# Date 2008-01-16 Time 01:15:28 PST -0800 (1200474928.29 s)
#phil __OFF__

Command line arguments: "../343.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22469
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 343

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 85.0941, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.97054
Completeness in resolution range: 0.953979
Completeness with d_max=infinity: 0.951061

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9401
                             d_min =   1.9705

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.97054
Completeness in resolution range: 0.953979
Completeness with d_max=infinity: 0.951061

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9406 -  4.2166 [2161/2190]  1944   217  10.0%
  bin  2:  4.2166 -  3.3593 [2065/2088]  1859   206  10.0%
  bin  3:  3.3593 -  2.9384 [2054/2079]  1845   209  10.2%
  bin  4:  2.9384 -  2.6714 [2008/2024]  1812   196   9.8%
  bin  5:  2.6714 -  2.4808 [2006/2050]  1801   205  10.2%
  bin  6:  2.4808 -  2.3351 [2010/2038]  1818   192   9.6%
  bin  7:  2.3351 -  2.2186 [1976/2012]  1775   201  10.2%
  bin  8:  2.2186 -  2.1223 [1996/2038]  1799   197   9.9%
  bin  9:  2.1223 -  2.0408 [1964/2010]  1766   198  10.1%
  bin 10:  2.0408 -  1.9705 [1349/2005]  1211   138  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/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:
        1.54 -     2.21: 21
        2.21 -     2.88: 1321
        2.88 -     3.56: 4491
        3.56 -     4.23: 9242
        4.23 -     4.90: 13438
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.539 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.540 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.747 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.761 3.040 -x+1,y+1/2,-z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.762 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28508 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_343/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5021   r_free= 0.4908   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.298832                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.7030 0.99   1400  158 0.4143 0.4145      6.6232      6.6671|
|  2:  4.7030 -  3.7524 0.99   1345  147 0.4395 0.4242      6.8365      6.8537|
|  3:  3.7524 -  3.2838 0.99   1322  149 0.4660 0.4361      6.7143      6.7154|
|  4:  3.2838 -  2.9862 0.99   1315  137 0.4813 0.4525      6.5333      6.4985|
|  5:  2.9862 -  2.7736 0.98   1300  149 0.5379 0.5412      6.4036       6.413|
|  6:  2.7736 -  2.6110 0.99   1300  146 0.5253 0.5237      6.2866      6.2048|
|  7:  2.6110 -  2.4808 0.98   1279  147 0.5316 0.4944      6.2762      6.1959|
|  8:  2.4808 -  2.3733 0.99   1299  136 0.5377 0.5136      6.1872      6.1709|
|  9:  2.3733 -  2.2822 0.99   1287  147 0.5542 0.5737      6.1266      6.1857|
| 10:  2.2822 -  2.2037 0.98   1277  141 0.5421 0.5613      6.1275      6.1335|
| 11:  2.2037 -  2.1350 0.97   1259  144 0.5490 0.5567      6.0421      6.0564|
| 12:  2.1350 -  2.0742 0.99   1281  142 0.5403 0.5246      5.9794      5.9898|
| 13:  2.0742 -  2.0197 0.94   1243  128 0.5464 0.5510      5.8825      5.9026|
| 14:  2.0197 -  1.9705 0.57    723   88 0.5725 0.4671      5.8965      5.7202|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.7030  1400   158  0.63  40.14   0.79     0.66      91815.47|
|  2:  4.7030 -  3.7524  1345   147  0.64  39.95   0.87     0.71     125877.83|
|  3:  3.7524 -  3.2838  1322   149  0.55  47.75   0.83     0.67     130451.63|
|  4:  3.2838 -  2.9862  1315   137  0.47  54.45   0.79     0.57     109710.80|
|  5:  2.9862 -  2.7736  1300   149  0.36  62.88   0.72     0.44      91787.29|
|  6:  2.7736 -  2.6110  1300   146  0.33  65.51   0.71     0.38      77330.62|
|  7:  2.6110 -  2.4808  1279   147  0.31  66.44   0.72     0.36      70767.41|
|  8:  2.4808 -  2.3733  1299   136  0.31  66.76   0.72     0.36      62919.74|
|  9:  2.3733 -  2.2822  1287   147  0.28  69.30   0.71     0.35      59915.63|
| 10:  2.2822 -  2.2037  1277   141  0.25  71.11   0.75     0.30      55397.15|
| 11:  2.2037 -  2.1350  1259   144  0.21  74.69   0.73     0.26      53551.03|
| 12:  2.1350 -  2.0742  1281   142  0.21  74.57   0.74     0.27      49556.52|
| 13:  2.0742 -  2.0197  1243   128  0.24  72.02   0.73     0.31      40269.42|
| 14:  2.0197 -  1.9705   723    88  0.35  63.67   0.71     0.39      28512.66|
|alpha:            min =        0.26 max =            0.71 mean =         0.44|
|beta:             min =    28512.66 max =       130451.63 mean =     76919.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.73|
|phase err.(test): min =        0.00 max =           89.99 mean =        61.78|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.127964             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.228   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.755857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.226   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.970 -  1.363:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.363 -  1.756:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.756 -  2.149:       80 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.149 -  2.542:      490 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.542 -  2.935:     1284 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.935 -  3.328:     2439 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.328 -  3.721:     3956 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.721 -  4.114:     5221 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.114 -  4.507:     6855 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.507 -  4.900:     8222 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.408 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.970 |       2.342 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    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 = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5065   r_free= 0.4967   ksol= 0.00   Bsol= 0.00   scale= 0.753    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.299014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4949   r_free= 0.4836   ksol= 0.33   Bsol= 6.24   scale= 0.978    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,11.20,7.67,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.293467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.375991             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.662889              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.569   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4949      final r-factor (work) = 0.4286          |
| start r-factor (free) = 0.4836      final r-factor (free) = 0.4450          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 108.1255 = 17.38 * 0.50 * 6.2980 + 1.00 * 53.4081                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.3300 = 17.38 * 0.50 * 6.2351 + 1.00 * 0.1595                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4286      final r-factor (work) = 0.3867          |
| start r-factor (free) = 0.4450      final r-factor (free) = 0.4354          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3830 = 1.66 * 1.00 * 6.2351 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2990 = 1.66 * 1.00 * 6.1802 + 1.00 * 0.0220                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.72   15.54    None  None   None       |
|    all(noH): 2823   0      0.00    99.72   15.54    None  None   None       |
|    Sol.    : 438    0      0.00    99.72   25.76    None  None   None       |
|    Mac.    : 2385   0      0.00    75.15   13.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.972: 1192   |   5:    49.859 -  59.831:   46        |
|      1:     9.972 -  19.944:  813   |   6:    59.831 -  69.803:   11        |
|      2:    19.944 -  29.916:  444   |   7:    69.803 -  79.775:    8        |
|      3:    29.916 -  39.887:  192   |   8:    79.775 -  89.747:    3        |
|      4:    39.887 -  49.859:  113   |   9:    89.747 -  99.719:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3867 r_free = 0.4354             target_work(ml) = 6.168         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3861 r_free = 0.4342             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3861   r_free= 0.4342   ksol= 0.33   Bsol= 6.24   scale= 1.115    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,11.20,7.67,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.167356                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3843   r_free= 0.4293   ksol= 0.30   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,6.93,4.85,0.00,0.00,0.00); trace/3= 5.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.167871                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.215348             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.396  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.645233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.249  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3843      final r-factor (work) = 0.3062          |
