# Date 2008-01-16 Time 01:47:16 PST -0800 (1200476836.85 s)
#phil __OFF__

Command line arguments: "../571.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13120
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 571

-------------------------------------------------------------------------------
  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: (69.8988, 47.3993, 88.5498, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (69.8988, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99079
Completeness in resolution range: 0.94464
Completeness with d_max=infinity: 0.941734

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0370
                             d_min =   1.9908

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: (69.8988, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99079
Completeness in resolution range: 0.94464
Completeness with d_max=infinity: 0.941734

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0375 -  4.2596 [2184/2211]  1964   220  10.1%
  bin  2:  4.2596 -  3.3937 [2082/2098]  1871   211  10.1%
  bin  3:  3.3937 -  2.9685 [2071/2090]  1869   202   9.8%
  bin  4:  2.9685 -  2.6988 [2050/2080]  1844   206  10.0%
  bin  5:  2.6988 -  2.5063 [2013/2032]  1813   200   9.9%
  bin  6:  2.5063 -  2.3591 [2027/2063]  1820   207  10.2%
  bin  7:  2.3591 -  2.2414 [2017/2050]  1818   199   9.9%
  bin  8:  2.2414 -  2.1441 [2002/2037]  1796   206  10.3%
  bin  9:  2.1441 -  2.0618 [1994/2021]  1803   191   9.6%
  bin 10:  2.0618 -  1.9908 [1149/2055]  1032   117  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/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: 0.12 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:
        1.36 -     2.07: 7
        2.07 -     2.78: 557
        2.78 -     3.49: 4420
        3.49 -     4.19: 9199
        4.19 -     4.90: 13698
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.364 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.643 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.651 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.692 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.692 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27876 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_571/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/model_refine_001.geo

CPU time processing inputs: 7.97


============================ 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 = 69.89875 47.3993 88.54975 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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4831   r_free= 0.4700   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.285868                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1415  157 0.3904 0.3711      6.6057       6.561|
|  2:  4.7508 -  3.7907 0.99   1369  153 0.4030 0.4716      6.7853      6.9558|
|  3:  3.7907 -  3.3174 0.99   1329  147 0.4523 0.4120      6.6917      6.6414|
|  4:  3.3174 -  3.0168 0.99   1327  140 0.4752 0.4307       6.521      6.4718|
|  5:  3.0168 -  2.8020 0.99   1303  153 0.5137 0.4716      6.3701      6.3817|
|  6:  2.8020 -  2.6378 0.99   1324  147 0.5109 0.5712       6.279      6.2221|
|  7:  2.6378 -  2.5063 0.99   1294  142 0.5100 0.4546      6.2249      6.1223|
|  8:  2.5063 -  2.3977 0.98   1298  148 0.5333 0.4463      6.2065      6.1484|
|  9:  2.3977 -  2.3057 0.98   1309  142 0.5212 0.5457      6.1159      6.1494|
| 10:  2.3057 -  2.2264 0.98   1295  136 0.5441 0.4642       6.115      6.0634|
| 11:  2.2264 -  2.1570 1.00   1288  154 0.5179 0.5497       6.024      6.0828|
| 12:  2.1570 -  2.0955 0.97   1281  134 0.5413 0.5266      5.9611      6.0118|
| 13:  2.0955 -  2.0405 0.97   1275  141 0.5287 0.5386      5.8924      5.8165|
| 14:  2.0405 -  1.9908 0.41    523   65 0.5245 0.4657      5.8888      5.7804|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7508  1415   157  0.71  33.37   0.79     0.72      66911.75|
|  2:  4.7508 -  3.7907  1369   153  0.70  35.49   0.87     0.75     108368.13|
|  3:  3.7907 -  3.3174  1329   147  0.60  43.91   0.81     0.71     113205.40|
|  4:  3.3174 -  3.0168  1327   140  0.51  51.23   0.78     0.59      99232.81|
|  5:  3.0168 -  2.8020  1303   153  0.41  58.69   0.73     0.48      80662.12|
|  6:  2.8020 -  2.6378  1324   147  0.36  63.12   0.72     0.41      75042.19|
|  7:  2.6378 -  2.5063  1294   142  0.38  61.14   0.73     0.43      63738.84|
|  8:  2.5063 -  2.3977  1298   148  0.43  57.93   0.72     0.49      53318.93|
|  9:  2.3977 -  2.3057  1309   142  0.43  57.75   0.70     0.50      48972.53|
| 10:  2.3057 -  2.2264  1295   136  0.37  62.30   0.72     0.43      47492.83|
| 11:  2.2264 -  2.1570  1288   154  0.31  67.09   0.74     0.38      49112.58|
| 12:  2.1570 -  2.0955  1281   134  0.30  67.95   0.73     0.38      44423.89|
| 13:  2.0955 -  2.0405  1275   141  0.33  65.16   0.72     0.41      37187.64|
| 14:  2.0405 -  1.9908   523    65  0.43  58.18   0.74     0.44      25773.08|
|alpha:            min =        0.38 max =            0.75 mean =         0.51|
|beta:             min =    25773.08 max =       113205.40 mean =     67383.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.97 mean =        55.57|
|phase err.(test): min =        0.00 max =           89.91 mean =        55.78|
|-----------------------------------------------------------------------------|

