# Date 2008-01-16 Time 03:08:12 PST -0800 (1200481692.24 s)
#phil __OFF__

Command line arguments: "../1117.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15729
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1117

-------------------------------------------------------------------------------
  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: (71.655, 46.2261, 86.822, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 1.97375
Completeness in resolution range: 0.939205
Completeness with d_max=infinity: 0.936511

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2319
                             d_min =   1.9737

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: (71.655, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 1.97375
Completeness in resolution range: 0.939205
Completeness with d_max=infinity: 0.936511

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2323 -  4.2249 [2193/2220]  1973   220  10.0%
  bin  2:  4.2249 -  3.3653 [2111/2131]  1901   210   9.9%
  bin  3:  3.3653 -  2.9434 [2072/2091]  1865   207  10.0%
  bin  4:  2.9434 -  2.6759 [2060/2090]  1851   209  10.1%
  bin  5:  2.6759 -  2.4850 [2045/2064]  1848   197   9.6%
  bin  6:  2.4850 -  2.3390 [2028/2053]  1818   210  10.4%
  bin  7:  2.3390 -  2.2222 [2044/2072]  1836   208  10.2%
  bin  8:  2.2222 -  2.1258 [2003/2039]  1803   200  10.0%
  bin  9:  2.1258 -  2.0441 [2017/2059]  1824   193   9.6%
  bin 10:  2.0441 -  1.9737 [1016/2038]   911   105  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/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:
        1.81 -     2.42: 28
        2.42 -     3.04: 2177
        3.04 -     3.66: 4691
        3.66 -     4.28: 9008
        4.28 -     4.90: 12268
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.990 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.144 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28167 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_1117/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 71.655 46.22605 86.82195 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: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4809   r_free= 0.4736   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.283787                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7130 0.99   1419  159 0.4040 0.3944      6.5948      6.5893|
|  2:  4.7130 -  3.7594 0.99   1365  151 0.3950 0.3997      6.8035      6.7788|
|  3:  3.7594 -  3.2896 0.99   1340  146 0.4297 0.4043      6.6495       6.634|
|  4:  3.2896 -  2.9913 0.99   1343  154 0.4717 0.4510      6.5305      6.5156|
|  5:  2.9913 -  2.7783 0.99   1336  149 0.5119 0.5030      6.3718       6.379|
|  6:  2.7783 -  2.6154 0.99   1315  144 0.5085 0.5148      6.2746      6.2138|
|  7:  2.6154 -  2.4850 0.99   1320  140 0.5347 0.4980      6.2517      6.1913|
|  8:  2.4850 -  2.3772 0.98   1307  152 0.5228 0.4903      6.1704      6.1828|
|  9:  2.3772 -  2.2860 0.98   1286  145 0.5248 0.5158      6.1202      6.1577|
| 10:  2.2860 -  2.2074 1.00   1307  152 0.5281 0.4718      6.0958      6.0624|
| 11:  2.2074 -  2.1385 0.98   1308  133 0.5152 0.5454      6.0429      6.0467|
| 12:  2.1385 -  2.0776 0.98   1279  148 0.5315 0.5832      5.9452      6.0049|
| 13:  2.0776 -  2.0230 0.95   1257  132 0.5409 0.5179      5.8768      5.7981|
| 14:  2.0230 -  1.9737 0.34    448   54 0.5560 0.5096      5.9011      5.8234|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2323 -  4.7130  1419   159  0.68  36.27   0.78     0.73      79571.74|
|  2:  4.7130 -  3.7594  1365   151  0.71  34.19   0.87     0.78     104832.81|
|  3:  3.7594 -  3.2896  1340   146  0.61  43.30   0.85     0.73     111415.91|
|  4:  3.2896 -  2.9913  1343   154  0.52  50.49   0.78     0.62     100174.12|
|  5:  2.9913 -  2.7783  1336   149  0.42  58.16   0.73     0.51      83485.84|
|  6:  2.7783 -  2.6154  1315   144  0.38  60.99   0.71     0.45      73043.70|
|  7:  2.6154 -  2.4850  1320   140  0.34  64.25   0.73     0.40      66792.68|
|  8:  2.4850 -  2.3772  1307   152  0.33  65.38   0.72     0.39      60993.67|
|  9:  2.3772 -  2.2860  1286   145  0.34  64.47   0.72     0.39      54344.74|
| 10:  2.2860 -  2.2074  1307   152  0.34  64.67   0.74     0.40      49644.39|
| 11:  2.2074 -  2.1385  1308   133  0.29  68.08   0.78     0.36      49837.62|
| 12:  2.1385 -  2.0776  1279   148  0.26  70.95   0.73     0.33      46443.43|
| 13:  2.0776 -  2.0230  1257   132  0.27  69.80   0.70     0.36      39306.69|
| 14:  2.0230 -  1.9737   448    54  0.44  57.40   0.71     0.47      26585.48|
|alpha:            min =        0.33 max =            0.78 mean =         0.50|
|beta:             min =    26585.48 max =       111415.91 mean =     70107.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.97 mean =        57.45|
|phase err.(test): min =        0.00 max =           89.96 mean =        57.51|
|-----------------------------------------------------------------------------|

============================== 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 = 15.138867             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.287   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.310336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.842   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1507 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3946 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5042 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6515 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7689 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.923 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.792 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    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 = 12.004)------------------------------------------|
|    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: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4862   r_free= 0.4767   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.285165                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4736   r_free= 0.4597   ksol= 0.30   Bsol= 20.00   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.57,8.63,7.42,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277738                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.958587             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.545   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.241193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.657   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4736      final r-factor (work) = 0.3927          |
| start r-factor (free) = 0.4597      final r-factor (free) = 0.4074          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 94.6106 = 12.96 * 0.50 * 6.2797 + 1.00 * 53.9228                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.3103 = 12.96 * 0.50 * 6.1998 + 1.00 * 0.1400                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3927      final r-factor (work) = 0.3460          |
| start r-factor (free) = 0.4074      final r-factor (free) = 0.3995          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7096 = 1.24 * 1.00 * 6.1998 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6047 = 1.24 * 1.00 * 6.1122 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.74   14.36    None  None   None       |
|    all(noH): 2823   0      0.00    79.74   14.36    None  None   None       |
|    Sol.    : 438    0      0.00    79.74   28.28    None  None   None       |
|    Mac.    : 2385   0      0.00    72.26   11.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.974: 1072   |   5:    39.870 -  47.844:   83        |
|      1:     7.974 -  15.948:  791   |   6:    47.844 -  55.818:   31        |
|      2:    15.948 -  23.922:  443   |   7:    55.818 -  63.792:   27        |
|      3:    23.922 -  31.896:  236   |   8:    63.792 -  71.767:   10        |