| start r-factor (free) = 0.4293      final r-factor (free) = 0.3658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.9634 = 13.22 * 0.50 * 6.1754 + 1.00 * 0.1585                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.2728 = 13.22 * 0.50 * 6.0782 + 1.00 * 0.1100                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3062      final r-factor (work) = 0.2808          |
| start r-factor (free) = 0.3658      final r-factor (free) = 0.3421          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9433 = 0.65 * 1.00 * 6.0782 + 1.00 * 0.0215                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8607 = 0.65 * 1.00 * 5.9605 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.25   14.72    None  None   None       |
|    all(noH): 2823   0      0.00    99.25   14.72    None  None   None       |
|    Sol.    : 438    0      0.00    99.25   30.84    None  None   None       |
|    Mac.    : 2385   0      0.00    77.03   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.925: 1340   |   5:    49.623 -  59.548:   49        |
|      1:     9.925 -  19.849:  773   |   6:    59.548 -  69.472:   20        |
|      2:    19.849 -  29.774:  364   |   7:    69.472 -  79.397:    7        |
|      3:    29.774 -  39.698:  187   |   8:    79.397 -  89.321:    1        |
|      4:    39.698 -  49.623:   80   |   9:    89.321 -  99.246:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2808 r_free = 0.3421             target_work(ml) = 5.931         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2805 r_free = 0.3417             target_work(ml) = 5.930         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2805   r_free= 0.3417   ksol= 0.30   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.48,6.93,4.85,0.00,0.00,0.00); trace/3= 5.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.930286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2780   r_free= 0.3391   ksol= 0.31   Bsol= 40.85   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.53,4.08,2.77,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.928010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.597071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.750  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297975              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2780      final r-factor (work) = 0.2059          |
| start r-factor (free) = 0.3391      final r-factor (free) = 0.2576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7957 = 5.60 * 0.50 * 5.9623 + 1.00 * 0.1100                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3512 = 5.60 * 0.50 * 5.8147 + 1.00 * 0.0787                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2059      final r-factor (work) = 0.1880          |
| start r-factor (free) = 0.2576      final r-factor (free) = 0.2362          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7458 = 0.30 * 1.00 * 5.8147 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6864 = 0.30 * 1.00 * 5.6169 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.02   14.50    None  None   None       |
|    all(noH): 2823   0      0.00    97.02   14.50    None  None   None       |
|    Sol.    : 438    0      3.70    97.02   33.66    None  None   None       |
|    Mac.    : 2385   0      0.00    77.76   10.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.702: 1437   |   5:    48.508 -  58.209:   46        |
|      1:     9.702 -  19.403:  717   |   6:    58.209 -  67.911:   23        |
|      2:    19.403 -  29.105:  269   |   7:    67.911 -  77.612:    7        |
|      3:    29.105 -  38.806:  203   |   8:    77.612 -  87.314:    2        |
|      4:    38.806 -  48.508:  117   |   9:    87.314 -  97.015:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1880 r_free = 0.2362             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1876 r_free = 0.2363             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1876   r_free= 0.2363   ksol= 0.31   Bsol= 40.85   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.53,4.08,2.77,0.00,0.00,0.00); trace/3= 2.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.579167                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1867   r_free= 0.2349   ksol= 0.32   Bsol= 42.77   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,2.26,1.50,0.00,0.00,0.00); trace/3= 1.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.578471                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.691323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.525  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255637              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.008  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1867      final r-factor (work) = 0.1450          |
| start r-factor (free) = 0.2349      final r-factor (free) = 0.1914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2748 = 4.69 * 0.50 * 5.6257 + 1.00 * 0.0787                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9021 = 4.69 * 0.50 * 5.4688 + 1.00 * 0.0743                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1332          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4108 = 0.26 * 1.00 * 5.4688 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3686 = 0.26 * 1.00 * 5.3186 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    81.67   14.48    None  None   None       |
|    all(noH): 2823   0      0.54    81.67   14.48    None  None   None       |
|    Sol.    : 438    0      3.83    81.34   36.83    None  None   None       |
|    Mac.    : 2385   0      0.54    81.67   10.37    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:     0.540 -   8.653: 1291   |   5:    41.104 -  49.217:   98        |
|      1:     8.653 -  16.766:  865   |   6:    49.217 -  57.330:   67        |
|      2:    16.766 -  24.879:  219   |   7:    57.330 -  65.443:   35        |
|      3:    24.879 -  32.992:  115   |   8:    65.443 -  73.556:    9        |
|      4:    32.992 -  41.104:  116   |   9:    73.556 -  81.668:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1332 r_free = 0.1767             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1331 r_free = 0.1768             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1768   ksol= 0.32   Bsol= 42.77   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.10,2.26,1.50,0.00,0.00,0.00); trace/3= 1.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.277176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1777   ksol= 0.33   Bsol= 45.17   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,1.34,1.06,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.708160              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.085  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.177519              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.939  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1334      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2821 = 2.71 * 0.50 * 5.3231 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1688 = 2.71 * 0.50 * 5.2435 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9398 = 0.18 * 1.00 * 5.2435 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9329 = 0.18 * 1.00 * 5.2083 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    81.67   14.18    None  None   None       |
|    all(noH): 2823   0      0.70    81.67   14.18    None  None   None       |
|    Sol.    : 438    0      3.34    76.09   36.03    None  None   None       |
|    Mac.    : 2385   0      0.70    81.67   10.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.699 -   8.796: 1339   |   5:    41.184 -  49.280:   98        |
|      1:     8.796 -  16.893:  856   |   6:    49.280 -  57.377:   61        |
|      2:    16.893 -  24.990:  193   |   7:    57.377 -  65.474:   28        |
|      3:    24.990 -  33.087:  120   |   8:    65.474 -  73.571:    8        |
