# Date 2008-01-16 Time 02:16:39 PST -0800 (1200478599.05 s)
#phil __OFF__

Command line arguments: "../767.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16922
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 767

-------------------------------------------------------------------------------
  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, 46.4607, 87.6859, 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: 3.35, per 1000 atoms: 1.19


================================== 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, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.98275
Completeness in resolution range: 0.951107
Completeness with d_max=infinity: 0.948207

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9827

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, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.98275
Completeness in resolution range: 0.951107
Completeness with d_max=infinity: 0.948207

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2431 [2165/2189]  1945   220  10.2%
  bin  2:  4.2431 -  3.3803 [2071/2091]  1866   205   9.9%
  bin  3:  3.3803 -  2.9566 [2065/2084]  1860   205   9.9%
  bin  4:  2.9566 -  2.6880 [2026/2056]  1824   202  10.0%
  bin  5:  2.6880 -  2.4962 [2013/2032]  1813   200   9.9%
  bin  6:  2.4962 -  2.3496 [2013/2038]  1808   205  10.2%
  bin  7:  2.3496 -  2.2323 [2002/2030]  1799   203  10.1%
  bin  8:  2.2323 -  2.1354 [1982/2018]  1785   197   9.9%
  bin  9:  2.1354 -  2.0534 [1988/2030]  1793   195   9.8%
  bin 10:  2.0534 -  1.9827 [1264/2028]  1137   127  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 23
        2.42 -     3.04: 2174
        3.04 -     3.66: 4681
        3.66 -     4.28: 8958
        4.28 -     4.90: 12332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.985 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.099 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.102 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.172 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28163 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_767/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/model_refine_001.geo

CPU time processing inputs: 10.05


============================ 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 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4609   r_free= 0.4424   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.259238                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7328 0.99   1405  155 0.3839 0.3543      6.5797      6.4965|
|  2:  4.7328 -  3.7759 0.99   1353  153 0.3567 0.3581      6.7066      6.7343|
|  3:  3.7759 -  3.3043 0.99   1323  141 0.4029 0.3577      6.6183      6.5624|
|  4:  3.3043 -  3.0047 0.99   1317  151 0.4500 0.4124      6.5033      6.4386|
|  5:  3.0047 -  2.7908 0.99   1308  148 0.4914 0.4427      6.3457      6.3304|
|  6:  2.7908 -  2.6272 0.99   1311  142 0.4850 0.5161      6.2573      6.1953|
|  7:  2.6272 -  2.4962 0.99   1291  142 0.5076 0.5045      6.2206       6.217|
|  8:  2.4962 -  2.3880 0.98   1281  144 0.5159 0.4712      6.1762      6.1644|
|  9:  2.3880 -  2.2964 0.98   1289  143 0.4966 0.5280      6.0982        6.15|
| 10:  2.2964 -  2.2174 1.00   1282  144 0.5249 0.4675      6.1121      6.0476|
| 11:  2.2174 -  2.1483 0.98   1295  141 0.5154 0.5060      6.0292      6.0269|
| 12:  2.1483 -  2.0870 0.98   1262  144 0.5165 0.5151      5.9649      5.9998|
| 13:  2.0870 -  2.0322 0.99   1285  141 0.5194 0.4766      5.8659      5.7855|
| 14:  2.0322 -  1.9827 0.48    628   70 0.5332 0.5365      5.8841      5.7938|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7328  1405   155  0.73  31.50   0.80     0.77      61623.46|
|  2:  4.7328 -  3.7759  1353   153  0.76  29.99   0.89     0.82      82140.12|
|  3:  3.7759 -  3.3043  1323   141  0.68  36.96   0.86     0.78      86964.19|
|  4:  3.3043 -  3.0047  1317   151  0.60  43.55   0.80     0.68      78900.94|
|  5:  3.0047 -  2.7908  1308   148  0.51  51.41   0.75     0.59      68413.96|
|  6:  2.7908 -  2.6272  1311   142  0.46  54.89   0.73     0.52      62971.12|
|  7:  2.6272 -  2.4962  1291   142  0.41  58.78   0.74     0.48      61025.84|
|  8:  2.4962 -  2.3880  1281   144  0.40  59.81   0.73     0.46      55884.58|
|  9:  2.3880 -  2.2964  1289   143  0.42  58.11   0.74     0.49      49688.03|
| 10:  2.2964 -  2.2174  1282   144  0.43  57.69   0.75     0.50      43315.24|
| 11:  2.2174 -  2.1483  1295   141  0.42  58.29   0.76     0.52      40926.19|
| 12:  2.1483 -  2.0870  1262   144  0.40  59.85   0.76     0.49      38867.49|
| 13:  2.0870 -  2.0322  1285   141  0.37  62.48   0.72     0.46      34573.81|
| 14:  2.0322 -  1.9827   628    70  0.39  60.55   0.73     0.42      28872.26|
|alpha:            min =        0.42 max =            0.82 mean =         0.58|
|beta:             min =    28872.26 max =        86964.19 mean =     58042.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.10|
|phase err.(test): min =        0.00 max =           89.97 mean =        51.33|
|-----------------------------------------------------------------------------|