|      4:    31.896 -  39.870:  122   |   9:    71.767 -  79.741:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3460 r_free = 0.3995             target_work(ml) = 6.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3456 r_free = 0.4005             target_work(ml) = 6.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3456   r_free= 0.4005   ksol= 0.30   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.57,8.63,7.42,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.095237                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3427   r_free= 0.3966   ksol= 0.34   Bsol= 47.97   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.33,4.66,4.48,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.095563                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.851439             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.920   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490600              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.414  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3427      final r-factor (work) = 0.2480          |
| start r-factor (free) = 0.3966      final r-factor (free) = 0.3027          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.2733 = 10.85 * 0.50 * 6.1067 + 1.00 * 0.1400                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4995 = 10.85 * 0.50 * 5.9724 + 1.00 * 0.0950                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2480      final r-factor (work) = 0.2177          |
| start r-factor (free) = 0.3027      final r-factor (free) = 0.2786          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9485 = 0.49 * 1.00 * 5.9724 + 1.00 * 0.0185                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8399 = 0.49 * 1.00 * 5.7638 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.67   13.59    None  None   None       |
|    all(noH): 2823   0      0.00    82.67   13.59    None  None   None       |
|    Sol.    : 438    0      0.00    82.67   34.38    None  None   None       |
|    Mac.    : 2385   0      0.00    80.57   9.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.267: 1320   |   5:    41.335 -  49.602:   99        |
|      1:     8.267 -  16.534:  783   |   6:    49.602 -  57.869:   45        |
|      2:    16.534 -  24.801:  263   |   7:    57.869 -  66.136:   22        |
|      3:    24.801 -  33.068:  163   |   8:    66.136 -  74.403:    8        |
|      4:    33.068 -  41.335:  118   |   9:    74.403 -  82.670:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2177 r_free = 0.2786             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2174 r_free = 0.2778             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2174   r_free= 0.2778   ksol= 0.34   Bsol= 47.97   scale= 1.059   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.33,4.66,4.48,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.721194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2152   r_free= 0.2747   ksol= 0.32   Bsol= 54.38   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,2.22,3.33,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.719104                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.896799              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.205  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2152      final r-factor (work) = 0.1665          |
| start r-factor (free) = 0.2747      final r-factor (free) = 0.2167          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4523 = 2.90 * 0.50 * 5.7700 + 1.00 * 0.0950                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1973 = 2.90 * 0.50 * 5.6181 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1665      final r-factor (work) = 0.1557          |
| start r-factor (free) = 0.2167      final r-factor (free) = 0.2053          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3446 = 0.42 * 1.00 * 5.6181 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2790 = 0.42 * 1.00 * 5.4548 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.52   13.65    None  None   None       |
|    all(noH): 2823   0      0.00    82.52   13.65    None  None   None       |
|    Sol.    : 438    0      2.60    82.52   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    80.71   9.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.252: 1383   |   5:    41.261 -  49.514:  117        |
|      1:     8.252 -  16.505:  754   |   6:    49.514 -  57.766:   51        |
|      2:    16.505 -  24.757:  226   |   7:    57.766 -  66.018:   26        |
|      3:    24.757 -  33.009:  129   |   8:    66.018 -  74.270:    7        |
|      4:    33.009 -  41.261:  128   |   9:    74.270 -  82.522:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1557 r_free = 0.2053             target_work(ml) = 5.430         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1556 r_free = 0.2050             target_work(ml) = 5.430         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2050   ksol= 0.32   Bsol= 54.38   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,2.22,3.33,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.429694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1553   r_free= 0.2042   ksol= 0.33   Bsol= 54.38   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,1.26,2.64,0.00,0.00,0.00); trace/3= 1.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.428604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.797783              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.371   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1553      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9675 = 1.80 * 0.50 * 5.4595 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8878 = 1.80 * 0.50 * 5.3763 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1374      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4790 = 0.27 * 1.00 * 5.3763 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4663 = 0.27 * 1.00 * 5.3154 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.82   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    82.82   13.51    None  None   None       |
|    Sol.    : 438    0      2.79    78.24   36.60    None  None   None       |
|    Mac.    : 2385   0      0.00    82.82   9.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.282: 1429   |   5:    41.409 -  49.690:  106        |
|      1:     8.282 -  16.564:  756   |   6:    49.690 -  57.972:   65        |
|      2:    16.564 -  24.845:  198   |   7:    57.972 -  66.254:   33        |
|      3:    24.845 -  33.127:  117   |   8:    66.254 -  74.536:    7        |
|      4:    33.127 -  41.409:  108   |   9:    74.536 -  82.817:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1336 r_free = 0.1804             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1336 r_free = 0.1805             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1805   ksol= 0.33   Bsol= 54.38   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,1.26,2.64,0.00,0.00,0.00); trace/3= 1.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.297163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1804   ksol= 0.32   Bsol= 53.21   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,1.08,2.64,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.296874                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.772396              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.261  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.502290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.245   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7649 = 1.77 * 0.50 * 5.3147 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7250 = 1.77 * 0.50 * 5.2669 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6614 = 0.50 * 1.00 * 5.2669 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6387 = 0.50 * 1.00 * 5.2304 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.55   13.63    None  None   None       |
|    all(noH): 2823   0      0.00    85.55   13.63    None  None   None       |
|    Sol.    : 438    0      2.68    82.05   37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    85.55   9.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.555: 1489   |   5:    42.773 -  51.328:   96        |
|      1:     8.555 -  17.109:  723   |   6:    51.328 -  59.882:   69        |
|      2:    17.109 -  25.664:  180   |   7:    59.882 -  68.437:   28        |
|      3:    25.664 -  34.219:  109   |   8:    68.437 -  76.992:   11        |