============================== 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 = 14.375053             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.600   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.265145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.621   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.936:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.936 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1486 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2585 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3844 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5000 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.529:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.529 -  4.900:     7610 |
|-----------------------------------------------------------------------------|
|-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 |       54.359 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.887 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    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 = 12.170)------------------------------------------|
|    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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4885   r_free= 0.4720   ksol= 0.00   Bsol= 0.00   scale= 0.753    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.288809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4741   r_free= 0.4596   ksol= 0.31   Bsol= 10.16   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.52,12.04,0.00,0.00,0.00); trace/3= 8.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.279736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.575732             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.140404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.200   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4741      final r-factor (work) = 0.3905          |
| start r-factor (free) = 0.4596      final r-factor (free) = 0.4158          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.8797 = 12.58 * 0.50 * 6.2853 + 1.00 * 54.3586                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.0673 = 12.58 * 0.50 * 6.1896 + 1.00 * 0.1478                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3905      final r-factor (work) = 0.3458          |
| start r-factor (free) = 0.4158      final r-factor (free) = 0.3958          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0731 = 1.14 * 1.00 * 6.1896 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9783 = 1.14 * 1.00 * 6.1039 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.82   13.79    None  None   None       |
|    all(noH): 2823   0      0.00    81.82   13.79    None  None   None       |
|    Sol.    : 438    0      0.00    81.82   27.14    None  None   None       |
|    Mac.    : 2385   0      0.00    71.85   11.34    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 -   8.182: 1171   |   5:    40.909 -  49.090:   60        |
|      1:     8.182 -  16.364:  788   |   6:    49.090 -  57.272:   46        |
|      2:    16.364 -  24.545:  402   |   7:    57.272 -  65.454:   15        |
|      3:    24.545 -  32.727:  216   |   8:    65.454 -  73.636:    5        |
|      4:    32.727 -  40.909:  113   |   9:    73.636 -  81.817:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3458 r_free = 0.3958             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3453 r_free = 0.3967             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3453   r_free= 0.3967   ksol= 0.31   Bsol= 10.16   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,8.52,12.04,0.00,0.00,0.00); trace/3= 8.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.082783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3420   r_free= 0.3922   ksol= 0.32   Bsol= 47.34   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,4.75,7.93,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.082954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.269628              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.911   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.512320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.366  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3420      final r-factor (work) = 0.2683          |
| start r-factor (free) = 0.3922      final r-factor (free) = 0.3235          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2182 = 5.27 * 0.50 * 6.0992 + 1.00 * 0.1478                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8264 = 5.27 * 0.50 * 5.9747 + 1.00 * 0.0843                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2683      final r-factor (work) = 0.2483          |
| start r-factor (free) = 0.3235      final r-factor (free) = 0.3027          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0783 = 0.51 * 1.00 * 5.9747 + 1.00 * 0.0174                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0089 = 0.51 * 1.00 * 5.8490 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.82   13.44    None  None   None       |
|    all(noH): 2823   0      0.00    81.82   13.44    None  None   None       |
|    Sol.    : 438    0      0.00    81.82   32.20    None  None   None       |
|    Mac.    : 2385   0      0.00    68.70   9.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.182: 1295   |   5:    40.909 -  49.090:   95        |
|      1:     8.182 -  16.364:  750   |   6:    49.090 -  57.272:   38        |
|      2:    16.364 -  24.545:  329   |   7:    57.272 -  65.454:   14        |
|      3:    24.545 -  32.727:  175   |   8:    65.454 -  73.635:    8        |
|      4:    32.727 -  40.909:  115   |   9:    73.635 -  81.817:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2483 r_free = 0.3027             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2480 r_free = 0.3031             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2480   r_free= 0.3031   ksol= 0.32   Bsol= 47.34   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,4.75,7.93,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.825359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2470   r_free= 0.3034   ksol= 0.34   Bsol= 70.19   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,3.15,5.38,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.827031                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.977394              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.791   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.401510              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.220  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2470      final r-factor (work) = 0.1808          |
| start r-factor (free) = 0.3034      final r-factor (free) = 0.2324          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6465 = 4.98 * 0.50 * 5.8513 + 1.00 * 0.0843                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2681 = 4.98 * 0.50 * 5.7011 + 1.00 * 0.0796                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1808      final r-factor (work) = 0.1652          |
| start r-factor (free) = 0.2324      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3014 = 0.40 * 1.00 * 5.7011 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2237 = 0.40 * 1.00 * 5.5058 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.85   13.29    None  None   None       |
|    all(noH): 2823   0      0.00    79.85   13.29    None  None   None       |
|    Sol.    : 438    0      1.86    79.85   35.77    None  None   None       |
|    Mac.    : 2385   0      0.00    69.91   9.17     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 -   7.985: 1400   |   5:    39.925 -  47.910:  114        |
|      1:     7.985 -  15.970:  757   |   6:    47.910 -  55.894:   64        |
|      2:    15.970 -  23.955:  210   |   7:    55.894 -  63.879:   25        |
|      3:    23.955 -  31.940:  121   |   8:    63.879 -  71.864:   11        |
|      4:    31.940 -  39.925:  116   |   9:    71.864 -  79.849:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1652 r_free = 0.2149             target_work(ml) = 5.471         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1650 r_free = 0.2148             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1650   r_free= 0.2148   ksol= 0.34   Bsol= 70.19   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,3.15,5.38,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.470251                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1643   r_free= 0.2138   ksol= 0.33   Bsol= 68.80   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.16,3.94,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.469970                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.198351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.504  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.099944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.427   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1643      final r-factor (work) = 0.1335          |
| start r-factor (free) = 0.2138      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6486 = 4.20 * 0.50 * 5.5112 + 1.00 * 0.0796                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3899 = 4.20 * 0.50 * 5.3862 + 1.00 * 0.0832                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9491 = 1.10 * 1.00 * 5.3862 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9126 = 1.10 * 1.00 * 5.2747 + 1.00 * 0.1106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.88   13.42    None  None   None       |