============================== 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 = 9.619719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.854295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.781   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1482 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2620 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3890 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5080 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6533 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7626 |
|-----------------------------------------------------------------------------|
|-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 |       54.037 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.732 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4678   r_free= 0.4455   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.263219                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4522   r_free= 0.4290   ksol= 0.35   Bsol= 15.95   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,8.65,10.53,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.253519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.358366              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.985   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.813689              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.104   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4522      final r-factor (work) = 0.3535          |
| start r-factor (free) = 0.4290      final r-factor (free) = 0.3707          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.2005 = 8.36 * 0.50 * 6.2604 + 1.00 * 54.0371                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7595 = 8.36 * 0.50 * 6.1329 + 1.00 * 0.1289                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3535      final r-factor (work) = 0.2999          |
| start r-factor (free) = 0.3707      final r-factor (free) = 0.3460          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0047 = 0.81 * 1.00 * 6.1329 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8981 = 0.81 * 1.00 * 6.0022 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.02   12.11    None  None   None       |
|    all(noH): 2823   0      0.00    69.02   12.11    None  None   None       |
|    Sol.    : 438    0      0.00    69.02   27.37    None  None   None       |
|    Mac.    : 2385   0      0.00    57.00   9.30     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 -   6.902: 1160   |   5:    34.512 -  41.414:   85        |
|      1:     6.902 -  13.805:  783   |   6:    41.414 -  48.317:   49        |
|      2:    13.805 -  20.707:  398   |   7:    48.317 -  55.219:   29        |
|      3:    20.707 -  27.610:  199   |   8:    55.219 -  62.122:    9        |
|      4:    27.610 -  34.512:  109   |   9:    62.122 -  69.024:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2999 r_free = 0.3460             target_work(ml) = 5.972         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2994 r_free = 0.3460             target_work(ml) = 5.971         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2994   r_free= 0.3460   ksol= 0.35   Bsol= 15.95   scale= 1.111   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,8.65,10.53,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.971058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2944   r_free= 0.3405   ksol= 0.34   Bsol= 46.77   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,4.35,6.55,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.969903                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.541603              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.826   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.757  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2944      final r-factor (work) = 0.2016          |
| start r-factor (free) = 0.3405      final r-factor (free) = 0.2513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7619 = 4.54 * 0.50 * 6.0036 + 1.00 * 0.1289                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2535 = 4.54 * 0.50 * 5.8057 + 1.00 * 0.0699                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2016      final r-factor (work) = 0.1801          |
| start r-factor (free) = 0.2513      final r-factor (free) = 0.2291          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0835 = 0.36 * 1.00 * 5.8057 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0011 = 0.36 * 1.00 * 5.5855 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.93   11.90    None  None   None       |
|    all(noH): 2823   0      0.00    72.93   11.90    None  None   None       |
|    Sol.    : 438    0      0.00    72.93   31.87    None  None   None       |
|    Mac.    : 2385   0      0.00    59.05   8.23     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 -   7.293: 1405   |   5:    36.466 -  43.759:  109        |
|      1:     7.293 -  14.586:  732   |   6:    43.759 -  51.052:   51        |
|      2:    14.586 -  21.879:  226   |   7:    51.052 -  58.345:   29        |
|      3:    21.879 -  29.173:  124   |   8:    58.345 -  65.638:    4        |
|      4:    29.173 -  36.466:  141   |   9:    65.638 -  72.931:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1801 r_free = 0.2291             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1801 r_free = 0.2291             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1801   r_free= 0.2291   ksol= 0.34   Bsol= 46.77   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,4.35,6.55,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.540579                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1789   r_free= 0.2281   ksol= 0.33   Bsol= 54.68   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.72,4.53,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.540991                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.555822              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.116  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.763320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.414  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1789      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.2281      final r-factor (free) = 0.1806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0170 = 3.56 * 0.50 * 5.5948 + 1.00 * 0.0700                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7155 = 3.56 * 0.50 * 5.4253 + 1.00 * 0.0697                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1354      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1806      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.4277 = 3.76 * 1.00 * 5.4253 + 1.00 * 0.0104                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.8266 = 3.76 * 1.00 * 5.2644 + 1.00 * 0.0150                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.20   13.04    None  None   None       |
|    all(noH): 2823   0      0.00    81.20   13.04    None  None   None       |
|    Sol.    : 438    0      1.07    81.20   38.38    None  None   None       |
|    Mac.    : 2385   0      0.00    80.88   8.39     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 -   8.120: 1561   |   5:    40.599 -  48.719:   81        |
|      1:     8.120 -  16.240:  637   |   6:    48.719 -  56.839:   84        |
|      2:    16.240 -  24.359:  177   |   7:    56.839 -  64.958:   44        |
|      3:    24.359 -  32.479:  111   |   8:    64.958 -  73.078:   24        |
|      4:    32.479 -  40.599:   89   |   9:    73.078 -  81.198:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1253 r_free = 0.1736             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1737             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1737   ksol= 0.33   Bsol= 54.68   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,2.72,4.53,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.246126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1737   ksol= 0.32   Bsol= 54.68   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.44,4.20,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.245708                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.309043              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.457  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.063  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1737      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1471 = 2.31 * 0.50 * 5.2637 + 1.00 * 0.0700                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0925 = 2.31 * 0.50 * 5.2239 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9127 = 0.17 * 1.00 * 5.2239 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9070 = 0.17 * 1.00 * 5.2123 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.52   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    77.52   12.07    None  None   None       |