|      4:    34.219 -  42.773:  111   |   9:    76.992 -  85.546:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1226 r_free = 0.1689             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1225 r_free = 0.1687             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1687   ksol= 0.32   Bsol= 53.21   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,1.08,2.64,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.226989                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7130 0.99   1419  159 0.1011 0.1378      5.4012      5.5986|
|  2:  4.7130 -  3.7594 0.99   1365  151 0.0901 0.1131      5.4791       5.641|
|  3:  3.7594 -  3.2896 0.99   1340  146 0.1143 0.1609       5.531      5.8577|
|  4:  3.2896 -  2.9913 0.99   1343  154 0.1346 0.1762      5.5172      5.6633|
|  5:  2.9913 -  2.7783 0.99   1336  149 0.1475 0.1868      5.4058      5.6259|
|  6:  2.7783 -  2.6154 0.99   1315  144 0.1368 0.2074      5.2811       5.555|
|  7:  2.6154 -  2.4850 0.99   1320  140 0.1396 0.1692      5.2488      5.3558|
|  8:  2.4850 -  2.3772 0.98   1307  152 0.1294 0.1959      5.1498      5.4407|
|  9:  2.3772 -  2.2860 0.98   1286  145 0.1364 0.2018      5.1442      5.4029|
| 10:  2.2860 -  2.2074 1.00   1307  152 0.1256 0.1685      5.0387      5.2207|
| 11:  2.2074 -  2.1385 0.98   1308  133 0.1232 0.2008      5.0276      5.4077|
| 12:  2.1385 -  2.0776 0.98   1279  148 0.1242 0.1805      4.9433       5.189|
| 13:  2.0776 -  2.0230 0.95   1257  132 0.1301 0.1799      4.8721       5.098|
| 14:  2.0230 -  1.9737 0.34    448   54 0.1140 0.1633      4.7716      4.9477|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2323 -  4.7130  1419   159  0.94   9.52   0.97     0.95       7701.40|
|  2:  4.7130 -  3.7594  1365   151  0.95   8.39   1.01     0.99       9751.92|
|  3:  3.7594 -  3.2896  1340   146  0.93  12.00   1.03     1.03      11327.87|
|  4:  3.2896 -  2.9913  1343   154  0.91  15.15   1.01     0.98      11417.72|
|  5:  2.9913 -  2.7783  1336   149  0.89  17.17   0.99     0.97       9535.26|
|  6:  2.7783 -  2.6154  1315   144  0.89  17.57   0.98     0.96       8068.09|
|  7:  2.6154 -  2.4850  1320   140  0.89  16.96   0.99     0.96       7217.67|
|  8:  2.4850 -  2.3772  1307   152  0.89  17.32   0.98     0.94       6260.55|
|  9:  2.3772 -  2.2860  1286   145  0.89  17.78   1.00     0.95       6241.41|
| 10:  2.2860 -  2.2074  1307   152  0.89  17.58   1.00     0.96       5261.32|
| 11:  2.2074 -  2.1385  1308   133  0.89  17.37   0.99     0.93       5006.60|
| 12:  2.1385 -  2.0776  1279   148  0.90  17.07   1.00     1.01       4554.70|
| 13:  2.0776 -  2.0230  1257   132  0.88  18.54   0.99     0.96       3991.92|
| 14:  2.0230 -  1.9737   448    54  0.90  16.62   0.98     0.95       3289.04|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3289.04 max =        11417.72 mean =      7349.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.78 mean =        15.52|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1684   ksol= 0.32   Bsol= 55.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.73,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227054                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1684   ksol= 0.32   Bsol= 55.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.73,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.227054                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7130 0.99   1419  159 0.1020 0.1327      5.3966      5.5735|
|  2:  4.7130 -  3.7594 0.99   1365  151 0.0909 0.1148       5.481      5.6491|
|  3:  3.7594 -  3.2896 0.99   1340  146 0.1147 0.1603      5.5331      5.8568|
|  4:  3.2896 -  2.9913 0.99   1343  154 0.1346 0.1768      5.5171      5.6662|
|  5:  2.9913 -  2.7783 0.99   1336  149 0.1474 0.1867      5.4067       5.624|
|  6:  2.7783 -  2.6154 0.99   1315  144 0.1369 0.2067      5.2811      5.5535|
|  7:  2.6154 -  2.4850 0.99   1320  140 0.1396 0.1691      5.2488      5.3552|
|  8:  2.4850 -  2.3772 0.98   1307  152 0.1292 0.1961      5.1495       5.442|
|  9:  2.3772 -  2.2860 0.98   1286  145 0.1363 0.2017      5.1444      5.4026|
| 10:  2.2860 -  2.2074 1.00   1307  152 0.1257 0.1684      5.0393      5.2218|
| 11:  2.2074 -  2.1385 0.98   1308  133 0.1233 0.2007      5.0283      5.4086|
| 12:  2.1385 -  2.0776 0.98   1279  148 0.1241 0.1806      4.9436      5.1892|
| 13:  2.0776 -  2.0230 0.95   1257  132 0.1301 0.1796      4.8719      5.0975|
| 14:  2.0230 -  1.9737 0.34    448   54 0.1140 0.1632      4.7711      4.9475|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2323 -  4.7130  1419   159  0.94   9.44   0.97     0.95       7364.94|
|  2:  4.7130 -  3.7594  1365   151  0.95   8.28   1.01     1.00       9578.25|
|  3:  3.7594 -  3.2896  1340   146  0.93  11.99   1.03     1.03      11332.15|
|  4:  3.2896 -  2.9913  1343   154  0.91  15.17   1.01     0.99      11428.33|
|  5:  2.9913 -  2.7783  1336   149  0.89  17.18   0.99     0.97       9548.40|
|  6:  2.7783 -  2.6154  1315   144  0.89  17.57   0.98     0.96       8055.57|
|  7:  2.6154 -  2.4850  1320   140  0.89  16.98   0.99     0.96       7226.49|
|  8:  2.4850 -  2.3772  1307   152  0.89  17.34   0.98     0.94       6270.32|
|  9:  2.3772 -  2.2860  1286   145  0.89  17.79   1.00     0.95       6245.86|
| 10:  2.2860 -  2.2074  1307   152  0.89  17.61   1.00     0.96       5276.40|
| 11:  2.2074 -  2.1385  1308   133  0.89  17.39   0.99     0.93       5014.35|
| 12:  2.1385 -  2.0776  1279   148  0.90  17.08   1.00     1.01       4561.56|
| 13:  2.0776 -  2.0230  1257   132  0.88  18.54   0.99     0.96       3989.50|
| 14:  2.0230 -  1.9737   448    54  0.90  16.61   0.98     0.95       3284.47|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3284.47 max =        11428.33 mean =      7314.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.51|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    87.36   15.44    None  None   None       |
|    all(noH): 2823   0      1.81    87.36   15.44    None  None   None       |
|    Sol.    : 438    0      4.49    83.86   39.31    None  None   None       |
|    Mac.    : 2385   0      1.81    87.36   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.811 -  10.366: 1489   |   5:    44.585 -  53.139:   96        |
|      1:    10.366 -  18.921:  723   |   6:    53.139 -  61.694:   69        |
|      2:    18.921 -  27.475:  180   |   7:    61.694 -  70.248:   28        |
|      3:    27.475 -  36.030:  109   |   8:    70.248 -  78.803:   11        |
|      4:    36.030 -  44.585:  111   |   9:    78.803 -  87.358:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.402 - 4.751
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 331
   mapped sites are within: 0.724 - 4.751

peak=   10.298 closest distance to " CB  VAL A 230 " =    1.459
peak=    7.704 closest distance to " CG2 VAL A 296 " =    1.186
peak=    7.340 closest distance to " CG  ARG A 138 " =    1.214
peak=    6.790 closest distance to " CD2 LEU A   5 " =    1.273
peak=    5.848 closest distance to " NH1 ARG A 138 " =    1.027
peak=    5.703 closest distance to " NE2 GLN A  11 " =    1.131
peak=    5.427 closest distance to " CD1AILE A 234 " =    1.072
peak=    5.392 closest distance to " O   HOH Z 232 " =    2.268
peak=    5.375 closest distance to " CG  LEU A   5 " =    1.255
peak=    5.335 closest distance to " CG  PRO A  54 " =    1.412
peak=    5.230 closest distance to " O   HOH Z   7 " =    1.590
peak=    5.198 closest distance to " O   HOH Z 222 " =    1.308
peak=    5.088 closest distance to " O   HOH Z 144 " =    2.111
peak=    5.042 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.000 closest distance to " CB  PRO A  54 " =    1.058
peak=    4.942 closest distance to " O   HOH Z 111 " =    1.716
peak=    4.917 closest distance to " CD  ARG A 138 " =    1.070
peak=    4.916 closest distance to " CG  PRO A 198 " =    1.295
peak=    4.910 closest distance to " CB  ASN A 148 " =    1.398
peak=    4.776 closest distance to " O   HOH Z 410 " =    1.589
peak=    4.776 closest distance to " O   HOH Z 130 " =    1.057
peak=    4.765 closest distance to " CG  LEU A 228 " =    1.184
peak=    4.761 closest distance to " O   HOH Z 287 " =    1.952
peak=    4.709 closest distance to " O   HOH Z 427 " =    2.778
peak=    4.697 closest distance to " O   HOH Z 425 " =    1.592
peak=    4.618 closest distance to " O   HOH Z 369 " =    2.006
peak=    4.566 closest distance to " O   HOH Z 298 " =    1.987
