# Date 2008-01-16 Time 02:20:38 PST -0800 (1200478838.39 s)
#phil __OFF__

Command line arguments: "../791.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23814
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 791

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.00219
Completeness in resolution range: 0.960057
Completeness with d_max=infinity: 0.957102

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0022

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.00219
Completeness in resolution range: 0.960057
Completeness with d_max=infinity: 0.957102

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.2841 [2148/2172]  1929   219  10.2%
  bin  2:  4.2841 -  3.4132 [2053/2073]  1849   204   9.9%
  bin  3:  3.4132 -  2.9855 [2030/2049]  1832   198   9.8%
  bin  4:  2.9855 -  2.7143 [2013/2043]  1810   203  10.1%
  bin  5:  2.7143 -  2.5207 [1997/2016]  1796   201  10.1%
  bin  6:  2.5207 -  2.3726 [2007/2032]  1802   205  10.2%
  bin  7:  2.3726 -  2.2542 [1971/1999]  1776   195   9.9%
  bin  8:  2.2542 -  2.1564 [1968/2004]  1772   196  10.0%
  bin  9:  2.1564 -  2.0736 [1957/1999]  1765   192   9.8%
  bin 10:  2.0736 -  2.0022 [1445/2017]  1299   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 9
        2.22 -     2.89: 1310
        2.89 -     3.56: 4371
        3.56 -     4.23: 9054
        4.23 -     4.90: 13144
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.553 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.720 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.720 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.767 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27883 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_791/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 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: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4652   r_free= 0.4567   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.267484                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.3890 0.3498      6.6015      6.4952|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.3688 0.4019      6.7402      6.8607|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.4221 0.4034      6.6544      6.6269|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.4576 0.4128      6.5166      6.4257|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.4918 0.4541      6.3632      6.3726|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.4834 0.5633       6.265      6.2214|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.5047 0.5002      6.2279      6.1607|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.5211 0.4517      6.1849      6.1599|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.4982 0.5769      6.1068      6.1736|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.5226 0.4609      6.1174      6.0449|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.5020 0.5029      6.0154      6.0535|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.5191 0.4766      5.9699      6.0096|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.5117 0.5300      5.8775      5.8402|
| 14:  2.0521 -  2.0022 0.60    780   91 0.5252 0.4918      5.8743      5.7519|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7782  1392   154  0.73  31.72   0.79     0.76      61520.81|
|  2:  4.7782 -  3.8125  1339   152  0.74  31.80   0.88     0.79      91982.93|
|  3:  3.8125 -  3.3365  1303   142  0.65  39.55   0.83     0.75      97155.15|
|  4:  3.3365 -  3.0341  1310   145  0.56  47.02   0.80     0.63      88669.46|
|  5:  3.0341 -  2.8181  1296   147  0.46  54.66   0.75     0.53      74760.49|
|  6:  2.8181 -  2.6529  1298   143  0.41  58.92   0.72     0.46      69874.45|
|  7:  2.6529 -  2.5207  1278   142  0.40  60.07   0.73     0.45      62869.94|
|  8:  2.5207 -  2.4114  1279   138  0.41  59.09   0.72     0.47      54847.99|
|  9:  2.4114 -  2.3189  1274   145  0.43  57.82   0.74     0.49      49716.60|
| 10:  2.3189 -  2.2391  1296   141  0.42  58.70   0.74     0.48      44909.20|
| 11:  2.2391 -  2.1693  1257   140  0.39  60.44   0.75     0.47      43608.26|
| 12:  2.1693 -  2.1075  1252   144  0.39  60.71   0.74     0.48      39330.49|
| 13:  2.1075 -  2.0521  1276   135  0.38  61.69   0.71     0.46      34512.52|
| 14:  2.0521 -  2.0022   780    91  0.40  60.33   0.73     0.43      28609.18|
|alpha:            min =        0.43 max =            0.79 mean =         0.55|
|beta:             min =    28609.18 max =        97155.15 mean =     61349.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.97 mean =        52.58|
|phase err.(test): min =        0.00 max =           89.99 mean =        52.88|
|-----------------------------------------------------------------------------|

============================== 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 = 11.689940             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.203   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.981603              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.463   (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 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 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:     2568 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3868 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5009 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6474 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7611 |
|-----------------------------------------------------------------------------|
|-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 |       54.391 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.759 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    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 = 12.207)------------------------------------------|
|    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: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4711   r_free= 0.4569   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.271175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4553   r_free= 0.4431   ksol= 0.33   Bsol= 21.03   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.78,7.00,12.46,0.00,0.00,0.00); trace/3= 8.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.260582                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.536278             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.920123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.452   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4553      final r-factor (work) = 0.3653          |
| start r-factor (free) = 0.4431      final r-factor (free) = 0.3895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.4121 = 10.54 * 0.50 * 6.2680 + 1.00 * 54.3913                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.5638 = 10.54 * 0.50 * 6.1553 + 1.00 * 0.1369                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3653      final r-factor (work) = 0.3141          |
| start r-factor (free) = 0.3895      final r-factor (free) = 0.3629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6780 = 0.92 * 1.00 * 6.1553 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5787 = 0.92 * 1.00 * 6.0468 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.83   12.60    None  None   None       |
|    all(noH): 2823   0      0.00    71.83   12.60    None  None   None       |
|    Sol.    : 438    0      0.00    71.83   27.30    None  None   None       |
|    Mac.    : 2385   0      0.00    61.23   9.90     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 -   7.184: 1187   |   5:    35.917 -  43.101:   81        |
|      1:     7.184 -  14.367:  731   |   6:    43.101 -  50.284:   52        |
|      2:    14.367 -  21.550:  372   |   7:    50.284 -  57.468:   25        |
|      3:    21.550 -  28.734:  242   |   8:    57.468 -  64.651:   11        |