|    Sol.    : 438    0      1.76    72.53   34.04    None  None   None       |
|    Mac.    : 2385   0      0.00    77.52   8.03     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 -   7.752: 1574   |   5:    38.760 -  46.513:   77        |
|      1:     7.752 -  15.504:  648   |   6:    46.513 -  54.265:   73        |
|      2:    15.504 -  23.256:  170   |   7:    54.265 -  62.017:   29        |
|      3:    23.256 -  31.008:  118   |   8:    62.017 -  69.769:   17        |
|      4:    31.008 -  38.760:  109   |   9:    69.769 -  77.521:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1636             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1634             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1634   ksol= 0.32   Bsol= 54.68   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.44,4.20,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196664                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1633   ksol= 0.33   Bsol= 54.68   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,2.28,4.09,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.735683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.652  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.326   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5843 = 1.74 * 0.50 * 5.2117 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5615 = 1.74 * 0.50 * 5.1896 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8964 = 0.36 * 1.00 * 5.1896 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9073 = 0.36 * 1.00 * 5.1793 + 1.00 * 0.0251                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.94   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    78.94   12.10    None  None   None       |
|    Sol.    : 438    0      1.63    71.29   34.38    None  None   None       |
|    Mac.    : 2385   0      0.00    78.94   8.01     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 -   7.894: 1610   |   5:    39.468 -  47.361:   85        |
|      1:     7.894 -  15.787:  614   |   6:    47.361 -  55.255:   70        |
|      2:    15.787 -  23.681:  167   |   7:    55.255 -  63.148:   27        |
|      3:    23.681 -  31.574:  114   |   8:    63.148 -  71.042:   20        |
|      4:    31.574 -  39.468:  114   |   9:    71.042 -  78.936:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1615             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1616             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1616   ksol= 0.33   Bsol= 54.68   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,2.28,4.09,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7328 0.99   1405  155 0.1015 0.1329      5.4099      5.5584|
|  2:  4.7328 -  3.7759 0.99   1353  153 0.0892 0.1186      5.4674      5.6607|
|  3:  3.7759 -  3.3043 0.99   1323  141 0.1103 0.1513      5.5135      5.8488|
|  4:  3.3043 -  3.0047 0.99   1317  151 0.1249 0.1751       5.474       5.646|
|  5:  3.0047 -  2.7908 0.99   1308  148 0.1380 0.1750      5.3638      5.5964|
|  6:  2.7908 -  2.6272 0.99   1311  142 0.1237 0.2039      5.2221      5.5066|
|  7:  2.6272 -  2.4962 0.99   1291  142 0.1357 0.1604      5.2187      5.3637|
|  8:  2.4962 -  2.3880 0.98   1281  144 0.1214 0.1681      5.1147      5.3534|
|  9:  2.3880 -  2.2964 0.98   1289  143 0.1270 0.1933      5.0987      5.3676|
| 10:  2.2964 -  2.2174 1.00   1282  144 0.1177 0.1656      4.9826      5.1928|
| 11:  2.2174 -  2.1483 0.98   1295  141 0.1187 0.1836      4.9708      5.3004|
| 12:  2.1483 -  2.0870 0.98   1262  144 0.1179 0.1760       4.899      5.2198|
| 13:  2.0870 -  2.0322 0.99   1285  141 0.1148 0.1605         4.8      5.0168|
| 14:  2.0322 -  1.9827 0.48    628   70 0.0995 0.1589      4.6731      4.8795|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7328  1405   155  0.94   9.40   0.97     0.95       7459.77|
|  2:  4.7328 -  3.7759  1353   153  0.95   8.29   1.01     1.00       9489.32|
|  3:  3.7759 -  3.3043  1323   141  0.93  11.81   1.02     1.01      11106.13|
|  4:  3.3043 -  3.0047  1317   151  0.92  14.10   1.00     0.98      10804.90|
|  5:  3.0047 -  2.7908  1308   148  0.90  16.59   0.99     0.97       8990.77|
|  6:  2.7908 -  2.6272  1311   142  0.90  16.45   0.97     0.95       7265.52|
|  7:  2.6272 -  2.4962  1291   142  0.90  16.17   0.98     0.95       6648.35|
|  8:  2.4962 -  2.3880  1281   144  0.90  16.22   0.99     0.96       5861.73|
|  9:  2.3880 -  2.2964  1289   143  0.90  16.32   1.00     0.96       5654.01|
| 10:  2.2964 -  2.2174  1282   144  0.89  16.56   1.00     0.96       4665.79|
| 11:  2.2174 -  2.1483  1295   141  0.90  16.46   0.99     0.94       4477.24|
| 12:  2.1483 -  2.0870  1262   144  0.90  16.01   1.01     1.00       4098.73|
| 13:  2.0870 -  2.0322  1285   141  0.90  16.57   0.99     0.97       3474.60|
| 14:  2.0322 -  1.9827   628    70  0.92  14.17   0.98     0.95       2637.49|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2637.49 max =        11106.13 mean =      6805.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.61|
|phase err.(test): min =        0.00 max =           88.85 mean =        14.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1616   ksol= 0.33   Bsol= 57.59   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.61,1.19,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180682                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1616   ksol= 0.33   Bsol= 57.59   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.61,1.19,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180682                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7328 0.99   1405  155 0.1015 0.1329        5.41      5.5586|
|  2:  4.7328 -  3.7759 0.99   1353  153 0.0893 0.1186      5.4676      5.6608|
|  3:  3.7759 -  3.3043 0.99   1323  141 0.1103 0.1513      5.5135       5.849|
|  4:  3.3043 -  3.0047 0.99   1317  151 0.1249 0.1751      5.4741       5.646|
|  5:  3.0047 -  2.7908 0.99   1308  148 0.1379 0.1749      5.3638      5.5962|
|  6:  2.7908 -  2.6272 0.99   1311  142 0.1237 0.2040      5.2221      5.5067|
|  7:  2.6272 -  2.4962 0.99   1291  142 0.1357 0.1605      5.2188      5.3639|
|  8:  2.4962 -  2.3880 0.98   1281  144 0.1214 0.1681      5.1147      5.3533|
|  9:  2.3880 -  2.2964 0.98   1289  143 0.1270 0.1933      5.0986      5.3676|
| 10:  2.2964 -  2.2174 1.00   1282  144 0.1177 0.1656      4.9825      5.1927|
| 11:  2.2174 -  2.1483 0.98   1295  141 0.1187 0.1835      4.9706      5.3002|
| 12:  2.1483 -  2.0870 0.98   1262  144 0.1179 0.1760      4.8988      5.2196|
| 13:  2.0870 -  2.0322 0.99   1285  141 0.1148 0.1605      4.7999      5.0168|
| 14:  2.0322 -  1.9827 0.48    628   70 0.0996 0.1589      4.6732      4.8795|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7328  1405   155  0.94   9.40   0.98     0.95       7462.65|
|  2:  4.7328 -  3.7759  1353   153  0.95   8.29   1.01     1.00       9492.70|
|  3:  3.7759 -  3.3043  1323   141  0.93  11.81   1.02     1.02      11109.26|
|  4:  3.3043 -  3.0047  1317   151  0.92  14.10   1.00     0.98      10805.40|
|  5:  3.0047 -  2.7908  1308   148  0.90  16.59   0.99     0.97       8990.21|
|  6:  2.7908 -  2.6272  1311   142  0.90  16.45   0.97     0.95       7264.84|
|  7:  2.6272 -  2.4962  1291   142  0.90  16.17   0.99     0.95       6648.97|
|  8:  2.4962 -  2.3880  1281   144  0.90  16.22   0.99     0.97       5862.39|
|  9:  2.3880 -  2.2964  1289   143  0.90  16.33   1.00     0.96       5654.96|
| 10:  2.2964 -  2.2174  1282   144  0.89  16.56   1.00     0.97       4664.59|
| 11:  2.2174 -  2.1483  1295   141  0.90  16.45   0.99     0.94       4475.84|
| 12:  2.1483 -  2.0870  1262   144  0.90  16.01   1.01     1.00       4097.11|
| 13:  2.0870 -  2.0322  1285   141  0.90  16.57   1.00     0.97       3473.90|
| 14:  2.0322 -  1.9827   628    70  0.92  14.17   0.98     0.95       2637.25|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2637.25 max =        11109.26 mean =      6806.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.61|
|phase err.(test): min =        0.00 max =           88.85 mean =        14.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.995)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.92    81.85   15.02    None  None   None       |
|    all(noH): 2823   0      2.92    81.85   15.02    None  None   None       |
|    Sol.    : 438    0      4.54    74.21   37.30    None  None   None       |
|    Mac.    : 2385   0      2.92    81.85   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.919 -  10.812: 1610   |   5:    42.386 -  50.280:   85        |
|      1:    10.812 -  18.706:  614   |   6:    50.280 -  58.173:   70        |
|      2:    18.706 -  26.599:  167   |   7:    58.173 -  66.067:   27        |
|      3:    26.599 -  34.493:  114   |   8:    66.067 -  73.961:   20        |
|      4:    34.493 -  42.386:  114   |   9:    73.961 -  81.854:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.294 - 4.834
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.707 - 4.834