peak=    4.520 closest distance to " CB  GLN A 183 " =    1.213
peak=    4.515 closest distance to " CB  VAL A 230 " =    1.194
peak=    4.507 closest distance to " O   HOH Z   2 " =    1.916
peak=    4.500 closest distance to " CB  ASP A 124 " =    0.814
peak=    4.464 closest distance to " O   HOH Z   9 " =    1.526
peak=    4.405 closest distance to " CD2 LEU A 228 " =    1.219
peak=    4.398 closest distance to " O   HOH Z  55 " =    2.207
peak=    4.395 closest distance to " NH1AARG A 145 " =    1.125
peak=    4.384 closest distance to " O   HOH Z 183 " =    1.368
peak=    4.329 closest distance to " CG  PRO A 280 " =    0.931
peak=    4.325 closest distance to " CB  SER A   3 " =    1.525
peak=    4.305 closest distance to " CB  SER A  63 " =    1.270
peak=    4.266 closest distance to " CG  PRO A 213 " =    1.298
peak=    4.259 closest distance to " CD2 TRP A 179 " =    2.325
peak=    4.254 closest distance to " NH1 ARG A  56 " =    1.070
peak=    4.214 closest distance to " CG  PRO A 243 " =    1.143
peak=    4.176 closest distance to " CG  LEU A 167 " =    1.229
peak=    4.172 closest distance to " CB  TRP A 266 " =    0.981
peak=    4.165 closest distance to " O   PRO A 198 " =    1.570
peak=    4.161 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.143 closest distance to " CB  ARG A 275 " =    0.959
peak=    4.141 closest distance to " CB  ASN A  39 " =    0.974
peak=    4.121 closest distance to " CB  SER A 216 " =    0.979
peak=    4.111 closest distance to " O   HOH Z 316 " =    3.016
peak=    4.096 closest distance to " O   HOH Z  78 " =    1.575
peak=    4.096 closest distance to " ND1 HIS A  86 " =    1.771
peak=    4.093 closest distance to " O   HOH Z 411 " =    3.193
peak=    4.085 closest distance to " CA  VAL A 296 " =    1.145
peak=    4.083 closest distance to " O   HOH Z 423 " =    1.616
peak=    4.045 closest distance to " O   HOH Z 126 " =    2.100
peak=    4.045 closest distance to " O   HOH Z  44 " =    2.379
peak=    4.038 closest distance to " O   HOH Z 437 " =    2.108
peak=    4.015 closest distance to " CB  GLU A 128 " =    1.119
peak=    3.978 closest distance to " O   HOH Z 368 " =    2.047
peak=    3.949 closest distance to " CB  SER A 210 " =    0.892
peak=    3.938 closest distance to " CD  ARG A  66 " =    2.308
peak=    3.921 closest distance to " CB  VAL A 265 " =    1.327
peak=    3.914 closest distance to " CB  VAL A 202 " =    1.565
peak=    3.897 closest distance to " ND2 ASN A 187 " =    1.551
peak=    3.894 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.890 closest distance to " NH1 ARG A  14 " =    0.942
peak=    3.881 closest distance to " O   ASP A 132 " =    3.891
peak=    3.878 closest distance to " CG2 THR A 221 " =    1.107
peak=    3.853 closest distance to " CD  ARG A 159 " =    0.791
peak=    3.853 closest distance to " CA  ILE A 234 " =    1.017
peak=    3.851 closest distance to " OG  SER A  62 " =    2.845
peak=    3.848 closest distance to " O   HOH Z 392 " =    1.286
peak=    3.840 closest distance to " O   HOH Z 156 " =    2.947
peak=    3.839 closest distance to " CE3 TRP A 274 " =    1.314
peak=    3.834 closest distance to " O   HOH Z  68 " =    1.975
peak=    3.833 closest distance to " O   HOH Z 193 " =    1.650
peak=    3.821 closest distance to " O   HOH Z 217 " =    3.032
peak=    3.821 closest distance to " CB  ASN A 187 " =    1.146
peak=    3.816 closest distance to " CD1 ILE A  33 " =    1.813
peak=    3.808 closest distance to " CG  GLN A  88 " =    1.041
peak=    3.784 closest distance to " CB  ASN A 142 " =    0.940
peak=    3.777 closest distance to " CB  ALA A 104 " =    0.804
peak=    3.770 closest distance to " CA  SER A  87 " =    0.905
peak=    3.770 closest distance to " O   HOH Z  78 " =    2.217
peak=    3.766 closest distance to " CG1 ILE A 151 " =    1.168
peak=    3.759 closest distance to " O   PRO A 198 " =    1.295
peak=    3.759 closest distance to " O   HOH Z 126 " =    1.582
peak=    3.753 closest distance to " O   HOH Z  88 " =    3.264
peak=    3.745 closest distance to " CB  ARG A 138 " =    1.490
peak=    3.743 closest distance to " CA  TYR A 116 " =    1.469
peak=    3.742 closest distance to " CB  SER A 212 " =    1.282
peak=    3.741 closest distance to " CB  LEU A 237 " =    0.873
peak=    3.738 closest distance to " CA  ALA A  51 " =    1.028
peak=    3.736 closest distance to " CZ  PHE A 218 " =    1.071
peak=    3.734 closest distance to " O   HOH Z 158 " =    2.916
peak=    3.702 closest distance to " CB  LEU A 143 " =    1.170
peak=    3.696 closest distance to " CB  LEU A 228 " =    1.218
peak=    3.690 closest distance to " O   HOH Z  61 " =    1.665
peak=    3.688 closest distance to " CD BLYS A 290 " =    1.019
peak=    3.684 closest distance to " O   HOH Z 133 " =    2.521
peak=    3.680 closest distance to " O   HOH Z 261 " =    2.229
peak=    3.678 closest distance to " O   HOH Z   1 " =    2.022
peak=    3.673 closest distance to " CB  VAL A 250 " =    1.074
peak=    3.667 closest distance to " O   HOH Z  59 " =    1.934
peak=    3.663 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.648 closest distance to " O   HOH Z  57 " =    1.202
peak=    3.643 closest distance to " O   HOH Z 132 " =    2.497
peak=    3.642 closest distance to " O   HOH Z 362 " =    2.477
peak=    3.637 closest distance to " O   HOH Z   3 " =    2.037
peak=    3.634 closest distance to " OH  TYR A 186 " =    1.045
peak=    3.631 closest distance to " CB  MET A  47 " =    1.232
peak=    3.624 closest distance to " NH2AARG A 190 " =    1.673
peak=    3.623 closest distance to " CA  TYR A  30 " =    0.970
peak=    3.615 closest distance to " ND2 ASN A 249 " =    0.799
peak=    3.611 closest distance to " N   PHE A 130 " =    1.308
peak=    3.607 closest distance to " OD2 ASP A 286 " =    2.816
peak=    3.603 closest distance to " O   HOH Z 184 " =    1.537
peak=    3.600 closest distance to " CD  GLN A 240 " =    1.701
peak=    3.595 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.594 closest distance to " CB  MET A  40 " =    0.858
peak=    3.579 closest distance to " O   HOH Z 284 " =    1.611
peak=    3.575 closest distance to " NE  ARG A  56 " =    3.561
peak=    3.573 closest distance to " CA  ASN A 127 " =    1.154
peak=    3.565 closest distance to " NE AARG A 275 " =    1.467
peak=    3.563 closest distance to " O   HOH Z 361 " =    1.383
peak=    3.555 closest distance to " CB  GLU A 152 " =    1.401
peak=    3.553 closest distance to " O   HOH Z 332 " =    1.618
peak=    3.551 closest distance to " O   HOH Z  63 " =    1.294
peak=    3.550 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.549 closest distance to " CA  ALA A 299 " =    0.981
peak=    3.544 closest distance to " O   HOH Z 350 " =    1.585
peak=    3.542 closest distance to " O   HOH Z 282 " =    1.833
peak=    3.541 closest distance to " O   HOH Z 148 " =    1.520
peak=    3.536 closest distance to " O   MET A 105 " =    1.816
peak=    3.527 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.523 closest distance to " CB  GLU A 277 " =    3.617
peak=    3.521 closest distance to " CA  ARG A 195 " =    1.280
peak=    3.519 closest distance to " CB  ARG A  79 " =    1.449
peak=    3.516 closest distance to " O   HOH Z 146 " =    1.444
peak=    3.507 closest distance to " O   HOH Z 258 " =    2.146
peak=    3.503 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.494 closest distance to " O   TYR A 116 " =    1.197
peak=    3.489 closest distance to " CG1 ILE A  49 " =    1.581
peak=    3.486 closest distance to " O   HOH Z 380 " =    1.705
peak=    3.478 closest distance to " CA  ALA A  21 " =    1.212
peak=    3.474 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.473 closest distance to " O   HOH Z 175 " =    2.220
peak=    3.469 closest distance to " CB  THR A  82 " =    1.186
peak=    3.469 closest distance to " CZ  PHE A 192 " =    0.958
peak=    3.467 closest distance to " O   HOH Z 122 " =    1.946
peak=    3.466 closest distance to " O   SER A  87 " =    2.351
peak=    3.466 closest distance to " CA  GLY A 267 " =    1.076
peak=    3.465 closest distance to " N   ALA A 256 " =    1.105
peak=    3.459 closest distance to " N   TYR A  15 " =    0.935
peak=    3.453 closest distance to " CB  GLN A 103 " =    1.117
peak=    3.450 closest distance to " NZ ALYS A 290 " =    1.002
peak=    3.446 closest distance to " CG BARG A 102 " =    1.946