|      4:    28.734 -  35.917:  119   |   9:    64.651 -  71.835:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3141 r_free = 0.3629             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3137 r_free = 0.3641             target_work(ml) = 6.016         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3137   r_free= 0.3641   ksol= 0.33   Bsol= 21.03   scale= 1.090   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.78,7.00,12.46,0.00,0.00,0.00); trace/3= 8.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.016161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3111   r_free= 0.3606   ksol= 0.34   Bsol= 55.73   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,3.94,8.97,0.00,0.00,0.00); trace/3= 5.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.016896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.822784              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.353   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441691              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.353  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3111      final r-factor (work) = 0.2261          |
| start r-factor (free) = 0.3606      final r-factor (free) = 0.2812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7528 = 6.82 * 0.50 * 6.0432 + 1.00 * 0.1369                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1401 = 6.82 * 0.50 * 5.8753 + 1.00 * 0.0970                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2261      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.2812      final r-factor (free) = 0.2536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6102 = 0.44 * 1.00 * 5.8753 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5239 = 0.44 * 1.00 * 5.6857 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.66   12.38    None  None   None       |
|    all(noH): 2823   0      0.00    73.66   12.38    None  None   None       |
|    Sol.    : 438    0      0.00    73.66   33.20    None  None   None       |
|    Mac.    : 2385   0      0.00    60.45   8.55     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 -   7.366: 1375   |   5:    36.831 -  44.198:  107        |
|      1:     7.366 -  14.733:  722   |   6:    44.198 -  51.564:   68        |
|      2:    14.733 -  22.099:  258   |   7:    51.564 -  58.930:   33        |
|      3:    22.099 -  29.465:  130   |   8:    58.930 -  66.296:   15        |
|      4:    29.465 -  36.831:  113   |   9:    66.296 -  73.663:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2017 r_free = 0.2536             target_work(ml) = 5.643         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2015 r_free = 0.2535             target_work(ml) = 5.643         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2015   r_free= 0.2535   ksol= 0.34   Bsol= 55.73   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,3.94,8.97,0.00,0.00,0.00); trace/3= 5.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.642504                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1992   r_free= 0.2536   ksol= 0.32   Bsol= 65.88   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,2.75,5.47,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.641760                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.360798              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.402   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.583685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1992      final r-factor (work) = 0.1601          |
| start r-factor (free) = 0.2536      final r-factor (free) = 0.2097          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8188 = 2.36 * 0.50 * 5.6945 + 1.00 * 0.0970                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6089 = 2.36 * 0.50 * 5.5480 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1601      final r-factor (work) = 0.1498          |
| start r-factor (free) = 0.2097      final r-factor (free) = 0.1991          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2507 = 0.58 * 1.00 * 5.5480 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1739 = 0.58 * 1.00 * 5.4095 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.99   12.93    None  None   None       |
|    all(noH): 2823   0      0.00    82.99   12.93    None  None   None       |
|    Sol.    : 438    0      1.40    82.99   37.12    None  None   None       |
|    Mac.    : 2385   0      0.00    72.00   8.49     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 -   8.299: 1543   |   5:    41.495 -  49.794:  101        |
|      1:     8.299 -  16.598:  664   |   6:    49.794 -  58.093:   73        |
|      2:    16.598 -  24.897:  180   |   7:    58.093 -  66.393:   39        |
|      3:    24.897 -  33.196:  112   |   8:    66.393 -  74.692:   10        |
|      4:    33.196 -  41.495:   97   |   9:    74.692 -  82.991:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1498 r_free = 0.1991             target_work(ml) = 5.389         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1497 r_free = 0.1989             target_work(ml) = 5.389         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1989   ksol= 0.32   Bsol= 65.88   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,2.75,5.47,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.389332                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1982   ksol= 0.33   Bsol= 65.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.36,4.53,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.387736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.200014              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.904  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.868  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1982      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0112 = 2.20 * 0.50 * 5.4101 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9279 = 2.20 * 0.50 * 5.3290 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4661 = 0.27 * 1.00 * 5.3290 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4459 = 0.27 * 1.00 * 5.2697 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.17   12.53    None  None   None       |
|    all(noH): 2823   0      0.00    83.17   12.53    None  None   None       |
|    Sol.    : 438    0      1.25    83.17   36.12    None  None   None       |
|    Mac.    : 2385   0      0.00    71.94   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.317: 1618   |   5:    41.587 -  49.904:   89        |
|      1:     8.317 -  16.635:  626   |   6:    49.904 -  58.222:   65        |
|      2:    16.635 -  24.952:  160   |   7:    58.222 -  66.539:   32        |
|      3:    24.952 -  33.270:  114   |   8:    66.539 -  74.857:   10        |
|      4:    33.270 -  41.587:  105   |   9:    74.857 -  83.174:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1739             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1287 r_free = 0.1738             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1738   ksol= 0.33   Bsol= 65.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.00,2.36,4.53,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.257503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1739   ksol= 0.33   Bsol= 65.88   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.41,4.34,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.257444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.847400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.154  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.011630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.527  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1286      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1739      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5682 = 2.85 * 0.50 * 5.2695 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5158 = 2.85 * 0.50 * 5.2256 + 1.00 * 0.0761                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1662      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2980 = 1.01 * 1.00 * 5.2256 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2701 = 1.01 * 1.00 * 5.1953 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.99   12.66    None  None   None       |
|    all(noH): 2823   0      0.00    91.99   12.66    None  None   None       |
|    Sol.    : 438    0      0.87    91.99   37.02    None  None   None       |
|    Mac.    : 2385   0      0.00    77.73   8.19     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 -   9.199: 1746   |   5:    45.995 -  55.194:   97        |
|      1:     9.199 -  18.398:  532   |   6:    55.194 -  64.393:   49        |
|      2:    18.398 -  27.597:  154   |   7:    64.393 -  73.592:   22        |
|      3:    27.597 -  36.796:  123   |   8:    73.592 -  82.791:    7        |
