# Date 2008-01-16 Time 00:27:21 PST -0800 (1200472041.63 s)
#phil __OFF__

Command line arguments: "../33.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9360
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 33

-------------------------------------------------------------------------------
  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: (68.4938, 46.4607, 84.2302, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (68.4938, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95046
Completeness in resolution range: 0.971484
Completeness with d_max=infinity: 0.96841

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6191
                             d_min =   1.9505

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: (68.4938, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95046
Completeness in resolution range: 0.971484
Completeness with d_max=infinity: 0.96841

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6195 -  4.1726 [2114/2141]  1903   211  10.0%
  bin  2:  4.1726 -  3.3248 [2031/2047]  1827   204  10.0%
  bin  3:  3.3248 -  2.9082 [2016/2035]  1813   203  10.1%
  bin  4:  2.9082 -  2.6441 [1981/2011]  1789   192   9.7%
  bin  5:  2.6441 -  2.4555 [1972/1991]  1771   201  10.2%
  bin  6:  2.4555 -  2.3113 [1962/1998]  1767   195   9.9%
  bin  7:  2.3113 -  2.1960 [1957/1990]  1763   194   9.9%
  bin  8:  2.1960 -  2.1007 [1946/1981]  1748   198  10.2%
  bin  9:  2.1007 -  2.0200 [1937/1964]  1743   194  10.0%
  bin 10:  2.0200 -  1.9505 [1673/2006]  1506   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/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: 0.15 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:
        0.71 -     1.55: 11
        1.55 -     2.39: 76
        2.39 -     3.23: 3369
        3.23 -     4.06: 9767
        4.06 -     4.90: 16059
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.715 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.993 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.347 3.440 -x+1,y-1/2,-z+1/2
  " O   HOH Z 401 " - " CA  GLY A  91 "  1.347 3.440 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.386 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29277 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_33/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/model_refine_001.geo

CPU time processing inputs: 11.36


============================ 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 = 68.49375 46.4607 84.23025 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: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5127   r_free= 0.5008   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.304288                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.4243 0.4256      6.6381      6.6661|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.4591 0.4548      6.8528      6.8675|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.4853 0.4563      6.7381      6.8045|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.4926 0.5003      6.5675      6.5279|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.5404 0.5585      6.4137      6.3948|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.5446 0.5328      6.3141      6.2714|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.5366 0.5113      6.2612       6.181|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.5543 0.5384      6.2139       6.209|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.5496 0.5391      6.1289       6.143|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.5657 0.5090      6.1362      6.1101|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.5518 0.5668      6.0582      6.1186|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.5355 0.4585      5.9879      6.0098|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.5587 0.5332      5.9122      5.8914|
| 14:  1.9991 -  1.9505 0.78    993  118 0.5466 0.5255      5.8573      5.7571|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.62  41.44   0.79     0.65      94593.26|
|  2:  4.6535 -  3.7135  1322   146  0.60  43.49   0.85     0.68     146759.57|
|  3:  3.7135 -  3.2500  1299   146  0.49  52.61   0.84     0.64     155098.51|
|  4:  3.2500 -  2.9555  1287   139  0.41  58.76   0.81     0.53     129274.32|
|  5:  2.9555 -  2.7452  1274   142  0.36  63.14   0.72     0.45      96462.39|
|  6:  2.7452 -  2.5843  1279   146  0.34  64.59   0.71     0.40      78113.35|
|  7:  2.5843 -  2.4555  1268   139  0.32  66.24   0.74     0.37      70876.15|
|  8:  2.4555 -  2.3491  1267   143  0.31  66.81   0.73     0.37      62659.55|
|  9:  2.3491 -  2.2590  1264   139  0.29  67.96   0.73     0.37      58691.21|
| 10:  2.2590 -  2.1813  1244   135  0.31  66.83   0.75     0.38      51905.95|
| 11:  2.1813 -  2.1133  1266   147  0.27  69.98   0.77     0.35      50926.48|
| 12:  2.1133 -  2.0530  1253   128  0.26  70.72   0.75     0.33      47406.05|
| 13:  2.0530 -  1.9991  1240   138  0.21  74.23   0.75     0.28      42081.00|
| 14:  1.9991 -  1.9505   993   118  0.20  75.31   0.75     0.23      33605.91|
|alpha:            min =        0.23 max =            0.68 mean =         0.44|
|beta:             min =    33605.91 max =       155098.51 mean =     81229.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.57|
|phase err.(test): min =        0.00 max =           90.00 mean =        63.07|
|-----------------------------------------------------------------------------|