peak=    3.444 closest distance to " O   HOH Z  30 " =    1.804
peak=    3.440 closest distance to " O   HOH Z 193 " =    1.956
peak=    3.436 closest distance to " NE1 TRP A 274 " =    0.975
peak=    3.435 closest distance to " ND1 HIS A  81 " =    1.718
peak=    3.429 closest distance to " O   HOH Z  80 " =    1.509
peak=    3.428 closest distance to " CB  THR A 157 " =    1.130
peak=    3.426 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.422 closest distance to " O   HOH Z 236 " =    1.668
peak=    3.421 closest distance to " CB  GLN A  88 " =    1.365
peak=    3.419 closest distance to " O   HOH Z 109 " =    2.467
peak=    3.418 closest distance to " O   HOH Z 133 " =    1.760
peak=    3.417 closest distance to " O   HOH Z 173 " =    1.723
peak=    3.412 closest distance to " O   HOH Z 214 " =    2.077
peak=    3.411 closest distance to " CB  ASP A 140 " =    0.923
peak=    3.410 closest distance to " CA  ALA A 160 " =    0.943
peak=    3.403 closest distance to " CB  SER A 276 " =    1.163
peak=    3.400 closest distance to " O   HOH Z 195 " =    1.443
peak=    3.399 closest distance to " CD1 LEU A   5 " =    1.365
peak=    3.394 closest distance to " CG2BVAL A  41 " =    1.262
peak=    3.391 closest distance to " O   HOH Z 148 " =    2.381
peak=    3.389 closest distance to " O   HOH Z 170 " =    1.097
peak=    3.388 closest distance to " O   HOH Z 345 " =    3.316
peak=    3.388 closest distance to " CG2 VAL A 257 " =    0.905
peak=    3.387 closest distance to " O   HOH Z 280 " =    3.026
peak=    3.381 closest distance to " CD  ARG A 195 " =    3.434
peak=    3.381 closest distance to " O   HOH Z 110 " =    1.644
peak=    3.379 closest distance to " CE  MET A  93 " =    1.540
peak=    3.376 closest distance to " N   SER A 271 " =    0.973
peak=    3.376 closest distance to " CD  ARG A  14 " =    1.231
peak=    3.373 closest distance to " CB  ALA A   1 " =    4.751
peak=    3.372 closest distance to " CA  ARG A 102 " =    1.139
peak=    3.371 closest distance to " O   HOH Z 290 " =    1.127
peak=    3.369 closest distance to " OD1 ASN A  69 " =    2.654
peak=    3.366 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.362 closest distance to " CZ3 TRP A  92 " =    1.256
peak=    3.359 closest distance to " O   HOH Z 263 " =    1.646
peak=    3.356 closest distance to " N   ASN A 127 " =    1.341
peak=    3.350 closest distance to " O   HOH Z 419 " =    1.814
peak=    3.343 closest distance to " CD  ARG A  24 " =    1.140
peak=    3.341 closest distance to " CA  GLU A 152 " =    0.941
peak=    3.341 closest distance to " OG BSER A 212 " =    2.785
peak=    3.340 closest distance to " CA  ALA A 295 " =    1.097
peak=    3.340 closest distance to " O   HOH Z 172 " =    2.861
peak=    3.338 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.338 closest distance to " OG  SER A  97 " =    3.073
peak=    3.337 closest distance to " CB  TRP A 179 " =    1.464
peak=    3.336 closest distance to " O   HOH Z  10 " =    1.799
peak=    3.335 closest distance to " O   HOH Z 222 " =    2.157
peak=    3.335 closest distance to " CA  MET A  40 " =    1.049
peak=    3.334 closest distance to " O   HOH Z 391 " =    3.062
peak=    3.333 closest distance to " CE3 TRP A  85 " =    1.110
peak=    3.331 closest distance to " O   HOH Z 302 " =    1.619
peak=    3.330 closest distance to " O   HOH Z  20 " =    1.894
peak=    3.328 closest distance to " O   HOH Z 409 " =    2.510
peak=    3.328 closest distance to " O   HOH Z 235 " =    1.611
peak=    3.327 closest distance to " OD1BASN A 224 " =    2.341
peak=    3.323 closest distance to " CA  ARG A  36 " =    1.228
peak=    3.323 closest distance to " O   HOH Z 180 " =    2.081
peak=    3.322 closest distance to " O   HOH Z 154 " =    1.801
peak=    3.320 closest distance to " CG  ARG A 159 " =    1.012
peak=    3.319 closest distance to " O   HOH Z 281 " =    1.693
peak=    3.318 closest distance to " CB  LEU A 255 " =    0.871
peak=    3.316 closest distance to " O   HOH Z 389 " =    1.895
peak=    3.313 closest distance to " CA  LYS A 117 " =    1.098
peak=    3.312 closest distance to " O   HOH Z 427 " =    1.265
peak=    3.311 closest distance to " O   HOH Z 185 " =    1.873
peak=    3.311 closest distance to " O   HOH Z 305 " =    3.501
peak=    3.306 closest distance to " O   ASN A 209 " =    1.478
peak=    3.300 closest distance to " O   HOH Z 112 " =    1.424
peak=    3.300 closest distance to " CE3 TRP A 150 " =    1.036
peak=    3.299 closest distance to " O   HOH Z 371 " =    1.664
peak=    3.298 closest distance to " O   HOH Z  85 " =    1.956
peak=    3.298 closest distance to " CB  LEU A  83 " =    0.827
peak=    3.298 closest distance to " O   HOH Z   9 " =    1.625
peak=    3.295 closest distance to " O   HOH Z  40 " =    2.128
peak=    3.294 closest distance to " O   HOH Z 119 " =    1.537
peak=    3.294 closest distance to " O   ALA A 165 " =    1.473
peak=    3.293 closest distance to " CB  GLU A 236 " =    1.035
peak=    3.286 closest distance to " CB  TYR A  30 " =    1.410
peak=    3.285 closest distance to " O   HOH Z 371 " =    2.773
peak=    3.285 closest distance to " CB  GLN A  89 " =    1.202
peak=    3.283 closest distance to " CA  LEU A 282 " =    1.057
peak=    3.282 closest distance to " CA  TYR A 186 " =    1.570
peak=    3.281 closest distance to " O   HOH Z 403 " =    1.554
peak=    3.280 closest distance to " CA  ALA A 154 " =    1.030
peak=    3.280 closest distance to " O   HOH Z 303 " =    1.880
peak=    3.279 closest distance to " O   HOH Z 225 " =    1.397
peak=    3.279 closest distance to " O   HOH Z 403 " =    1.226
peak=    3.277 closest distance to " O   HOH Z 207 " =    2.493
peak=    3.277 closest distance to " CA  ILE A 106 " =    0.806
peak=    3.274 closest distance to " NE2 HIS A 207 " =    1.174
peak=    3.273 closest distance to " OD1 ASN A 217 " =    1.529
peak=    3.271 closest distance to " O   HOH Z 392 " =    1.899
peak=    3.269 closest distance to " O   HOH Z 252 " =    1.712
peak=    3.267 closest distance to " CA  MET A  47 " =    1.145
peak=    3.266 closest distance to " NH2AARG A 145 " =    1.101
peak=    3.264 closest distance to " O   HOH Z 310 " =    2.180
peak=    3.261 closest distance to " CB  PRO A 243 " =    1.191
peak=    3.260 closest distance to " O   HOH Z 435 " =    2.294
peak=    3.259 closest distance to " CD  LYS A 166 " =    1.372
peak=    3.258 closest distance to " O   HOH Z 417 " =    1.209
peak=    3.257 closest distance to " CG  LYS A  76 " =    1.706
peak=    3.257 closest distance to " CB  TRP A 150 " =    1.248
peak=    3.251 closest distance to " O   HOH Z  44 " =    2.672
peak=    3.249 closest distance to " O   HOH Z  58 " =    1.937
peak=    3.249 closest distance to " C   LYS A 290 " =    1.368
peak=    3.247 closest distance to " O   HOH Z 181 " =    2.289
peak=    3.247 closest distance to " O   HOH Z 153 " =    3.748
peak=    3.244 closest distance to " OG BSER A 134 " =    2.808
peak=    3.239 closest distance to " CA  ASP A 162 " =    0.985
peak=    3.235 closest distance to " O   HOH Z 215 " =    1.318
peak=    3.232 closest distance to " O   HOH Z 295 " =    1.611
peak=    3.231 closest distance to " CB  ALA A 248 " =    1.255
peak=    3.230 closest distance to " O   ALA A 291 " =    1.425
peak=    3.227 closest distance to " O   HOH Z 145 " =    3.780
peak=    3.225 closest distance to " CA  LEU A 101 " =    1.480
peak=    3.224 closest distance to " O   HOH Z 116 " =    1.787
peak=    3.224 closest distance to " CB  PHE A  16 " =    1.100
peak=    3.223 closest distance to " O   HOH Z   1 " =    1.887
peak=    3.222 closest distance to " CB  ALA A 291 " =    1.415
peak=    3.219 closest distance to " O   HOH Z 425 " =    2.088
peak=    3.217 closest distance to " CA  ALA A 291 " =    0.936
peak=    3.217 closest distance to " CA  ASN A 215 " =    1.266
peak=    3.217 closest distance to " OE2 GLU A   2 " =    1.808
peak=    3.214 closest distance to " CB  ARG A 190 " =    1.763
peak=    3.214 closest distance to " CB  ALA A  10 " =    1.005
peak=    3.207 closest distance to " CA  ARG A 139 " =    1.009
peak=    3.206 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    3.204 closest distance to " O   HOH Z 115 " =    1.671
peak=    3.200 closest distance to " O   ALA A  10 " =    1.601