peak=   11.192 closest distance to " CB  VAL A 230 " =    1.475
peak=    7.951 closest distance to " CG2 VAL A 296 " =    1.229
peak=    6.073 closest distance to " CG  LEU A   5 " =    1.262
peak=    6.069 closest distance to " CD2 LEU A   5 " =    1.244
peak=    6.031 closest distance to " NH2 ARG A  56 " =    2.151
peak=    5.795 closest distance to " CG  PRO A  54 " =    1.403
peak=    5.596 closest distance to " O   HOH Z 142 " =    2.083
peak=    5.530 closest distance to " NE2 GLN A  11 " =    1.203
peak=    5.245 closest distance to " CB  PRO A  54 " =    1.039
peak=    5.233 closest distance to " O   HOH Z 232 " =    2.331
peak=    5.197 closest distance to " CB  GLN A 223 " =    1.447
peak=    5.162 closest distance to " CG  LEU A 228 " =    1.143
peak=    5.153 closest distance to " O   HOH Z   9 " =    1.808
peak=    4.922 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.781 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.721 closest distance to " ND2 ASN A 187 " =    1.618
peak=    4.561 closest distance to " O   HOH Z 427 " =    2.820
peak=    4.507 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.502 closest distance to " CB  ASN A 148 " =    1.363
peak=    4.492 closest distance to " CB  SER A  63 " =    1.277
peak=    4.482 closest distance to " O   HOH Z 265 " =    2.146
peak=    4.453 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.417 closest distance to " CG  PRO A 213 " =    1.254
peak=    4.406 closest distance to " CB  ASN A 142 " =    1.045
peak=    4.372 closest distance to " CB  TRP A 266 " =    1.034
peak=    4.364 closest distance to " O   HOH Z 126 " =    2.025
peak=    4.354 closest distance to " O   HOH Z 425 " =    1.434
peak=    4.349 closest distance to " O   HOH Z 369 " =    2.119
peak=    4.342 closest distance to " CZ  PHE A 218 " =    1.092
peak=    4.323 closest distance to " CB  VAL A 265 " =    1.353
peak=    4.308 closest distance to " O   HOH Z 303 " =    2.138
peak=    4.307 closest distance to " O   HOH Z 287 " =    2.162
peak=    4.267 closest distance to " CD2 LEU A 228 " =    1.196
peak=    4.260 closest distance to " CA  VAL A 296 " =    1.100
peak=    4.246 closest distance to " O   PRO A 198 " =    1.573
peak=    4.189 closest distance to " CB  ASP A 124 " =    0.790
peak=    4.186 closest distance to " O   HOH Z 346 " =    1.607
peak=    4.183 closest distance to " O   HOH Z 313 " =    1.908
peak=    4.155 closest distance to " CB  ARG A  79 " =    1.475
peak=    4.143 closest distance to " N   PHE A 130 " =    1.254
peak=    4.126 closest distance to " CB  VAL A 230 " =    1.163
peak=    4.085 closest distance to " O   SER A  87 " =    2.353
peak=    4.070 closest distance to " CB  SER A   3 " =    1.351
peak=    4.069 closest distance to " CG  LEU A 167 " =    1.225
peak=    4.068 closest distance to " CG2 VAL A 257 " =    0.949
peak=    4.049 closest distance to " CB  ASN A  39 " =    0.898
peak=    4.023 closest distance to " O   HOH Z  61 " =    1.655
peak=    4.021 closest distance to " OG  SER A  97 " =    2.998
peak=    4.020 closest distance to " O   HOH Z 298 " =    1.746
peak=    3.983 closest distance to " CA  TYR A  30 " =    1.016
peak=    3.979 closest distance to " CB  ARG A 190 " =    1.450
peak=    3.977 closest distance to " CA  THR A 264 " =    0.808
peak=    3.975 closest distance to " O   HOH Z  43 " =    1.921
peak=    3.964 closest distance to " O   HOH Z 248 " =    1.604
peak=    3.960 closest distance to " O   HOH Z  78 " =    1.600
peak=    3.953 closest distance to " O   HOH Z 209 " =    2.300
peak=    3.948 closest distance to " O   HOH Z 214 " =    2.176
peak=    3.948 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.931 closest distance to " CB  GLU A 128 " =    0.994
peak=    3.919 closest distance to " O   HOH Z 234 " =    3.764
peak=    3.914 closest distance to " O   HOH Z 353 " =    2.533
peak=    3.911 closest distance to " CB  SER A 216 " =    0.813
peak=    3.908 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.903 closest distance to " O   HOH Z 368 " =    2.098
peak=    3.900 closest distance to " NH1AARG A 145 " =    1.156
peak=    3.894 closest distance to " CA  SER A  87 " =    0.994
peak=    3.862 closest distance to " CB BVAL A  41 " =    1.213
peak=    3.849 closest distance to " OG ASER A 258 " =    3.098
peak=    3.826 closest distance to " CD  ARG A 159 " =    0.739
peak=    3.820 closest distance to " O   HOH Z 411 " =    3.700
peak=    3.819 closest distance to " CA  ALA A  51 " =    0.982
peak=    3.791 closest distance to " O   HOH Z 261 " =    1.965
peak=    3.779 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.777 closest distance to " O   HOH Z   1 " =    1.811
peak=    3.774 closest distance to " O   HOH Z 158 " =    3.223
peak=    3.774 closest distance to " CB  SER A 212 " =    1.339
peak=    3.747 closest distance to " CZ3 TRP A 266 " =    1.140
peak=    3.738 closest distance to " CB  SER A 210 " =    0.790
peak=    3.738 closest distance to " O   HOH Z  10 " =    1.741
peak=    3.725 closest distance to " O   HOH Z 286 " =    2.417
peak=    3.720 closest distance to " CB  VAL A 202 " =    1.576
peak=    3.719 closest distance to " CG2AVAL A  72 " =    1.618
peak=    3.713 closest distance to " CB  LYS A 117 " =    1.256
peak=    3.691 closest distance to " CD  LYS A 166 " =    1.296
peak=    3.688 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.674 closest distance to " O   HOH Z 380 " =    1.732
peak=    3.661 closest distance to " CA  ARG A 195 " =    1.158
peak=    3.656 closest distance to " NE2 HIS A 207 " =    1.181
peak=    3.654 closest distance to " CA  ASN A 215 " =    1.105
peak=    3.651 closest distance to " O   HOH Z  21 " =    1.801
peak=    3.650 closest distance to " CB  ALA A 104 " =    0.722
peak=    3.648 closest distance to " N   ASN A  39 " =    1.151
peak=    3.646 closest distance to " OD1 ASN A  69 " =    2.581
peak=    3.645 closest distance to " CG  MET A 185 " =    1.159
peak=    3.645 closest distance to " CB  GLU A 277 " =    3.607
peak=    3.644 closest distance to " CB  ASN A 187 " =    1.076
peak=    3.643 closest distance to " O   PHE A 192 " =    1.345
peak=    3.640 closest distance to " CB  ASP A 140 " =    0.913
peak=    3.634 closest distance to " CD  ARG A  66 " =    2.368
peak=    3.624 closest distance to " O   HOH Z 437 " =    1.727
peak=    3.614 closest distance to " O   HOH Z   7 " =    1.320
peak=    3.614 closest distance to " O   HOH Z  88 " =    3.082
peak=    3.610 closest distance to " CA  ARG A  36 " =    1.109
peak=    3.597 closest distance to " O   HOH Z 389 " =    1.838
peak=    3.592 closest distance to " CB  ARG A  79 " =    0.916
peak=    3.581 closest distance to " CB  ASN A 110 " =    1.058
peak=    3.580 closest distance to " CD  ARG A 269 " =    1.004
peak=    3.568 closest distance to " O   HOH Z 193 " =    1.857
peak=    3.563 closest distance to " O   HOH Z   2 " =    1.624
peak=    3.554 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.546 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.544 closest distance to " O   HOH Z  30 " =    1.551
peak=    3.539 closest distance to " CB  TRP A 179 " =    1.494
peak=    3.539 closest distance to " CD1 ILE A  33 " =    1.771
peak=    3.539 closest distance to " CZ  PHE A  38 " =    1.123
peak=    3.537 closest distance to " CB  GLN A  88 " =    1.240
peak=    3.531 closest distance to " CB  ALA A 291 " =    1.300
peak=    3.530 closest distance to " CA  LYS A 117 " =    1.189
peak=    3.530 closest distance to " CB  LEU A 228 " =    1.230
peak=    3.528 closest distance to " O   HOH Z 280 " =    3.074
peak=    3.526 closest distance to " CB  THR A 157 " =    1.161
peak=    3.522 closest distance to " CB  MET A  40 " =    0.825
peak=    3.521 closest distance to " O   HOH Z   3 " =    2.065
peak=    3.517 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.515 closest distance to " CB  GLU A  46 " =    0.947
peak=    3.514 closest distance to " OE2 GLU A   2 " =    1.916
peak=    3.512 closest distance to " CG  GLN A  88 " =    1.050
peak=    3.508 closest distance to " CA  TYR A 116 " =    1.379
peak=    3.505 closest distance to " O  BHOH Z 338 " =    2.396
peak=    3.504 closest distance to " O   HOH Z 171 " =    4.094
peak=    3.501 closest distance to " N   SER A 135 " =    1.311
peak=    3.495 closest distance to " O   HOH Z  78 " =    2.167
peak=    3.491 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.485 closest distance to " CG1 ILE A  49 " =    1.488
peak=    3.484 closest distance to " CA  ALA A 233 " =    1.294
peak=    3.481 closest distance to " O   HOH Z  68 " =    2.121
peak=    3.476 closest distance to " CG1 VAL A 153 " =    0.994
peak=    3.475 closest distance to " O   HOH Z 251 " =    1.592
peak=    3.472 closest distance to " CG1 ILE A 151 " =    1.114
peak=    3.470 closest distance to " CE3 TRP A 150 " =    1.001
peak=    3.462 closest distance to " O   HOH Z 260 " =    1.519
peak=    3.461 closest distance to " CG2 ILE A 239 " =    0.707
peak=    3.459 closest distance to " CA  ASP A 162 " =    1.003
peak=    3.459 closest distance to " O   HOH Z 366 " =    2.906
peak=    3.458 closest distance to " O   HOH Z 368 " =    3.591
peak=    3.455 closest distance to " O   HOH Z 421 " =    2.154
peak=    3.447 closest distance to " O   HOH Z 406 " =    1.570
peak=    3.447 closest distance to " OG BSER A 164 " =    2.259
peak=    3.446 closest distance to " O   HOH Z  92 " =    2.465
peak=    3.445 closest distance to " C   ALA A 299 " =    0.944
peak=    3.439 closest distance to " CD2 LEU A 255 " =    1.771
peak=    3.438 closest distance to " CB  LEU A 143 " =    1.181
peak=    3.432 closest distance to " O   HOH Z 250 " =    1.375
peak=    3.432 closest distance to " O   HOH Z 409 " =    2.925
peak=    3.432 closest distance to " CD2 TRP A 179 " =    1.271
peak=    3.427 closest distance to " CD1 LEU A  96 " =    0.752
peak=    3.426 closest distance to " O   HOH Z 193 " =    1.825