|      4:    33.087 -  41.184:  114   |   9:    73.571 -  81.668:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1645             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1646             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1646   ksol= 0.33   Bsol= 45.17   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,1.34,1.06,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201935                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.7030 0.99   1400  158 0.1025 0.1303      5.4112      5.5539|
|  2:  4.7030 -  3.7524 0.99   1345  147 0.0910 0.1121      5.4855      5.6787|
|  3:  3.7524 -  3.2838 0.99   1322  149 0.1116 0.1654       5.535      5.9142|
|  4:  3.2838 -  2.9862 0.99   1315  137 0.1350 0.1664      5.5235      5.7157|
|  5:  2.9862 -  2.7736 0.98   1300  149 0.1474 0.1671       5.415      5.5234|
|  6:  2.7736 -  2.6110 0.99   1300  146 0.1410 0.2214      5.3085      5.5793|
|  7:  2.6110 -  2.4808 0.98   1279  147 0.1314 0.1688      5.2255      5.4108|
|  8:  2.4808 -  2.3733 0.99   1299  136 0.1258 0.1801      5.1301      5.3716|
|  9:  2.3733 -  2.2822 0.99   1287  147 0.1265 0.1847      5.0764      5.3498|
| 10:  2.2822 -  2.2037 0.98   1277  141 0.1233 0.1882      5.0424      5.3023|
| 11:  2.2037 -  2.1350 0.97   1259  144 0.1242 0.1777        4.98      5.2402|
| 12:  2.1350 -  2.0742 0.99   1281  142 0.1191 0.1785       4.899      5.1672|
| 13:  2.0742 -  2.0197 0.94   1243  128 0.1197 0.1738      4.8063      5.0834|
| 14:  2.0197 -  1.9705 0.57    723   88 0.1058 0.1671      4.6968      4.9095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.7030  1400   158  0.94   9.34   0.98     0.96       7639.52|
|  2:  4.7030 -  3.7524  1345   147  0.95   8.62   1.02     1.00       9866.09|
|  3:  3.7524 -  3.2838  1322   149  0.93  12.30   1.02     1.01      11962.89|
|  4:  3.2838 -  2.9862  1315   137  0.91  15.23   1.01     0.99      11686.01|
|  5:  2.9862 -  2.7736  1300   149  0.89  17.48   0.99     0.96       9673.81|
|  6:  2.7736 -  2.6110  1300   146  0.89  17.44   0.98     0.94       8173.51|
|  7:  2.6110 -  2.4808  1279   147  0.90  16.56   0.98     0.95       6899.41|
|  8:  2.4808 -  2.3733  1299   136  0.90  16.18   1.01     0.98       6020.80|
|  9:  2.3733 -  2.2822  1287   147  0.89  17.13   1.01     0.98       5572.13|
| 10:  2.2822 -  2.2037  1277   141  0.89  16.72   1.00     0.97       5183.41|
| 11:  2.2037 -  2.1350  1259   144  0.89  16.87   1.01     0.98       4640.82|
| 12:  2.1350 -  2.0742  1281   142  0.91  15.40   1.01     0.98       3950.45|
| 13:  2.0742 -  2.0197  1243   128  0.90  16.39   1.01     1.01       3380.84|
| 14:  2.0197 -  1.9705   723    88  0.91  15.31   0.99     0.95       2713.59|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2713.59 max =        11962.89 mean =      7138.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.00|
|phase err.(test): min =        0.00 max =           89.90 mean =        14.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1646   ksol= 0.32   Bsol= 45.45   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.55,0.42,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201863                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1646   ksol= 0.32   Bsol= 45.45   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,0.55,0.42,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201863                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.7030 0.99   1400  158 0.1023 0.1300      5.4093      5.5521|
|  2:  4.7030 -  3.7524 0.99   1345  147 0.0911 0.1123      5.4858      5.6801|
|  3:  3.7524 -  3.2838 0.99   1322  149 0.1117 0.1656      5.5359      5.9152|
|  4:  3.2838 -  2.9862 0.99   1315  137 0.1349 0.1663      5.5235      5.7157|
|  5:  2.9862 -  2.7736 0.98   1300  149 0.1474 0.1669      5.4148      5.5228|
|  6:  2.7736 -  2.6110 0.99   1300  146 0.1409 0.2211      5.3079      5.5785|
|  7:  2.6110 -  2.4808 0.98   1279  147 0.1313 0.1690      5.2251      5.4107|
|  8:  2.4808 -  2.3733 0.99   1299  136 0.1257 0.1799      5.1301      5.3715|
|  9:  2.3733 -  2.2822 0.99   1287  147 0.1263 0.1850      5.0763       5.351|
| 10:  2.2822 -  2.2037 0.98   1277  141 0.1233 0.1882      5.0425      5.3033|
| 11:  2.2037 -  2.1350 0.97   1259  144 0.1241 0.1776      4.9802      5.2399|
| 12:  2.1350 -  2.0742 0.99   1281  142 0.1191 0.1787      4.8992      5.1678|
| 13:  2.0742 -  2.0197 0.94   1243  128 0.1198 0.1736      4.8069      5.0829|
| 14:  2.0197 -  1.9705 0.57    723   88 0.1058 0.1668       4.697      4.9093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9406 -  4.7030  1400   158  0.94   9.31   0.98     0.96       7597.74|
|  2:  4.7030 -  3.7524  1345   147  0.95   8.62   1.02     1.00       9858.39|
|  3:  3.7524 -  3.2838  1322   149  0.93  12.33   1.02     1.01      11992.71|
|  4:  3.2838 -  2.9862  1315   137  0.91  15.23   1.01     0.99      11691.28|
|  5:  2.9862 -  2.7736  1300   149  0.89  17.47   0.99     0.96       9661.94|
|  6:  2.7736 -  2.6110  1300   146  0.89  17.42   0.98     0.94       8163.41|
|  7:  2.6110 -  2.4808  1279   147  0.90  16.55   0.98     0.94       6894.90|
|  8:  2.4808 -  2.3733  1299   136  0.90  16.19   1.00     0.98       6024.35|
|  9:  2.3733 -  2.2822  1287   147  0.89  17.13   1.01     0.98       5578.74|
| 10:  2.2822 -  2.2037  1277   141  0.89  16.73   1.00     0.96       5184.64|
| 11:  2.2037 -  2.1350  1259   144  0.89  16.88   1.00     0.97       4645.69|
| 12:  2.1350 -  2.0742  1281   142  0.91  15.41   1.00     0.98       3954.49|
| 13:  2.0742 -  2.0197  1243   128  0.90  16.39   1.01     1.01       3382.37|
| 14:  2.0197 -  1.9705   723    88  0.91  15.31   0.98     0.95       2710.53|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2710.53 max =        11992.71 mean =      7136.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.99|
|phase err.(test): min =        0.00 max =           89.88 mean =        14.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    82.27   14.79    None  None   None       |
|    all(noH): 2823   0      1.30    82.27   14.79    None  None   None       |
|    Sol.    : 438    0      3.94    76.69   36.63    None  None   None       |
|    Mac.    : 2385   0      1.30    82.27   10.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.303 -   9.400: 1339   |   5:    41.787 -  49.884:   98        |
|      1:     9.400 -  17.496:  856   |   6:    49.884 -  57.980:   61        |
|      2:    17.496 -  25.593:  193   |   7:    57.980 -  66.077:   28        |
|      3:    25.593 -  33.690:  120   |   8:    66.077 -  74.174:    8        |
|      4:    33.690 -  41.787:  114   |   9:    74.174 -  82.271:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.491 - 5.092
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 332
   mapped sites are within: 0.761 - 5.092

peak=    9.356 closest distance to " CG2 VAL A 230 " =    1.379
peak=    8.263 closest distance to " O   HOH Z 120 " =    1.561
peak=    6.801 closest distance to " CG2 VAL A 296 " =    1.160
peak=    6.120 closest distance to " CD1AILE A 234 " =    1.255
peak=    6.020 closest distance to " O   HOH Z 402 " =    1.707
peak=    5.606 closest distance to " CG  LEU A   5 " =    1.375
peak=    5.459 closest distance to " O   HOH Z 247 " =    1.513
peak=    5.212 closest distance to " O   HOH Z 403 " =    1.924
peak=    5.130 closest distance to " O   HOH Z 124 " =    1.707
peak=    5.130 closest distance to " CB  VAL A 296 " =    1.064
peak=    5.070 closest distance to " CB  SER A  63 " =    1.151
peak=    4.951 closest distance to " O   HOH Z 142 " =    1.656
peak=    4.939 closest distance to " O   HOH Z 209 " =    2.325
peak=    4.905 closest distance to " O   HOH Z 272 " =    1.989
peak=    4.853 closest distance to " O   HOH Z 193 " =    1.753
peak=    4.829 closest distance to " CG  PRO A  54 " =    1.231
peak=    4.804 closest distance to " O   HOH Z 154 " =    1.770
peak=    4.747 closest distance to " NH2 ARG A  56 " =    2.303
peak=    4.671 closest distance to " CB  ARG A 275 " =    0.917
peak=    4.617 closest distance to " O   HOH Z 128 " =    1.625
peak=    4.614 closest distance to " CD2 LEU A   5 " =    1.259
peak=    4.610 closest distance to " CB  VAL A 230 " =    1.266
peak=    4.572 closest distance to " O   HOH Z  80 " =    2.081
peak=    4.554 closest distance to " O   HOH Z  67 " =    2.078
peak=    4.532 closest distance to " CB  GLN A 223 " =    1.378
peak=    4.525 closest distance to " O   HOH Z 278 " =    1.209
peak=    4.440 closest distance to " C   PRO A 198 " =    1.459
peak=    4.423 closest distance to " O   HOH Z 126 " =    1.585
peak=    4.407 closest distance to " CB  ARG A 275 " =    1.297
peak=    4.395 closest distance to " O   HOH Z 357 " =    2.021