|    all(noH): 2823   0      0.00    84.88   13.42    None  None   None       |
|    Sol.    : 438    0      1.33    84.88   37.55    None  None   None       |
|    Mac.    : 2385   0      0.00    71.42   8.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.488: 1505   |   5:    42.439 -  50.927:  118        |
|      1:     8.488 -  16.976:  684   |   6:    50.927 -  59.415:   65        |
|      2:    16.976 -  25.464:  193   |   7:    59.415 -  67.903:   22        |
|      3:    25.464 -  33.952:  112   |   8:    67.903 -  76.391:   11        |
|      4:    33.952 -  42.439:  109   |   9:    76.391 -  84.879:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1755             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1755             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1755   ksol= 0.33   Bsol= 68.80   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.16,3.94,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.261837                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1756   ksol= 0.33   Bsol= 66.48   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.16,2.05,3.66,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.260063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.398074              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.104  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.983433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.025   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1266      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1756      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4066 = 2.40 * 0.50 * 5.2737 + 1.00 * 0.0832                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3623 = 2.40 * 0.50 * 5.2497 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4344 = 1.98 * 1.00 * 5.2497 + 1.00 * 0.0219                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3867 = 1.98 * 1.00 * 5.2291 + 1.00 * 0.0151                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.98   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    93.98   13.51    None  None   None       |
|    Sol.    : 438    0      1.23    93.98   38.55    None  None   None       |
|    Mac.    : 2385   0      0.00    81.08   8.91     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.398: 1681   |   5:    46.988 -  56.385:   96        |
|      1:     9.398 -  18.795:  572   |   6:    56.385 -  65.783:   56        |
|      2:    18.795 -  28.193:  176   |   7:    65.783 -  75.180:   27        |
|      3:    28.193 -  37.590:  110   |   8:    75.180 -  84.578:    7        |
|      4:    37.590 -  46.988:   96   |   9:    84.578 -  93.975:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1701             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1213 r_free = 0.1700             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1700   ksol= 0.33   Bsol= 66.48   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.16,2.05,3.66,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228531                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1415  157 0.0997 0.1329      5.4084       5.567|
|  2:  4.7508 -  3.7907 0.99   1369  153 0.0883 0.1098      5.4651      5.6743|
|  3:  3.7907 -  3.3174 0.99   1329  147 0.1140 0.1587      5.5279      5.8655|
|  4:  3.3174 -  3.0168 0.99   1327  140 0.1284 0.1758       5.497      5.6934|
|  5:  3.0168 -  2.8020 0.99   1303  153 0.1472 0.1689      5.4209      5.5611|
|  6:  2.8020 -  2.6378 0.99   1324  147 0.1354 0.2289      5.3018      5.6293|
|  7:  2.6378 -  2.5063 0.99   1294  142 0.1413 0.1762      5.2679      5.4019|
|  8:  2.5063 -  2.3977 0.98   1298  148 0.1268 0.1781      5.1702      5.3964|
|  9:  2.3977 -  2.3057 0.98   1309  142 0.1307 0.2210      5.1168       5.461|
| 10:  2.3057 -  2.2264 0.98   1295  136 0.1269 0.1700      5.0564      5.2169|
| 11:  2.2264 -  2.1570 1.00   1288  154 0.1276 0.2043        5.03      5.3918|
| 12:  2.1570 -  2.0955 0.97   1281  134 0.1280 0.1756      4.9751        5.24|
| 13:  2.0955 -  2.0405 0.97   1275  141 0.1211 0.1924      4.8716       5.083|
| 14:  2.0405 -  1.9908 0.41    523   65 0.1059 0.1931       4.749      5.0792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7508  1415   157  0.94   9.65   0.96     0.94       7920.05|
|  2:  4.7508 -  3.7907  1369   153  0.95   8.55   1.00     0.98       9643.16|
|  3:  3.7907 -  3.3174  1329   147  0.93  12.10   1.02     1.02      11355.28|
|  4:  3.3174 -  3.0168  1327   140  0.91  14.37   1.00     0.98      11141.03|
|  5:  3.0168 -  2.8020  1303   153  0.89  17.61   0.99     0.96       9995.80|
|  6:  2.8020 -  2.6378  1324   147  0.88  18.70   0.97     0.94       8835.88|
|  7:  2.6378 -  2.5063  1294   142  0.89  17.36   0.98     0.94       7566.20|
|  8:  2.5063 -  2.3977  1298   148  0.89  17.14   0.98     0.95       6654.44|
|  9:  2.3977 -  2.3057  1309   142  0.89  17.56   0.99     0.95       5981.87|
| 10:  2.3057 -  2.2264  1295   136  0.88  17.99   0.98     0.93       5415.23|
| 11:  2.2264 -  2.1570  1288   154  0.88  18.47   0.98     0.93       5369.81|
| 12:  2.1570 -  2.0955  1281   134  0.89  17.90   0.98     0.96       4904.01|
| 13:  2.0955 -  2.0405  1275   141  0.88  18.44   0.97     0.94       4121.96|
| 14:  2.0405 -  1.9908   523    65  0.90  15.93   0.94     0.90       3109.86|
|alpha:            min =        0.90 max =            1.02 mean =         0.95|
|beta:             min =     3109.86 max =        11355.28 mean =      7507.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.54 mean =        15.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1699   ksol= 0.33   Bsol= 65.24   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.26,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228614                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1699   ksol= 0.33   Bsol= 65.24   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.26,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228614                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1415  157 0.0995 0.1329      5.4062      5.5662|
|  2:  4.7508 -  3.7907 0.99   1369  153 0.0882 0.1096      5.4645      5.6726|
|  3:  3.7907 -  3.3174 0.99   1329  147 0.1140 0.1589      5.5278      5.8665|
|  4:  3.3174 -  3.0168 0.99   1327  140 0.1285 0.1760      5.4977      5.6942|
|  5:  3.0168 -  2.8020 0.99   1303  153 0.1472 0.1691      5.4216      5.5618|
|  6:  2.8020 -  2.6378 0.99   1324  147 0.1354 0.2291      5.3023      5.6298|
|  7:  2.6378 -  2.5063 0.99   1294  142 0.1413 0.1766      5.2687      5.4031|
|  8:  2.5063 -  2.3977 0.98   1298  148 0.1269 0.1782       5.171      5.3969|
|  9:  2.3977 -  2.3057 0.98   1309  142 0.1307 0.2212      5.1172      5.4611|
| 10:  2.3057 -  2.2264 0.98   1295  136 0.1269 0.1700      5.0565      5.2172|
| 11:  2.2264 -  2.1570 1.00   1288  154 0.1276 0.2039      5.0299      5.3912|
| 12:  2.1570 -  2.0955 0.97   1281  134 0.1280 0.1754      4.9749      5.2394|
| 13:  2.0955 -  2.0405 0.97   1275  141 0.1210 0.1925      4.8716      5.0834|
| 14:  2.0405 -  1.9908 0.41    523   65 0.1059 0.1928      4.7501      5.0786|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7508  1415   157  0.94   9.62   0.97     0.94       7890.82|
|  2:  4.7508 -  3.7907  1369   153  0.95   8.54   1.01     0.99       9624.94|
|  3:  3.7907 -  3.3174  1329   147  0.93  12.10   1.02     1.02      11353.06|
|  4:  3.3174 -  3.0168  1327   140  0.91  14.38   1.01     0.99      11153.62|
|  5:  3.0168 -  2.8020  1303   153  0.89  17.62   1.00     0.97      10014.78|
|  6:  2.8020 -  2.6378  1324   147  0.88  18.72   0.98     0.95       8845.60|
|  7:  2.6378 -  2.5063  1294   142  0.89  17.38   0.99     0.95       7581.59|
|  8:  2.5063 -  2.3977  1298   148  0.89  17.16   0.99     0.95       6665.28|
|  9:  2.3977 -  2.3057  1309   142  0.89  17.59   1.00     0.96       5992.77|
| 10:  2.3057 -  2.2264  1295   136  0.88  17.98   0.99     0.94       5412.54|
| 11:  2.2264 -  2.1570  1288   154  0.88  18.47   0.99     0.94       5366.04|
| 12:  2.1570 -  2.0955  1281   134  0.89  17.89   0.99     0.98       4901.05|
| 13:  2.0955 -  2.0405  1275   141  0.88  18.44   0.98     0.95       4121.59|
| 14:  2.0405 -  1.9908   523    65  0.90  15.93   0.96     0.91       3110.01|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3110.01 max =        11353.06 mean =      7508.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.55 mean =        15.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.51    96.49   16.02    None  None   None       |
|    all(noH): 2823   0      2.51    96.49   16.02    None  None   None       |
|    Sol.    : 438    0      3.74    96.49   41.06    None  None   None       |
|    Mac.    : 2385   0      2.51    83.59   11.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.510 -  11.908: 1681   |   5:    49.498 -  58.895:   96        |
|      1:    11.908 -  21.305:  572   |   6:    58.895 -  68.293:   56        |
|      2:    21.305 -  30.703:  176   |   7:    68.293 -  77.690:   27        |
|      3:    30.703 -  40.100:  110   |   8:    77.690 -  87.088:    7        |
|      4:    40.100 -  49.498:   96   |   9:    87.088 -  96.485:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.189 - 5.483
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 318
   mapped sites are within: 0.711 - 5.483