peak=    3.425 closest distance to " O   HOH Z 435 " =    2.050
peak=    3.421 closest distance to " NE2 GLN A  73 " =    3.923
peak=    3.417 closest distance to " O   HOH Z 203 " =    1.785
peak=    3.415 closest distance to " O   HOH Z  97 " =    2.085
peak=    3.413 closest distance to " O   HOH Z 193 " =    1.729
peak=    3.412 closest distance to " CE1 TYR A 186 " =    1.290
peak=    3.412 closest distance to " CA  ARG A 159 " =    1.268
peak=    3.412 closest distance to " CD1 LEU A 300 " =    1.114
peak=    3.411 closest distance to " O   ASN A  74 " =    1.553
peak=    3.410 closest distance to " CA  ALA A 154 " =    1.064
peak=    3.406 closest distance to " NZ  LYS A 117 " =    3.033
peak=    3.406 closest distance to " CG2 ILE A  20 " =    1.567
peak=    3.405 closest distance to " CA  ILE A 234 " =    0.927
peak=    3.403 closest distance to " CA  PHE A 283 " =    1.179
peak=    3.401 closest distance to " O   HOH Z 130 " =    1.028
peak=    3.396 closest distance to " CA  LEU A 282 " =    1.146
peak=    3.393 closest distance to " NH1 ARG A 138 " =    1.092
peak=    3.392 closest distance to " O   HOH Z 148 " =    3.487
peak=    3.392 closest distance to " CB  HIS A 108 " =    0.810
peak=    3.392 closest distance to " CB  ASN A 215 " =    1.255
peak=    3.388 closest distance to " CG2 THR A 221 " =    1.020
peak=    3.388 closest distance to " O   HOH Z  90 " =    2.265
peak=    3.384 closest distance to " CD  ARG A  66 " =    2.495
peak=    3.380 closest distance to " CG BARG A 102 " =    1.874
peak=    3.377 closest distance to " CG  MET A 185 " =    1.004
peak=    3.375 closest distance to " O   HOH Z 258 " =    2.201
peak=    3.372 closest distance to " O   HOH Z 126 " =    1.461
peak=    3.368 closest distance to " O   HOH Z 197 " =    3.264
peak=    3.366 closest distance to " CB  PRO A  90 " =    1.152
peak=    3.366 closest distance to " O   HOH Z 359 " =    1.377
peak=    3.358 closest distance to " NH2AARG A 275 " =    3.557
peak=    3.352 closest distance to " O   HOH Z 128 " =    1.796
peak=    3.352 closest distance to " O   HOH Z 371 " =    2.781
peak=    3.350 closest distance to " CB  VAL A 268 " =    0.823
peak=    3.349 closest distance to " CB  LEU A  83 " =    0.755
peak=    3.346 closest distance to " O   HOH Z 419 " =    1.922
peak=    3.340 closest distance to " CB  VAL A 250 " =    1.139
peak=    3.337 closest distance to " N   ALA A 256 " =    1.099
peak=    3.335 closest distance to " O   HOH Z 172 " =    3.163
peak=    3.332 closest distance to " O   HOH Z 294 " =    1.558
peak=    3.331 closest distance to " O   HOH Z 303 " =    2.992
peak=    3.329 closest distance to " CB  ASN A 173 " =    1.031
peak=    3.328 closest distance to " CA  ASN A 217 " =    1.292
peak=    3.326 closest distance to " O   HOH Z 261 " =    1.473
peak=    3.322 closest distance to " O   HOH Z 285 " =    2.375
peak=    3.321 closest distance to " CD1 LEU A 281 " =    1.065
peak=    3.321 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.320 closest distance to " NZ  LYS A  48 " =    1.302
peak=    3.320 closest distance to " O   HOH Z 290 " =    1.116
peak=    3.320 closest distance to " O   HOH Z 273 " =    2.928
peak=    3.318 closest distance to " CD1 LEU A 228 " =    2.052
peak=    3.318 closest distance to " CG2 ILE A 120 " =    1.181
peak=    3.315 closest distance to " O   HOH Z 132 " =    2.603
peak=    3.313 closest distance to " O   HOH Z 263 " =    1.716
peak=    3.309 closest distance to " CG AARG A 275 " =    1.228
peak=    3.306 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.306 closest distance to " O   HOH Z 130 " =    2.007
peak=    3.303 closest distance to " O   HOH Z 403 " =    1.554
peak=    3.303 closest distance to " O   HOH Z  40 " =    1.912
peak=    3.302 closest distance to " O   HOH Z 187 " =    2.294
peak=    3.301 closest distance to " O   HOH Z 147 " =    1.781
peak=    3.300 closest distance to " O   HOH Z  88 " =    3.297
peak=    3.298 closest distance to " O   ASP A 124 " =    1.075
peak=    3.286 closest distance to " CB  TRP A 150 " =    1.445
peak=    3.275 closest distance to " CG1 VAL A 296 " =    1.225
peak=    3.273 closest distance to " CB  PRO A 243 " =    1.371
peak=    3.271 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.268 closest distance to " O   HOH Z 196 " =    1.391
peak=    3.266 closest distance to " CB  THR A  82 " =    1.353
peak=    3.263 closest distance to " OG  SER A  62 " =    2.964
peak=    3.262 closest distance to " O   TYR A 116 " =    1.313
peak=    3.260 closest distance to " NH2BARG A 190 " =    1.512
peak=    3.260 closest distance to " O   HOH Z 109 " =    2.560
peak=    3.259 closest distance to " CB  GLN A  89 " =    1.240
peak=    3.257 closest distance to " O   LEU A 228 " =    2.018
peak=    3.256 closest distance to " N   GLN A 278 " =    1.298
peak=    3.254 closest distance to " N   SER A 271 " =    0.989
peak=    3.250 closest distance to " CB  SER A  62 " =    1.057
peak=    3.250 closest distance to " CA  LYS A 290 " =    1.231
peak=    3.250 closest distance to " O   HOH Z 305 " =    3.469
peak=    3.247 closest distance to " O   HOH Z 145 " =    1.809
peak=    3.246 closest distance to " CG  GLN A 278 " =    1.350
peak=    3.246 closest distance to " CA  ASN A 127 " =    1.044
peak=    3.243 closest distance to " CA  ILE A 106 " =    0.758
peak=    3.240 closest distance to " O   CYS A 168 " =    1.176
peak=    3.239 closest distance to " ND1 HIS A  86 " =    1.718
peak=    3.238 closest distance to " O   PRO A  90 " =    1.696
peak=    3.230 closest distance to " CA  ALA A  21 " =    1.097
peak=    3.229 closest distance to " O   HOH Z 423 " =    1.554
peak=    3.228 closest distance to " CZ  PHE A 192 " =    0.932
peak=    3.222 closest distance to " OE2 GLU A  53 " =    1.962
peak=    3.221 closest distance to " CG  GLU A  37 " =    0.826
peak=    3.221 closest distance to " N   ASN A 127 " =    1.272
peak=    3.218 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.217 closest distance to " CA  ALA A 295 " =    1.074
peak=    3.209 closest distance to " CB  ALA A  43 " =    0.858
peak=    3.202 closest distance to " OG1 THR A 264 " =    0.761
peak=    3.200 closest distance to " CD2 TYR A 186 " =    1.104
peak=    3.200 closest distance to " OG1 THR A 279 " =    1.371
peak=    3.199 closest distance to " N   ARG A 156 " =    1.305
peak=    3.197 closest distance to " CB  THR A  31 " =    1.562
peak=    3.196 closest distance to " O   HOH Z 116 " =    3.057
peak=    3.193 closest distance to " O   ALA A 158 " =    1.444
peak=    3.192 closest distance to " O   THR A 251 " =    1.126
peak=    3.191 closest distance to " O   HOH Z  59 " =    1.777
peak=    3.190 closest distance to " CB  ALA A 114 " =    1.114
peak=    3.186 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.186 closest distance to " CA  ALA A 160 " =    1.044
peak=    3.179 closest distance to " O   SER A 164 " =    1.306
peak=    3.178 closest distance to " CB  ALA A 227 " =    0.964
peak=    3.174 closest distance to " CG  ARG A 159 " =    0.954
peak=    3.168 closest distance to " CA  ARG A 102 " =    1.153
peak=    3.166 closest distance to " CB  ILE A 120 " =    1.345
peak=    3.166 closest distance to " O   HOH Z 329 " =    4.067
peak=    3.166 closest distance to " CB  ALA A  34 " =    1.077
peak=    3.161 closest distance to " CB  GLN A 278 " =    0.893
peak=    3.161 closest distance to " O   HOH Z 213 " =    2.145
peak=    3.158 closest distance to " O   HOH Z 299 " =    4.239
peak=    3.154 closest distance to " O   HOH Z 162 " =    3.890
peak=    3.153 closest distance to " CD1 ILE A 199 " =    1.019
peak=    3.153 closest distance to " O   HOH Z 153 " =    3.772
peak=    3.151 closest distance to " CD  LYS A  76 " =    1.856
peak=    3.150 closest distance to " CG  MET A 113 " =    1.266
peak=    3.147 closest distance to " CA  MET A 105 " =    0.946
peak=    3.146 closest distance to " CB  TYR A 247 " =    0.947
peak=    3.145 closest distance to " CD1 LEU A 261 " =    1.217
peak=    3.143 closest distance to " CA  VAL A  41 " =    0.790
peak=    3.143 closest distance to " O   PHE A  61 " =    1.392
peak=    3.132 closest distance to " CB  SER A  26 " =    1.759
peak=    3.130 closest distance to " CD1 ILE A 106 " =    0.867
peak=    3.129 closest distance to " CD1 ILE A 263 " =    1.171
peak=    3.127 closest distance to " O   HOH Z 148 " =    2.191
peak=    3.125 closest distance to " CG2 ILE A 151 " =    0.861
peak=    3.120 closest distance to " O   HOH Z 188 " =    1.953
peak=    3.119 closest distance to " CB  ALA A   1 " =    4.834
peak=    3.111 closest distance to " O   HOH Z 116 " =    1.728
peak=    3.111 closest distance to " O   HOH Z 173 " =    2.159
peak=    3.109 closest distance to " O   MET A 105 " =    1.762
peak=    3.107 closest distance to " O   HOH Z 423 " =    2.577
peak=    3.104 closest distance to " CG  MET A 188 " =    0.875
peak=    3.104 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.102 closest distance to " O   GLY A  75 " =    1.462
peak=    3.099 closest distance to " CB  TYR A 116 " =    0.870
peak=    3.097 closest distance to " O   HOH Z   4 " =    1.659
peak=    3.097 closest distance to " CB  PHE A 204 " =    0.829
peak=    3.092 closest distance to " N   ASP A 162 " =    1.171
peak=    3.090 closest distance to " O   HOH Z 344 " =    2.968
peak=    3.088 closest distance to " O   HOH Z 371 " =    1.594
peak=    3.086 closest distance to " C   GLN A  88 " =    1.435
peak=    3.064 closest distance to " O   HOH Z 325 " =    2.239
peak=    3.060 closest distance to " NH2AARG A 145 " =    1.227
peak=    3.059 closest distance to " O   HOH Z 345 " =    3.433
peak=    3.056 closest distance to " OH  TYR A 214 " =    1.256
peak=    3.053 closest distance to " NH2BARG A 145 " =    1.964
peak=    3.042 closest distance to " O   HOH Z 154 " =    2.264
peak=    3.016 closest distance to " O   HOH Z 175 " =    2.130
peak=    3.002 closest distance to " O   HOH Z 264 " =    1.544