peak=    4.387 closest distance to " O   SER A  87 " =    2.349
peak=    4.377 closest distance to " O   HOH Z 389 " =    2.021
peak=    4.361 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.330 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.318 closest distance to " O   HOH Z  40 " =    1.903
peak=    4.318 closest distance to " O   HOH Z 155 " =    1.692
peak=    4.318 closest distance to " O   HOH Z 134 " =    2.001
peak=    4.314 closest distance to " CB  PRO A  54 " =    0.888
peak=    4.313 closest distance to " O   HOH Z 327 " =    1.749
peak=    4.312 closest distance to " O   HOH Z 210 " =    1.134
peak=    4.299 closest distance to " O   HOH Z 316 " =    2.304
peak=    4.298 closest distance to " CG  ARG A  66 " =    1.070
peak=    4.278 closest distance to " O   HOH Z 102 " =    1.372
peak=    4.265 closest distance to " O   HOH Z 346 " =    1.531
peak=    4.262 closest distance to " O   HOH Z 234 " =    3.617
peak=    4.261 closest distance to " CG  PRO A 198 " =    1.234
peak=    4.247 closest distance to " CG  LEU A 228 " =    1.303
peak=    4.244 closest distance to " CD2 LEU A 228 " =    1.177
peak=    4.222 closest distance to " O   HOH Z  47 " =    1.601
peak=    4.203 closest distance to " O   HOH Z  48 " =    1.887
peak=    4.201 closest distance to " O   HOH Z 423 " =    1.873
peak=    4.196 closest distance to " O   HOH Z  11 " =    1.314
peak=    4.190 closest distance to " O   HOH Z  85 " =    1.695
peak=    4.188 closest distance to " O   HOH Z 232 " =    2.458
peak=    4.187 closest distance to " CB  GLN A 183 " =    1.331
peak=    4.183 closest distance to " O   HOH Z 404 " =    1.505
peak=    4.174 closest distance to " O   HOH Z  49 " =    1.159
peak=    4.166 closest distance to " CB  PRO A 198 " =    1.099
peak=    4.134 closest distance to " O   HOH Z 316 " =    1.161
peak=    4.132 closest distance to " O   HOH Z 236 " =    1.393
peak=    4.126 closest distance to " O   HOH Z  48 " =    1.697
peak=    4.119 closest distance to " CB  GLU A 152 " =    1.117
peak=    4.101 closest distance to " O   HOH Z  15 " =    2.182
peak=    4.082 closest distance to " O   HOH Z 130 " =    2.802
peak=    4.081 closest distance to " O   HOH Z 411 " =    3.268
peak=    4.074 closest distance to " CG2 VAL A 296 " =    1.735
peak=    4.071 closest distance to " O   HOH Z 414 " =    2.349
peak=    4.068 closest distance to " OD1 ASN A  60 " =    1.493
peak=    4.063 closest distance to " CA  VAL A  41 " =    0.844
peak=    4.061 closest distance to " O   GLY A  91 " =    1.365
peak=    4.059 closest distance to " O   HOH Z 126 " =    2.541
peak=    4.057 closest distance to " OE1 GLU A   2 " =    2.072
peak=    4.057 closest distance to " NE2 GLN A  11 " =    1.006
peak=    4.056 closest distance to " O   HOH Z 245 " =    1.434
peak=    4.048 closest distance to " CB  SER A   3 " =    1.300
peak=    4.044 closest distance to " O   HOH Z 345 " =    2.682
peak=    4.041 closest distance to " O   HOH Z 156 " =    3.130
peak=    4.034 closest distance to " O   HOH Z 406 " =    1.747
peak=    4.025 closest distance to " O   HOH Z 408 " =    1.772
peak=    4.009 closest distance to " O   HOH Z 263 " =    1.573
peak=    4.004 closest distance to " O   HOH Z 433 " =    1.612
peak=    3.996 closest distance to " CG1 ILE A  33 " =    1.295
peak=    3.986 closest distance to " CG2 THR A 221 " =    1.187
peak=    3.961 closest distance to " O   HOH Z 189 " =    2.597
peak=    3.949 closest distance to " O   HOH Z 303 " =    2.337
peak=    3.940 closest distance to " CD2 TRP A 179 " =    1.391
peak=    3.932 closest distance to " O   HOH Z  59 " =    2.301
peak=    3.932 closest distance to " O   HOH Z  46 " =    1.337
peak=    3.927 closest distance to " O   HOH Z 279 " =    1.293
peak=    3.926 closest distance to " O   HOH Z 334 " =    1.545
peak=    3.921 closest distance to " CB  TRP A 179 " =    1.155
peak=    3.920 closest distance to " O   HOH Z  43 " =    1.527
peak=    3.909 closest distance to " NH2BARG A 145 " =    2.104
peak=    3.903 closest distance to " O   HOH Z  97 " =    1.932
peak=    3.898 closest distance to " NZ  LYS A 117 " =    3.045
peak=    3.883 closest distance to " O   HOH Z   9 " =    2.328
peak=    3.873 closest distance to " O   HOH Z 227 " =    1.707
peak=    3.872 closest distance to " O   ASP A 124 " =    1.559
peak=    3.852 closest distance to " O   HOH Z  97 " =    2.327
peak=    3.848 closest distance to " CB  ALA A 100 " =    1.267
peak=    3.848 closest distance to " CB  ASN A 187 " =    1.390
peak=    3.847 closest distance to " OE1 GLN A  11 " =    1.837
peak=    3.838 closest distance to " O   HOH Z 394 " =    1.640
peak=    3.835 closest distance to " CG1BVAL A  72 " =    1.706
peak=    3.832 closest distance to " O   HOH Z 412 " =    3.795
peak=    3.829 closest distance to " O   HOH Z 203 " =    1.720
peak=    3.828 closest distance to " O   HOH Z 163 " =    1.473
peak=    3.818 closest distance to " CE  LYS A 119 " =    1.099
peak=    3.802 closest distance to " O   HOH Z 130 " =    1.209
peak=    3.790 closest distance to " CE1 HIS A 108 " =    1.115
peak=    3.785 closest distance to " CB  SER A 141 " =    1.007
peak=    3.776 closest distance to " CA  ASP A 191 " =    0.893
peak=    3.774 closest distance to " CA  ALA A  21 " =    1.242
peak=    3.765 closest distance to " CD  ARG A 159 " =    0.791
peak=    3.761 closest distance to " O   HOH Z  54 " =    2.378
peak=    3.746 closest distance to " O   HOH Z 271 " =    2.396
peak=    3.742 closest distance to " O   HOH Z  66 " =    2.171
peak=    3.733 closest distance to " O   HOH Z 166 " =    1.770
peak=    3.732 closest distance to " O   HOH Z 193 " =    2.110
peak=    3.720 closest distance to " NH2 ARG A 156 " =    1.090
peak=    3.720 closest distance to " O   HOH Z 132 " =    2.403
peak=    3.711 closest distance to " CD  ARG A 195 " =    1.044
peak=    3.700 closest distance to " O   HOH Z 380 " =    1.939
peak=    3.699 closest distance to " OG1 THR A 294 " =    2.211
peak=    3.699 closest distance to " O   HOH Z 197 " =    2.104
peak=    3.698 closest distance to " CD  LYS A 166 " =    1.479
peak=    3.696 closest distance to " O   HOH Z  48 " =    2.315
peak=    3.694 closest distance to " O   HOH Z 409 " =    3.146
peak=    3.692 closest distance to " CB  SER A  26 " =    1.699
peak=    3.681 closest distance to " OD1 ASN A  69 " =    2.521
peak=    3.673 closest distance to " O   HOH Z 345 " =    1.809
peak=    3.665 closest distance to " O   HOH Z 426 " =    1.475
peak=    3.663 closest distance to " O   HOH Z 128 " =    1.750
peak=    3.659 closest distance to " CG  PRO A 243 " =    1.182
peak=    3.656 closest distance to " O   HOH Z  71 " =    2.032
peak=    3.654 closest distance to " O   HOH Z 423 " =    2.951
peak=    3.649 closest distance to " O   HOH Z 368 " =    2.087
peak=    3.643 closest distance to " O   HOH Z 136 " =    1.321
peak=    3.639 closest distance to " N   ASN A  39 " =    1.264
peak=    3.638 closest distance to " CD  ARG A 269 " =    1.244
peak=    3.635 closest distance to " ND2 ASN A 187 " =    1.734
peak=    3.630 closest distance to " O   HOH Z 332 " =    1.585
peak=    3.629 closest distance to " O   HOH Z 315 " =    1.876
peak=    3.625 closest distance to " CB  ALA A 256 " =    1.011
peak=    3.623 closest distance to " CB  ASN A 148 " =    1.341
peak=    3.621 closest distance to " CG2 THR A 220 " =    0.761
peak=    3.617 closest distance to " O   HOH Z 395 " =    1.444
peak=    3.615 closest distance to " O   HOH Z 344 " =    1.839
peak=    3.614 closest distance to " O   HOH Z 241 " =    1.739
peak=    3.614 closest distance to " CB  ARG A 139 " =    0.955
peak=    3.607 closest distance to " O   HOH Z 403 " =    1.485
peak=    3.593 closest distance to " C   VAL A 265 " =    1.332
peak=    3.591 closest distance to " CG1 VAL A 153 " =    1.096
peak=    3.588 closest distance to " O   HOH Z 248 " =    1.668
peak=    3.574 closest distance to " O   HOH Z 273 " =    2.616
peak=    3.573 closest distance to " O   HOH Z  54 " =    1.504
peak=    3.571 closest distance to " CA  ASN A 176 " =    1.054
peak=    3.555 closest distance to " O   HOH Z 298 " =    5.092
peak=    3.548 closest distance to " CB  THR A  31 " =    1.471
peak=    3.542 closest distance to " O   HOH Z 435 " =    1.945
peak=    3.540 closest distance to " CB  GLU A 128 " =    1.109
peak=    3.537 closest distance to " NH2AARG A 275 " =    3.851
peak=    3.535 closest distance to " O   HOH Z 126 " =    1.771
peak=    3.533 closest distance to " O   HOH Z 383 " =    1.959
peak=    3.532 closest distance to " CD1 LEU A   5 " =    1.498