peak=   10.393 closest distance to " CB  VAL A 230 " =    1.461
peak=    5.598 closest distance to " CB  GLN A 223 " =    1.514
peak=    5.502 closest distance to " CG  LEU A   5 " =    1.212
peak=    5.500 closest distance to " CB  VAL A 296 " =    1.080
peak=    5.453 closest distance to " NH2 ARG A  56 " =    2.156
peak=    5.204 closest distance to " CG  LEU A 228 " =    1.275
peak=    5.090 closest distance to " CG  PRO A  54 " =    1.385
peak=    5.066 closest distance to " O   HOH Z 210 " =    1.101
peak=    5.013 closest distance to " CG  PRO A 280 " =    0.943
peak=    4.991 closest distance to " CG2 VAL A 296 " =    1.030
peak=    4.942 closest distance to " CD2 LEU A   5 " =    1.107
peak=    4.883 closest distance to " CG1 VAL A 296 " =    1.183
peak=    4.863 closest distance to " CD1AILE A 234 " =    0.993
peak=    4.796 closest distance to " NE2 GLN A  11 " =    1.040
peak=    4.779 closest distance to " O   HOH Z 248 " =    1.352
peak=    4.719 closest distance to " O   HOH Z 142 " =    1.813
peak=    4.563 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.535 closest distance to " CZ  PHE A 218 " =    1.191
peak=    4.505 closest distance to " O   HOH Z 128 " =    1.490
peak=    4.504 closest distance to " O   HOH Z 126 " =    1.605
peak=    4.421 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.400 closest distance to " O   HOH Z 265 " =    1.969
peak=    4.399 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.395 closest distance to " CG  PRO A 243 " =    1.121
peak=    4.391 closest distance to " CB  ARG A 190 " =    1.660
peak=    4.383 closest distance to " CG  PRO A 198 " =    1.288
peak=    4.372 closest distance to " CD2 LEU A 228 " =    1.225
peak=    4.351 closest distance to " CB  ASN A 142 " =    1.233
peak=    4.338 closest distance to " CA  TYR A  30 " =    1.005
peak=    4.334 closest distance to " CB  GLU A 277 " =    3.780
peak=    4.315 closest distance to " O   HOH Z 251 " =    1.747
peak=    4.310 closest distance to " CZ3 TRP A 266 " =    1.129
peak=    4.292 closest distance to " O   HOH Z 412 " =    3.936
peak=    4.271 closest distance to " O   HOH Z  76 " =    1.280
peak=    4.267 closest distance to " O   HOH Z 232 " =    2.253
peak=    4.251 closest distance to " O   HOH Z 369 " =    2.194
peak=    4.232 closest distance to " CA  ALA A  51 " =    0.947
peak=    4.207 closest distance to " CB  ASN A 148 " =    1.456
peak=    4.168 closest distance to " CB  SER A  63 " =    1.135
peak=    4.154 closest distance to " CD2 TRP A 179 " =    1.295
peak=    4.137 closest distance to " O   HOH Z 368 " =    2.442
peak=    4.124 closest distance to " O   HOH Z 403 " =    1.651
peak=    4.115 closest distance to " O   HOH Z 402 " =    1.425
peak=    4.106 closest distance to " O   SER A  87 " =    2.445
peak=    4.099 closest distance to " O   PRO A 198 " =    1.530
peak=    4.094 closest distance to " CG  MET A 185 " =    1.247
peak=    4.086 closest distance to " O   HOH Z 261 " =    2.400
peak=    4.067 closest distance to " O   HOH Z 154 " =    1.603
peak=    4.066 closest distance to " O   HOH Z 313 " =    1.852
peak=    4.056 closest distance to " CB  VAL A 230 " =    1.185
peak=    4.052 closest distance to " O   HOH Z 214 " =    3.125
peak=    4.042 closest distance to " O   HOH Z 214 " =    1.478
peak=    3.967 closest distance to " CB  TYR A 169 " =    0.747
peak=    3.959 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.944 closest distance to " O   HOH Z 406 " =    1.518
peak=    3.942 closest distance to " CE  LYS A  76 " =    0.899
peak=    3.938 closest distance to " O   HOH Z 287 " =    1.888
peak=    3.933 closest distance to " OG BSER A 164 " =    2.301
peak=    3.933 closest distance to " O   HOH Z 359 " =    1.912
peak=    3.912 closest distance to " O   HOH Z 427 " =    2.980
peak=    3.912 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.904 closest distance to " O   HOH Z 346 " =    1.456
peak=    3.896 closest distance to " O   HOH Z 280 " =    2.916
peak=    3.895 closest distance to " NH2AARG A 145 " =    1.141
peak=    3.889 closest distance to " CD1 LEU A  96 " =    0.795
peak=    3.875 closest distance to " O   HOH Z 422 " =    2.591
peak=    3.874 closest distance to " CB  PRO A  90 " =    1.228
peak=    3.870 closest distance to " O  BHOH Z  74 " =    1.249
peak=    3.869 closest distance to " O   HOH Z 425 " =    1.456
peak=    3.868 closest distance to " CG  PRO A 213 " =    1.143
peak=    3.861 closest distance to " CB  ARG A  79 " =    1.434
peak=    3.852 closest distance to " O   HOH Z  78 " =    1.685
peak=    3.849 closest distance to " O   HOH Z  43 " =    2.030
peak=    3.839 closest distance to " O   HOH Z 238 " =    1.090
peak=    3.835 closest distance to " CG  ARG A  66 " =    2.508
peak=    3.835 closest distance to " O   HOH Z 188 " =    2.873
peak=    3.832 closest distance to " CB  GLU A 128 " =    1.154
peak=    3.830 closest distance to " O   HOH Z   4 " =    1.643
peak=    3.814 closest distance to " ND2 ASN A 249 " =    0.916
peak=    3.809 closest distance to " CG AARG A 275 " =    1.224
peak=    3.805 closest distance to " CB  VAL A 265 " =    1.199
peak=    3.800 closest distance to " N   ASN A  39 " =    1.297
peak=    3.794 closest distance to " CA  ARG A  36 " =    1.025
peak=    3.793 closest distance to " CG2AVAL A 121 " =    2.233
peak=    3.789 closest distance to " CA  ARG A 195 " =    1.230
peak=    3.787 closest distance to " O   HOH Z  63 " =    1.833
peak=    3.782 closest distance to " CA  ALA A 295 " =    1.029
peak=    3.778 closest distance to " O   HOH Z  49 " =    1.118
peak=    3.777 closest distance to " CD  ARG A 269 " =    0.996
peak=    3.777 closest distance to " ND2 ASN A 187 " =    1.720
peak=    3.776 closest distance to " CA  TYR A 116 " =    1.358
peak=    3.774 closest distance to " O   HOH Z 417 " =    3.107
peak=    3.773 closest distance to " CZ  PHE A  38 " =    1.168
peak=    3.754 closest distance to " O  BHOH Z 338 " =    2.211
peak=    3.753 closest distance to " CG2 ILE A 234 " =    0.873
peak=    3.740 closest distance to " CA  ALA A 160 " =    0.949
peak=    3.739 closest distance to " CB  GLU A 152 " =    1.166
peak=    3.739 closest distance to " CD  LYS A 166 " =    1.386
peak=    3.731 closest distance to " NZ  LYS A  48 " =    1.189
peak=    3.730 closest distance to " O   ASP A 124 " =    1.228
peak=    3.699 closest distance to " CB  ASP A 124 " =    0.821
peak=    3.695 closest distance to " CA  ILE A 106 " =    0.786
peak=    3.682 closest distance to " O   HOH Z 368 " =    3.494
peak=    3.678 closest distance to " O   HOH Z 126 " =    1.956
peak=    3.669 closest distance to " O   HOH Z 199 " =    1.641
peak=    3.666 closest distance to " NE2 HIS A 207 " =    1.082
peak=    3.665 closest distance to " CB  GLU A  46 " =    0.982
peak=    3.660 closest distance to " NE2 GLN A  77 " =    3.288
peak=    3.653 closest distance to " CG  PHE A 204 " =    0.920
peak=    3.652 closest distance to " NH1AARG A 145 " =    1.248
peak=    3.652 closest distance to " O   HOH Z 234 " =    3.656
peak=    3.651 closest distance to " O   HOH Z 327 " =    2.446
peak=    3.646 closest distance to " CB AVAL A  41 " =    0.881
peak=    3.646 closest distance to " CB  GLN A  89 " =    1.188
peak=    3.643 closest distance to " O   HOH Z 303 " =    2.183
peak=    3.640 closest distance to " O   HOH Z 247 " =    1.328
peak=    3.639 closest distance to " O   HOH Z 258 " =    1.895
peak=    3.638 closest distance to " O   HOH Z  19 " =    2.195
peak=    3.635 closest distance to " CB  VAL A 202 " =    1.490
peak=    3.628 closest distance to " CG1 VAL A 153 " =    1.024
peak=    3.628 closest distance to " CG  GLN A  58 " =    0.936
peak=    3.623 closest distance to " O   HOH Z 298 " =    1.836
peak=    3.607 closest distance to " CG  ARG A 138 " =    1.406
peak=    3.605 closest distance to " CB  ASP A 298 " =    1.193
peak=    3.599 closest distance to " CD1 ILE A 199 " =    1.177
peak=    3.596 closest distance to " CG1 ILE A  49 " =    1.714
peak=    3.595 closest distance to " O   HOH Z 353 " =    2.712
peak=    3.592 closest distance to " O   HOH Z 371 " =    2.716
peak=    3.589 closest distance to " O   HOH Z 290 " =    1.045
peak=    3.586 closest distance to " CB  TRP A 266 " =    1.059
peak=    3.583 closest distance to " O   HOH Z 203 " =    1.759
peak=    3.579 closest distance to " O   HOH Z 299 " =    4.306
peak=    3.568 closest distance to " OG  SER A 276 " =    1.367
peak=    3.562 closest distance to " OG BSER A 134 " =    2.736
peak=    3.557 closest distance to " CB  LYS A 117 " =    1.291
peak=    3.546 closest distance to " CB  SER A   3 " =    1.456
peak=    3.541 closest distance to " CA  SER A  87 " =    1.022
peak=    3.533 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.527 closest distance to " OG  SER A 245 " =    1.562
peak=    3.524 closest distance to " O   HOH Z 316 " =    3.163
peak=    3.523 closest distance to " O   HOH Z 154 " =    2.267
peak=    3.520 closest distance to " O   HOH Z 193 " =    1.457
peak=    3.519 closest distance to " CB  THR A  52 " =    0.855
peak=    3.518 closest distance to " O   ASP A 200 " =    1.611
peak=    3.517 closest distance to " CB  SER A 273 " =    0.954
peak=    3.516 closest distance to " O   HOH Z 365 " =    2.716
peak=    3.516 closest distance to " CB  ASN A 110 " =    1.123
peak=    3.510 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.501 closest distance to " O   HOH Z 207 " =    1.096
peak=    3.500 closest distance to " NZ  LYS A 117 " =    3.016
peak=    3.497 closest distance to " CE1 TYR A 186 " =    1.268
peak=    3.496 closest distance to " CA  ASP A 162 " =    0.991
peak=    3.492 closest distance to " CA  LYS A 117 " =    1.289
peak=    3.489 closest distance to " O   HOH Z 171 " =    3.972