peak=    3.194 closest distance to " O   HOH Z 422 " =    2.681
peak=    3.193 closest distance to " CB  GLU A 236 " =    1.214
peak=    3.192 closest distance to " O   HOH Z 124 " =    1.824
peak=    3.187 closest distance to " O   HOH Z 326 " =    2.081
peak=    3.184 closest distance to " NH2 ARG A  79 " =    1.570
peak=    3.180 closest distance to " N   ARG A 156 " =    1.307
peak=    3.180 closest distance to " O   HOH Z 411 " =    1.413
peak=    3.175 closest distance to " O   THR A 251 " =    1.193
peak=    3.173 closest distance to " CA  ARG A 156 " =    1.028
peak=    3.171 closest distance to " O   HOH Z 368 " =    3.580
peak=    3.170 closest distance to " O   HOH Z 344 " =    2.981
peak=    3.168 closest distance to " O   HOH Z 106 " =    3.942
peak=    3.163 closest distance to " CB  ASN A 110 " =    1.117
peak=    3.157 closest distance to " NE2 GLN A  58 " =    3.615
peak=    3.156 closest distance to " ND2 ASN A  60 " =    3.117
peak=    3.155 closest distance to " CB  LEU A 300 " =    0.917
peak=    3.154 closest distance to " O   HOH Z 359 " =    1.302
peak=    3.154 closest distance to " O   THR A 294 " =    1.104
peak=    3.144 closest distance to " O   HOH Z 359 " =    4.074
peak=    3.138 closest distance to " CA  TYR A  30 " =    1.087
peak=    3.131 closest distance to " O   HOH Z 405 " =    1.478
peak=    3.125 closest distance to " O   HOH Z 244 " =    1.599
peak=    3.122 closest distance to " CA  ALA A 158 " =    1.166
peak=    3.121 closest distance to " CB  THR A 235 " =    0.992
peak=    3.121 closest distance to " CB  ILE A 120 " =    1.362
peak=    3.118 closest distance to " O   HOH Z 374 " =    1.039
peak=    3.109 closest distance to " CA  ALA A 184 " =    1.132
peak=    3.104 closest distance to " O   HOH Z  51 " =    1.780
peak=    3.097 closest distance to " OD1 ASN A  45 " =    1.517
peak=    3.093 closest distance to " CD1 LEU A 167 " =    1.218
peak=    3.086 closest distance to " CA  THR A 264 " =    0.724
peak=    3.075 closest distance to " O   ALA A 158 " =    1.523
peak=    3.071 closest distance to " O   HOH Z 368 " =    4.316
peak=    3.070 closest distance to " CB  SER A  62 " =    1.090
peak=    3.066 closest distance to " OH  TYR A 214 " =    1.359
peak=    3.061 closest distance to " O   HOH Z 130 " =    3.545
peak=    3.027 closest distance to " OG ASER A 212 " =    1.441
peak=    3.019 closest distance to " CB  ALA A 227 " =    0.934

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.407 - 5.616
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 190
   mapped sites are within: 0.734 - 5.616

peak=   -5.346 closest distance to " CD  ARG A 138 " =    1.138
peak=   -5.056 closest distance to " CG2 VAL A 230 " =    0.868
peak=   -4.333 closest distance to " O   PRO A 198 " =    1.225
peak=   -4.289 closest distance to " OE1 GLN A  88 " =    1.019
peak=   -4.177 closest distance to " CD  ARG A  14 " =    3.068
peak=   -4.176 closest distance to " CG  ARG A 138 " =    0.919
peak=   -4.176 closest distance to " O   HOH Z 231 " =    1.707
peak=   -4.172 closest distance to " CD  ARG A 156 " =    2.050
peak=   -4.156 closest distance to " CB  PRO A 243 " =    2.615
peak=   -4.056 closest distance to " O   HOH Z 102 " =    1.188
peak=   -4.025 closest distance to " OG  SER A  87 " =    1.446
peak=   -4.007 closest distance to " O   HOH Z 290 " =    1.146
peak=   -3.963 closest distance to " CD  GLN A 223 " =    2.481
peak=   -3.960 closest distance to " O   HOH Z 411 " =    5.147
peak=   -3.958 closest distance to " O   GLY A 203 " =    2.527
peak=   -3.928 closest distance to " CD1 TYR A 247 " =    2.820
peak=   -3.901 closest distance to " N   ALA A  43 " =    2.585
peak=   -3.895 closest distance to " CB  ALA A  43 " =    2.516
peak=   -3.878 closest distance to " O   HOH Z 377 " =    1.535
peak=   -3.854 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.836 closest distance to " OG  SER A  97 " =    2.217
peak=   -3.826 closest distance to " O   HOH Z 351 " =    1.457
peak=   -3.799 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.795 closest distance to " CA  ASP A  27 " =    2.463
peak=   -3.783 closest distance to " O   HOH Z  65 " =    1.038
peak=   -3.773 closest distance to " CG2 VAL A 296 " =    1.207
peak=   -3.769 closest distance to " O   HOH Z 389 " =    2.145
peak=   -3.763 closest distance to " N   THR A 157 " =    1.494
peak=   -3.760 closest distance to " CD2 LEU A   5 " =    0.950
peak=   -3.744 closest distance to " O   GLY A  80 " =    2.480
peak=   -3.725 closest distance to " OG BSER A 134 " =    1.541
peak=   -3.722 closest distance to " O   HOH Z  43 " =    1.699
peak=   -3.707 closest distance to " O   HOH Z 275 " =    1.835
peak=   -3.707 closest distance to " O   HOH Z 185 " =    2.167
peak=   -3.707 closest distance to " CE2 TYR A  30 " =    2.682
peak=   -3.702 closest distance to " NH2AARG A 275 " =    5.616
peak=   -3.692 closest distance to " CB  ALA A 248 " =    1.977
peak=   -3.688 closest distance to " CB  ALA A   9 " =    2.532
peak=   -3.681 closest distance to " CB  PHE A 130 " =    1.303
peak=   -3.668 closest distance to " O   HOH Z 211 " =    1.342
peak=   -3.662 closest distance to " CG  GLN A  88 " =    0.815
peak=   -3.659 closest distance to " O   HOH Z 435 " =    3.045
peak=   -3.635 closest distance to " O   ILE A  49 " =    1.749
peak=   -3.617 closest distance to " CB  PRO A 163 " =    2.384
peak=   -3.614 closest distance to " CB  ALA A 161 " =    2.654
peak=   -3.607 closest distance to " O   HOH Z 394 " =    1.505
peak=   -3.591 closest distance to " O   HOH Z 359 " =    1.626
peak=   -3.572 closest distance to " C   ALA A 158 " =    1.386
peak=   -3.567 closest distance to " O   HOH Z 111 " =    2.047
peak=   -3.551 closest distance to " O   HOH Z 166 " =    1.871
peak=   -3.543 closest distance to " O   HOH Z 292 " =    1.581
peak=   -3.538 closest distance to " CB  TYR A  15 " =    2.137
peak=   -3.538 closest distance to " CG2 VAL A 202 " =    2.786
peak=   -3.537 closest distance to " O   PRO A 163 " =    1.930
peak=   -3.536 closest distance to " CD1 LEU A 228 " =    2.376
peak=   -3.534 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.533 closest distance to " CG1 VAL A 296 " =    1.327
peak=   -3.524 closest distance to " C   LEU A 222 " =    0.874
peak=   -3.522 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.517 closest distance to " CE2 TYR A 116 " =    3.142
peak=   -3.516 closest distance to " O   SER A  22 " =    2.531
peak=   -3.515 closest distance to " O   HOH Z 176 " =    0.734
peak=   -3.511 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.510 closest distance to " O   HOH Z 198 " =    2.573
peak=   -3.509 closest distance to " OG ASER A 134 " =    1.098
peak=   -3.508 closest distance to " CZ3 TRP A 179 " =    1.175
peak=   -3.503 closest distance to " C   MET A 188 " =    1.472
peak=   -3.503 closest distance to " CA  GLY A  98 " =    1.962
peak=   -3.499 closest distance to " CG2 ILE A  49 " =    2.839
peak=   -3.499 closest distance to " CB  VAL A 230 " =    1.031
peak=   -3.497 closest distance to " CB  TRP A  85 " =    2.477
peak=   -3.495 closest distance to " O   GLY A  17 " =    1.274
peak=   -3.481 closest distance to " O   HOH Z 389 " =    4.661
peak=   -3.472 closest distance to " OH  TYR A 214 " =    1.068
peak=   -3.469 closest distance to " OD1 ASN A  60 " =    0.942
peak=   -3.463 closest distance to " CZ  PHE A  38 " =    2.555
peak=   -3.459 closest distance to " O   HOH Z  44 " =    2.281
peak=   -3.453 closest distance to " C   HIS A 108 " =    1.076
peak=   -3.446 closest distance to " O   HOH Z 201 " =    1.734
peak=   -3.441 closest distance to " O   HOH Z 282 " =    4.933
peak=   -3.438 closest distance to " O   HOH Z 407 " =    3.342
peak=   -3.425 closest distance to " CG  TRP A 266 " =    1.747
peak=   -3.423 closest distance to " OE1 GLN A  88 " =    1.368
peak=   -3.418 closest distance to " O   SER A 135 " =    1.451
peak=   -3.417 closest distance to " CB  ALA A 227 " =    2.450
peak=   -3.409 closest distance to " O   HOH Z  39 " =    1.100
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.305
peak=   -3.406 closest distance to " CD  PRO A 213 " =    2.115
peak=   -3.405 closest distance to " O   HOH Z  52 " =    1.328
peak=   -3.403 closest distance to " CZ2 TRP A 274 " =    0.850