peak=    3.527 closest distance to " CE1 TYR A 186 " =    1.309
peak=    3.526 closest distance to " NH1BARG A 190 " =    2.023
peak=    3.522 closest distance to " O   HOH Z  61 " =    1.577
peak=    3.519 closest distance to " CB  GLN A  58 " =    0.997
peak=    3.518 closest distance to " O   HOH Z  39 " =    1.221
peak=    3.515 closest distance to " CB BVAL A  41 " =    1.045
peak=    3.513 closest distance to " CB  SER A  62 " =    0.801
peak=    3.505 closest distance to " O   HOH Z 146 " =    1.441
peak=    3.503 closest distance to " CB  VAL A 202 " =    1.440
peak=    3.502 closest distance to " CG1 ILE A  49 " =    1.583
peak=    3.497 closest distance to " O   HOH Z 421 " =    1.965
peak=    3.496 closest distance to " O   HOH Z 250 " =    1.699
peak=    3.491 closest distance to " OG BSER A 210 " =    1.217
peak=    3.484 closest distance to " O   HOH Z 359 " =    1.807
peak=    3.477 closest distance to " CD  PRO A  54 " =    0.992
peak=    3.456 closest distance to " O   HOH Z 402 " =    2.566
peak=    3.452 closest distance to " O   HOH Z  19 " =    1.903
peak=    3.451 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.447 closest distance to " O   HOH Z 365 " =    2.945
peak=    3.446 closest distance to " CB  ARG A  79 " =    1.322
peak=    3.441 closest distance to " O   HOH Z 207 " =    2.668
peak=    3.439 closest distance to " ND1 HIS A  81 " =    1.472
peak=    3.435 closest distance to " CA  ARG A 195 " =    1.081
peak=    3.433 closest distance to " O   HOH Z 146 " =    1.375
peak=    3.430 closest distance to " O   HOH Z 271 " =    1.437
peak=    3.430 closest distance to " O   HOH Z 214 " =    2.242
peak=    3.428 closest distance to " CD2 LEU A 255 " =    1.190
peak=    3.425 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.420 closest distance to " O   HOH Z 425 " =    1.403
peak=    3.417 closest distance to " O   HOH Z 257 " =    2.114
peak=    3.416 closest distance to " O   HOH Z 369 " =    2.059
peak=    3.414 closest distance to " O   HOH Z   4 " =    1.566
peak=    3.412 closest distance to " CB  TRP A 266 " =    1.136
peak=    3.408 closest distance to " O   HOH Z  35 " =    2.132
peak=    3.406 closest distance to " O   HOH Z 301 " =    1.978
peak=    3.405 closest distance to " O   HOH Z 280 " =    3.059
peak=    3.403 closest distance to " O   HOH Z 155 " =    2.671
peak=    3.398 closest distance to " CB  ARG A 269 " =    1.523
peak=    3.397 closest distance to " O   HOH Z 236 " =    1.735
peak=    3.396 closest distance to " CD2 LEU A 297 " =    0.872
peak=    3.390 closest distance to " CB  ALA A 248 " =    1.337
peak=    3.381 closest distance to " O   HOH Z 291 " =    1.545
peak=    3.380 closest distance to " O   GLY A  23 " =    2.328
peak=    3.378 closest distance to " NH2 ARG A  79 " =    1.272
peak=    3.376 closest distance to " O   HOH Z  44 " =    1.919
peak=    3.374 closest distance to " CB  LEU A   5 " =    1.143
peak=    3.373 closest distance to " CE BMET A  47 " =    1.399
peak=    3.373 closest distance to " O   HOH Z 358 " =    2.188
peak=    3.372 closest distance to " O   HOH Z 147 " =    1.828
peak=    3.363 closest distance to " CB  ALA A  71 " =    1.211
peak=    3.361 closest distance to " NH1 ARG A  14 " =    1.102
peak=    3.360 closest distance to " CD1 LEU A 222 " =    0.803
peak=    3.353 closest distance to " O   HOH Z 112 " =    1.680
peak=    3.352 closest distance to " O   HOH Z  59 " =    1.825
peak=    3.348 closest distance to " O   HOH Z 339 " =    1.313
peak=    3.347 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.346 closest distance to " O   HOH Z  66 " =    1.577
peak=    3.345 closest distance to " NE1 TRP A 274 " =    0.893
peak=    3.337 closest distance to " O   HOH Z 427 " =    3.021
peak=    3.337 closest distance to " C   SER A  32 " =    1.087
peak=    3.331 closest distance to " O   HOH Z 361 " =    2.796
peak=    3.327 closest distance to " CG2 THR A 294 " =    1.382
peak=    3.317 closest distance to " CG2 THR A  42 " =    0.808
peak=    3.312 closest distance to " CA  ARG A  66 " =    0.961
peak=    3.312 closest distance to " CA  ILE A 263 " =    0.948
peak=    3.312 closest distance to " CD  LYS A 119 " =    1.847
peak=    3.310 closest distance to " O   HOH Z 261 " =    2.012
peak=    3.300 closest distance to " CB  LEU A 228 " =    1.460
peak=    3.300 closest distance to " O   HOH Z 326 " =    1.451
peak=    3.300 closest distance to " O   HOH Z 132 " =    1.064
peak=    3.296 closest distance to " O   HOH Z 295 " =    1.522
peak=    3.296 closest distance to " CD AARG A 102 " =    2.410
peak=    3.287 closest distance to " O   HOH Z 156 " =    2.170
peak=    3.286 closest distance to " O   HOH Z 234 " =    1.824
peak=    3.285 closest distance to " CG  MET A 185 " =    1.149
peak=    3.283 closest distance to " OG  SER A  62 " =    2.950
peak=    3.281 closest distance to " CB  ALA A 137 " =    1.313
peak=    3.280 closest distance to " O   HOH Z 173 " =    2.304
peak=    3.279 closest distance to " CG2 ILE A 234 " =    2.071
peak=    3.275 closest distance to " O   HOH Z 280 " =    2.502
peak=    3.273 closest distance to " O   HOH Z 261 " =    2.045
peak=    3.273 closest distance to " O   HOH Z 162 " =    1.758
peak=    3.271 closest distance to " NZ  LYS A 117 " =    1.385
peak=    3.268 closest distance to " O   HOH Z 428 " =    3.973
peak=    3.267 closest distance to " O   HOH Z  88 " =    3.222
peak=    3.266 closest distance to " O   TRP A 274 " =    1.944
peak=    3.265 closest distance to " O   HOH Z 313 " =    1.779
peak=    3.260 closest distance to " CG2 VAL A 197 " =    1.098
peak=    3.258 closest distance to " NZ  LYS A  76 " =    0.953
peak=    3.257 closest distance to " O   HOH Z 362 " =    3.286
peak=    3.257 closest distance to " O   HOH Z 261 " =    2.109
peak=    3.256 closest distance to " CG2 ILE A 106 " =    0.780
peak=    3.256 closest distance to " O   HOH Z 417 " =    3.165
peak=    3.254 closest distance to " O   HOH Z 374 " =    2.556
peak=    3.251 closest distance to " O   HOH Z  78 " =    1.552
peak=    3.244 closest distance to " OG BSER A 164 " =    2.056
peak=    3.240 closest distance to " CD1 LEU A  96 " =    0.790
peak=    3.239 closest distance to " N   SER A 164 " =    1.054
peak=    3.239 closest distance to " OG  SER A 245 " =    1.418
peak=    3.237 closest distance to " CD AARG A 190 " =    1.702
peak=    3.232 closest distance to " O   HOH Z 253 " =    1.826
peak=    3.229 closest distance to " CB  MET A  40 " =    0.772
peak=    3.228 closest distance to " O   HOH Z 419 " =    2.414
peak=    3.224 closest distance to " O   HOH Z 252 " =    1.844
peak=    3.224 closest distance to " CG2 ILE A  20 " =    1.367
peak=    3.222 closest distance to " O   ALA A 165 " =    1.248
peak=    3.222 closest distance to " O   HOH Z 355 " =    1.825
peak=    3.220 closest distance to " OH  TYR A  30 " =    1.113
peak=    3.220 closest distance to " CD2 HIS A  81 " =    1.242
peak=    3.218 closest distance to " CB  GLN A 278 " =    0.916
peak=    3.218 closest distance to " O   HOH Z 109 " =    2.057
peak=    3.215 closest distance to " O   HOH Z 425 " =    2.163
peak=    3.212 closest distance to " CG  GLN A  58 " =    2.554
peak=    3.210 closest distance to " CB  ARG A  79 " =    0.769
peak=    3.206 closest distance to " OD2 ASP A 286 " =    2.709
peak=    3.200 closest distance to " CA  SER A 210 " =    1.457
peak=    3.196 closest distance to " CA  VAL A 126 " =    0.850
peak=    3.196 closest distance to " CG1BVAL A 121 " =    1.286
peak=    3.193 closest distance to " CA  ALA A 295 " =    1.045
peak=    3.193 closest distance to " O   HOH Z 438 " =    2.529
peak=    3.191 closest distance to " O   HOH Z 255 " =    1.552
peak=    3.188 closest distance to " CD  GLN A 194 " =    1.599
peak=    3.186 closest distance to " O   HOH Z 260 " =    1.459
peak=    3.185 closest distance to " CB  ARG A 259 " =    1.921
peak=    3.181 closest distance to " O   HOH Z 194 " =    2.028
peak=    3.180 closest distance to " O   HOH Z 387 " =    2.467
peak=    3.180 closest distance to " CG2AVAL A 121 " =    1.948
peak=    3.178 closest distance to " CB  PHE A 204 " =    1.114
peak=    3.177 closest distance to " O   ALA A 158 " =    1.237
peak=    3.174 closest distance to " O   HOH Z 298 " =    1.848
peak=    3.173 closest distance to " N   ASP A 162 " =    1.413
peak=    3.171 closest distance to " CB  GLN A  73 " =    1.216
peak=    3.171 closest distance to " O  BHOH Z  74 " =    1.367
peak=    3.159 closest distance to " CZ3 TRP A  85 " =    1.054
peak=    3.157 closest distance to " CA  CYS A 260 " =    1.930