|      4:    36.796 -  45.995:   90   |   9:    82.791 -  91.989:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1665             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1664             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1664   ksol= 0.33   Bsol= 65.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.41,4.34,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.196983                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.1019 0.1367      5.4148      5.5795|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.0858 0.1179      5.4575       5.696|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.1108 0.1513      5.5217      5.8428|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.1276 0.1811      5.4908      5.6866|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.1405 0.1623      5.3831       5.558|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.1294 0.2228      5.2655       5.595|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.1362 0.1714      5.2424      5.3708|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.1262 0.1747       5.153      5.4307|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.1259 0.1992      5.1142      5.3997|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.1201 0.1739      5.0157      5.2254|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.1213 0.1831      5.0001      5.2729|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.1194 0.1897      4.9278      5.3031|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.1153 0.1705      4.8269      5.0414|
| 14:  2.0521 -  2.0022 0.60    780   91 0.1017 0.1735      4.6907      4.9595|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7782  1392   154  0.94   9.68   0.97     0.95       7843.63|
|  2:  4.7782 -  3.8125  1339   152  0.95   8.42   1.00     0.99       9826.46|
|  3:  3.8125 -  3.3365  1303   142  0.93  11.89   1.02     1.01      11383.85|
|  4:  3.3365 -  3.0341  1310   145  0.92  14.21   1.00     0.98      11003.25|
|  5:  3.0341 -  2.8181  1296   147  0.90  16.58   0.99     0.97       9168.11|
|  6:  2.8181 -  2.6529  1298   143  0.89  17.18   0.97     0.94       7932.15|
|  7:  2.6529 -  2.5207  1278   142  0.89  16.95   0.98     0.94       7159.19|
|  8:  2.5207 -  2.4114  1279   138  0.89  16.88   0.98     0.95       6377.16|
|  9:  2.4114 -  2.3189  1274   145  0.90  16.74   1.00     0.95       6004.71|
| 10:  2.3189 -  2.2391  1296   141  0.89  17.24   0.99     0.95       4994.24|
| 11:  2.2391 -  2.1693  1257   140  0.89  17.33   0.98     0.94       4960.03|
| 12:  2.1693 -  2.1075  1252   144  0.90  16.93   0.99     0.98       4435.99|
| 13:  2.1075 -  2.0521  1276   135  0.89  17.18   0.98     0.95       3719.07|
| 14:  2.0521 -  2.0022   780    91  0.92  14.37   0.96     0.92       2711.38|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2711.38 max =        11383.85 mean =      7123.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.07|
|phase err.(test): min =        0.00 max =           88.78 mean =        14.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1662   ksol= 0.33   Bsol= 65.14   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.56,1.32,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.196394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1662   ksol= 0.33   Bsol= 65.14   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.56,1.32,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.196394                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7782 0.99   1392  154 0.1003 0.1360      5.4069      5.5689|
|  2:  4.7782 -  3.8125 0.99   1339  152 0.0867 0.1162      5.4592      5.6847|
|  3:  3.8125 -  3.3365 0.99   1303  142 0.1107 0.1505       5.518      5.8451|
|  4:  3.3365 -  3.0341 0.99   1310  145 0.1277 0.1828       5.492      5.6905|
|  5:  3.0341 -  2.8181 0.99   1296  147 0.1404 0.1619      5.3845       5.557|
|  6:  2.8181 -  2.6529 0.99   1298  143 0.1295 0.2228       5.266      5.5956|
|  7:  2.6529 -  2.5207 0.99   1278  142 0.1361 0.1718      5.2426      5.3704|
|  8:  2.5207 -  2.4114 0.98   1279  138 0.1262 0.1750      5.1533       5.431|
|  9:  2.4114 -  2.3189 0.98   1274  145 0.1257 0.1991      5.1138         5.4|
| 10:  2.3189 -  2.2391 1.00   1296  141 0.1200 0.1739      5.0158      5.2254|
| 11:  2.2391 -  2.1693 0.97   1257  140 0.1212 0.1831      4.9999      5.2726|
| 12:  2.1693 -  2.1075 0.98   1252  144 0.1193 0.1893      4.9274       5.302|
| 13:  2.1075 -  2.0521 0.99   1276  135 0.1152 0.1707      4.8266      5.0418|
| 14:  2.0521 -  2.0022 0.60    780   91 0.1017 0.1734      4.6908       4.959|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.7782  1392   154  0.94   9.70   0.97     0.94       7843.24|
|  2:  4.7782 -  3.8125  1339   152  0.95   8.34   1.01     0.99       9681.97|
|  3:  3.8125 -  3.3365  1303   142  0.93  11.79   1.02     1.02      11215.82|
|  4:  3.3365 -  3.0341  1310   145  0.91  14.27   1.00     0.98      11046.41|
|  5:  3.0341 -  2.8181  1296   147  0.90  16.60   1.00     0.97       9199.70|
|  6:  2.8181 -  2.6529  1298   143  0.89  17.18   0.98     0.95       7934.31|
|  7:  2.6529 -  2.5207  1278   142  0.89  16.96   0.98     0.94       7163.77|
|  8:  2.5207 -  2.4114  1279   138  0.89  16.89   0.99     0.96       6381.47|
|  9:  2.4114 -  2.3189  1274   145  0.90  16.74   1.00     0.96       6007.09|
| 10:  2.3189 -  2.2391  1296   141  0.89  17.24   0.99     0.95       4992.24|
| 11:  2.2391 -  2.1693  1257   140  0.89  17.33   0.99     0.94       4958.19|
| 12:  2.1693 -  2.1075  1252   144  0.90  16.93   1.00     0.99       4434.36|
| 13:  2.1075 -  2.0521  1276   135  0.89  17.18   0.99     0.96       3716.52|
| 14:  2.0521 -  2.0022   780    91  0.92  14.37   0.97     0.93       2710.88|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2710.88 max =        11215.82 mean =      7105.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.07|
|phase err.(test): min =        0.00 max =           87.54 mean =        14.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.09    95.08   15.75    None  None   None       |
|    all(noH): 2823   0      3.09    95.08   15.75    None  None   None       |
|    Sol.    : 438    0      3.95    95.08   40.11    None  None   None       |
|    Mac.    : 2385   0      3.09    80.82   11.28    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:     3.086 -  12.285: 1746   |   5:    49.081 -  58.280:   97        |
|      1:    12.285 -  21.484:  532   |   6:    58.280 -  67.479:   49        |
|      2:    21.484 -  30.683:  154   |   7:    67.479 -  76.677:   22        |
|      3:    30.683 -  39.882:  123   |   8:    76.677 -  85.876:    7        |
|      4:    39.882 -  49.081:   90   |   9:    85.876 -  95.075:    3        |
|                               =>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: 0.219 - 4.944
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 318
   mapped sites are within: 0.708 - 4.944

peak=   10.623 closest distance to " CB  VAL A 230 " =    1.438
peak=    5.884 closest distance to " CD2 LEU A   5 " =    1.162
peak=    5.530 closest distance to " NE2 GLN A  11 " =    1.111
peak=    5.487 closest distance to " CG  LEU A   5 " =    1.218
peak=    5.327 closest distance to " CG  LEU A 228 " =    1.174
peak=    5.292 closest distance to " O   HOH Z 248 " =    1.440
peak=    5.208 closest distance to " NH2 ARG A  56 " =    2.121
peak=    5.190 closest distance to " O   HOH Z 142 " =    1.969
peak=    5.167 closest distance to " CB  VAL A 296 " =    1.068
peak=    5.135 closest distance to " CB  GLN A 223 " =    1.506
peak=    5.085 closest distance to " CG2 VAL A 296 " =    1.052
peak=    5.071 closest distance to " CG  PRO A  54 " =    1.349
peak=    4.995 closest distance to " CB  GLN A 183 " =    1.275
peak=    4.796 closest distance to " O   HOH Z 265 " =    2.117
peak=    4.659 closest distance to " O   HOH Z   9 " =    1.615
peak=    4.611 closest distance to " CB  PRO A  54 " =    0.968
peak=    4.607 closest distance to " CB  ASN A 148 " =    1.473
peak=    4.604 closest distance to " CZ  PHE A 218 " =    1.128
peak=    4.508 closest distance to " O   HOH Z 369 " =    2.149
peak=    4.456 closest distance to " CB  ASN A 142 " =    1.091
peak=    4.454 closest distance to " O   SER A  87 " =    2.353
peak=    4.407 closest distance to " O   HOH Z 425 " =    1.512
peak=    4.406 closest distance to " CB  ARG A 190 " =    1.496
peak=    4.387 closest distance to " O   HOH Z 313 " =    1.890