peak=    3.486 closest distance to " CD  LYS A  76 " =    2.057
peak=    3.484 closest distance to " O   HOH Z 383 " =    1.887
peak=    3.477 closest distance to " CB  SER A  26 " =    1.827
peak=    3.477 closest distance to " O   HOH Z  48 " =    1.670
peak=    3.474 closest distance to " CG  LEU A 167 " =    1.172
peak=    3.468 closest distance to " CD2 LEU A 297 " =    0.875
peak=    3.466 closest distance to " CD2 LEU A   5 " =    0.711
peak=    3.465 closest distance to " CE3 TRP A 150 " =    1.167
peak=    3.464 closest distance to " O   HOH Z 361 " =    2.534
peak=    3.454 closest distance to " O   HOH Z  80 " =    1.867
peak=    3.453 closest distance to " O   HOH Z 391 " =    2.961
peak=    3.449 closest distance to " CG  GLU A  37 " =    0.917
peak=    3.446 closest distance to " CB  ASP A 140 " =    1.282
peak=    3.444 closest distance to " O   HOH Z 337 " =    1.911
peak=    3.443 closest distance to " CD  LYS A 119 " =    1.698
peak=    3.438 closest distance to " O   HOH Z  44 " =    2.202
peak=    3.438 closest distance to " O   ALA A 165 " =    1.394
peak=    3.436 closest distance to " CB  PHE A 204 " =    1.025
peak=    3.423 closest distance to " CB  SER A 210 " =    0.788
peak=    3.408 closest distance to " O   HOH Z 393 " =    3.156
peak=    3.407 closest distance to " CD  ARG A 139 " =    1.175
peak=    3.397 closest distance to " CB  ASN A 285 " =    1.024
peak=    3.392 closest distance to " O   HOH Z 189 " =    2.965
peak=    3.391 closest distance to " OD1 ASN A  69 " =    2.494
peak=    3.386 closest distance to " O   HOH Z 193 " =    1.773
peak=    3.383 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.383 closest distance to " O   HOH Z 145 " =    2.393
peak=    3.382 closest distance to " O   PHE A 192 " =    1.347
peak=    3.381 closest distance to " CA  ALA A 158 " =    1.385
peak=    3.377 closest distance to " NH2 ARG A 156 " =    1.108
peak=    3.375 closest distance to " CB  ASN A 215 " =    1.226
peak=    3.375 closest distance to " O   HOH Z 361 " =    3.701
peak=    3.367 closest distance to " CA  VAL A 125 " =    1.203
peak=    3.359 closest distance to " CA  ALA A  21 " =    1.150
peak=    3.358 closest distance to " O   HOH Z 193 " =    1.706
peak=    3.351 closest distance to " CG1 ILE A  20 " =    1.261
peak=    3.350 closest distance to " CA  GLY A 267 " =    1.031
peak=    3.347 closest distance to " O   HOH Z 172 " =    3.838
peak=    3.346 closest distance to " CA  ASN A 217 " =    1.110
peak=    3.342 closest distance to " CB  SER A 288 " =    1.490
peak=    3.339 closest distance to " CA  MET A 105 " =    1.060
peak=    3.330 closest distance to " O   HOH Z  83 " =    1.523
peak=    3.330 closest distance to " CD1 ILE A  33 " =    1.720
peak=    3.328 closest distance to " CG2 VAL A 257 " =    0.724
peak=    3.323 closest distance to " CZ3 TRP A 274 " =    4.487
peak=    3.322 closest distance to " CB  MET A  40 " =    0.795
peak=    3.321 closest distance to " CA  VAL A  41 " =    0.764
peak=    3.320 closest distance to " CB  ASP A 107 " =    1.158
peak=    3.316 closest distance to " O   ASN A  74 " =    1.444
peak=    3.314 closest distance to " O   GLN A  88 " =    1.644
peak=    3.313 closest distance to " O   CYS A 168 " =    1.137
peak=    3.305 closest distance to " O   THR A 220 " =    1.287
peak=    3.304 closest distance to " O   THR A 182 " =    1.418
peak=    3.298 closest distance to " O   HOH Z 421 " =    3.119
peak=    3.289 closest distance to " O   HOH Z  35 " =    2.495
peak=    3.289 closest distance to " O   HOH Z 430 " =    5.483
peak=    3.285 closest distance to " CA  ALA A 291 " =    0.867
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.207
peak=    3.279 closest distance to " CA  GLU A 152 " =    0.848
peak=    3.276 closest distance to " CB  ALA A   9 " =    1.657
peak=    3.275 closest distance to " CB  TRP A 179 " =    1.408
peak=    3.269 closest distance to " CG2 VAL A 197 " =    1.046
peak=    3.269 closest distance to " CG2AVAL A  72 " =    1.843
peak=    3.267 closest distance to " O   HOH Z 392 " =    2.704
peak=    3.267 closest distance to " O   GLU A   2 " =    1.524
peak=    3.263 closest distance to " CA  ALA A 154 " =    1.071
peak=    3.263 closest distance to " CB  ASN A 173 " =    1.093
peak=    3.262 closest distance to " CG  MET A 185 " =    1.006
peak=    3.260 closest distance to " OH  TYR A 116 " =    1.096
peak=    3.258 closest distance to " O   HOH Z 162 " =    1.396
peak=    3.258 closest distance to " CA  ASN A 127 " =    1.199
peak=    3.257 closest distance to " O   HOH Z   1 " =    2.372
peak=    3.256 closest distance to " OE2 GLU A  53 " =    1.944
peak=    3.253 closest distance to " N   PHE A 130 " =    1.299
peak=    3.252 closest distance to " O   HOH Z 158 " =    3.221
peak=    3.245 closest distance to " O   HOH Z 285 " =    2.149
peak=    3.241 closest distance to " O   HOH Z  61 " =    1.744
peak=    3.240 closest distance to " CG2 VAL A 126 " =    0.847
peak=    3.237 closest distance to " O   HOH Z 345 " =    3.361
peak=    3.236 closest distance to " O   HOH Z 187 " =    2.285
peak=    3.236 closest distance to " CB  PRO A 243 " =    1.144
peak=    3.232 closest distance to " O   HOH Z  21 " =    1.751
peak=    3.230 closest distance to " CG1AVAL A 121 " =    0.801
peak=    3.229 closest distance to " CG  GLN A  11 " =    1.722
peak=    3.228 closest distance to " O   HOH Z 148 " =    3.404
peak=    3.227 closest distance to " O   HOH Z 407 " =    2.422
peak=    3.225 closest distance to " O   HOH Z 109 " =    2.654
peak=    3.224 closest distance to " ND2AASN A 224 " =    0.898
peak=    3.223 closest distance to " ND2 ASN A 249 " =    1.848
peak=    3.221 closest distance to " NE1 TRP A  92 " =    1.793
peak=    3.217 closest distance to " OG  SER A  62 " =    2.830
peak=    3.216 closest distance to " CG2 ILE A  20 " =    1.502
peak=    3.216 closest distance to " O   HOH Z 141 " =    1.573
peak=    3.215 closest distance to " N   ASP A 162 " =    1.245
peak=    3.215 closest distance to " CB  SER A  62 " =    1.011
peak=    3.213 closest distance to " CA  ASP A 140 " =    1.389
peak=    3.213 closest distance to " CA  THR A 264 " =    0.719
peak=    3.212 closest distance to " O   HOH Z 438 " =    2.623
peak=    3.212 closest distance to " O   HOH Z 146 " =    1.437
peak=    3.205 closest distance to " CZ3 TRP A  85 " =    1.040
peak=    3.201 closest distance to " CB  ARG A 145 " =    0.910
peak=    3.197 closest distance to " O   HOH Z 258 " =    1.586
peak=    3.196 closest distance to " O   HOH Z 245 " =    1.326
peak=    3.196 closest distance to " O   HOH Z 371 " =    2.547
peak=    3.196 closest distance to " CA  ASP A 191 " =    1.235
peak=    3.190 closest distance to " CD BLYS A 290 " =    0.996
peak=    3.189 closest distance to " CA  ARG A 275 " =    1.813
peak=    3.188 closest distance to " O   HOH Z  40 " =    1.875
peak=    3.186 closest distance to " CB  ALA A  43 " =    0.853
peak=    3.184 closest distance to " CA  GLN A  94 " =    0.794
peak=    3.183 closest distance to " O   GLY A  91 " =    1.287
peak=    3.181 closest distance to " CG2 THR A 221 " =    1.296
peak=    3.181 closest distance to " CG  GLN A  58 " =    3.114
peak=    3.179 closest distance to " O   HOH Z 117 " =    0.994
peak=    3.176 closest distance to " O   HOH Z   9 " =    1.153
peak=    3.172 closest distance to " O   HOH Z 305 " =    3.547
peak=    3.171 closest distance to " NH2 ARG A  56 " =    1.141
peak=    3.169 closest distance to " CA  ARG A 139 " =    1.156
peak=    3.168 closest distance to " O   HOH Z 421 " =    3.015
peak=    3.167 closest distance to " CA  ASN A  74 " =    1.155
peak=    3.165 closest distance to " O   HOH Z 293 " =    1.984
peak=    3.162 closest distance to " O   ALA A 158 " =    1.154
peak=    3.159 closest distance to " CH2 TRP A  70 " =    0.961
peak=    3.156 closest distance to " CB  THR A  31 " =    1.511
peak=    3.150 closest distance to " CA  VAL A 153 " =    1.064
peak=    3.148 closest distance to " O   HOH Z 357 " =    2.136
peak=    3.143 closest distance to " CB  PHE A 283 " =    0.904
peak=    3.141 closest distance to " O   HOH Z 272 " =    1.789
peak=    3.141 closest distance to " O   HOH Z 213 " =    1.845
peak=    3.140 closest distance to " O   PRO A 213 " =    1.424
peak=    3.137 closest distance to " NE2 GLN A  58 " =    4.585
peak=    3.129 closest distance to " CG1 VAL A 257 " =    1.290
peak=    3.128 closest distance to " CB  ARG A 156 " =    1.229
peak=    3.122 closest distance to " CD  ARG A 195 " =    1.013
peak=    3.114 closest distance to " O   HOH Z 116 " =    1.796
peak=    3.114 closest distance to " CA  LEU A 282 " =    1.189
peak=    3.106 closest distance to " CB  ALA A 242 " =    0.859
peak=    3.105 closest distance to " O   HOH Z 102 " =    1.230
peak=    3.104 closest distance to " CG  LEU A 281 " =    1.025
peak=    3.097 closest distance to " CB  ARG A 102 " =    0.939
peak=    3.095 closest distance to " N   ALA A 256 " =    1.110
peak=    3.076 closest distance to " CA  ILE A 234 " =    0.968
peak=    3.073 closest distance to " CG1 ILE A  33 " =    1.240
peak=    3.066 closest distance to " CG2 ILE A  20 " =    1.326
peak=    3.062 closest distance to " CA  LYS A 290 " =    1.084
peak=    3.060 closest distance to " O   HOH Z 394 " =    1.464
peak=    3.057 closest distance to " O   HOH Z  40 " =    1.550
peak=    3.052 closest distance to " O   HOH Z 130 " =    2.364
peak=    3.050 closest distance to " CG  GLN A  55 " =    2.631
peak=    3.046 closest distance to " O   HOH Z 366 " =    2.591
peak=    3.043 closest distance to " O   ASN A 284 " =    1.893
peak=    3.036 closest distance to " O   HOH Z 263 " =    1.621
peak=    3.018 closest distance to " O   HOH Z 117 " =    2.000
peak=    3.018 closest distance to " O   HOH Z 201 " =    2.820