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.739 - 5.491
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.739 - 5.491

peak=   -5.197 closest distance to " CG2 VAL A 230 " =    0.755
peak=   -4.461 closest distance to " CD  ARG A  14 " =    3.260
peak=   -4.157 closest distance to " CB  PHE A 192 " =    1.832
peak=   -4.147 closest distance to " CB  PRO A 243 " =    2.672
peak=   -4.143 closest distance to " CD  ARG A 156 " =    2.037
peak=   -4.130 closest distance to " O   HOH Z 211 " =    1.154
peak=   -4.121 closest distance to " OG BSER A 134 " =    1.224
peak=   -4.095 closest distance to " O   VAL A  67 " =    2.539
peak=   -4.075 closest distance to " O   HOH Z 231 " =    1.838
peak=   -4.071 closest distance to " CD  GLN A  58 " =    0.948
peak=   -4.021 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -3.984 closest distance to " O   HOH Z 266 " =    5.491
peak=   -3.983 closest distance to " CB  ALA A 248 " =    2.123
peak=   -3.976 closest distance to " CG2 VAL A 202 " =    2.749
peak=   -3.968 closest distance to " O   HOH Z 290 " =    1.124
peak=   -3.931 closest distance to " CG2 VAL A 296 " =    1.420
peak=   -3.930 closest distance to " CB  ALA A  43 " =    2.599
peak=   -3.927 closest distance to " O   PRO A 198 " =    1.161
peak=   -3.915 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.905 closest distance to " CA  GLY A 241 " =    2.396
peak=   -3.856 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.844 closest distance to " CE2 TYR A  30 " =    2.655
peak=   -3.835 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.803 closest distance to " O   TYR A 247 " =    2.866
peak=   -3.791 closest distance to " O   ARG A 145 " =    1.483
peak=   -3.788 closest distance to " CB  VAL A 230 " =    1.139
peak=   -3.779 closest distance to " O   HOH Z 185 " =    2.317
peak=   -3.769 closest distance to " C   HIS A 108 " =    1.231
peak=   -3.761 closest distance to " CG2 ILE A  49 " =    2.828
peak=   -3.759 closest distance to " OG  SER A  97 " =    2.284
peak=   -3.753 closest distance to " CE BMET A  47 " =    1.569
peak=   -3.750 closest distance to " CB  ALA A 248 " =    2.406
peak=   -3.743 closest distance to " CG1 VAL A 112 " =    2.891
peak=   -3.734 closest distance to " N   ALA A  43 " =    2.468
peak=   -3.733 closest distance to " CB  ALA A 161 " =    2.566
peak=   -3.713 closest distance to " ND2 ASN A  45 " =    1.246
peak=   -3.697 closest distance to " ND2 ASN A  45 " =    1.924
peak=   -3.694 closest distance to " O   HOH Z  52 " =    1.496
peak=   -3.689 closest distance to " O   GLY A 203 " =    2.454
peak=   -3.679 closest distance to " CE3 TRP A 150 " =    2.205
peak=   -3.675 closest distance to " CD1 LEU A 255 " =    2.883
peak=   -3.673 closest distance to " CD2 LEU A   5 " =    1.090
peak=   -3.650 closest distance to " O   HOH Z 166 " =    2.243
peak=   -3.648 closest distance to " O   HOH Z 231 " =    1.165
peak=   -3.646 closest distance to " O   HOH Z 166 " =    2.073
peak=   -3.622 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -3.622 closest distance to " O   HOH Z 140 " =    1.400
peak=   -3.621 closest distance to " N   THR A 157 " =    1.450
peak=   -3.620 closest distance to " O   HOH Z 359 " =    3.142
peak=   -3.609 closest distance to " O   HOH Z  73 " =    2.173
peak=   -3.603 closest distance to " CD  GLN A 223 " =    2.131
peak=   -3.600 closest distance to " CD  PRO A 213 " =    2.040
peak=   -3.594 closest distance to " CA  GLY A 203 " =    2.486
peak=   -3.583 closest distance to " O   VAL A 189 " =    2.547
peak=   -3.560 closest distance to " CA  VAL A  67 " =    2.903
peak=   -3.559 closest distance to " O   HOH Z 103 " =    1.791
peak=   -3.559 closest distance to " O   HOH Z  51 " =    1.014
peak=   -3.558 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -3.549 closest distance to " O   HOH Z 176 " =    0.739
peak=   -3.528 closest distance to " CG  ASP A 231 " =    0.761
peak=   -3.526 closest distance to " O   HOH Z 345 " =    2.147
peak=   -3.520 closest distance to " O   HOH Z  11 " =    1.898
peak=   -3.515 closest distance to " O   HOH Z 262 " =    2.854
peak=   -3.514 closest distance to " CD1 LEU A 101 " =    2.360
peak=   -3.506 closest distance to " CB  PRO A 163 " =    2.498
peak=   -3.500 closest distance to " C   LEU A 222 " =    0.831
peak=   -3.499 closest distance to " C   MET A 188 " =    1.429
peak=   -3.494 closest distance to " OH  TYR A 172 " =    1.811
peak=   -3.487 closest distance to " CA  GLY A 241 " =    3.146
peak=   -3.481 closest distance to " N   ALA A 226 " =    2.112
peak=   -3.481 closest distance to " O   SER A  22 " =    2.349
peak=   -3.479 closest distance to " CG  TRP A 266 " =    1.863
peak=   -3.478 closest distance to " CG1 VAL A 250 " =    2.799
peak=   -3.459 closest distance to " OD1 ASN A 148 " =    1.367
peak=   -3.459 closest distance to " CZ2 TRP A 274 " =    0.937
peak=   -3.455 closest distance to " O   HOH Z 281 " =    2.644
peak=   -3.454 closest distance to " ND2 ASN A 187 " =    1.481
peak=   -3.446 closest distance to " O   HOH Z 389 " =    2.115
peak=   -3.446 closest distance to " O   HOH Z 371 " =    2.248
peak=   -3.444 closest distance to " O   HOH Z  60 " =    2.213
peak=   -3.439 closest distance to " O   HOH Z 191 " =    5.473
peak=   -3.436 closest distance to " O   HOH Z 389 " =    1.413
peak=   -3.435 closest distance to " O   HOH Z  44 " =    2.294
peak=   -3.433 closest distance to " ND2 ASN A 249 " =    2.470
peak=   -3.427 closest distance to " CB  PRO A 280 " =    2.100
peak=   -3.424 closest distance to " OG  SER A  87 " =    1.413
peak=   -3.421 closest distance to " O   GLY A  17 " =    1.226
peak=   -3.421 closest distance to " O   HOH Z  38 " =    1.798
peak=   -3.420 closest distance to " O   HOH Z 102 " =    1.621
peak=   -3.413 closest distance to " C   ASP A 231 " =    2.586
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.401 closest distance to " NH2AARG A 275 " =    5.276
peak=   -3.392 closest distance to " O   HOH Z 350 " =    1.866
peak=   -3.390 closest distance to " O   PRO A 163 " =    1.941
peak=   -3.384 closest distance to " O   HOH Z 359 " =    1.588
peak=   -3.377 closest distance to " O   ASP A  27 " =    1.891
peak=   -3.376 closest distance to " CD1 LEU A 228 " =    2.318
peak=   -3.373 closest distance to " CD  GLU A 277 " =    1.211