peak=    4.384 closest distance to " O   HOH Z 427 " =    3.000
peak=    4.367 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.300 closest distance to " CG  PRO A 243 " =    1.124
peak=    4.298 closest distance to " O   HOH Z 368 " =    2.307
peak=    4.237 closest distance to " O   HOH Z 251 " =    1.680
peak=    4.210 closest distance to " CB  GLU A 277 " =    3.713
peak=    4.166 closest distance to " CA  ALA A  51 " =    0.964
peak=    4.113 closest distance to " O   HOH Z 126 " =    1.973
peak=    4.111 closest distance to " O   HOH Z 359 " =    1.701
peak=    4.110 closest distance to " NH1 ARG A 138 " =    1.074
peak=    4.107 closest distance to " O   HOH Z 346 " =    1.597
peak=    4.106 closest distance to " CZ3 TRP A 266 " =    1.177
peak=    4.095 closest distance to " CG1 VAL A 296 " =    1.236
peak=    4.091 closest distance to " CB  ASP A 124 " =    0.787
peak=    4.088 closest distance to " CD2 LEU A 228 " =    1.133
peak=    4.056 closest distance to " CB  SER A  63 " =    1.179
peak=    4.051 closest distance to " O   HOH Z 126 " =    1.606
peak=    4.033 closest distance to " CG  PRO A 198 " =    1.272
peak=    4.025 closest distance to " O  BHOH Z 338 " =    2.309
peak=    4.022 closest distance to " CB  VAL A 265 " =    1.287
peak=    4.020 closest distance to " CG  MET A 185 " =    1.261
peak=    4.009 closest distance to " CG2 ILE A 234 " =    1.002
peak=    4.000 closest distance to " NH2AARG A 145 " =    1.136
peak=    3.989 closest distance to " O   HOH Z 287 " =    2.070
peak=    3.984 closest distance to " CA  TYR A  30 " =    0.993
peak=    3.983 closest distance to " O   HOH Z 303 " =    2.080
peak=    3.980 closest distance to " O   PRO A 198 " =    1.568
peak=    3.980 closest distance to " CB  ARG A 275 " =    0.946
peak=    3.979 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.961 closest distance to " O   HOH Z 406 " =    1.619
peak=    3.958 closest distance to " CB  ARG A  79 " =    1.479
peak=    3.954 closest distance to " O   HOH Z 298 " =    1.835
peak=    3.945 closest distance to " ND2 ASN A 187 " =    1.557
peak=    3.942 closest distance to " O   HOH Z 411 " =    3.883
peak=    3.935 closest distance to " O   HOH Z 261 " =    1.936
peak=    3.924 closest distance to " CG  PRO A 213 " =    1.142
peak=    3.905 closest distance to " CD2 TRP A 179 " =    1.239
peak=    3.903 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.901 closest distance to " CB  TRP A 266 " =    1.070
peak=    3.894 closest distance to " O   HOH Z 188 " =    2.901
peak=    3.880 closest distance to " O   HOH Z 214 " =    2.575
peak=    3.880 closest distance to " O   HOH Z 290 " =    1.142
peak=    3.876 closest distance to " CA  VAL A 125 " =    1.211
peak=    3.872 closest distance to " O   HOH Z 422 " =    2.622
peak=    3.855 closest distance to " CB  GLN A  89 " =    1.173
peak=    3.840 closest distance to " CG AARG A 275 " =    1.324
peak=    3.837 closest distance to " CB  ASP A 140 " =    0.993
peak=    3.834 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.834 closest distance to " CA  ARG A 195 " =    1.206
peak=    3.833 closest distance to " O   HOH Z  92 " =    2.331
peak=    3.829 closest distance to " NH1AARG A 145 " =    1.221
peak=    3.822 closest distance to " O   HOH Z 207 " =    1.177
peak=    3.819 closest distance to " O   HOH Z 353 " =    2.605
peak=    3.804 closest distance to " O   HOH Z  78 " =    1.657
peak=    3.798 closest distance to " CB  GLU A  46 " =    0.939
peak=    3.774 closest distance to " CB  GLU A 128 " =    0.951
peak=    3.766 closest distance to " O   HOH Z 258 " =    1.995
peak=    3.757 closest distance to " CD  LYS A 166 " =    1.333
peak=    3.737 closest distance to " O   HOH Z 273 " =    2.911
peak=    3.734 closest distance to " O   HOH Z  80 " =    1.710
peak=    3.733 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.719 closest distance to " CB  GLU A 152 " =    1.172
peak=    3.705 closest distance to " O   HOH Z 365 " =    2.885
peak=    3.700 closest distance to " CD1 ILE A  33 " =    1.836
peak=    3.698 closest distance to " CB  VAL A 202 " =    1.573
peak=    3.696 closest distance to " CG AARG A 102 " =    1.209
peak=    3.683 closest distance to " CB AVAL A  41 " =    1.185
peak=    3.678 closest distance to " CB  LEU A  83 " =    0.750
peak=    3.669 closest distance to " CB  SER A 212 " =    1.301
peak=    3.669 closest distance to " O   ASP A 124 " =    1.096
peak=    3.665 closest distance to " O   HOH Z   4 " =    1.547
peak=    3.661 closest distance to " O   HOH Z 158 " =    3.201
peak=    3.658 closest distance to " N   ALA A 256 " =    1.167
peak=    3.648 closest distance to " O   HOH Z  43 " =    2.032
peak=    3.648 closest distance to " CB  VAL A 230 " =    1.186
peak=    3.638 closest distance to " CB  SER A   3 " =    1.358
peak=    3.635 closest distance to " O   HOH Z 193 " =    1.873
peak=    3.631 closest distance to " O   HOH Z 214 " =    1.350
peak=    3.631 closest distance to " O   HOH Z  76 " =    1.174
peak=    3.621 closest distance to " CG  GLN A  58 " =    0.990
peak=    3.611 closest distance to " N   PHE A 130 " =    1.277
peak=    3.603 closest distance to " N   ASN A  39 " =    1.227
peak=    3.602 closest distance to " O   PHE A 192 " =    1.382
peak=    3.598 closest distance to " NE2 HIS A 207 " =    1.206
peak=    3.586 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.582 closest distance to " O   HOH Z  61 " =    1.761
peak=    3.582 closest distance to " CG  GLU A  37 " =    0.959
peak=    3.581 closest distance to " CB  PRO A  90 " =    1.195
peak=    3.576 closest distance to " O   HOH Z 280 " =    2.992
peak=    3.572 closest distance to " CA  TYR A 116 " =    1.421
peak=    3.568 closest distance to " CB  ALA A   9 " =    1.642
peak=    3.562 closest distance to " O   HOH Z  90 " =    2.274
peak=    3.559 closest distance to " CB  ASN A  39 " =    0.933
peak=    3.555 closest distance to " O   HOH Z  59 " =    2.265
peak=    3.555 closest distance to " O   HOH Z 213 " =    1.957
peak=    3.554 closest distance to " CZ  PHE A  38 " =    1.172
peak=    3.551 closest distance to " O   HOH Z 234 " =    3.619
peak=    3.549 closest distance to " CG  LEU A   5 " =    0.722
peak=    3.548 closest distance to " O   HOH Z  68 " =    2.121
peak=    3.540 closest distance to " ND2 ASN A 249 " =    0.882
peak=    3.540 closest distance to " CB  ASN A 110 " =    1.192
peak=    3.532 closest distance to " CG2 ILE A  20 " =    1.527
peak=    3.528 closest distance to " O   HOH Z 166 " =    3.891
peak=    3.526 closest distance to " O   HOH Z 371 " =    2.764
peak=    3.526 closest distance to " CA  ARG A  36 " =    1.144
peak=    3.521 closest distance to " O   HOH Z 368 " =    3.395
peak=    3.518 closest distance to " CG1 ILE A  49 " =    1.538
peak=    3.514 closest distance to " O   HOH Z 133 " =    2.837
peak=    3.513 closest distance to " OD1 ASN A  69 " =    2.523
peak=    3.512 closest distance to " O   HOH Z 261 " =    1.680
peak=    3.510 closest distance to " CA  LEU A 282 " =    1.153
peak=    3.507 closest distance to " CD  ARG A 269 " =    0.924
peak=    3.504 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.500 closest distance to " CA  ALA A 295 " =    1.160
peak=    3.500 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.495 closest distance to " O   HOH Z 272 " =    1.769
peak=    3.494 closest distance to " OG  SER A 276 " =    1.248
peak=    3.490 closest distance to " CB  SER A  62 " =    1.091
peak=    3.489 closest distance to " CB  LYS A 117 " =    1.214
peak=    3.480 closest distance to " CB  ASP A 298 " =    1.186
peak=    3.479 closest distance to " CA  ASP A 162 " =    0.989
peak=    3.468 closest distance to " OE2 GLU A  53 " =    1.966
peak=    3.461 closest distance to " NH2 ARG A  56 " =    1.096
peak=    3.460 closest distance to " CB  TRP A 179 " =    1.472
peak=    3.458 closest distance to " CD  ARG A  66 " =    2.629
peak=    3.447 closest distance to " O   HOH Z  30 " =    1.420
peak=    3.446 closest distance to " O   HOH Z   3 " =    1.946
peak=    3.445 closest distance to " CB  LEU A 143 " =    1.261
peak=    3.442 closest distance to " OE1 GLN A  55 " =    1.503
peak=    3.437 closest distance to " CA  THR A 264 " =    0.793
peak=    3.431 closest distance to " CD BLYS A 290 " =    1.036
peak=    3.423 closest distance to " O   HOH Z 285 " =    2.155