peak=    3.157 closest distance to " O   HOH Z 281 " =    4.238
peak=    3.156 closest distance to " OH  TYR A 116 " =    1.177
peak=    3.152 closest distance to " CB  ARG A 190 " =    1.727
peak=    3.150 closest distance to " OD2 ASP A 298 " =    3.908
peak=    3.149 closest distance to " CG1 VAL A 296 " =    1.065
peak=    3.144 closest distance to " CB  ASN A 148 " =    1.697
peak=    3.143 closest distance to " OG BSER A 258 " =    3.225
peak=    3.140 closest distance to " O   HOH Z  38 " =    1.604
peak=    3.130 closest distance to " CD1 ILE A  33 " =    1.531
peak=    3.129 closest distance to " O   HOH Z 163 " =    1.768
peak=    3.129 closest distance to " O   HOH Z 131 " =    2.393
peak=    3.127 closest distance to " CG2 VAL A 112 " =    1.711
peak=    3.123 closest distance to " O   HOH Z 248 " =    1.538
peak=    3.116 closest distance to " O   HOH Z 185 " =    1.621
peak=    3.112 closest distance to " O   HOH Z 420 " =    2.100
peak=    3.111 closest distance to " CG2 ILE A 120 " =    1.375
peak=    3.098 closest distance to " CB  ALA A   9 " =    1.541
peak=    3.091 closest distance to " O   HOH Z 197 " =    2.187
peak=    3.087 closest distance to " O   HOH Z 170 " =    1.627
peak=    3.087 closest distance to " O   HOH Z 293 " =    1.659
peak=    3.083 closest distance to " SG ACYS A 201 " =    0.888
peak=    3.056 closest distance to " O   HOH Z 409 " =    2.414
peak=    3.036 closest distance to " O   HOH Z 145 " =    2.674
peak=    3.034 closest distance to " CA  ARG A  36 " =    1.036
peak=    3.034 closest distance to " NH1 ARG A 138 " =    1.366
peak=    3.023 closest distance to " O   HOH Z 227 " =    2.009

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.576 - 5.033
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 218
   mapped sites are within: 0.733 - 5.033

peak=   -5.462 closest distance to " CG2 VAL A 230 " =    0.798
peak=   -4.617 closest distance to " O   PRO A 163 " =    2.033
peak=   -4.536 closest distance to " O   HOH Z 155 " =    1.544
peak=   -4.469 closest distance to " CD  ARG A 156 " =    1.993
peak=   -4.441 closest distance to " O   HOH Z 290 " =    0.837
peak=   -4.312 closest distance to " CG2BVAL A  41 " =    2.653
peak=   -4.307 closest distance to " O   HOH Z 166 " =    1.728
peak=   -4.222 closest distance to " C   THR A 279 " =    1.206
peak=   -4.090 closest distance to " CD1 PHE A  59 " =    1.922
peak=   -4.081 closest distance to " SG  CYS A 254 " =    3.153
peak=   -4.034 closest distance to " O   HOH Z 266 " =    4.469
peak=   -4.026 closest distance to " C   HIS A 108 " =    1.225
peak=   -4.008 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.987 closest distance to " CG1 VAL A 112 " =    2.455
peak=   -3.975 closest distance to " O   VAL A  67 " =    2.604
peak=   -3.908 closest distance to " OXT GLY A 302 " =    2.730
peak=   -3.903 closest distance to " O   HOH Z  71 " =    1.266
peak=   -3.848 closest distance to " O   HOH Z 423 " =    2.276
peak=   -3.848 closest distance to " CG  MET A  93 " =    2.501
peak=   -3.840 closest distance to " CD2 LEU A 300 " =    2.719
peak=   -3.827 closest distance to " O   HOH Z 136 " =    2.069
peak=   -3.808 closest distance to " O   HOH Z 351 " =    1.460
peak=   -3.795 closest distance to " CG2 THR A 182 " =    2.240
peak=   -3.764 closest distance to " CZ  TYR A 169 " =    1.844
peak=   -3.751 closest distance to " NH2 ARG A  66 " =    1.329
peak=   -3.734 closest distance to " OG  SER A  97 " =    2.344
peak=   -3.725 closest distance to " O   HOH Z 166 " =    1.176
peak=   -3.724 closest distance to " CB  ALA A 161 " =    2.406
peak=   -3.711 closest distance to " O   HOH Z  20 " =    1.369
peak=   -3.709 closest distance to " O   HOH Z 126 " =    1.865
peak=   -3.698 closest distance to " CG  ASP A 231 " =    0.815
peak=   -3.691 closest distance to " O   HOH Z 377 " =    1.145
peak=   -3.689 closest distance to " O   HOH Z 151 " =    1.159
peak=   -3.675 closest distance to " N   ALA A 226 " =    1.950
peak=   -3.664 closest distance to " OG1 THR A   4 " =    1.842
peak=   -3.657 closest distance to " O   ASN A 187 " =    1.513
peak=   -3.643 closest distance to " CD2 LEU A 237 " =    2.674
peak=   -3.640 closest distance to " CD  GLN A  58 " =    1.328
peak=   -3.640 closest distance to " N   GLN A  58 " =    1.822
peak=   -3.635 closest distance to " O   HOH Z 426 " =    1.778
peak=   -3.629 closest distance to " O   HOH Z  92 " =    1.431
peak=   -3.622 closest distance to " O   HOH Z   6 " =    2.008
peak=   -3.621 closest distance to " O   ALA A   1 " =    1.972
peak=   -3.620 closest distance to " O   HOH Z  52 " =    2.131
peak=   -3.615 closest distance to " CB  ALA A 248 " =    1.945
peak=   -3.588 closest distance to " O   HOH Z 124 " =    1.526
peak=   -3.583 closest distance to " O   HOH Z 103 " =    1.915
peak=   -3.580 closest distance to " O   HOH Z 411 " =    1.631
peak=   -3.569 closest distance to " CB  PHE A 208 " =    2.292
peak=   -3.569 closest distance to " O   HOH Z 196 " =    2.348
peak=   -3.568 closest distance to " O   HOH Z 174 " =    1.974
peak=   -3.558 closest distance to " C   GLY A  91 " =    1.388
peak=   -3.555 closest distance to " CG  ARG A 219 " =    2.403
peak=   -3.555 closest distance to " O   HOH Z 407 " =    3.211
peak=   -3.549 closest distance to " O   HOH Z 165 " =    2.064
peak=   -3.548 closest distance to " CH2 TRP A 179 " =    1.280
peak=   -3.548 closest distance to " OG ASER A 134 " =    1.329
peak=   -3.545 closest distance to " O  BHOH Z 338 " =    1.499
peak=   -3.542 closest distance to " CG2 VAL A 296 " =    0.982
peak=   -3.534 closest distance to " OE2 GLU A   2 " =    1.479
peak=   -3.526 closest distance to " NE1 TRP A 266 " =    2.300
peak=   -3.511 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.507 closest distance to " O   HOH Z 407 " =    1.290
peak=   -3.505 closest distance to " CE  MET A 105 " =    2.001
peak=   -3.503 closest distance to " N   THR A 235 " =    1.249
peak=   -3.492 closest distance to " O   ALA A 256 " =    1.498
peak=   -3.487 closest distance to " CD  GLN A  73 " =    0.740
peak=   -3.484 closest distance to " OG BSER A 134 " =    1.702
peak=   -3.479 closest distance to " O   HOH Z 120 " =    1.094
peak=   -3.471 closest distance to " CD1 LEU A 228 " =    2.233
peak=   -3.464 closest distance to " O   PRO A 198 " =    1.283
peak=   -3.463 closest distance to " OD1 ASN A 249 " =    2.172
peak=   -3.457 closest distance to " NH2 ARG A  79 " =    1.953
peak=   -3.451 closest distance to " NE2 GLN A 194 " =    1.724
peak=   -3.446 closest distance to " CG  GLN A  11 " =    1.264
peak=   -3.440 closest distance to " CE1 HIS A  81 " =    1.280
peak=   -3.439 closest distance to " O   HOH Z  39 " =    1.375
peak=   -3.433 closest distance to " O   HOH Z 150 " =    1.532
peak=   -3.427 closest distance to " N   SER A 210 " =    1.357
peak=   -3.427 closest distance to " O   TYR A  15 " =    1.735
peak=   -3.425 closest distance to " CD1 TRP A 179 " =    1.125
peak=   -3.424 closest distance to " C   LEU A 143 " =    1.133
peak=   -3.422 closest distance to " C   GLY A 133 " =    1.256
peak=   -3.421 closest distance to " N   ALA A 248 " =    1.841
peak=   -3.416 closest distance to " CG  ASP A  50 " =    2.222
peak=   -3.412 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.411 closest distance to " ND2 ASN A  60 " =    1.378
peak=   -3.409 closest distance to " OG BSER A 210 " =    1.382
peak=   -3.407 closest distance to " NH2 ARG A  66 " =    4.885
peak=   -3.406 closest distance to " CD2 LEU A 237 " =    2.839
peak=   -3.402 closest distance to " O   HOH Z 196 " =    2.113
peak=   -3.401 closest distance to " O   HOH Z 377 " =    2.086
peak=   -3.398 closest distance to " O   HOH Z 311 " =    3.591
peak=   -3.397 closest distance to " O   HOH Z  15 " =    1.550
peak=   -3.387 closest distance to " O   VAL A 174 " =    2.055
peak=   -3.386 closest distance to " O   HOH Z  60 " =    1.976
peak=   -3.385 closest distance to " O   HOH Z 171 " =    2.190
peak=   -3.378 closest distance to " CB  PRO A 163 " =    2.858
peak=   -3.372 closest distance to " CD1 PHE A 130 " =    2.247
peak=   -3.371 closest distance to " O   TRP A  92 " =    1.981
peak=   -3.370 closest distance to " N   ARG A  66 " =    1.713
peak=   -3.369 closest distance to " CB  ALA A 291 " =    2.189
peak=   -3.369 closest distance to " CA  GLY A 133 " =    2.022
peak=   -3.364 closest distance to " CD1 TYR A 169 " =    2.245
peak=   -3.363 closest distance to " CD  GLN A 223 " =    0.785
peak=   -3.362 closest distance to " CA  SER A 276 " =    1.448
peak=   -3.357 closest distance to " CD2 PHE A 192 " =    2.076