peak=   -3.372 closest distance to " CA  GLY A  98 " =    1.855
peak=   -3.368 closest distance to " O   HOH Z 407 " =    3.060
peak=   -3.367 closest distance to " CG2 ILE A 263 " =    2.414
peak=   -3.354 closest distance to " CA  ASP A  27 " =    2.410
peak=   -3.346 closest distance to " NH2 ARG A  79 " =    2.067
peak=   -3.342 closest distance to " CB  TRP A  85 " =    2.625
peak=   -3.325 closest distance to " CG1 VAL A 125 " =    1.928
peak=   -3.322 closest distance to " O   MET A  40 " =    2.820
peak=   -3.321 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.313 closest distance to " C   ALA A 158 " =    1.472
peak=   -3.311 closest distance to " O   HOH Z 198 " =    2.143
peak=   -3.310 closest distance to " CE  MET A 105 " =    2.346
peak=   -3.304 closest distance to " CD  ARG A 139 " =    1.654
peak=   -3.298 closest distance to " O   HOH Z 377 " =    0.769
peak=   -3.296 closest distance to " O   HOH Z 134 " =    3.917
peak=   -3.291 closest distance to " OXT GLY A 302 " =    3.078
peak=   -3.285 closest distance to " ND2 ASN A 252 " =    1.925
peak=   -3.284 closest distance to " N   ALA A 248 " =    1.573
peak=   -3.278 closest distance to " O   HOH Z 412 " =    4.306
peak=   -3.274 closest distance to " O   HOH Z  63 " =    1.812
peak=   -3.274 closest distance to " O   HOH Z   9 " =    3.044
peak=   -3.270 closest distance to " O   HOH Z 131 " =    4.069
peak=   -3.251 closest distance to " CE2 TRP A  70 " =    2.197
peak=   -3.250 closest distance to " O   HOH Z   9 " =    1.706
peak=   -3.247 closest distance to " CA  SER A 135 " =    1.383
peak=   -3.241 closest distance to " CD2 HIS A 207 " =    2.294
peak=   -3.241 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.241 closest distance to " CD2 PHE A 225 " =    1.080
peak=   -3.239 closest distance to " O   SER A 271 " =    2.256
peak=   -3.238 closest distance to " O   HOH Z 390 " =    2.298
peak=   -3.237 closest distance to " OG  SER A  62 " =    4.434
peak=   -3.236 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.235 closest distance to " CD1 TYR A 169 " =    2.529
peak=   -3.229 closest distance to " NE2 GLN A 278 " =    1.851
peak=   -3.228 closest distance to " O   HOH Z 295 " =    1.583
peak=   -3.228 closest distance to " N   SER A 212 " =    1.956
peak=   -3.215 closest distance to " CG1 VAL A 197 " =    2.363
peak=   -3.212 closest distance to " O   HOH Z 114 " =    2.870
peak=   -3.211 closest distance to " OD1 ASN A 187 " =    1.683
peak=   -3.210 closest distance to " CG  LEU A 228 " =    1.005
peak=   -3.208 closest distance to " CB  ASN A  69 " =    1.353
peak=   -3.203 closest distance to " O   HOH Z 318 " =    2.058
peak=   -3.203 closest distance to " OH  TYR A 214 " =    1.163
peak=   -3.203 closest distance to " O   HOH Z 253 " =    3.902
peak=   -3.200 closest distance to " O   HOH Z 384 " =    2.487
peak=   -3.198 closest distance to " O   HOH Z 100 " =    1.098
peak=   -3.196 closest distance to " CG  HIS A  86 " =    1.113
peak=   -3.189 closest distance to " O   PHE A 218 " =    1.701
peak=   -3.188 closest distance to " CG  MET A 105 " =    0.943
peak=   -3.185 closest distance to " O   HOH Z 426 " =    1.652
peak=   -3.183 closest distance to " O   HOH Z  89 " =    2.998
peak=   -3.182 closest distance to " NH2 ARG A  79 " =    1.557
peak=   -3.180 closest distance to " SG BCYS A 201 " =    2.132
peak=   -3.180 closest distance to " O   SER A 135 " =    1.405
peak=   -3.180 closest distance to " CB  ALA A 291 " =    2.322
peak=   -3.179 closest distance to " O   HOH Z 275 " =    1.413
peak=   -3.176 closest distance to " OG  SER A 206 " =    1.754
peak=   -3.170 closest distance to " O   HOH Z 357 " =    1.960
peak=   -3.166 closest distance to " O   HOH Z 166 " =    1.536
peak=   -3.165 closest distance to " CD1 LEU A   5 " =    2.617
peak=   -3.161 closest distance to " O   HOH Z 216 " =    1.340
peak=   -3.161 closest distance to " CG  GLN A  88 " =    0.760
peak=   -3.160 closest distance to " O   HOH Z 189 " =    2.144
peak=   -3.155 closest distance to " N   THR A  52 " =    1.729
peak=   -3.154 closest distance to " N   ASP A 270 " =    1.521
peak=   -3.146 closest distance to " ND2 ASN A  60 " =    1.702
peak=   -3.144 closest distance to " CA  GLY A 133 " =    1.953
peak=   -3.143 closest distance to " CD  LYS A 289 " =    2.458
peak=   -3.143 closest distance to " NE2 GLN A 194 " =    1.879
peak=   -3.141 closest distance to " CD  PRO A 243 " =    2.083
peak=   -3.137 closest distance to " O   HOH Z 346 " =    1.821
peak=   -3.134 closest distance to " N   GLN A  58 " =    1.874
peak=   -3.133 closest distance to " O   ALA A  51 " =    1.403
peak=   -3.128 closest distance to " OG BSER A 134 " =    1.801
peak=   -3.128 closest distance to " O   HOH Z 353 " =    2.006
peak=   -3.125 closest distance to " O   HOH Z 313 " =    1.445
peak=   -3.124 closest distance to " O   HOH Z 123 " =    2.552
peak=   -3.124 closest distance to " O   HOH Z  43 " =    1.754
peak=   -3.119 closest distance to " CG2 THR A 178 " =    2.200
peak=   -3.119 closest distance to " O   HOH Z  65 " =    1.172
peak=   -3.112 closest distance to " CG  PHE A 283 " =    2.649
peak=   -3.109 closest distance to " CZ  TYR A 169 " =    1.698
peak=   -3.107 closest distance to " CG1 VAL A 296 " =    1.394
peak=   -3.106 closest distance to " CD1 ILE A 239 " =    2.373
peak=   -3.103 closest distance to " CB  ALA A  10 " =    2.302
peak=   -3.100 closest distance to " O   HOH Z 174 " =    2.428
peak=   -3.100 closest distance to " CG2 THR A  42 " =    1.737
peak=   -3.099 closest distance to " OG  SER A  63 " =    1.203
peak=   -3.097 closest distance to " CE  LYS A  76 " =    2.599
peak=   -3.090 closest distance to " O   HOH Z 380 " =    1.191
peak=   -3.081 closest distance to " O   HOH Z 423 " =    1.215
peak=   -3.080 closest distance to " CB  CYS A 201 " =    2.329
peak=   -3.072 closest distance to " O   HOH Z 149 " =    2.354
peak=   -3.053 closest distance to " CD2 PHE A  61 " =    2.045
peak=   -3.052 closest distance to " O   TRP A  70 " =    1.400
peak=   -3.046 closest distance to " CA  GLY A 302 " =    2.863
peak=   -3.039 closest distance to " OD1 ASP A 171 " =    1.688
peak=   -3.028 closest distance to " O   HOH Z 340 " =    1.857
peak=   -3.023 closest distance to " NH2 ARG A 219 " =    1.685