peak=    3.423 closest distance to " CA  SER A  87 " =    0.996
peak=    3.422 closest distance to " CB  THR A  82 " =    1.314
peak=    3.422 closest distance to " CB  MET A  40 " =    0.769
peak=    3.421 closest distance to " CB  TRP A 150 " =    1.362
peak=    3.418 closest distance to " CB  THR A  31 " =    1.599
peak=    3.417 closest distance to " CB  THR A  52 " =    0.831
peak=    3.409 closest distance to " CD1 LEU A 300 " =    1.112
peak=    3.406 closest distance to " O   ASN A 284 " =    1.724
peak=    3.404 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.402 closest distance to " O   HOH Z 329 " =    4.249
peak=    3.402 closest distance to " CG2AVAL A 121 " =    2.427
peak=    3.395 closest distance to " O   HOH Z 227 " =    1.727
peak=    3.394 closest distance to " O   HOH Z  40 " =    1.666
peak=    3.392 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.387 closest distance to " CA  ALA A 129 " =    1.408
peak=    3.385 closest distance to " CA  LYS A 117 " =    1.291
peak=    3.382 closest distance to " O   HOH Z 199 " =    1.583
peak=    3.380 closest distance to " CB  GLN A  88 " =    1.228
peak=    3.378 closest distance to " CG  MET A 185 " =    0.991
peak=    3.377 closest distance to " O   HOH Z 391 " =    2.858
peak=    3.376 closest distance to " CE3 TRP A 150 " =    1.057
peak=    3.374 closest distance to " CB  SER A  97 " =    1.106
peak=    3.372 closest distance to " O   HOH Z 148 " =    3.442
peak=    3.368 closest distance to " CA  ASN A 127 " =    1.126
peak=    3.367 closest distance to " O   HOH Z  88 " =    3.461
peak=    3.365 closest distance to " CE1 TYR A 186 " =    1.222
peak=    3.361 closest distance to " OE2 GLU A   2 " =    1.963
peak=    3.357 closest distance to " CG BARG A 102 " =    1.853
peak=    3.357 closest distance to " O   HOH Z  10 " =    1.788
peak=    3.356 closest distance to " O   HOH Z 417 " =    3.363
peak=    3.349 closest distance to " O   HOH Z   1 " =    1.964
peak=    3.345 closest distance to " CA  GLY A 267 " =    0.952
peak=    3.345 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.344 closest distance to " CA  MET A 105 " =    0.971
peak=    3.344 closest distance to " O   ASN A  74 " =    1.371
peak=    3.343 closest distance to " O   HOH Z 145 " =    1.189
peak=    3.343 closest distance to " C   ALA A 299 " =    0.880
peak=    3.342 closest distance to " CA  ASN A  74 " =    1.249
peak=    3.339 closest distance to " NE2 GLN A  77 " =    3.347
peak=    3.338 closest distance to " CB  ASN A 187 " =    1.131
peak=    3.338 closest distance to " O   HOH Z 126 " =    1.751
peak=    3.335 closest distance to " O   HOH Z 316 " =    3.130
peak=    3.335 closest distance to " O   ALA A 165 " =    1.498
peak=    3.334 closest distance to " CD1 ILE A 199 " =    1.058
peak=    3.331 closest distance to " O   HOH Z 172 " =    3.636
peak=    3.320 closest distance to " O   MET A 105 " =    1.700
peak=    3.319 closest distance to " CA  ILE A 234 " =    0.994
peak=    3.318 closest distance to " CB  SER A  26 " =    1.838
peak=    3.314 closest distance to " N   ASP A 162 " =    1.244
peak=    3.312 closest distance to " CB  ALA A 104 " =    0.744
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.208
peak=    3.303 closest distance to " OG BSER A 134 " =    2.930
peak=    3.302 closest distance to " O   HOH Z 211 " =    1.107
peak=    3.295 closest distance to " O   HOH Z 299 " =    4.376
peak=    3.294 closest distance to " N   SER A 135 " =    1.443
peak=    3.292 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.291 closest distance to " O   HOH Z  21 " =    1.730
peak=    3.290 closest distance to " CA  ASN A 217 " =    1.313
peak=    3.289 closest distance to " CB  ALA A   1 " =    4.944
peak=    3.288 closest distance to " O   HOH Z 171 " =    4.113
peak=    3.288 closest distance to " O   HOH Z  78 " =    2.277
peak=    3.287 closest distance to " O   HOH Z 403 " =    1.604
peak=    3.286 closest distance to " O   HOH Z 128 " =    2.183
peak=    3.282 closest distance to " CA  HIS A  86 " =    0.714
peak=    3.281 closest distance to " O  BHOH Z  74 " =    1.286
peak=    3.280 closest distance to " O   GLN A  88 " =    1.679
peak=    3.279 closest distance to " CB  SER A 288 " =    1.468
peak=    3.277 closest distance to " NZ  LYS A 117 " =    3.117
peak=    3.275 closest distance to " CZ3 TRP A 274 " =    4.571
peak=    3.272 closest distance to " O   HOH Z  88 " =    3.017
peak=    3.272 closest distance to " O   HOH Z 423 " =    1.752
peak=    3.268 closest distance to " O   HOH Z 263 " =    1.698
peak=    3.267 closest distance to " CA  ALA A 160 " =    1.059
peak=    3.262 closest distance to " CB  SER A 216 " =    0.883
peak=    3.262 closest distance to " O   HOH Z 162 " =    3.777
peak=    3.259 closest distance to " CB  PRO A 243 " =    1.642
peak=    3.259 closest distance to " CB  ASP A 171 " =    1.161
peak=    3.255 closest distance to " O   ASP A 200 " =    1.555
peak=    3.254 closest distance to " CG  PHE A 204 " =    0.929
peak=    3.254 closest distance to " CA  ARG A 139 " =    1.086
peak=    3.253 closest distance to " CE  LYS A  48 " =    1.150
peak=    3.253 closest distance to " CA  ALA A 158 " =    1.261
peak=    3.252 closest distance to " O   HOH Z 197 " =    3.109
peak=    3.251 closest distance to " O   HOH Z 203 " =    1.712
peak=    3.248 closest distance to " ND2BASN A 224 " =    0.795
peak=    3.248 closest distance to " NZ  LYS A 117 " =    1.377
peak=    3.244 closest distance to " O   HOH Z 394 " =    3.750
peak=    3.241 closest distance to " CA  ASP A 140 " =    1.650
peak=    3.241 closest distance to " O   HOH Z 305 " =    3.443
peak=    3.240 closest distance to " OG BSER A 164 " =    2.249
peak=    3.240 closest distance to " CA  ASP A 124 " =    0.708
peak=    3.237 closest distance to " OG  SER A 245 " =    1.631
peak=    3.235 closest distance to " CD1 LEU A   5 " =    1.430
peak=    3.234 closest distance to " O   PHE A  61 " =    1.384
peak=    3.230 closest distance to " CA  ALA A  21 " =    1.165
peak=    3.229 closest distance to " O   ALA A 158 " =    1.354
peak=    3.226 closest distance to " CA  LEU A  83 " =    1.160
peak=    3.223 closest distance to " CA  ALA A 154 " =    1.121
peak=    3.219 closest distance to " O   HOH Z 368 " =    4.093
peak=    3.216 closest distance to " CB  VAL A 268 " =    0.829
peak=    3.215 closest distance to " CD  LYS A 119 " =    2.167
peak=    3.214 closest distance to " CG1 ILE A 151 " =    1.131
peak=    3.208 closest distance to " O   GLU A   2 " =    1.494
peak=    3.208 closest distance to " CG2AVAL A  72 " =    1.789
peak=    3.207 closest distance to " ND2 ASN A 249 " =    1.858
peak=    3.205 closest distance to " CB  GLN A 205 " =    1.080
peak=    3.199 closest distance to " CA  ASN A 215 " =    1.111
peak=    3.197 closest distance to " CB  ASN A 215 " =    1.184
peak=    3.196 closest distance to " O   HOH Z 357 " =    2.787
peak=    3.195 closest distance to " O   HOH Z 250 " =    1.236
peak=    3.191 closest distance to " O   HOH Z  44 " =    2.169
peak=    3.190 closest distance to " CE1 HIS A  81 " =    1.729
peak=    3.187 closest distance to " CA  ARG A 159 " =    1.208
peak=    3.184 closest distance to " O   HOH Z 187 " =    2.306
peak=    3.180 closest distance to " CB  ALA A 227 " =    0.950
peak=    3.179 closest distance to " O   HOH Z 147 " =    1.724
peak=    3.179 closest distance to " O   LEU A 228 " =    1.911
peak=    3.173 closest distance to " NH1 ARG A  14 " =    0.912
peak=    3.173 closest distance to " NE2 GLN A  73 " =    1.271
peak=    3.172 closest distance to " CD  LYS A  76 " =    1.974
peak=    3.171 closest distance to " O   HOH Z 215 " =    2.935
peak=    3.170 closest distance to " CA  GLN A  94 " =    0.764
peak=    3.156 closest distance to " CB  TYR A 116 " =    0.896
peak=    3.146 closest distance to " O   HOH Z  49 " =    1.050
peak=    3.146 closest distance to " CB  PHE A 204 " =    0.937
peak=    3.143 closest distance to " O   THR A 220 " =    1.307
peak=    3.141 closest distance to " CD  ARG A  66 " =    2.489
peak=    3.138 closest distance to " CB  LEU A 300 " =    0.878
peak=    3.135 closest distance to " O   ILE A  49 " =    1.174
peak=    3.134 closest distance to " CB  THR A 235 " =    1.414
peak=    3.133 closest distance to " CB  LEU A 228 " =    1.268
peak=    3.128 closest distance to " O   PRO A  90 " =    1.535
peak=    3.127 closest distance to " NH2AARG A 275 " =    3.421