peak=   -3.357 closest distance to " CD  ARG A 139 " =    1.556
peak=   -3.357 closest distance to " OG BSER A 212 " =    1.654
peak=   -3.356 closest distance to " O   HOH Z 234 " =    4.111
peak=   -3.355 closest distance to " NE2 GLN A  88 " =    1.046
peak=   -3.353 closest distance to " ND2 ASN A  39 " =    1.084
peak=   -3.352 closest distance to " CA  GLY A 203 " =    2.218
peak=   -3.352 closest distance to " O   HOH Z 120 " =    0.970
peak=   -3.351 closest distance to " O   HOH Z  49 " =    0.876
peak=   -3.350 closest distance to " NH2AARG A 275 " =    4.777
peak=   -3.348 closest distance to " OG BSER A 134 " =    1.419
peak=   -3.348 closest distance to " O   VAL A 197 " =    1.338
peak=   -3.346 closest distance to " O   MET A  40 " =    2.772
peak=   -3.343 closest distance to " O   HOH Z  78 " =    1.624
peak=   -3.336 closest distance to " OD1 ASN A 148 " =    1.580
peak=   -3.332 closest distance to " CH2 TRP A 150 " =    1.063
peak=   -3.325 closest distance to " ND2 ASN A  69 " =    1.575
peak=   -3.324 closest distance to " O   ALA A 161 " =    1.582
peak=   -3.324 closest distance to " OG  SER A  26 " =    1.115
peak=   -3.323 closest distance to " CD  ARG A  36 " =    1.838
peak=   -3.320 closest distance to " O   HOH Z 424 " =    2.856
peak=   -3.318 closest distance to " O   SER A 146 " =    0.901
peak=   -3.317 closest distance to " OG  SER A   3 " =    1.514
peak=   -3.317 closest distance to " O   HOH Z 340 " =    1.087
peak=   -3.304 closest distance to " C   ASN A 285 " =    2.188
peak=   -3.299 closest distance to " CE BMET A  47 " =    1.494
peak=   -3.290 closest distance to " CB  CYS A 254 " =    2.619
peak=   -3.290 closest distance to " O   HOH Z 313 " =    2.227
peak=   -3.289 closest distance to " O   GLY A 241 " =    2.252
peak=   -3.285 closest distance to " CB  ALA A 291 " =    2.393
peak=   -3.284 closest distance to " CG1 VAL A  78 " =    2.715
peak=   -3.282 closest distance to " NH2 ARG A 159 " =    2.258
peak=   -3.281 closest distance to " CG  ARG A 269 " =    2.198
peak=   -3.281 closest distance to " O   GLY A 196 " =    0.945
peak=   -3.280 closest distance to " CD1 LEU A  25 " =    2.453
peak=   -3.279 closest distance to " SG  CYS A 260 " =    2.522
peak=   -3.272 closest distance to " O   SER A 273 " =    1.206
peak=   -3.264 closest distance to " CD1 TYR A 247 " =    2.321
peak=   -3.261 closest distance to " O   HOH Z 426 " =    2.887
peak=   -3.261 closest distance to " O   HOH Z 313 " =    1.313
peak=   -3.255 closest distance to " O   ARG A 219 " =    1.857
peak=   -3.254 closest distance to " O   SER A 210 " =    1.873
peak=   -3.252 closest distance to " O   ASP A 191 " =    1.395
peak=   -3.248 closest distance to " OD1 ASN A  39 " =    2.187
peak=   -3.248 closest distance to " CA  ALA A 137 " =    2.472
peak=   -3.247 closest distance to " O   HOH Z  56 " =    2.208
peak=   -3.246 closest distance to " NH1 ARG A 195 " =    2.528
peak=   -3.242 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.242 closest distance to " C   VAL A 265 " =    0.851
peak=   -3.240 closest distance to " N   VAL A 230 " =    1.086
peak=   -3.235 closest distance to " OG  SER A 206 " =    1.423
peak=   -3.233 closest distance to " O   HOH Z 139 " =    3.447
peak=   -3.230 closest distance to " O   HOH Z 388 " =    2.054
peak=   -3.230 closest distance to " O   HOH Z  10 " =    1.570
peak=   -3.228 closest distance to " OXT GLY A 302 " =    3.574
peak=   -3.226 closest distance to " O   HOH Z  17 " =    1.030
peak=   -3.217 closest distance to " CD2 PHE A  59 " =    2.558
peak=   -3.211 closest distance to " O   ASN A  45 " =    1.844
peak=   -3.206 closest distance to " N   VAL A 189 " =    1.642
peak=   -3.205 closest distance to " O   HOH Z 292 " =    2.678
peak=   -3.205 closest distance to " NH1 ARG A 195 " =    2.271
peak=   -3.196 closest distance to " O   HOH Z 422 " =    1.402
peak=   -3.193 closest distance to " O   HOH Z 221 " =    1.220
peak=   -3.192 closest distance to " CA  VAL A 197 " =    0.955
peak=   -3.190 closest distance to " N   HIS A 115 " =    2.076
peak=   -3.188 closest distance to " O   HOH Z 166 " =    1.338
peak=   -3.188 closest distance to " CD  LYS A 289 " =    2.459
peak=   -3.188 closest distance to " OG1 THR A  82 " =    1.251
peak=   -3.186 closest distance to " CG  MET A 105 " =    0.811
peak=   -3.171 closest distance to " CD1 PHE A  59 " =    2.223
peak=   -3.170 closest distance to " CA  LYS A 166 " =    2.172
peak=   -3.169 closest distance to " CG2 VAL A 189 " =    1.892
peak=   -3.168 closest distance to " O   HOH Z 301 " =    2.205
peak=   -3.166 closest distance to " OG  SER A  62 " =    1.219
peak=   -3.160 closest distance to " N   THR A 157 " =    1.610
peak=   -3.156 closest distance to " O   HOH Z 297 " =    2.762
peak=   -3.154 closest distance to " CB  LEU A 167 " =    2.201
peak=   -3.153 closest distance to " CA  GLY A 133 " =    2.289
peak=   -3.152 closest distance to " O   HOH Z 126 " =    1.446
peak=   -3.148 closest distance to " CA  VAL A 296 " =    0.987
peak=   -3.142 closest distance to " CD  ARG A 195 " =    5.033
peak=   -3.140 closest distance to " C   SER A 206 " =    1.611
peak=   -3.139 closest distance to " NH2BARG A 145 " =    2.455
peak=   -3.139 closest distance to " O   ALA A  51 " =    1.561
peak=   -3.136 closest distance to " O   HOH Z 412 " =    4.954
peak=   -3.133 closest distance to " O   HOH Z  11 " =    1.534
peak=   -3.131 closest distance to " O   HOH Z  30 " =    0.976
peak=   -3.125 closest distance to " O   HOH Z 427 " =    1.400
peak=   -3.124 closest distance to " O   HOH Z 174 " =    4.410
peak=   -3.121 closest distance to " N   SER A 271 " =    1.432
peak=   -3.117 closest distance to " C   ALA A 158 " =    1.308
peak=   -3.116 closest distance to " CD2 TYR A 293 " =    1.999
peak=   -3.113 closest distance to " O   HOH Z  39 " =    1.574
peak=   -3.111 closest distance to " O   HOH Z 425 " =    1.155
peak=   -3.106 closest distance to " O   HOH Z 372 " =    2.520
peak=   -3.105 closest distance to " CE2 TRP A 274 " =    1.203
peak=   -3.102 closest distance to " O   PRO A 198 " =    1.146
peak=   -3.097 closest distance to " O   HOH Z 198 " =    1.158
peak=   -3.088 closest distance to " O   HOH Z 360 " =    2.484
peak=   -3.088 closest distance to " CD  PRO A 243 " =    1.965
peak=   -3.081 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.078 closest distance to " C   GLN A 144 " =    0.869
peak=   -3.077 closest distance to " C   PHE A 155 " =    0.733
peak=   -3.077 closest distance to " CA  PRO A 243 " =    2.814
peak=   -3.066 closest distance to " O   HOH Z 146 " =    1.129
peak=   -3.066 closest distance to " O   GLY A  80 " =    2.590
peak=   -3.057 closest distance to " O   HOH Z 397 " =    1.209
peak=   -3.026 closest distance to " O   HOH Z 184 " =    1.331

================= 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    :  0.5021 0.4908   6.298832e+00   6.288383e+00
   1_bss:  0.4949 0.4836   6.293467e+00   6.282964e+00
   1_xyz:  0.4286 0.4450   6.220754e+00   6.242983e+00
   1_adp:  0.3867 0.4354   6.168355e+00   6.231513e+00
   1_occ:  0.3861 0.4342   6.167356e+00   6.231381e+00
   2_bss:  0.3843 0.4293   6.167871e+00   6.230225e+00
   2_xyz:  0.3062 0.3658   5.993235e+00   6.119911e+00
   2_adp:  0.2808 0.3421   5.930733e+00   6.071878e+00
   2_occ:  0.2805 0.3417   5.930286e+00   6.071408e+00
   3_bss:  0.2780 0.3391   5.928010e+00   6.068029e+00
   3_xyz:  0.2059 0.2576   5.661379e+00   5.836595e+00
   3_adp:  0.1880 0.2362   5.579942e+00   5.762487e+00
   3_occ:  0.1876 0.2363   5.579167e+00   5.763034e+00
   4_bss:  0.1867 0.2349   5.578471e+00   5.760366e+00
   4_xyz:  0.1450 0.1914   5.355303e+00   5.572637e+00
   4_adp:  0.1332 0.1767   5.277309e+00   5.496533e+00
   4_occ:  0.1331 0.1768   5.277176e+00   5.497026e+00
   5_bss:  0.1334 0.1777   5.280911e+00   5.500111e+00
   5_xyz:  0.1218 0.1664   5.212378e+00   5.445146e+00
   5_adp:  0.1206 0.1645   5.202121e+00   5.433749e+00
   5_occ:  0.1205 0.1646   5.201935e+00   5.433950e+00
   5_bss:  0.1205 0.1646   5.201863e+00   5.434010e+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:  0.334   6.236   6.987  11.199   7.673   0.000   0.000   0.000
   1_xyz:  0.334   6.236   6.987  11.199   7.673   0.000   0.000   0.000
   1_adp:  0.334   6.236   6.987  11.199   7.673   0.000   0.000   0.000
   1_occ:  0.334   6.236   6.987  11.199   7.673   0.000   0.000   0.000
   2_bss:  0.304  20.001   3.482   6.928   4.846   0.000   0.000   0.000
   2_xyz:  0.304  20.001   3.482   6.928   4.846   0.000   0.000   0.000
   2_adp:  0.304  20.001   3.482   6.928   4.846   0.000   0.000   0.000