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 224         
Filter by distance & map next to the model:
   mapped sites are within: 0.773 - 5.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 224
   mapped sites are within: 0.773 - 5.691

peak=   -5.038 closest distance to " SG  CYS A 254 " =    3.319
peak=   -4.821 closest distance to " CG2 VAL A 230 " =    0.773
peak=   -4.594 closest distance to " CB  PRO A 243 " =    2.791
peak=   -4.409 closest distance to " O   HOH Z 193 " =    0.815
peak=   -4.401 closest distance to " O   HOH Z 196 " =    2.270
peak=   -4.358 closest distance to " CD  ARG A 156 " =    2.111
peak=   -4.358 closest distance to " O   HOH Z 211 " =    1.131
peak=   -4.355 closest distance to " CG  GLN A  58 " =    1.080
peak=   -4.248 closest distance to " O   VAL A  67 " =    2.708
peak=   -4.230 closest distance to " CA  ASP A 298 " =    1.075
peak=   -4.155 closest distance to " CG1 VAL A 250 " =    2.752
peak=   -4.146 closest distance to " C   HIS A 108 " =    1.190
peak=   -4.123 closest distance to " OG BSER A 134 " =    1.468
peak=   -4.079 closest distance to " CG1 VAL A 296 " =    1.134
peak=   -4.070 closest distance to " O   SER A 271 " =    2.222
peak=   -4.040 closest distance to " O   PRO A 198 " =    1.278
peak=   -4.034 closest distance to " O   PRO A 163 " =    2.214
peak=   -4.014 closest distance to " OG  SER A  97 " =    2.366
peak=   -4.009 closest distance to " CE2 PHE A  61 " =    2.649
peak=   -4.009 closest distance to " CD2 TYR A 293 " =    1.962
peak=   -3.989 closest distance to " CG1 VAL A 112 " =    2.688
peak=   -3.977 closest distance to " O   HOH Z 394 " =    1.634
peak=   -3.975 closest distance to " O   HOH Z 166 " =    1.786
peak=   -3.957 closest distance to " O   HOH Z 411 " =    5.645
peak=   -3.949 closest distance to " CE2 TYR A  30 " =    2.701
peak=   -3.926 closest distance to " O   HOH Z 154 " =    1.406
peak=   -3.914 closest distance to " O   HOH Z 133 " =    1.034
peak=   -3.895 closest distance to " CE3 TRP A 150 " =    2.308
peak=   -3.889 closest distance to " CG  GLU A 277 " =    1.245
peak=   -3.886 closest distance to " CG2 ILE A  49 " =    2.946
peak=   -3.805 closest distance to " CG2 VAL A 189 " =    2.069
peak=   -3.802 closest distance to " O   HOH Z  37 " =    1.884
peak=   -3.797 closest distance to " OXT GLY A 302 " =    2.904
peak=   -3.779 closest distance to " CG  PRO A 243 " =    1.663
peak=   -3.765 closest distance to " CE2 TRP A  70 " =    2.048
peak=   -3.763 closest distance to " OE1 GLN A 223 " =    2.419
peak=   -3.753 closest distance to " O   HOH Z 231 " =    2.263
peak=   -3.736 closest distance to " O   HOH Z 285 " =    1.986
peak=   -3.724 closest distance to " OE1 GLN A  88 " =    0.855
peak=   -3.723 closest distance to " O   HOH Z 110 " =    1.409
peak=   -3.723 closest distance to " O   HOH Z  10 " =    1.578
peak=   -3.718 closest distance to " CG  ARG A 269 " =    2.319
peak=   -3.711 closest distance to " CH2 TRP A 179 " =    1.209
peak=   -3.711 closest distance to " O   HOH Z  73 " =    2.504
peak=   -3.700 closest distance to " O   HOH Z 119 " =    2.168
peak=   -3.688 closest distance to " CB  VAL A 230 " =    1.096
peak=   -3.688 closest distance to " O   HOH Z  68 " =    1.289
peak=   -3.680 closest distance to " CD  PRO A 243 " =    1.928
peak=   -3.675 closest distance to " O   HOH Z 295 " =    1.603
peak=   -3.675 closest distance to " O   HOH Z 128 " =    1.043
peak=   -3.664 closest distance to " O   HOH Z 128 " =    2.562
peak=   -3.659 closest distance to " O   HOH Z 351 " =    1.787
peak=   -3.655 closest distance to " CG2 ILE A  20 " =    3.041
peak=   -3.654 closest distance to " O   HOH Z 198 " =    1.942
peak=   -3.652 closest distance to " O   HOH Z 359 " =    2.812
peak=   -3.640 closest distance to " O   HOH Z 216 " =    1.098
peak=   -3.630 closest distance to " C   ILE A 239 " =    2.119
peak=   -3.628 closest distance to " O   HOH Z 127 " =    1.159
peak=   -3.621 closest distance to " CB  PHE A 192 " =    2.120
peak=   -3.620 closest distance to " O   HOH Z 102 " =    1.521
peak=   -3.619 closest distance to " O   SER A 210 " =    1.677
peak=   -3.611 closest distance to " CB  ALA A 161 " =    2.530
peak=   -3.609 closest distance to " O   GLY A  17 " =    1.167
peak=   -3.595 closest distance to " CG  GLN A 103 " =    2.479
peak=   -3.591 closest distance to " O   HOH Z 131 " =    4.088
peak=   -3.589 closest distance to " O   HOH Z 431 " =    2.070
peak=   -3.587 closest distance to " NE2 GLN A  11 " =    1.662
peak=   -3.559 closest distance to " NE  ARG A  66 " =    4.351
peak=   -3.559 closest distance to " CA  GLY A 241 " =    2.391
peak=   -3.558 closest distance to " O   TYR A 186 " =    1.841
peak=   -3.550 closest distance to " O   HOH Z 149 " =    1.993
peak=   -3.544 closest distance to " CB  ALA A  10 " =    2.265
peak=   -3.543 closest distance to " CD1 LEU A 101 " =    2.355
peak=   -3.527 closest distance to " O   HOH Z 348 " =    2.280
peak=   -3.520 closest distance to " CG  GLU A  53 " =    1.581
peak=   -3.518 closest distance to " O   HOH Z 191 " =    5.691
peak=   -3.518 closest distance to " OD1 ASN A 148 " =    1.407
peak=   -3.507 closest distance to " CD1 PHE A  59 " =    2.078
peak=   -3.497 closest distance to " O   HOH Z 174 " =    2.301
peak=   -3.493 closest distance to " CZ3 TRP A 274 " =    2.459
peak=   -3.488 closest distance to " O   HOH Z 106 " =    1.910
peak=   -3.485 closest distance to " CB  HIS A  86 " =    1.181
peak=   -3.475 closest distance to " O   HOH Z 275 " =    1.824
peak=   -3.461 closest distance to " CZ  PHE A  38 " =    2.430
peak=   -3.458 closest distance to " O   ALA A 227 " =    1.424
peak=   -3.450 closest distance to " O   HOH Z 286 " =    1.936
peak=   -3.448 closest distance to " CA  GLY A 203 " =    2.437
peak=   -3.442 closest distance to " CE3 TRP A  70 " =    1.850
peak=   -3.441 closest distance to " O   HOH Z 423 " =    2.370
peak=   -3.441 closest distance to " N   THR A  52 " =    1.571
peak=   -3.439 closest distance to " O   HOH Z 107 " =    0.976
peak=   -3.434 closest distance to " O   HOH Z 290 " =    1.118
peak=   -3.434 closest distance to " NE2 GLN A 194 " =    1.993
peak=   -3.426 closest distance to " ND2 ASN A  45 " =    1.202
peak=   -3.423 closest distance to " O   ALA A  34 " =    2.656
peak=   -3.422 closest distance to " CE BMET A  47 " =    1.572
peak=   -3.420 closest distance to " O   HOH Z 340 " =    1.648
peak=   -3.419 closest distance to " CG2AVAL A  41 " =    2.897
peak=   -3.416 closest distance to " C   ALA A 158 " =    1.169
peak=   -3.415 closest distance to " O   ILE A 106 " =    1.920
peak=   -3.406 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -3.402 closest distance to " O   HOH Z 136 " =    2.592
peak=   -3.399 closest distance to " O   HOH Z  19 " =    2.286
peak=   -3.382 closest distance to " O   HOH Z 244 " =    1.442
peak=   -3.369 closest distance to " N   ALA A 226 " =    2.040
peak=   -3.368 closest distance to " O   HOH Z 407 " =    2.874
peak=   -3.366 closest distance to " O   HOH Z 210 " =    0.985
peak=   -3.356 closest distance to " O   HOH Z 177 " =    1.839
peak=   -3.354 closest distance to " ND2BASN A 224 " =    1.890
peak=   -3.353 closest distance to " CD  GLU A 236 " =    1.173