peak=    3.125 closest distance to " CB  ALA A 291 " =    1.220
peak=    3.123 closest distance to " OG  SER A  62 " =    2.954
peak=    3.119 closest distance to " O   HOH Z 141 " =    1.559
peak=    3.118 closest distance to " O   HOH Z 337 " =    1.751
peak=    3.110 closest distance to " O   HOH Z 112 " =    1.486
peak=    3.106 closest distance to " O   THR A 182 " =    1.417
peak=    3.106 closest distance to " O   HOH Z 350 " =    1.558
peak=    3.099 closest distance to " CA  GLY A 211 " =    1.384
peak=    3.098 closest distance to " CB  GLU A  37 " =    0.950
peak=    3.095 closest distance to " N   GLN A 278 " =    1.549
peak=    3.090 closest distance to " OG BSER A  99 " =    2.248
peak=    3.084 closest distance to " CZ3 TRP A  92 " =    1.379
peak=    3.082 closest distance to " O   SER A 164 " =    1.329
peak=    3.079 closest distance to " CZ3 TRP A  85 " =    0.968
peak=    3.074 closest distance to " CZ  PHE A 192 " =    1.004
peak=    3.074 closest distance to " O   HOH Z 148 " =    2.137
peak=    3.072 closest distance to " O   HOH Z 116 " =    1.782
peak=    3.046 closest distance to " O   HOH Z 258 " =    1.248
peak=    3.044 closest distance to " CG  GLN A  55 " =    2.479
peak=    3.030 closest distance to " CA  ALA A 233 " =    1.610
peak=    3.029 closest distance to " CE1 PHE A 218 " =    1.229
peak=    3.026 closest distance to " O   HOH Z 193 " =    1.429
peak=    3.010 closest distance to " CE  MET A  40 " =    1.075

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.704 - 5.604
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.704 - 5.604

peak=   -4.711 closest distance to " CG2 VAL A 230 " =    0.745
peak=   -4.701 closest distance to " O   HOH Z 211 " =    0.741
peak=   -4.698 closest distance to " CD  ARG A  14 " =    3.264
peak=   -4.400 closest distance to " CB  PRO A 243 " =    2.707
peak=   -4.354 closest distance to " CD  GLN A  58 " =    0.959
peak=   -4.294 closest distance to " O   HOH Z 193 " =    1.162
peak=   -4.285 closest distance to " CG1 VAL A 296 " =    1.159
peak=   -4.109 closest distance to " CG  GLN A 223 " =    2.286
peak=   -4.097 closest distance to " O   HOH Z 411 " =    5.604
peak=   -4.060 closest distance to " CD  ARG A 156 " =    2.080
peak=   -4.039 closest distance to " O   HOH Z 196 " =    2.371
peak=   -4.021 closest distance to " C   HIS A 108 " =    1.235
peak=   -4.013 closest distance to " CG1 VAL A 112 " =    2.672
peak=   -4.000 closest distance to " O   HOH Z 231 " =    2.088
peak=   -3.976 closest distance to " O   VAL A  67 " =    2.703
peak=   -3.935 closest distance to " CB  VAL A 230 " =    1.174
peak=   -3.933 closest distance to " OG  SER A  97 " =    2.375
peak=   -3.921 closest distance to " CA  ASP A 298 " =    1.087
peak=   -3.912 closest distance to " O   HOH Z 359 " =    2.837
peak=   -3.911 closest distance to " CG1 VAL A 112 " =    2.757
peak=   -3.899 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.897 closest distance to " CZ2 TRP A  92 " =    2.827
peak=   -3.890 closest distance to " O   HOH Z  73 " =    2.438
peak=   -3.853 closest distance to " CG2 VAL A 202 " =    2.840
peak=   -3.851 closest distance to " O   HOH Z 100 " =    0.971
peak=   -3.833 closest distance to " O   HOH Z 133 " =    1.137
peak=   -3.830 closest distance to " OG BSER A 134 " =    1.400
peak=   -3.816 closest distance to " O   HOH Z 394 " =    1.568
peak=   -3.799 closest distance to " O   HOH Z 166 " =    1.902
peak=   -3.791 closest distance to " O   VAL A  67 " =    2.926
peak=   -3.786 closest distance to " CB  ALA A 161 " =    2.469
peak=   -3.783 closest distance to " CD1 LEU A 101 " =    2.381
peak=   -3.783 closest distance to " CG1 VAL A 250 " =    2.759
peak=   -3.779 closest distance to " CE3 TRP A 150 " =    2.303
peak=   -3.741 closest distance to " O   HOH Z 238 " =    0.892
peak=   -3.728 closest distance to " CB  PHE A 192 " =    1.965
peak=   -3.727 closest distance to " CD2 TYR A 293 " =    2.035
peak=   -3.722 closest distance to " O   HOH Z 351 " =    1.629
peak=   -3.716 closest distance to " O   MET A  40 " =    2.844
peak=   -3.708 closest distance to " CE2 TYR A  30 " =    2.603
peak=   -3.696 closest distance to " O   PRO A 163 " =    2.142
peak=   -3.695 closest distance to " OD1 ASN A 148 " =    1.397
peak=   -3.685 closest distance to " O   HOH Z 216 " =    0.998
peak=   -3.678 closest distance to " O   HOH Z 127 " =    1.014
peak=   -3.677 closest distance to " CA  GLY A 241 " =    2.395
peak=   -3.674 closest distance to " O   HOH Z 295 " =    1.605
peak=   -3.657 closest distance to " O   HOH Z 103 " =    1.832
peak=   -3.652 closest distance to " CG  GLU A 277 " =    1.258
peak=   -3.649 closest distance to " CA  ALA A 158 " =    1.322
peak=   -3.645 closest distance to " CG2 VAL A 296 " =    1.157
peak=   -3.645 closest distance to " CB  GLN A  11 " =    1.746
peak=   -3.644 closest distance to " O   HOH Z 149 " =    2.072
peak=   -3.643 closest distance to " O   HOH Z 115 " =    1.707
peak=   -3.640 closest distance to " CE BMET A  47 " =    1.340
peak=   -3.639 closest distance to " CD2 PHE A 225 " =    1.131
peak=   -3.639 closest distance to " CG2 THR A 178 " =    2.458
peak=   -3.637 closest distance to " O   HOH Z 106 " =    1.778
peak=   -3.626 closest distance to " N   THR A  52 " =    1.676
peak=   -3.624 closest distance to " CB  ALA A  43 " =    2.664
peak=   -3.622 closest distance to " O   HOH Z 377 " =    2.065
peak=   -3.616 closest distance to " OE1 GLN A  88 " =    1.005
peak=   -3.616 closest distance to " O   HOH Z 102 " =    1.694
peak=   -3.616 closest distance to " CB  HIS A  86 " =    1.087
peak=   -3.611 closest distance to " O   SER A 271 " =    2.121
peak=   -3.611 closest distance to " O   HOH Z 290 " =    1.259
peak=   -3.577 closest distance to " CE2 TRP A  70 " =    2.228
peak=   -3.574 closest distance to " O   HOH Z  11 " =    1.784
peak=   -3.570 closest distance to " O   HOH Z 435 " =    2.913
peak=   -3.537 closest distance to " CZ3 TRP A 179 " =    1.230
peak=   -3.535 closest distance to " CE3 TRP A  70 " =    1.746
peak=   -3.522 closest distance to " O   HOH Z 198 " =    1.933
peak=   -3.502 closest distance to " O   HOH Z 429 " =    1.991
peak=   -3.501 closest distance to " O   HOH Z  52 " =    1.602
peak=   -3.496 closest distance to " CD1 LEU A 228 " =    2.338
peak=   -3.477 closest distance to " ND2 ASN A 249 " =    2.478
peak=   -3.462 closest distance to " CG  TRP A 266 " =    1.812
peak=   -3.460 closest distance to " O   HOH Z 131 " =    3.996
peak=   -3.448 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.447 closest distance to " C   LEU A 143 " =    1.118
peak=   -3.442 closest distance to " O   ALA A 227 " =    1.490
peak=   -3.431 closest distance to " CG  ARG A 269 " =    2.304
peak=   -3.429 closest distance to " CD2 PHE A  61 " =    2.053
peak=   -3.428 closest distance to " C   MET A 188 " =    1.482
peak=   -3.427 closest distance to " NE  ARG A  66 " =    4.154
peak=   -3.425 closest distance to " CE2 PHE A  61 " =    2.689
peak=   -3.420 closest distance to " O   HOH Z 177 " =    1.853
peak=   -3.418 closest distance to " CB  TRP A  85 " =    2.730
peak=   -3.415 closest distance to " O   HOH Z 191 " =    5.585
peak=   -3.413 closest distance to " O   HOH Z 110 " =    1.271
peak=   -3.409 closest distance to " CA  GLY A 241 " =    3.256
peak=   -3.405 closest distance to " O   HOH Z  68 " =    1.360
peak=   -3.404 closest distance to " N   ALA A 226 " =    2.114
peak=   -3.403 closest distance to " O   HOH Z 236 " =    1.384
peak=   -3.401 closest distance to " CD  GLN A 223 " =    1.347
peak=   -3.394 closest distance to " CB  PRO A 163 " =    2.429
peak=   -3.393 closest distance to " O   HOH Z 185 " =    2.450
peak=   -3.389 closest distance to " OG  SER A  62 " =    4.356
peak=   -3.380 closest distance to " CD2 LEU A 237 " =    2.780
peak=   -3.380 closest distance to " O   GLY A  80 " =    2.618
peak=   -3.370 closest distance to " O   HOH Z  93 " =    2.376
peak=   -3.363 closest distance to " CG2BVAL A  41 " =    1.836
peak=   -3.362 closest distance to " CG1 VAL A 125 " =    1.879
peak=   -3.361 closest distance to " O   ASP A  27 " =    1.964
peak=   -3.358 closest distance to " O   HOH Z 111 " =    1.617
peak=   -3.354 closest distance to " O   HOH Z 252 " =    3.825
peak=   -3.348 closest distance to " O   VAL A 189 " =    2.675
peak=   -3.346 closest distance to " O   HOH Z 251 " =    5.029