================= 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    :  0.4609 0.4424   6.259238e+00   6.231423e+00
   1_bss:  0.4522 0.4290   6.253519e+00   6.221212e+00
   1_xyz:  0.3535 0.3707   6.094492e+00   6.117832e+00
   1_adp:  0.2999 0.3460   5.972210e+00   6.068830e+00
   1_occ:  0.2994 0.3460   5.971058e+00   6.069116e+00
   2_bss:  0.2944 0.3405   5.969903e+00   6.065836e+00
   2_xyz:  0.2016 0.2513   5.643013e+00   5.809522e+00
   2_adp:  0.1801 0.2291   5.540676e+00   5.721862e+00
   2_occ:  0.1801 0.2291   5.540579e+00   5.722668e+00
   3_bss:  0.1789 0.2281   5.540991e+00   5.722843e+00
   3_xyz:  0.1354 0.1806   5.300802e+00   5.517316e+00
   3_adp:  0.1253 0.1736   5.246348e+00   5.480698e+00
   3_occ:  0.1252 0.1737   5.246126e+00   5.480416e+00
   4_bss:  0.1252 0.1737   5.245708e+00   5.480497e+00
   4_xyz:  0.1180 0.1673   5.203646e+00   5.445914e+00
   4_adp:  0.1192 0.1636   5.197475e+00   5.423323e+00
   4_occ:  0.1191 0.1634   5.196664e+00   5.422412e+00
   5_bss:  0.1190 0.1633   5.196595e+00   5.422340e+00
   5_xyz:  0.1174 0.1616   5.184730e+00   5.414457e+00
   5_adp:  0.1162 0.1615   5.180935e+00   5.416656e+00
   5_occ:  0.1161 0.1616   5.180681e+00   5.416480e+00
   5_bss:  0.1161 0.1616   5.180682e+00   5.416485e+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:  0.347  15.953   7.221   8.652  10.526   0.000   0.000   0.000
   1_xyz:  0.347  15.953   7.221   8.652  10.526   0.000   0.000   0.000
   1_adp:  0.347  15.953   7.221   8.652  10.526   0.000   0.000   0.000
   1_occ:  0.347  15.953   7.221   8.652  10.526   0.000   0.000   0.000
   2_bss:  0.339  46.774   3.652   4.354   6.549   0.000   0.000   0.000
   2_xyz:  0.339  46.774   3.652   4.354   6.549   0.000   0.000   0.000
   2_adp:  0.339  46.774   3.652   4.354   6.549   0.000   0.000   0.000
   2_occ:  0.339  46.774   3.652   4.354   6.549   0.000   0.000   0.000
   3_bss:  0.334  54.675   2.524   2.719   4.529   0.000   0.000   0.000
   3_xyz:  0.334  54.675   2.524   2.719   4.529   0.000   0.000   0.000
   3_adp:  0.334  54.675   2.524   2.719   4.529   0.000   0.000   0.000
   3_occ:  0.334  54.675   2.524   2.719   4.529   0.000   0.000   0.000
   4_bss:  0.324  54.675   2.367   2.436   4.202   0.000   0.000   0.000
   4_xyz:  0.324  54.675   2.367   2.436   4.202   0.000   0.000   0.000
   4_adp:  0.324  54.675   2.367   2.436   4.202   0.000   0.000   0.000
   4_occ:  0.324  54.675   2.367   2.436   4.202   0.000   0.000   0.000
   5_bss:  0.330  54.675   2.291   2.280   4.090   0.000   0.000   0.000
   5_xyz:  0.330  54.675   2.291   2.280   4.090   0.000   0.000   0.000
   5_adp:  0.330  54.675   2.291   2.280   4.090   0.000   0.000   0.000
   5_occ:  0.330  54.675   2.291   2.280   4.090   0.000   0.000   0.000
   5_bss:  0.330  57.594  -0.578  -0.611   1.188  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.127 0.5070  0.5792    58040.976
   1_bss:  50.966 0.5075  0.7525    56043.301
   1_xyz:  40.778 0.6323  0.9050    37898.485
   1_adp:  36.258 0.6865  1.0028    31934.885
   1_occ:  36.286 0.6861  1.0009    31934.329
   2_bss:  35.913 0.6903  0.8758    31411.775
   2_xyz:  24.958 0.8113  0.9912    15991.625
   2_adp:  21.955 0.8428  1.0091    13106.928
   2_occ:  21.974 0.8426  1.0087    13109.480
   3_bss:  21.936 0.8431  0.9533    13144.994
   3_xyz:  16.904 0.8901  0.9842     8325.317
   3_adp:  16.105 0.8972  0.9824     7758.054
   3_occ:  16.103 0.8972  0.9823     7754.353
   4_bss:  16.112 0.8972  0.9727     7767.352
   4_xyz:  15.292 0.9044  0.9751     7185.004
   4_adp:  14.726 0.9094  0.9762     6920.531
   4_occ:  14.712 0.9095  0.9762     6905.318
   5_bss:  14.710 0.9095  0.9724     6905.204
   5_xyz:  14.510 0.9112  0.9728     6784.258
   5_adp:  14.547 0.9109  0.9691     6806.615
   5_occ:  14.549 0.9109  0.9690     6805.573
   5_bss:  14.549 0.9109  0.9701     6806.038
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4037e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4037e+01
   1_xyz:   1.606  0.012  0.104 18.246  0.006  4.111   1.2890e-01
   1_adp:   1.606  0.012  0.104 18.246  0.006  4.111   1.2890e-01
   1_occ:   1.606  0.012  0.104 18.246  0.006  4.111   1.2890e-01
   2_bss:   1.606  0.012  0.104 18.246  0.006  4.111   1.2890e-01
   2_xyz:   1.064  0.008  0.078 16.298  0.004  4.127   6.9946e-02
   2_adp:   1.064  0.008  0.078 16.298  0.004  4.127   6.9946e-02
   2_occ:   1.064  0.008  0.078 16.298  0.004  4.127   6.9946e-02
   3_bss:   1.064  0.008  0.078 16.298  0.004  4.127   6.9946e-02
   3_xyz:   1.082  0.008  0.084 16.001  0.004  4.129   6.9726e-02
   3_adp:   1.082  0.008  0.084 16.001  0.004  4.129   6.9726e-02
   3_occ:   1.082  0.008  0.084 16.001  0.004  4.129   6.9726e-02
   4_bss:   1.082  0.008  0.084 16.001  0.004  4.129   6.9726e-02
   4_xyz:   0.985  0.007  0.079 15.530  0.004  4.119   6.1350e-02
   4_adp:   0.985  0.007  0.079 15.530  0.004  4.119   6.1350e-02
   4_occ:   0.985  0.007  0.079 15.530  0.004  4.119   6.1350e-02
   5_bss:   0.985  0.007  0.079 15.530  0.004  4.119   6.1350e-02
   5_xyz:   0.962  0.007  0.078 15.241  0.003  4.121   5.7711e-02
   5_adp:   0.962  0.007  0.078 15.241  0.003  4.121   5.7711e-02
   5_occ:   0.962  0.007  0.078 15.241  0.003  4.121   5.7711e-02
   5_bss:   0.962  0.007  0.078 15.241  0.003  4.121   5.7711e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0060e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0060e+00
   1_xyz:  13.054  0.159  0.395 85.794  0.031  2.181   9.4086e-02
   1_adp:  13.054  0.159  0.395 85.794  0.031  2.181   9.4086e-02
   1_occ:  13.054  0.159  0.395 85.794  0.031  2.181   9.4086e-02
   2_bss:  13.054  0.159  0.395 85.794  0.031  2.181   9.4086e-02
   2_xyz:   6.292  0.057  0.239 85.842  0.042  2.312   4.9294e-02
   2_adp:   6.292  0.057  0.239 85.842  0.042  2.312   4.9294e-02
   2_occ:   6.292  0.057  0.239 85.842  0.042  2.312   4.9294e-02
   3_bss:   6.292  0.057  0.239 85.842  0.042  2.312   4.9294e-02
   3_xyz:   9.389  0.062  0.471 82.287  0.027  2.264   5.8383e-02
   3_adp:   9.389  0.062  0.471 82.287  0.027  2.264   5.8383e-02
   3_occ:   9.389  0.062  0.471 82.287  0.027  2.264   5.8383e-02
   4_bss:   9.389  0.062  0.471 82.287  0.027  2.264   5.8383e-02
   4_xyz:   7.005  0.041  0.454 82.595  0.039  2.350   4.7853e-02
   4_adp:   7.005  0.041  0.454 82.595  0.039  2.350   4.7853e-02
   4_occ:   7.005  0.041  0.454 82.595  0.039  2.350   4.7853e-02
   5_bss:   7.005  0.041  0.454 82.595  0.039  2.350   4.7853e-02
   5_xyz:   7.221  0.042  0.444 83.364  0.038  2.322   3.5052e-02
   5_adp:   7.221  0.042  0.444 83.364  0.038  2.322   3.5052e-02
   5_occ:   7.221  0.042  0.444 83.364  0.038  2.322   3.5052e-02
   5_bss:   7.221  0.042  0.444 83.364  0.038  2.322   3.5052e-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:  69.02   0.00  12.11  57.00   0.00   9.30  69.02   0.00  27.37
   1_occ:  69.02   0.00  12.11  57.00   0.00   9.30  69.02   0.00  27.37
   2_bss:  69.02   0.00  12.11  57.00   0.00   9.30  69.02   0.00  27.37
   2_xyz:  69.02   0.00  12.11  57.00   0.00   9.30  69.02   0.00  27.37
   2_adp:  72.93   0.00  11.90  59.05   0.00   8.23  72.93   0.00  31.87
   2_occ:  72.93   0.00  11.90  59.05   0.00   8.23  72.93   0.00  31.87
   3_bss:  72.93   0.00  11.90  59.05   0.00   8.23  72.93   0.00  31.87
   3_xyz:  72.93   0.00  11.90  59.05   0.00   8.23  72.93   0.00  31.87
   3_adp:  81.20   0.00  13.04  80.88   0.00   8.39  81.20   1.07  38.38
   3_occ:  81.20   0.00  13.04  80.88   0.00   8.39  81.20   1.07  38.38
   4_bss:  81.20   0.00  13.04  80.88   0.00   8.39  81.20   1.07  38.38
   4_xyz:  81.20   0.00  13.04  80.88   0.00   8.39  81.20   1.07  38.38
   4_adp:  77.52   0.00  12.07  77.52   0.00   8.03  72.53   1.76  34.04
   4_occ:  77.52   0.00  12.07  77.52   0.00   8.03  72.53   1.76  34.04
   5_bss:  77.52   0.00  12.07  77.52   0.00   8.03  72.53   1.76  34.04
   5_xyz:  77.52   0.00  12.07  77.52   0.00   8.03  72.53   1.76  34.04
   5_adp:  78.94   0.00  12.10  78.94   0.00   8.01  71.29   1.63  34.38
   5_occ:  78.94   0.00  12.10  78.94   0.00   8.01  71.29   1.63  34.38
   5_bss:  81.85   2.92  15.02  81.85   2.92  10.93  74.21   4.54  37.30
------------------------------------------------------------------------
 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:    1.237    0.012    0.405
   1_adp:    1.237    0.012    0.405
   1_occ:    1.237    0.012    0.405
   2_bss:    1.237    0.012    0.405
   2_xyz:    1.514    0.015    0.547
   2_adp:    1.514    0.015    0.547
   2_occ:    1.514    0.015    0.547
   3_bss:    1.514    0.015    0.547
   3_xyz:    1.553    0.044    0.606
   3_adp:    1.553    0.044    0.606
   3_occ:    1.553    0.044    0.606
   4_bss:    1.553    0.044    0.606
   4_xyz:    1.648    0.038    0.619
   4_adp:    1.648    0.038    0.619
   4_occ:    1.648    0.038    0.619
   5_bss:    1.648    0.038    0.619
   5_xyz:    1.728    0.038    0.629
   5_adp:    1.728    0.038    0.629
   5_occ:    1.728    0.038    0.629
   5_bss:    1.728    0.038    0.629
------------------------------------------------------------------------

CPU time actual refinement: 345.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/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_767/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_767/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.15 
  Macro-tasks:
    bulk solvent and scale       = 41.76  
    individual site refinement   = 148.38 
    weights calculation          = 32.57  
    collect and process          = 6.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 229.37 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 105.83 
    alpha_beta                      = 8.53   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 119.10 
    fmodel                         = 7.55   
    r_factors                      = 0.19   
    phase_errors                   = 10.48  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.93 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.709 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    689 calls, 105.43 s
gradients_fft:          634 calls, 104.14 s

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

# Date 2008-01-16 Time 02:22:36 PST -0800 (1200478956.82 s)
Start R-work = 0.4609, R-free = 0.4424 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1788 (no bulk solvent and anisotropic scale)

Start R-work = 0.4522, R-free = 0.4290
Final R-work = 0.1161, R-free = 0.1616