peak=   -3.347 closest distance to " CB  ALA A  43 " =    2.679
peak=   -3.339 closest distance to " O   ASP A  27 " =    2.041
peak=   -3.338 closest distance to " O   HOH Z 390 " =    1.460
peak=   -3.337 closest distance to " O   GLN A 240 " =    2.486
peak=   -3.334 closest distance to " O   HOH Z 165 " =    1.983
peak=   -3.334 closest distance to " CZ  TYR A 169 " =    1.835
peak=   -3.329 closest distance to " C   MET A 188 " =    1.429
peak=   -3.328 closest distance to " NE2 GLN A  88 " =    1.127
peak=   -3.322 closest distance to " O   HOH Z 111 " =    1.643
peak=   -3.322 closest distance to " O   HOH Z 251 " =    4.978
peak=   -3.313 closest distance to " CD  LYS A 289 " =    2.432
peak=   -3.308 closest distance to " CZ2 TRP A 274 " =    1.076
peak=   -3.305 closest distance to " O   HOH Z 301 " =    2.495
peak=   -3.304 closest distance to " CB  ALA A  51 " =    1.889
peak=   -3.304 closest distance to " O   SER A   3 " =    1.106
peak=   -3.302 closest distance to " O   HOH Z 166 " =    1.793
peak=   -3.301 closest distance to " O   HOH Z 139 " =    5.385
peak=   -3.298 closest distance to " ND2 ASN A  69 " =    1.998
peak=   -3.296 closest distance to " OD1 ASN A 173 " =    1.407
peak=   -3.296 closest distance to " CA  HIS A  86 " =    2.300
peak=   -3.294 closest distance to " CD2 HIS A 207 " =    2.135
peak=   -3.292 closest distance to " CG2 VAL A 202 " =    2.814
peak=   -3.288 closest distance to " CB  ALA A 248 " =    2.280
peak=   -3.288 closest distance to " O   HOH Z 357 " =    2.097
peak=   -3.283 closest distance to " CG  LYS A 166 " =    2.127
peak=   -3.281 closest distance to " O   HOH Z 236 " =    1.507
peak=   -3.280 closest distance to " O   HOH Z  52 " =    1.698
peak=   -3.278 closest distance to " CB  ALA A 248 " =    2.140
peak=   -3.277 closest distance to " CD1 ILE A 199 " =    2.435
peak=   -3.276 closest distance to " CB  ALA A 129 " =    2.473
peak=   -3.274 closest distance to " CG2 VAL A 296 " =    1.171
peak=   -3.273 closest distance to " O   GLN A  94 " =    2.360
peak=   -3.269 closest distance to " CG  LEU A  83 " =    2.094
peak=   -3.265 closest distance to " O   GLY A  80 " =    2.674
peak=   -3.263 closest distance to " O   HOH Z 115 " =    1.801
peak=   -3.263 closest distance to " CD2 PHE A 225 " =    1.065
peak=   -3.260 closest distance to " O   HOH Z 250 " =    1.873
peak=   -3.260 closest distance to " O   HOH Z 292 " =    1.845
peak=   -3.260 closest distance to " O   HOH Z 174 " =    3.712
peak=   -3.248 closest distance to " N   ALA A  43 " =    2.749
peak=   -3.245 closest distance to " ND2 ASN A 249 " =    2.329
peak=   -3.245 closest distance to " ND2 ASN A 187 " =    1.638
peak=   -3.242 closest distance to " NH2 ARG A  79 " =    2.347
peak=   -3.239 closest distance to " CE1 TYR A 247 " =    2.687
peak=   -3.237 closest distance to " O   HOH Z 114 " =    3.264
peak=   -3.236 closest distance to " CB  PRO A 163 " =    2.518
peak=   -3.235 closest distance to " CA  VAL A 296 " =    1.027
peak=   -3.234 closest distance to " O   VAL A 189 " =    2.703
peak=   -3.232 closest distance to " CB  SER A 210 " =    1.101
peak=   -3.231 closest distance to " O   HOH Z 434 " =    1.703
peak=   -3.231 closest distance to " NE2 GLN A 103 " =    1.656
peak=   -3.230 closest distance to " O   HOH Z   6 " =    1.539
peak=   -3.227 closest distance to " O   HOH Z 156 " =    3.468
peak=   -3.225 closest distance to " O   HOH Z 252 " =    3.583
peak=   -3.223 closest distance to " CB  ASN A  39 " =    2.419
peak=   -3.219 closest distance to " O   SER A 276 " =    1.669
peak=   -3.217 closest distance to " CG  LEU A   5 " =    1.421
peak=   -3.212 closest distance to " O   HOH Z 426 " =    1.668
peak=   -3.211 closest distance to " O   HOH Z   6 " =    2.230
peak=   -3.211 closest distance to " O   VAL A 189 " =    1.812
peak=   -3.210 closest distance to " CG  ASP A 231 " =    1.061
peak=   -3.209 closest distance to " O   HOH Z  69 " =    2.027
peak=   -3.209 closest distance to " O   HOH Z  64 " =    1.578
peak=   -3.207 closest distance to " CD2 LEU A 237 " =    2.833
peak=   -3.207 closest distance to " CG1 VAL A 125 " =    1.870
peak=   -3.205 closest distance to " ND2 ASN A  45 " =    1.989
peak=   -3.202 closest distance to " NH2 ARG A  79 " =    1.530
peak=   -3.201 closest distance to " CA  GLY A 133 " =    2.328
peak=   -3.199 closest distance to " CA  GLY A 241 " =    3.188
peak=   -3.196 closest distance to " O   HOH Z  43 " =    1.567
peak=   -3.196 closest distance to " N   SER A 276 " =    1.426
peak=   -3.193 closest distance to " O   HOH Z 421 " =    3.477
peak=   -3.192 closest distance to " C   LEU A 143 " =    1.093
peak=   -3.192 closest distance to " OG  SER A  63 " =    1.224
peak=   -3.190 closest distance to " O   HOH Z 137 " =    1.754
peak=   -3.189 closest distance to " O   HOH Z 171 " =    2.240
peak=   -3.189 closest distance to " O   HOH Z 395 " =    1.415
peak=   -3.189 closest distance to " O   GLY A 203 " =    2.440
peak=   -3.188 closest distance to " NH2 ARG A 159 " =    2.341
peak=   -3.181 closest distance to " CA  SER A  62 " =    2.562
peak=   -3.179 closest distance to " CB  GLN A  55 " =    1.268
peak=   -3.179 closest distance to " O   HOH Z 185 " =    2.505
peak=   -3.178 closest distance to " CG  MET A 105 " =    0.995
peak=   -3.177 closest distance to " O   HOH Z 275 " =    1.620
peak=   -3.176 closest distance to " OD2 ASP A  50 " =    2.288
peak=   -3.176 closest distance to " CG1BVAL A  72 " =    2.003
peak=   -3.172 closest distance to " O   TRP A  70 " =    1.676
peak=   -3.172 closest distance to " O   HOH Z 244 " =    2.007
peak=   -3.170 closest distance to " O   HOH Z 100 " =    1.259
peak=   -3.170 closest distance to " O   HOH Z 140 " =    1.206
peak=   -3.165 closest distance to " CG  LEU A   5 " =    1.025
peak=   -3.165 closest distance to " CB  ASP A 171 " =    2.226
peak=   -3.162 closest distance to " CB  PHE A  38 " =    1.780
peak=   -3.158 closest distance to " O   GLU A 152 " =    1.347
peak=   -3.153 closest distance to " CZ  ARG A 259 " =    0.993
peak=   -3.148 closest distance to " CG2 THR A 178 " =    2.449
peak=   -3.145 closest distance to " OXT GLY A 302 " =    3.426
peak=   -3.140 closest distance to " CG  TRP A 266 " =    1.748
peak=   -3.138 closest distance to " CH2 TRP A 150 " =    1.185
peak=   -3.129 closest distance to " C   ASN A 285 " =    2.320
peak=   -3.114 closest distance to " O   HOH Z 265 " =    1.821
peak=   -3.113 closest distance to " O   HOH Z 346 " =    1.920
peak=   -3.108 closest distance to " O   HOH Z 378 " =    1.421
peak=   -3.103 closest distance to " O   HOH Z 278 " =    1.155
peak=   -3.091 closest distance to " OG  SER A  28 " =    2.037
peak=   -3.074 closest distance to " CD1 TYR A 247 " =    2.736
peak=   -3.064 closest distance to " ND2 ASN A  45 " =    1.422
peak=   -3.061 closest distance to " O   HOH Z 326 " =    5.088
peak=   -3.054 closest distance to " OD1 ASN A  39 " =    1.188
peak=   -3.050 closest distance to " O   SER A 141 " =    1.727
peak=   -3.048 closest distance to " O   HOH Z 162 " =    2.832
peak=   -3.043 closest distance to " N   ALA A 248 " =    2.523
peak=   -3.023 closest distance to " O   HOH Z 313 " =    1.845