peak=   -3.339 closest distance to " O   GLY A  17 " =    1.190
peak=   -3.338 closest distance to " O   HOH Z  44 " =    0.977
peak=   -3.336 closest distance to " NH2AARG A 275 " =    5.261
peak=   -3.333 closest distance to " CA  GLY A 203 " =    2.587
peak=   -3.331 closest distance to " O   HOH Z  10 " =    1.560
peak=   -3.326 closest distance to " CG2 VAL A 189 " =    1.951
peak=   -3.322 closest distance to " OH  TYR A 247 " =    1.902
peak=   -3.321 closest distance to " NE2 GLN A 194 " =    1.911
peak=   -3.320 closest distance to " O   HOH Z 176 " =    0.704
peak=   -3.314 closest distance to " OXT GLY A 302 " =    3.107
peak=   -3.313 closest distance to " CD2 LEU A 167 " =    1.861
peak=   -3.312 closest distance to " O   HOH Z 128 " =    2.541
peak=   -3.311 closest distance to " ND2 ASN A  45 " =    1.987
peak=   -3.311 closest distance to " O   HOH Z  11 " =    2.169
peak=   -3.310 closest distance to " O   HOH Z 145 " =    0.966
peak=   -3.305 closest distance to " CG  ARG A 259 " =    2.394
peak=   -3.298 closest distance to " OG  SER A 141 " =    1.776
peak=   -3.297 closest distance to " OD1 ASP A 171 " =    1.671
peak=   -3.294 closest distance to " N   ALA A  43 " =    2.650
peak=   -3.290 closest distance to " O   SER A 210 " =    1.733
peak=   -3.287 closest distance to " O   HOH Z 147 " =    1.934
peak=   -3.287 closest distance to " N   ALA A 248 " =    1.772
peak=   -3.285 closest distance to " O   HOH Z 431 " =    1.944
peak=   -3.282 closest distance to " CD  PRO A 243 " =    2.034
peak=   -3.277 closest distance to " CA  ASP A  27 " =    2.521
peak=   -3.272 closest distance to " O   HOH Z 371 " =    2.421
peak=   -3.272 closest distance to " O   HOH Z  69 " =    2.045
peak=   -3.272 closest distance to " O   HOH Z 350 " =    1.996
peak=   -3.270 closest distance to " ND2 ASN A  45 " =    1.324
peak=   -3.268 closest distance to " C   LEU A 222 " =    1.086
peak=   -3.267 closest distance to " CA  GLY A 133 " =    2.280
peak=   -3.263 closest distance to " CG1 VAL A  67 " =    2.927
peak=   -3.260 closest distance to " O   HOH Z 313 " =    1.608
peak=   -3.256 closest distance to " O   HOH Z 345 " =    2.192
peak=   -3.256 closest distance to " N   PHE A  59 " =    1.968
peak=   -3.255 closest distance to " CB  ALA A 129 " =    2.509
peak=   -3.252 closest distance to " O   HOH Z 256 " =    1.444
peak=   -3.251 closest distance to " O   HOH Z   9 " =    3.097
peak=   -3.251 closest distance to " O   HOH Z 128 " =    1.252
peak=   -3.250 closest distance to " CD1 ILE A  33 " =    2.569
peak=   -3.248 closest distance to " OH  TYR A 214 " =    1.226
peak=   -3.247 closest distance to " CG1 VAL A 265 " =    2.437
peak=   -3.243 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.235 closest distance to " O   HOH Z 407 " =    2.968
peak=   -3.232 closest distance to " NE2 GLN A  88 " =    1.074
peak=   -3.231 closest distance to " CD1 TYR A 247 " =    2.420
peak=   -3.229 closest distance to " O   HOH Z 285 " =    2.047
peak=   -3.228 closest distance to " O   GLY A 203 " =    2.490
peak=   -3.227 closest distance to " CD1 ILE A 199 " =    2.538
peak=   -3.216 closest distance to " OG1 THR A  82 " =    1.526
peak=   -3.210 closest distance to " CG  MET A 105 " =    0.982
peak=   -3.209 closest distance to " CA  SER A 135 " =    1.273
peak=   -3.207 closest distance to " CD  LYS A 289 " =    2.403
peak=   -3.198 closest distance to " O   HOH Z 434 " =    1.594
peak=   -3.197 closest distance to " CG  ASP A 231 " =    0.876
peak=   -3.193 closest distance to " NE2 GLN A  88 " =    2.132
peak=   -3.193 closest distance to " CD  PRO A 213 " =    2.113
peak=   -3.191 closest distance to " O   HOH Z  17 " =    1.706
peak=   -3.188 closest distance to " C   ASN A 285 " =    2.393
peak=   -3.186 closest distance to " O   HOH Z 412 " =    4.279
peak=   -3.183 closest distance to " OG BSER A 210 " =    1.572
peak=   -3.180 closest distance to " O   HOH Z 286 " =    1.908
peak=   -3.177 closest distance to " O   GLY A 211 " =    1.331
peak=   -3.177 closest distance to " CB  LYS A 289 " =    3.146
peak=   -3.171 closest distance to " OD1 ASN A 249 " =    2.497
peak=   -3.168 closest distance to " O   HOH Z 250 " =    1.769
peak=   -3.167 closest distance to " CD2 LEU A   5 " =    1.158
peak=   -3.164 closest distance to " CE1 TYR A 247 " =    2.621
peak=   -3.162 closest distance to " CG  PRO A 163 " =    2.217
peak=   -3.161 closest distance to " CD1 ILE A 239 " =    2.369
peak=   -3.160 closest distance to " N   SER A 276 " =    1.442
peak=   -3.159 closest distance to " CD1 LEU A   5 " =    2.563
peak=   -3.158 closest distance to " CD2 HIS A 207 " =    2.185
peak=   -3.158 closest distance to " O   HOH Z 259 " =    4.157
peak=   -3.154 closest distance to " CA  GLY A 241 " =    2.901
peak=   -3.152 closest distance to " O   ALA A 180 " =    1.417
peak=   -3.146 closest distance to " O   HOH Z 389 " =    1.535
peak=   -3.140 closest distance to " O   GLY A  80 " =    2.537
peak=   -3.139 closest distance to " O   HOH Z 292 " =    1.661
peak=   -3.134 closest distance to " O   HOH Z  17 " =    1.584
peak=   -3.134 closest distance to " O   HOH Z 357 " =    2.230
peak=   -3.133 closest distance to " C   ARG A 269 " =    1.534
peak=   -3.126 closest distance to " O   GLN A 240 " =    2.590
peak=   -3.124 closest distance to " C   GLU A 236 " =    1.016
peak=   -3.104 closest distance to " NE2 GLN A 278 " =    1.728
peak=   -3.096 closest distance to " O   HOH Z 265 " =    1.814
peak=   -3.088 closest distance to " O   TYR A 186 " =    1.773
peak=   -3.086 closest distance to " O   HOH Z 100 " =    0.748
peak=   -3.083 closest distance to " N   ASP A 191 " =    1.181
peak=   -3.081 closest distance to " O   HOH Z 140 " =    1.519
peak=   -3.077 closest distance to " O   PHE A 218 " =    1.531
peak=   -3.077 closest distance to " OD1 ASN A  39 " =    2.236
peak=   -3.076 closest distance to " N   ALA A 248 " =    2.337
peak=   -3.075 closest distance to " OG BSER A 134 " =    1.855
peak=   -3.070 closest distance to " O   HOH Z  89 " =    2.868
peak=   -3.065 closest distance to " NE2 GLN A 240 " =    1.692
peak=   -3.065 closest distance to " CD2 TYR A  15 " =    2.312
peak=   -3.055 closest distance to " O   HOH Z 189 " =    2.490
peak=   -3.051 closest distance to " NH2 ARG A 219 " =    1.740

================= 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    :  0.4652 0.4567   6.267484e+00   6.247768e+00
   1_bss:  0.4553 0.4431   6.260582e+00   6.234714e+00
   1_xyz:  0.3653 0.3895   6.125430e+00   6.159346e+00
   1_adp:  0.3141 0.3629   6.016781e+00   6.109077e+00
   1_occ:  0.3137 0.3641   6.016161e+00   6.111355e+00
   2_bss:  0.3111 0.3606   6.016896e+00   6.110177e+00
   2_xyz:  0.2261 0.2812   5.741584e+00   5.904462e+00
   2_adp:  0.2017 0.2536   5.642935e+00   5.824384e+00
   2_occ:  0.2015 0.2535   5.642504e+00   5.824604e+00
   3_bss:  0.1992 0.2536   5.641760e+00   5.824425e+00
   3_xyz:  0.1601 0.2097   5.442436e+00   5.642497e+00
   3_adp:  0.1498 0.1991   5.389249e+00   5.600042e+00
   3_occ:  0.1497 0.1989   5.389332e+00   5.600740e+00
   4_bss:  0.1494 0.1982   5.387736e+00   5.598842e+00
   4_xyz:  0.1303 0.1775   5.274369e+00   5.502046e+00
   4_adp:  0.1288 0.1739   5.258061e+00   5.480033e+00
   4_occ:  0.1287 0.1738   5.257503e+00   5.479433e+00
   5_bss:  0.1286 0.1739   5.257444e+00   5.479662e+00
   5_xyz:  0.1193 0.1662   5.203767e+00   5.441980e+00
   5_adp:  0.1174 0.1665   5.197370e+00   5.442932e+00
   5_occ:  0.1174 0.1664   5.196983e+00   5.442542e+00
   5_bss:  0.1173 0.1662   5.196394e+00   5.441184e+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:  0.325  21.027   6.780   6.998  12.461   0.000   0.000   0.000
   1_xyz:  0.325  21.027   6.780   6.998  12.461   0.000   0.000   0.000
   1_adp:  0.325  21.027   6.780   6.998  12.461   0.000   0.000   0.000
   1_occ:  0.325  21.027   6.780   6.998  12.461   0.000   0.000   0.000
   2_bss:  0.336  55.727   3.733   3.944   8.968   0.000   0.000   0.000
   2_xyz:  0.336  55.727   3.733   3.944   8.968   0.000   0.000   0.000
   2_adp:  0.336  55.727   3.733   3.944   8.968   0.000   0.000   0.000
   2_occ:  0.336  55.727   3.733   3.944   8.968   0.000   0.000   0.000
   3_bss:  0.321  65.876   2.308   2.747   5.465   0.000   0.000   0.000
   3_xyz:  0.321  65.876   2.308   2.747   5.465   0.000   0.000   0.000