   2_occ:  0.304  20.001   3.482   6.928   4.846   0.000   0.000   0.000
   3_bss:  0.315  40.855   1.533   4.077   2.766   0.000   0.000   0.000
   3_xyz:  0.315  40.855   1.533   4.077   2.766   0.000   0.000   0.000
   3_adp:  0.315  40.855   1.533   4.077   2.766   0.000   0.000   0.000
   3_occ:  0.315  40.855   1.533   4.077   2.766   0.000   0.000   0.000
   4_bss:  0.324  42.765   0.100   2.256   1.499   0.000   0.000   0.000
   4_xyz:  0.324  42.765   0.100   2.256   1.499   0.000   0.000   0.000
   4_adp:  0.324  42.765   0.100   2.256   1.499   0.000   0.000   0.000
   4_occ:  0.324  42.765   0.100   2.256   1.499   0.000   0.000   0.000
   5_bss:  0.328  45.172  -0.357   1.345   1.060   0.000   0.000   0.000
   5_xyz:  0.328  45.172  -0.357   1.345   1.060   0.000   0.000   0.000
   5_adp:  0.328  45.172  -0.357   1.345   1.060   0.000   0.000   0.000
   5_occ:  0.328  45.172  -0.357   1.345   1.060   0.000   0.000   0.000
   5_bss:  0.325  45.452  -0.967   0.547   0.421   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.737 0.3717  0.4353    76907.092
   1_bss:  62.459 0.3604  0.5349    75121.869
   1_xyz:  55.850 0.4440  0.6480    61468.622
   1_adp:  52.695 0.4846  0.7808    57630.353
   1_occ:  52.619 0.4855  0.7802    57371.518
   2_bss:  52.186 0.4909  0.7032    56648.907
   2_xyz:  40.958 0.6296  0.9003    37983.738
   2_adp:  36.816 0.6798  0.9555    32474.582
   2_occ:  36.790 0.6801  0.9554    32443.300
   3_bss:  36.462 0.6838  0.8861    31944.031
   3_xyz:  25.889 0.8018  0.9953    17291.772
   3_adp:  23.186 0.8305  1.0171    14664.111
   3_occ:  23.180 0.8306  1.0173    14676.179
   4_bss:  23.077 0.8315  0.9639    14540.352
   4_xyz:  18.206 0.8781  0.9927     9413.759
   4_adp:  16.396 0.8948  0.9998     8056.206
   4_occ:  16.404 0.8947  0.9997     8066.823
   5_bss:  16.465 0.8942  0.9776     8163.701
   5_xyz:  15.221 0.9052  0.9798     7266.277
   5_adp:  14.932 0.9078  0.9777     7132.703
   5_occ:  14.931 0.9078  0.9776     7137.253
   5_bss:  14.929 0.9078  0.9750     7135.477
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3408e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3408e+01
   1_xyz:   1.798  0.014  0.111 18.375  0.007  4.118   1.5949e-01
   1_adp:   1.798  0.014  0.111 18.375  0.007  4.118   1.5949e-01
   1_occ:   1.798  0.014  0.111 18.375  0.007  4.118   1.5949e-01
   2_bss:   1.798  0.014  0.111 18.375  0.007  4.118   1.5949e-01
   2_xyz:   1.371  0.011  0.092 16.896  0.006  4.105   1.1005e-01
   2_adp:   1.371  0.011  0.092 16.896  0.006  4.105   1.1005e-01
   2_occ:   1.371  0.011  0.092 16.896  0.006  4.105   1.1005e-01
   3_bss:   1.371  0.011  0.092 16.896  0.006  4.105   1.1005e-01
   3_xyz:   1.180  0.008  0.082 15.906  0.005  4.126   7.8686e-02
   3_adp:   1.180  0.008  0.082 15.906  0.005  4.126   7.8686e-02
   3_occ:   1.180  0.008  0.082 15.906  0.005  4.126   7.8686e-02
   4_bss:   1.180  0.008  0.082 15.906  0.005  4.126   7.8686e-02
   4_xyz:   1.122  0.008  0.082 15.726  0.004  4.121   7.4273e-02
   4_adp:   1.122  0.008  0.082 15.726  0.004  4.121   7.4273e-02
   4_occ:   1.122  0.008  0.082 15.726  0.004  4.121   7.4273e-02
   5_bss:   1.122  0.008  0.082 15.726  0.004  4.121   7.4273e-02
   5_xyz:   1.083  0.008  0.082 15.678  0.004  4.112   6.8699e-02
   5_adp:   1.083  0.008  0.082 15.678  0.004  4.112   6.8699e-02
   5_occ:   1.083  0.008  0.082 15.678  0.004  4.112   6.8699e-02
   5_bss:   1.083  0.008  0.082 15.678  0.004  4.112   6.8699e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.970   6.9199e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.970   6.9199e+00
   1_xyz:  16.158  0.174  0.545 87.006  0.052  2.166   1.0854e-01
   1_adp:  16.158  0.174  0.545 87.006  0.052  2.166   1.0854e-01
   1_occ:  16.158  0.174  0.545 87.006  0.052  2.166   1.0854e-01
   2_bss:  16.158  0.174  0.545 87.006  0.052  2.166   1.0854e-01
   2_xyz:   9.682  0.138  0.329 84.786  0.064  2.069   8.6090e-02
   2_adp:   9.682  0.138  0.329 84.786  0.064  2.069   8.6090e-02
   2_occ:   9.682  0.138  0.329 84.786  0.064  2.069   8.6090e-02
   3_bss:   9.682  0.138  0.329 84.786  0.064  2.069   8.6090e-02
   3_xyz:   7.153  0.056  0.332 88.447  0.040  2.185   7.2356e-02
   3_adp:   7.153  0.056  0.332 88.447  0.040  2.185   7.2356e-02
   3_occ:   7.153  0.056  0.332 88.447  0.040  2.185   7.2356e-02
   4_bss:   7.153  0.056  0.332 88.447  0.040  2.185   7.2356e-02
   4_xyz:   7.149  0.052  0.557 83.116  0.038  2.178   6.9556e-02
   4_adp:   7.149  0.052  0.557 83.116  0.038  2.178   6.9556e-02
   4_occ:   7.149  0.052  0.557 83.116  0.038  2.178   6.9556e-02
   5_bss:   7.149  0.052  0.557 83.116  0.038  2.178   6.9556e-02
   5_xyz:   7.373  0.054  0.566 83.171  0.040  2.285   4.5987e-02
   5_adp:   7.373  0.054  0.566 83.171  0.040  2.285   4.5987e-02
   5_occ:   7.373  0.054  0.566 83.171  0.040  2.285   4.5987e-02
   5_bss:   7.373  0.054  0.566 83.171  0.040  2.285   4.5987e-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:  99.72   0.00  15.54  75.15   0.00  13.67  99.72   0.00  25.76
   1_occ:  99.72   0.00  15.54  75.15   0.00  13.67  99.72   0.00  25.76
   2_bss:  99.72   0.00  15.54  75.15   0.00  13.67  99.72   0.00  25.76
   2_xyz:  99.72   0.00  15.54  75.15   0.00  13.67  99.72   0.00  25.76
   2_adp:  99.25   0.00  14.72  77.03   0.00  11.75  99.25   0.00  30.84
   2_occ:  99.25   0.00  14.72  77.03   0.00  11.75  99.25   0.00  30.84
   3_bss:  99.25   0.00  14.72  77.03   0.00  11.75  99.25   0.00  30.84
   3_xyz:  99.25   0.00  14.72  77.03   0.00  11.75  99.25   0.00  30.84
   3_adp:  97.02   0.00  14.50  77.76   0.00  10.98  97.02   3.70  33.66
   3_occ:  97.02   0.00  14.50  77.76   0.00  10.98  97.02   3.70  33.66
   4_bss:  97.02   0.00  14.50  77.76   0.00  10.98  97.02   3.70  33.66
   4_xyz:  97.02   0.00  14.50  77.76   0.00  10.98  97.02   3.70  33.66
   4_adp:  81.67   0.54  14.48  81.67   0.54  10.37  81.34   3.83  36.83
   4_occ:  81.67   0.54  14.48  81.67   0.54  10.37  81.34   3.83  36.83
   5_bss:  81.67   0.54  14.48  81.67   0.54  10.37  81.34   3.83  36.83
   5_xyz:  81.67   0.54  14.48  81.67   0.54  10.37  81.34   3.83  36.83
   5_adp:  81.67   0.70  14.18  81.67   0.70  10.17  76.09   3.34  36.03
   5_occ:  81.67   0.70  14.18  81.67   0.70  10.17  76.09   3.34  36.03
   5_bss:  82.27   1.30  14.79  82.27   1.30  10.77  76.69   3.94  36.63
------------------------------------------------------------------------
 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:    1.156    0.021    0.417
   1_adp:    1.156    0.021    0.417
   1_occ:    1.156    0.021    0.417
   2_bss:    1.156    0.021    0.417
   2_xyz:    1.851    0.026    0.636
   2_adp:    1.851    0.026    0.636
   2_occ:    1.851    0.026    0.636
   3_bss:    1.851    0.026    0.636
   3_xyz:    1.685    0.035    0.747
   3_adp:    1.685    0.035    0.747
   3_occ:    1.685    0.035    0.747
   4_bss:    1.685    0.035    0.747
   4_xyz:    1.792    0.038    0.828
   4_adp:    1.792    0.038    0.828
   4_occ:    1.792    0.038    0.828
   5_bss:    1.792    0.038    0.828
   5_xyz:    1.820    0.029    0.857
   5_adp:    1.820    0.029    0.857
   5_occ:    1.820    0.029    0.857
   5_bss:    1.820    0.029    0.857
------------------------------------------------------------------------

CPU time actual refinement: 336.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/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_343/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_343/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.26 
  Macro-tasks:
    bulk solvent and scale       = 45.16  
    individual site refinement   = 137.90 
    weights calculation          = 32.36  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.99 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 102.70 
    alpha_beta                      = 8.19   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 112.71 
    fmodel                         = 7.68   
    r_factors                      = 0.25   
    phase_errors                   = 10.22  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 245.58 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.751 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    625 calls, 102.41 s
gradients_fft:          571 calls,  99.63 s

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

# Date 2008-01-16 Time 01:21:18 PST -0800 (1200475278.50 s)
Start R-work = 0.5021, R-free = 0.4908 (no bulk solvent and anisotropic scale)
Final R-work = 0.1382, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4949, R-free = 0.4836
Final R-work = 0.1205, R-free = 0.1646