================= 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    :  0.4831 0.4700   6.285868e+00   6.270080e+00
   1_bss:  0.4741 0.4596   6.279736e+00   6.260736e+00
   1_xyz:  0.3905 0.4158   6.165109e+00   6.198406e+00
   1_adp:  0.3458 0.3958   6.083110e+00   6.163772e+00
   1_occ:  0.3453 0.3967   6.082783e+00   6.165447e+00
   2_bss:  0.3420 0.3922   6.082954e+00   6.164770e+00
   2_xyz:  0.2683 0.3235   5.882121e+00   6.022992e+00
   2_adp:  0.2483 0.3027   5.825609e+00   5.980793e+00
   2_occ:  0.2480 0.3031   5.825359e+00   5.981116e+00
   3_bss:  0.2470 0.3034   5.827031e+00   5.982181e+00
   3_xyz:  0.1808 0.2324   5.548113e+00   5.744869e+00
   3_adp:  0.1652 0.2149   5.470649e+00   5.675412e+00
   3_occ:  0.1650 0.2148   5.470251e+00   5.675509e+00
   4_bss:  0.1643 0.2138   5.469970e+00   5.673794e+00
   4_xyz:  0.1335 0.1797   5.296865e+00   5.522258e+00
   4_adp:  0.1269 0.1755   5.262397e+00   5.497194e+00
   4_occ:  0.1266 0.1755   5.261837e+00   5.497413e+00
   5_bss:  0.1266 0.1756   5.260063e+00   5.494979e+00
   5_xyz:  0.1230 0.1700   5.236229e+00   5.471075e+00
   5_adp:  0.1214 0.1701   5.228806e+00   5.467359e+00
   5_occ:  0.1213 0.1700   5.228531e+00   5.467030e+00
   5_bss:  0.1212 0.1699   5.228614e+00   5.467126e+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:  0.312  10.161   6.388   8.523  12.040   0.000   0.000   0.000
   1_xyz:  0.312  10.161   6.388   8.523  12.040   0.000   0.000   0.000
   1_adp:  0.312  10.161   6.388   8.523  12.040   0.000   0.000   0.000
   1_occ:  0.312  10.161   6.388   8.523  12.040   0.000   0.000   0.000
   2_bss:  0.325  47.344   2.722   4.748   7.929   0.000   0.000   0.000
   2_xyz:  0.325  47.344   2.722   4.748   7.929   0.000   0.000   0.000
   2_adp:  0.325  47.344   2.722   4.748   7.929   0.000   0.000   0.000
   2_occ:  0.325  47.344   2.722   4.748   7.929   0.000   0.000   0.000
   3_bss:  0.335  70.188   1.655   3.152   5.376   0.000   0.000   0.000
   3_xyz:  0.335  70.188   1.655   3.152   5.376   0.000   0.000   0.000
   3_adp:  0.335  70.188   1.655   3.152   5.376   0.000   0.000   0.000
   3_occ:  0.335  70.188   1.655   3.152   5.376   0.000   0.000   0.000
   4_bss:  0.333  68.799   1.066   2.155   3.937   0.000   0.000   0.000
   4_xyz:  0.333  68.799   1.066   2.155   3.937   0.000   0.000   0.000
   4_adp:  0.333  68.799   1.066   2.155   3.937   0.000   0.000   0.000
   4_occ:  0.333  68.799   1.066   2.155   3.937   0.000   0.000   0.000
   5_bss:  0.332  66.476   1.160   2.048   3.661   0.000   0.000   0.000
   5_xyz:  0.332  66.476   1.160   2.048   3.661   0.000   0.000   0.000
   5_adp:  0.332  66.476   1.160   2.048   3.661   0.000   0.000   0.000
   5_occ:  0.332  66.476   1.160   2.048   3.661   0.000   0.000   0.000
   5_bss:  0.325  65.238  -1.048  -0.264   1.312  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.592 0.4507  0.5142    67372.521
   1_bss:  54.599 0.4627  0.6888    65695.266
   1_xyz:  47.220 0.5540  0.8050    49688.822
   1_adp:  43.524 0.6002  0.9146    44352.621
   1_occ:  43.633 0.5988  0.9116    44563.934
   2_bss:  43.288 0.6031  0.8062    44253.222
   2_xyz:  34.187 0.7102  0.9322    28495.162
   2_adp:  31.485 0.7414  0.9585    25234.443
   2_occ:  31.511 0.7411  0.9579    25264.814
   3_bss:  31.427 0.7422  0.9022    25312.221
   3_xyz:  22.988 0.8318  0.9761    13988.969
   3_adp:  20.791 0.8543  0.9843    12086.524
   3_occ:  20.797 0.8542  0.9843    12077.309
   4_bss:  20.696 0.8551  0.9507    11988.446
   4_xyz:  17.042 0.8891  0.9682     8538.152
   4_adp:  16.427 0.8947  0.9625     8111.390
   4_occ:  16.434 0.8947  0.9623     8113.668
   5_bss:  16.397 0.8949  0.9596     8060.690
   5_xyz:  15.782 0.9004  0.9623     7584.790
   5_adp:  15.699 0.9013  0.9543     7513.225
   5_occ:  15.692 0.9013  0.9542     7506.609
   5_bss:  15.696 0.9013  0.9615     7507.789
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4359e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4359e+01
   1_xyz:   1.736  0.014  0.109 18.211  0.007  4.112   1.4783e-01
   1_adp:   1.736  0.014  0.109 18.211  0.007  4.112   1.4783e-01
   1_occ:   1.736  0.014  0.109 18.211  0.007  4.112   1.4783e-01
   2_bss:   1.736  0.014  0.109 18.211  0.007  4.112   1.4783e-01
   2_xyz:   1.215  0.009  0.077 16.002  0.004  4.111   8.4309e-02
   2_adp:   1.215  0.009  0.077 16.002  0.004  4.111   8.4309e-02
   2_occ:   1.215  0.009  0.077 16.002  0.004  4.111   8.4309e-02
   3_bss:   1.215  0.009  0.077 16.002  0.004  4.111   8.4309e-02
   3_xyz:   1.167  0.009  0.083 15.815  0.004  4.130   7.9636e-02
   3_adp:   1.167  0.009  0.083 15.815  0.004  4.130   7.9636e-02
   3_occ:   1.167  0.009  0.083 15.815  0.004  4.130   7.9636e-02
   4_bss:   1.167  0.009  0.083 15.815  0.004  4.130   7.9636e-02
   4_xyz:   1.173  0.011  0.089 15.841  0.004  4.117   8.3247e-02
   4_adp:   1.173  0.011  0.089 15.841  0.004  4.117   8.3247e-02
   4_occ:   1.173  0.011  0.089 15.841  0.004  4.117   8.3247e-02
   5_bss:   1.173  0.011  0.089 15.841  0.004  4.117   8.3247e-02
   5_xyz:   1.060  0.009  0.083 15.420  0.003  4.123   6.7752e-02
   5_adp:   1.060  0.009  0.083 15.420  0.003  4.123   6.7752e-02
   5_occ:   1.060  0.009  0.083 15.420  0.003  4.123   6.7752e-02
   5_bss:   1.060  0.009  0.083 15.420  0.003  4.123   6.7752e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0462e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0462e+00
   1_xyz:  15.525  0.168  0.482 86.201  0.049  2.179   1.0858e-01
   1_adp:  15.525  0.168  0.482 86.201  0.049  2.179   1.0858e-01
   1_occ:  15.525  0.168  0.482 86.201  0.049  2.179   1.0858e-01
   2_bss:  15.525  0.168  0.482 86.201  0.049  2.179   1.0858e-01
   2_xyz:   7.734  0.101  0.227 86.498  0.038  2.156   1.0361e-01
   2_adp:   7.734  0.101  0.227 86.498  0.038  2.156   1.0361e-01
   2_occ:   7.734  0.101  0.227 86.498  0.038  2.156   1.0361e-01
   3_bss:   7.734  0.101  0.227 86.498  0.038  2.156   1.0361e-01
   3_xyz:   8.000  0.057  0.317 82.108  0.034  2.256   1.0271e-01
   3_adp:   8.000  0.057  0.317 82.108  0.034  2.256   1.0271e-01
   3_occ:   8.000  0.057  0.317 82.108  0.034  2.256   1.0271e-01
   4_bss:   8.000  0.057  0.317 82.108  0.034  2.256   1.0271e-01
   4_xyz:   7.833  0.060  0.443 88.160  0.035  2.285   6.2055e-02
   4_adp:   7.833  0.060  0.443 88.160  0.035  2.285   6.2055e-02
   4_occ:   7.833  0.060  0.443 88.160  0.035  2.285   6.2055e-02
   5_bss:   7.833  0.060  0.443 88.160  0.035  2.285   6.2055e-02
   5_xyz:   7.345  0.044  0.417 80.898  0.032  2.339   4.2494e-02
   5_adp:   7.345  0.044  0.417 80.898  0.032  2.339   4.2494e-02
   5_occ:   7.345  0.044  0.417 80.898  0.032  2.339   4.2494e-02
   5_bss:   7.345  0.044  0.417 80.898  0.032  2.339   4.2494e-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:  81.82   0.00  13.79  71.85   0.00  11.34  81.82   0.00  27.14
   1_occ:  81.82   0.00  13.79  71.85   0.00  11.34  81.82   0.00  27.14
   2_bss:  81.82   0.00  13.79  71.85   0.00  11.34  81.82   0.00  27.14
   2_xyz:  81.82   0.00  13.79  71.85   0.00  11.34  81.82   0.00  27.14
   2_adp:  81.82   0.00  13.44  68.70   0.00   9.99  81.82   0.00  32.20
   2_occ:  81.82   0.00  13.44  68.70   0.00   9.99  81.82   0.00  32.20
   3_bss:  81.82   0.00  13.44  68.70   0.00   9.99  81.82   0.00  32.20
   3_xyz:  81.82   0.00  13.44  68.70   0.00   9.99  81.82   0.00  32.20
   3_adp:  79.85   0.00  13.29  69.91   0.00   9.17  79.85   1.86  35.77
   3_occ:  79.85   0.00  13.29  69.91   0.00   9.17  79.85   1.86  35.77
   4_bss:  79.85   0.00  13.29  69.91   0.00   9.17  79.85   1.86  35.77
   4_xyz:  79.85   0.00  13.29  69.91   0.00   9.17  79.85   1.86  35.77
   4_adp:  84.88   0.00  13.42  71.42   0.00   8.98  84.88   1.33  37.55
   4_occ:  84.88   0.00  13.42  71.42   0.00   8.98  84.88   1.33  37.55
   5_bss:  84.88   0.00  13.42  71.42   0.00   8.98  84.88   1.33  37.55
   5_xyz:  84.88   0.00  13.42  71.42   0.00   8.98  84.88   1.33  37.55
   5_adp:  93.98   0.00  13.51  81.08   0.00   8.91  93.98   1.23  38.55
   5_occ:  93.98   0.00  13.51  81.08   0.00   8.91  93.98   1.23  38.55
   5_bss:  96.49   2.51  16.02  83.59   2.51  11.42  96.49   3.74  41.06
------------------------------------------------------------------------
 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:    1.285    0.025    0.415
   1_adp:    1.285    0.025    0.415
   1_occ:    1.285    0.025    0.415
   2_bss:    1.285    0.025    0.415
   2_xyz:    1.989    0.037    0.571
   2_adp:    1.989    0.037    0.571
   2_occ:    1.989    0.037    0.571
   3_bss:    1.989    0.037    0.571
   3_xyz:    1.876    0.024    0.665
   3_adp:    1.876    0.024    0.665
   3_occ:    1.876    0.024    0.665
   4_bss:    1.876    0.024    0.665
   4_xyz:    1.996    0.046    0.729
   4_adp:    1.996    0.046    0.729
   4_occ:    1.996    0.046    0.729
   5_bss:    1.996    0.046    0.729
   5_xyz:    2.101    0.036    0.740
   5_adp:    2.101    0.036    0.740
   5_occ:    2.101    0.036    0.740
   5_bss:    2.101    0.036    0.740
------------------------------------------------------------------------

CPU time actual refinement: 273.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/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_571/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_571/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 273.47 
  Macro-tasks:
    bulk solvent and scale       = 36.04  
    individual site refinement   = 110.02 
    weights calculation          = 26.00  
    collect and process          = 5.39   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 177.54 
  Micro-tasks:
    mask                            = 2.00   
    f_calc                          = 82.91  
    alpha_beta                      = 7.20   
    target                          = 0.97   
    gradients_wrt_atomic_parameters = 91.48  
    fmodel                         = 5.84   
    r_factors                      = 0.20   
    phase_errors                   = 8.66   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 199.46 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.896 micro seconds
Total CPU time: 4.75 minutes
from_scatterers_fft:    634 calls, 82.57 s
gradients_fft:          579 calls, 80.45 s

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

# Date 2008-01-16 Time 01:52:01 PST -0800 (1200477121.44 s)
Start R-work = 0.4831, R-free = 0.4700 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1846 (no bulk solvent and anisotropic scale)

Start R-work = 0.4741, R-free = 0.4596
Final R-work = 0.1212, R-free = 0.1699