   3_adp:  0.321  65.876   2.308   2.747   5.465   0.000   0.000   0.000
   3_occ:  0.321  65.876   2.308   2.747   5.465   0.000   0.000   0.000
   4_bss:  0.333  65.876   2.004   2.361   4.527   0.000   0.000   0.000
   4_xyz:  0.333  65.876   2.004   2.361   4.527   0.000   0.000   0.000
   4_adp:  0.333  65.876   2.004   2.361   4.527   0.000   0.000   0.000
   4_occ:  0.333  65.876   2.004   2.361   4.527   0.000   0.000   0.000
   5_bss:  0.333  65.876   2.155   2.414   4.343   0.000   0.000   0.000
   5_xyz:  0.333  65.876   2.155   2.414   4.343   0.000   0.000   0.000
   5_adp:  0.333  65.876   2.155   2.414   4.343   0.000   0.000   0.000
   5_occ:  0.333  65.876   2.155   2.414   4.343   0.000   0.000   0.000
   5_bss:  0.327  65.136  -0.759  -0.562   1.322  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.611 0.4886  0.5521    61348.134
   1_bss:  51.639 0.5001  0.7341    59120.295
   1_xyz:  43.518 0.6000  0.8527    43222.915
   1_adp:  38.773 0.6576  0.9529    36472.909
   1_occ:  38.873 0.6564  0.9505    36667.719
   2_bss:  38.625 0.6594  0.8537    36366.651
   2_xyz:  28.441 0.7746  0.9786    20500.627
   2_adp:  25.106 0.8109  1.0074    16812.062
   2_occ:  25.134 0.8105  1.0068    16808.292
   3_bss:  25.017 0.8119  0.9381    16824.285
   3_xyz:  19.769 0.8643  0.9702    11055.852
   3_adp:  18.625 0.8753  0.9713    10105.385
   3_occ:  18.648 0.8750  0.9710    10107.557
   4_bss:  18.569 0.8757  0.9531    10022.598
   4_xyz:  16.419 0.8948  0.9632     8120.066
   4_adp:  15.851 0.9000  0.9612     7780.136
   4_occ:  15.838 0.9000  0.9613     7771.133
   5_bss:  15.837 0.9001  0.9617     7775.315
   5_xyz:  14.995 0.9072  0.9665     7150.508
   5_adp:  15.011 0.9072  0.9604     7128.676
   5_occ:  15.002 0.9073  0.9605     7122.754
   5_bss:  14.999 0.9073  0.9640     7105.236
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4391e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4391e+01
   1_xyz:   1.657  0.013  0.106 18.266  0.006  4.111   1.3691e-01
   1_adp:   1.657  0.013  0.106 18.266  0.006  4.111   1.3691e-01
   1_occ:   1.657  0.013  0.106 18.266  0.006  4.111   1.3691e-01
   2_bss:   1.657  0.013  0.106 18.266  0.006  4.111   1.3691e-01
   2_xyz:   1.265  0.011  0.084 16.438  0.005  4.113   9.7008e-02
   2_adp:   1.265  0.011  0.084 16.438  0.005  4.113   9.7008e-02
   2_occ:   1.265  0.011  0.084 16.438  0.005  4.113   9.7008e-02
   3_bss:   1.265  0.011  0.084 16.438  0.005  4.113   9.7008e-02
   3_xyz:   0.985  0.007  0.075 15.918  0.003  4.127   5.9990e-02
   3_adp:   0.985  0.007  0.075 15.918  0.003  4.127   5.9990e-02
   3_occ:   0.985  0.007  0.075 15.918  0.003  4.127   5.9990e-02
   4_bss:   0.985  0.007  0.075 15.918  0.003  4.127   5.9990e-02
   4_xyz:   1.035  0.008  0.080 15.845  0.003  4.136   6.6002e-02
   4_adp:   1.035  0.008  0.080 15.845  0.003  4.136   6.6002e-02
   4_occ:   1.035  0.008  0.080 15.845  0.003  4.136   6.6002e-02
   5_bss:   1.035  0.008  0.080 15.845  0.003  4.136   6.6002e-02
   5_xyz:   1.118  0.010  0.089 15.647  0.004  4.144   7.6064e-02
   5_adp:   1.118  0.010  0.089 15.647  0.004  4.144   7.6064e-02
   5_occ:   1.118  0.010  0.089 15.647  0.004  4.144   7.6064e-02
   5_bss:   1.118  0.010  0.089 15.647  0.004  4.144   7.6064e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0516e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0516e+00
   1_xyz:  14.425  0.156  0.421 88.076  0.036  2.142   1.0156e-01
   1_adp:  14.425  0.156  0.421 88.076  0.036  2.142   1.0156e-01
   1_occ:  14.425  0.156  0.421 88.076  0.036  2.142   1.0156e-01
   2_bss:  14.425  0.156  0.421 88.076  0.036  2.142   1.0156e-01
   2_xyz:   7.449  0.097  0.261 86.173  0.035  2.262   1.6830e-01
   2_adp:   7.449  0.097  0.261 86.173  0.035  2.262   1.6830e-01
   2_occ:   7.449  0.097  0.261 86.173  0.035  2.262   1.6830e-01
   3_bss:   7.449  0.097  0.261 86.173  0.035  2.262   1.6830e-01
   3_xyz:   6.958  0.044  0.236 88.684  0.041  2.307   4.2361e-02
   3_adp:   6.958  0.044  0.236 88.684  0.041  2.307   4.2361e-02
   3_occ:   6.958  0.044  0.236 88.684  0.041  2.307   4.2361e-02
   4_bss:   6.958  0.044  0.236 88.684  0.041  2.307   4.2361e-02
   4_xyz:   8.714  0.052  0.344 87.540  0.036  2.413   7.6291e-02
   4_adp:   8.714  0.052  0.344 87.540  0.036  2.413   7.6291e-02
   4_occ:   8.714  0.052  0.344 87.540  0.036  2.413   7.6291e-02
   5_bss:   8.714  0.052  0.344 87.540  0.036  2.413   7.6291e-02
   5_xyz:   7.302  0.062  0.504 88.843  0.037  2.340   5.0652e-02
   5_adp:   7.302  0.062  0.504 88.843  0.037  2.340   5.0652e-02
   5_occ:   7.302  0.062  0.504 88.843  0.037  2.340   5.0652e-02
   5_bss:   7.302  0.062  0.504 88.843  0.037  2.340   5.0652e-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:  71.83   0.00  12.60  61.23   0.00   9.90  71.83   0.00  27.30
   1_occ:  71.83   0.00  12.60  61.23   0.00   9.90  71.83   0.00  27.30
   2_bss:  71.83   0.00  12.60  61.23   0.00   9.90  71.83   0.00  27.30
   2_xyz:  71.83   0.00  12.60  61.23   0.00   9.90  71.83   0.00  27.30
   2_adp:  73.66   0.00  12.38  60.45   0.00   8.55  73.66   0.00  33.20
   2_occ:  73.66   0.00  12.38  60.45   0.00   8.55  73.66   0.00  33.20
   3_bss:  73.66   0.00  12.38  60.45   0.00   8.55  73.66   0.00  33.20
   3_xyz:  73.66   0.00  12.38  60.45   0.00   8.55  73.66   0.00  33.20
   3_adp:  82.99   0.00  12.93  72.00   0.00   8.49  82.99   1.40  37.12
   3_occ:  82.99   0.00  12.93  72.00   0.00   8.49  82.99   1.40  37.12
   4_bss:  82.99   0.00  12.93  72.00   0.00   8.49  82.99   1.40  37.12
   4_xyz:  82.99   0.00  12.93  72.00   0.00   8.49  82.99   1.40  37.12
   4_adp:  83.17   0.00  12.53  71.94   0.00   8.20  83.17   1.25  36.12
   4_occ:  83.17   0.00  12.53  71.94   0.00   8.20  83.17   1.25  36.12
   5_bss:  83.17   0.00  12.53  71.94   0.00   8.20  83.17   1.25  36.12
   5_xyz:  83.17   0.00  12.53  71.94   0.00   8.20  83.17   1.25  36.12
   5_adp:  91.99   0.00  12.66  77.73   0.00   8.19  91.99   0.87  37.02
   5_occ:  91.99   0.00  12.66  77.73   0.00   8.19  91.99   0.87  37.02
   5_bss:  95.08   3.09  15.75  80.82   3.09  11.28  95.08   3.95  40.11
------------------------------------------------------------------------
 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:    1.250    0.020    0.410
   1_adp:    1.250    0.020    0.410
   1_occ:    1.250    0.020    0.410
   2_bss:    1.250    0.020    0.410
   2_xyz:    1.818    0.053    0.585
   2_adp:    1.818    0.053    0.585
   2_occ:    1.818    0.053    0.585
   3_bss:    1.818    0.053    0.585
   3_xyz:    1.820    0.036    0.622
   3_adp:    1.820    0.036    0.622
   3_occ:    1.820    0.036    0.622
   4_bss:    1.820    0.036    0.622
   4_xyz:    1.987    0.026    0.659
   4_adp:    1.987    0.026    0.659
   4_occ:    1.987    0.026    0.659
   5_bss:    1.987    0.026    0.659
   5_xyz:    1.987    0.019    0.672
   5_adp:    1.987    0.019    0.672
   5_occ:    1.987    0.019    0.672
   5_bss:    1.987    0.019    0.672
------------------------------------------------------------------------

CPU time actual refinement: 329.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/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_791/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_791/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.15 
  Macro-tasks:
    bulk solvent and scale       = 39.97  
    individual site refinement   = 134.07 
    weights calculation          = 31.03  
    collect and process          = 6.50   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.67 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 101.17 
    alpha_beta                      = 8.16   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 111.73 
    fmodel                         = 7.40   
    r_factors                      = 0.20   
    phase_errors                   = 10.76  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 243.18 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.633 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    655 calls, 100.91 s
gradients_fft:          600 calls,  98.43 s

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

# Date 2008-01-16 Time 02:26:20 PST -0800 (1200479180.12 s)
Start R-work = 0.4652, R-free = 0.4567 (no bulk solvent and anisotropic scale)
Final R-work = 0.1347, R-free = 0.1821 (no bulk solvent and anisotropic scale)

Start R-work = 0.4553, R-free = 0.4431
Final R-work = 0.1173, R-free = 0.1662