peak=   -3.398 closest distance to " CA  GLY A 203 " =    2.348
peak=   -3.389 closest distance to " CG  GLN A 278 " =    2.280
peak=   -3.388 closest distance to " ND2 ASN A 187 " =    1.525
peak=   -3.380 closest distance to " O   HOH Z 139 " =    1.045
peak=   -3.379 closest distance to " CE1 TYR A 169 " =    2.618
peak=   -3.378 closest distance to " O   HOH Z 179 " =    2.278
peak=   -3.376 closest distance to " O   GLY A 211 " =    1.250
peak=   -3.370 closest distance to " O   VAL A 189 " =    2.428
peak=   -3.364 closest distance to " O   ARG A 145 " =    1.431
peak=   -3.362 closest distance to " CB  PRO A  54 " =    2.541
peak=   -3.353 closest distance to " O   HOH Z 353 " =    2.048
peak=   -3.349 closest distance to " O   HOH Z 298 " =    1.108
peak=   -3.344 closest distance to " C   ASN A 285 " =    2.393
peak=   -3.343 closest distance to " CB  ALA A 114 " =    2.396
peak=   -3.338 closest distance to " O   HOH Z 112 " =    1.428
peak=   -3.325 closest distance to " CG  PRO A 163 " =    2.422
peak=   -3.325 closest distance to " O   HOH Z 118 " =    1.853
peak=   -3.318 closest distance to " C   LYS A  76 " =    1.291
peak=   -3.315 closest distance to " CD1 LEU A 101 " =    2.717
peak=   -3.309 closest distance to " O   HOH Z  51 " =    0.954
peak=   -3.297 closest distance to " NZ  LYS A 166 " =    1.160
peak=   -3.290 closest distance to " O   VAL A  67 " =    2.577
peak=   -3.289 closest distance to " O   HOH Z 350 " =    1.779
peak=   -3.289 closest distance to " N   VAL A 125 " =    0.927
peak=   -3.285 closest distance to " O   HOH Z 359 " =    3.368
peak=   -3.284 closest distance to " O   HOH Z  11 " =    2.030
peak=   -3.284 closest distance to " O   HOH Z  52 " =    1.909
peak=   -3.284 closest distance to " CD  GLN A  58 " =    0.846
peak=   -3.282 closest distance to " OG  SER A 206 " =    1.613
peak=   -3.276 closest distance to " O   SER A  62 " =    2.337
peak=   -3.271 closest distance to " O   HOH Z 286 " =    1.773
peak=   -3.268 closest distance to " OG  SER A  28 " =    2.014
peak=   -3.264 closest distance to " O   HOH Z 275 " =    1.567
peak=   -3.260 closest distance to " O   HOH Z 368 " =    2.480
peak=   -3.255 closest distance to " CE2 PHE A 218 " =    2.526
peak=   -3.251 closest distance to " CZ  PHE A 130 " =    0.987
peak=   -3.249 closest distance to " CB  CYS A 254 " =    1.899
peak=   -3.245 closest distance to " O   HOH Z  90 " =    3.006
peak=   -3.243 closest distance to " CD  GLU A 277 " =    1.111
peak=   -3.242 closest distance to " CE BMET A  47 " =    1.660
peak=   -3.241 closest distance to " O   HOH Z 238 " =    0.861
peak=   -3.229 closest distance to " O   TYR A  30 " =    2.542
peak=   -3.226 closest distance to " O   HOH Z 193 " =    1.556
peak=   -3.226 closest distance to " CG1 VAL A 112 " =    2.552
peak=   -3.226 closest distance to " O   ASP A  27 " =    1.804
peak=   -3.222 closest distance to " CB  ALA A 248 " =    2.444
peak=   -3.222 closest distance to " OH  TYR A 247 " =    1.764
peak=   -3.214 closest distance to " C   LEU A 101 " =    1.045
peak=   -3.213 closest distance to " O   TRP A  70 " =    1.412
peak=   -3.211 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.200 closest distance to " O   HOH Z  60 " =    1.668
peak=   -3.199 closest distance to " O   HOH Z 313 " =    1.447
peak=   -3.196 closest distance to " O   HOH Z  73 " =    2.024
peak=   -3.194 closest distance to " N   ALA A 226 " =    2.128
peak=   -3.188 closest distance to " O   HOH Z 143 " =    1.312
peak=   -3.186 closest distance to " CD2 HIS A 207 " =    2.468
peak=   -3.180 closest distance to " O   HOH Z  32 " =    1.957
peak=   -3.176 closest distance to " O   HOH Z 389 " =    1.476
peak=   -3.176 closest distance to " O   SER A  87 " =    2.001
peak=   -3.175 closest distance to " CG1 VAL A  78 " =    2.302
peak=   -3.174 closest distance to " CG  ASP A 231 " =    0.768
peak=   -3.173 closest distance to " C   LEU A 143 " =    1.221
peak=   -3.171 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.171 closest distance to " C   GLU A 236 " =    0.908
peak=   -3.169 closest distance to " CG2AVAL A  41 " =    2.841
peak=   -3.169 closest distance to " CB  ALA A 244 " =    2.139
peak=   -3.164 closest distance to " O   HOH Z  38 " =    1.547
peak=   -3.160 closest distance to " O   HOH Z 241 " =    1.353
peak=   -3.159 closest distance to " O   HOH Z 417 " =    2.898
peak=   -3.155 closest distance to " N   GLY A  23 " =    2.314
peak=   -3.154 closest distance to " N   ASP A 270 " =    1.494
peak=   -3.144 closest distance to " O   HOH Z 216 " =    1.700
peak=   -3.143 closest distance to " O   HOH Z 131 " =    4.009
peak=   -3.142 closest distance to " OD2 ASP A 171 " =    2.623
peak=   -3.142 closest distance to " OD2 ASP A 171 " =    1.804
peak=   -3.141 closest distance to " CB  CYS A 201 " =    2.186
peak=   -3.140 closest distance to " O   HOH Z 134 " =    1.785
peak=   -3.137 closest distance to " O   HOH Z  52 " =    1.669
peak=   -3.135 closest distance to " ND2 ASN A  60 " =    1.529
peak=   -3.128 closest distance to " O   HOH Z 368 " =    1.489
peak=   -3.124 closest distance to " O   HOH Z 429 " =    1.793
peak=   -3.121 closest distance to " CE  LYS A  76 " =    2.710
peak=   -3.114 closest distance to " ND2 ASN A 209 " =    2.063
peak=   -3.114 closest distance to " CD2 LEU A 143 " =    2.635
peak=   -3.111 closest distance to " NH2 ARG A 219 " =    1.818
peak=   -3.106 closest distance to " CB  PHE A 283 " =    2.746
peak=   -3.104 closest distance to " CE2 TRP A  70 " =    2.365
peak=   -3.103 closest distance to " CD2 TYR A 293 " =    1.888
peak=   -3.103 closest distance to " O   HOH Z 297 " =    3.791
peak=   -3.101 closest distance to " CZ BARG A 275 " =    1.612
peak=   -3.097 closest distance to " O   HOH Z   2 " =    1.816
peak=   -3.097 closest distance to " O   HOH Z 184 " =    1.903
peak=   -3.092 closest distance to " OD1 ASN A 187 " =    1.478
peak=   -3.087 closest distance to " OG  SER A 245 " =    1.253
peak=   -3.083 closest distance to " CA  GLY A 133 " =    1.988
peak=   -3.074 closest distance to " CD2 LEU A 300 " =    2.547
peak=   -3.069 closest distance to " O   ALA A   1 " =    1.282

================= 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    :  0.4809 0.4736   6.283787e+00   6.269625e+00
   1_bss:  0.4736 0.4597   6.277738e+00   6.261295e+00
   1_xyz:  0.3927 0.4074   6.171799e+00   6.195857e+00
   1_adp:  0.3460 0.3995   6.095782e+00   6.179896e+00
   1_occ:  0.3456 0.4005   6.095237e+00   6.180434e+00
   2_bss:  0.3427 0.3966   6.095563e+00   6.179415e+00
   2_xyz:  0.2480 0.3027   5.821323e+00   5.971802e+00
   2_adp:  0.2177 0.2786   5.722310e+00   5.899496e+00
   2_occ:  0.2174 0.2778   5.721194e+00   5.898252e+00
   3_bss:  0.2152 0.2747   5.719104e+00   5.894158e+00
   3_xyz:  0.1665 0.2167   5.485631e+00   5.686961e+00
   3_adp:  0.1557 0.2053   5.430290e+00   5.639506e+00
   3_occ:  0.1556 0.2050   5.429694e+00   5.638496e+00
   4_bss:  0.1553 0.2042   5.428604e+00   5.636113e+00
   4_xyz:  0.1374 0.1871   5.326546e+00   5.545572e+00
   4_adp:  0.1336 0.1804   5.297178e+00   5.511139e+00
   4_occ:  0.1336 0.1805   5.297163e+00   5.511249e+00
   5_bss:  0.1335 0.1804   5.296874e+00   5.511205e+00
   5_xyz:  0.1247 0.1702   5.238565e+00   5.462926e+00
   5_adp:  0.1226 0.1689   5.227362e+00   5.456803e+00
   5_occ:  0.1225 0.1687   5.226989e+00   5.456148e+00
   5_bss:  0.1229 0.1684   5.227054e+00   5.454785e+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:  0.300  20.000   8.574   8.630   7.424   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.574   8.630   7.424   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.574   8.630   7.424   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.574   8.630   7.424   0.000   0.000   0.000
   2_bss:  0.336  47.972   5.333   4.657   4.478   0.000   0.000   0.000
   2_xyz:  0.336  47.972   5.333   4.657   4.478   0.000   0.000   0.000
   2_adp:  0.336  47.972   5.333   4.657   4.478   0.000   0.000   0.000
   2_occ:  0.336  47.972   5.333   4.657   4.478   0.000   0.000   0.000
   3_bss:  0.322  54.378   2.895   2.219   3.325   0.000   0.000   0.000
   3_xyz:  0.322  54.378   2.895   2.219   3.325   0.000   0.000   0.000
   3_adp:  0.322  54.378   2.895   2.219   3.325   0.000   0.000   0.000
   3_occ:  0.322  54.378   2.895   2.219   3.325   0.000   0.000   0.000
   4_bss:  0.332  54.378   1.855   1.257   2.640   0.000   0.000   0.000
   4_xyz:  0.332  54.378   1.855   1.257   2.640   0.000   0.000   0.000
   4_adp:  0.332  54.378   1.855   1.257   2.640   0.000   0.000   0.000
   4_occ:  0.332  54.378   1.855   1.257   2.640   0.000   0.000   0.000
   5_bss:  0.322  53.211   1.714   1.084   2.636   0.000   0.000   0.000
   5_xyz:  0.322  53.211   1.714   1.084   2.636   0.000   0.000   0.000
   5_adp:  0.322  53.211   1.714   1.084   2.636   0.000   0.000   0.000
   5_occ:  0.322  53.211   1.714   1.084   2.636   0.000   0.000   0.000
   5_bss:  0.322  55.022  -0.097  -0.727   0.824   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.455 0.4264  0.4997    70105.772
   1_bss:  57.609 0.4233  0.6279    68610.341
   1_xyz:  48.429 0.5386  0.7790    51214.548
   1_adp:  45.304 0.5779  0.8934    47840.465
   1_occ:  45.373 0.5770  0.8914    47928.489
   2_bss:  45.091 0.5804  0.7986    47541.500
   2_xyz:  32.034 0.7339  0.9706    24863.501
   2_adp:  28.504 0.7737  0.9967    20522.698
   2_occ:  28.455 0.7742  0.9962    20428.818
   3_bss:  28.273 0.7761  0.9294    20195.672
   3_xyz:  21.128 0.8502  0.9883    12063.250
   3_adp:  19.767 0.8641  0.9962    10981.179
   3_occ:  19.753 0.8642  0.9959    10952.047
   4_bss:  19.695 0.8646  0.9647    10872.576
   4_xyz:  17.605 0.8839  0.9715     8892.418
   4_adp:  16.763 0.8918  0.9711     8307.708
   4_occ:  16.773 0.8917  0.9708     8300.052
   5_bss:  16.767 0.8917  0.9670     8295.522
   5_xyz:  15.655 0.9014  0.9728     7471.408
   5_adp:  15.474 0.9031  0.9695     7361.701
   5_occ:  15.465 0.9031  0.9695     7350.200
   5_bss:  15.456 0.9031  0.9692     7314.470
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3923e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3923e+01
   1_xyz:   1.675  0.013  0.107 18.331  0.007  4.109   1.3996e-01
   1_adp:   1.675  0.013  0.107 18.331  0.007  4.109   1.3996e-01
   1_occ:   1.675  0.013  0.107 18.331  0.007  4.109   1.3996e-01
   2_bss:   1.675  0.013  0.107 18.331  0.007  4.109   1.3996e-01
   2_xyz:   1.253  0.010  0.090 16.792  0.005  4.109   9.5040e-02
   2_adp:   1.253  0.010  0.090 16.792  0.005  4.109   9.5040e-02
   2_occ:   1.253  0.010  0.090 16.792  0.005  4.109   9.5040e-02
   3_bss:   1.253  0.010  0.090 16.792  0.005  4.109   9.5040e-02
   3_xyz:   0.976  0.007  0.073 15.519  0.003  4.125   6.0009e-02
   3_adp:   0.976  0.007  0.073 15.519  0.003  4.125   6.0009e-02
   3_occ:   0.976  0.007  0.073 15.519  0.003  4.125   6.0009e-02
   4_bss:   0.976  0.007  0.073 15.519  0.003  4.125   6.0009e-02
   4_xyz:   0.934  0.006  0.074 15.230  0.003  4.111   5.5034e-02
   4_adp:   0.934  0.006  0.074 15.230  0.003  4.111   5.5034e-02
   4_occ:   0.934  0.006  0.074 15.230  0.003  4.111   5.5034e-02
   5_bss:   0.934  0.006  0.074 15.230  0.003  4.111   5.5034e-02
   5_xyz:   0.963  0.007  0.075 15.197  0.003  4.115   5.7445e-02
   5_adp:   0.963  0.007  0.075 15.197  0.003  4.115   5.7445e-02
   5_occ:   0.963  0.007  0.075 15.197  0.003  4.115   5.7445e-02
   5_bss:   0.963  0.007  0.075 15.197  0.003  4.115   5.7445e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9908e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9908e+00
   1_xyz:  13.476  0.168  0.418 88.095  0.040  2.233   1.0040e-01
   1_adp:  13.476  0.168  0.418 88.095  0.040  2.233   1.0040e-01
   1_occ:  13.476  0.168  0.418 88.095  0.040  2.233   1.0040e-01
   2_bss:  13.476  0.168  0.418 88.095  0.040  2.233   1.0040e-01
   2_xyz:   6.699  0.086  0.335 84.610  0.043  2.241   6.6902e-02
   2_adp:   6.699  0.086  0.335 84.610  0.043  2.241   6.6902e-02
   2_occ:   6.699  0.086  0.335 84.610  0.043  2.241   6.6902e-02
   3_bss:   6.699  0.086  0.335 84.610  0.043  2.241   6.6902e-02
   3_xyz:   8.033  0.045  0.342 81.671  0.024  2.278   5.9846e-02
   3_adp:   8.033  0.045  0.342 81.671  0.024  2.278   5.9846e-02
   3_occ:   8.033  0.045  0.342 81.671  0.024  2.278   5.9846e-02
   4_bss:   8.033  0.045  0.342 81.671  0.024  2.278   5.9846e-02
   4_xyz:   7.410  0.052  0.357 82.018  0.035  2.369   3.1310e-02
   4_adp:   7.410  0.052  0.357 82.018  0.035  2.369   3.1310e-02
   4_occ:   7.410  0.052  0.357 82.018  0.035  2.369   3.1310e-02
   5_bss:   7.410  0.052  0.357 82.018  0.035  2.369   3.1310e-02
   5_xyz:   8.039  0.058  0.397 83.634  0.026  2.331   4.1359e-02
   5_adp:   8.039  0.058  0.397 83.634  0.026  2.331   4.1359e-02
   5_occ:   8.039  0.058  0.397 83.634  0.026  2.331   4.1359e-02
   5_bss:   8.039  0.058  0.397 83.634  0.026  2.331   4.1359e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.74   0.00  14.36  72.26   0.00  11.80  79.74   0.00  28.28
   1_occ:  79.74   0.00  14.36  72.26   0.00  11.80  79.74   0.00  28.28
   2_bss:  79.74   0.00  14.36  72.26   0.00  11.80  79.74   0.00  28.28
   2_xyz:  79.74   0.00  14.36  72.26   0.00  11.80  79.74   0.00  28.28
   2_adp:  82.67   0.00  13.59  80.57   0.00   9.77  82.67   0.00  34.38
   2_occ:  82.67   0.00  13.59  80.57   0.00   9.77  82.67   0.00  34.38
   3_bss:  82.67   0.00  13.59  80.57   0.00   9.77  82.67   0.00  34.38
   3_xyz:  82.67   0.00  13.59  80.57   0.00   9.77  82.67   0.00  34.38
   3_adp:  82.52   0.00  13.65  80.71   0.00   9.54  82.52   2.60  36.00
   3_occ:  82.52   0.00  13.65  80.71   0.00   9.54  82.52   2.60  36.00
   4_bss:  82.52   0.00  13.65  80.71   0.00   9.54  82.52   2.60  36.00
   4_xyz:  82.52   0.00  13.65  80.71   0.00   9.54  82.52   2.60  36.00
   4_adp:  82.82   0.00  13.51  82.82   0.00   9.27  78.24   2.79  36.60
   4_occ:  82.82   0.00  13.51  82.82   0.00   9.27  78.24   2.79  36.60
   5_bss:  82.82   0.00  13.51  82.82   0.00   9.27  78.24   2.79  36.60
   5_xyz:  82.82   0.00  13.51  82.82   0.00   9.27  78.24   2.79  36.60
   5_adp:  85.55   0.00  13.63  85.55   0.00   9.24  82.05   2.68  37.50
   5_occ:  85.55   0.00  13.63  85.55   0.00   9.24  82.05   2.68  37.50
   5_bss:  87.36   1.81  15.44  87.36   1.81  11.06  83.86   4.49  39.31
------------------------------------------------------------------------
 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:    1.230    0.008    0.409
   1_adp:    1.230    0.008    0.409
   1_occ:    1.230    0.008    0.409
   2_bss:    1.230    0.008    0.409
   2_xyz:    1.487    0.035    0.605
   2_adp:    1.487    0.035    0.605
   2_occ:    1.487    0.035    0.605
   3_bss:    1.487    0.035    0.605
   3_xyz:    1.735    0.059    0.670
   3_adp:    1.735    0.059    0.670
   3_occ:    1.735    0.059    0.670
   4_bss:    1.735    0.059    0.670
   4_xyz:    1.880    0.012    0.710
   4_adp:    1.880    0.012    0.710
   4_occ:    1.880    0.012    0.710
   5_bss:    1.880    0.012    0.710
   5_xyz:    2.001    0.021    0.729
   5_adp:    2.001    0.021    0.729
   5_occ:    2.001    0.021    0.729
   5_bss:    2.001    0.021    0.729
------------------------------------------------------------------------

CPU time actual refinement: 349.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/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_1117/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1117/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.74 
  Macro-tasks:
    bulk solvent and scale       = 41.92  
    individual site refinement   = 146.41 
    weights calculation          = 32.08  
    collect and process          = 6.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.97 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 110.98 
    alpha_beta                      = 8.09   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 120.77 
    fmodel                         = 7.21   
    r_factors                      = 0.26   
    phase_errors                   = 10.50  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 261.63 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.904 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    647 calls, 110.61 s
gradients_fft:          591 calls, 107.22 s

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

# Date 2008-01-16 Time 03:14:15 PST -0800 (1200482055.90 s)
Start R-work = 0.4809, R-free = 0.4736 (no bulk solvent and anisotropic scale)
Final R-work = 0.1391, R-free = 0.1850 (no bulk solvent and anisotropic scale)

Start R-work = 0.4736, R-free = 0.4597
Final R-work = 0.1229, R-free = 0.1684