============================== 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 = 25.659929             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.368   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.954368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.706   (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 |  0.589 -  1.020:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.020 -  1.451:        4 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.451 -  1.882:       42 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.882 -  2.313:      224 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.313 -  2.744:      950 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.744 -  3.175:     2180 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.175 -  3.607:     3837 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.607 -  4.038:     5548 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.038 -  4.469:     7439 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.469 -  4.900:     9074 |
|-----------------------------------------------------------------------------|
|-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 |       52.436 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  0.589 |       3.917 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    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 = 11.144)------------------------------------------|
|    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: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5161   r_free= 0.5050   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.304716                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5043   r_free= 0.4933   ksol= 0.38   Bsol= 0.00   scale= 0.980    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.14,8.93,0.00,0.00,0.00); trace/3= 8.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.298470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.450467             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.492   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.718846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.432   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5043      final r-factor (work) = 0.4382          |
| start r-factor (free) = 0.4933      final r-factor (free) = 0.4537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 113.7189 = 19.45 * 0.50 * 6.3015 + 1.00 * 52.4357                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.8761 = 19.45 * 0.50 * 6.2414 + 1.00 * 0.1773                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4382      final r-factor (work) = 0.3986          |
| start r-factor (free) = 0.4537      final r-factor (free) = 0.4522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7422 = 1.72 * 1.00 * 6.2414 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6615 = 1.72 * 1.00 * 6.1899 + 1.00 * 0.0220                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.14   15.42    None  None   None       |
|    all(noH): 2823   0      0.00    79.14   15.42    None  None   None       |
|    Sol.    : 438    0      0.00    79.14   25.05    None  None   None       |
|    Mac.    : 2385   0      0.00    76.28   13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.914:  935   |   5:    39.568 -  47.482:   99        |
|      1:     7.914 -  15.827:  757   |   6:    47.482 -  55.396:   31        |
|      2:    15.827 -  23.741:  512   |   7:    55.396 -  63.309:   18        |
|      3:    23.741 -  31.655:  302   |   8:    63.309 -  71.223:   11        |
|      4:    31.655 -  39.568:  154   |   9:    71.223 -  79.137:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3986 r_free = 0.4522             target_work(ml) = 6.178         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3979 r_free = 0.4516             target_work(ml) = 6.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3979   r_free= 0.4516   ksol= 0.38   Bsol= 0.00   scale= 1.117    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.14,8.93,0.00,0.00,0.00); trace/3= 8.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.178037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3951   r_free= 0.4487   ksol= 0.36   Bsol= 24.11   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.21,5.48,0.00,0.00,0.00); trace/3= 4.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.178238                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.009648             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.060  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.720107              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.436  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3951      final r-factor (work) = 0.3120          |
| start r-factor (free) = 0.4487      final r-factor (free) = 0.3719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.6784 = 16.01 * 0.50 * 6.1839 + 1.00 * 0.1773                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.8988 = 16.01 * 0.50 * 6.0933 + 1.00 * 0.1226                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3120      final r-factor (work) = 0.2844          |
| start r-factor (free) = 0.3719      final r-factor (free) = 0.3498          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4097 = 0.72 * 1.00 * 6.0933 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3118 = 0.72 * 1.00 * 5.9610 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.04   14.88    None  None   None       |
|    all(noH): 2823   0      0.00    85.04   14.88    None  None   None       |
|    Sol.    : 438    0      0.00    84.12   31.48    None  None   None       |
|    Mac.    : 2385   0      0.00    85.04   11.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.504: 1179   |   5:    42.520 -  51.023:   74        |
|      1:     8.504 -  17.008:  739   |   6:    51.023 -  59.527:   37        |
|      2:    17.008 -  25.512:  395   |   7:    59.527 -  68.031:   22        |
|      3:    25.512 -  34.016:  228   |   8:    68.031 -  76.535:    5        |
|      4:    34.016 -  42.520:  141   |   9:    76.535 -  85.039:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2844 r_free = 0.3498             target_work(ml) = 5.935         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2840 r_free = 0.3498             target_work(ml) = 5.935         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2840   r_free= 0.3498   ksol= 0.36   Bsol= 24.11   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.21,5.48,0.00,0.00,0.00); trace/3= 4.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.934721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2818   r_free= 0.3491   ksol= 0.34   Bsol= 34.19   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.25,3.19,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.931772                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.621083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.301  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.220   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2086          |
| start r-factor (free) = 0.3491      final r-factor (free) = 0.2660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8321 = 7.62 * 0.50 * 5.9597 + 1.00 * 0.1226                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2687 = 7.62 * 0.50 * 5.8209 + 1.00 * 0.0880                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2086      final r-factor (work) = 0.1871          |
| start r-factor (free) = 0.2660      final r-factor (free) = 0.2394          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6863 = 0.29 * 1.00 * 5.8209 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6262 = 0.29 * 1.00 * 5.6317 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.85   14.07    None  None   None       |
|    all(noH): 2823   0      0.00    86.85   14.07    None  None   None       |
|    Sol.    : 438    0      2.50    79.55   35.34    None  None   None       |
|    Mac.    : 2385   0      0.00    86.85   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:     0.000 -   8.685: 1375   |   5:    43.423 -  52.108:   98        |
|      1:     8.685 -  17.369:  758   |   6:    52.108 -  60.793:   45        |
|      2:    17.369 -  26.054:  251   |   7:    60.793 -  69.477:   13        |
|      3:    26.054 -  34.739:  158   |   8:    69.477 -  78.162:    6        |
|      4:    34.739 -  43.423:  116   |   9:    78.162 -  86.847:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1871 r_free = 0.2394             target_work(ml) = 5.576         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1867 r_free = 0.2388             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1867   r_free= 0.2388   ksol= 0.34   Bsol= 34.19   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.25,3.19,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.575024                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1860   r_free= 0.2362   ksol= 0.32   Bsol= 32.14   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,1.25,1.97,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.569792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.591882              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.805   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.154026              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.844  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1860      final r-factor (work) = 0.1457          |
| start r-factor (free) = 0.2362      final r-factor (free) = 0.1909          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2066 = 3.59 * 0.50 * 5.6343 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8899 = 3.59 * 0.50 * 5.4685 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1457      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.1909      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8513 = 0.15 * 1.00 * 5.4685 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8288 = 0.15 * 1.00 * 5.3297 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.95   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    80.95   13.80    None  None   None       |
|    Sol.    : 438    0      3.43    80.95   35.85    None  None   None       |
|    Mac.    : 2385   0      0.00    80.47   9.75     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 -   8.095: 1311   |   5:    40.475 -  48.570:   88        |
|      1:     8.095 -  16.190:  843   |   6:    48.570 -  56.665:   73        |
|      2:    16.190 -  24.285:  222   |   7:    56.665 -  64.760:   23        |
|      3:    24.285 -  32.380:  134   |   8:    64.760 -  72.855:    6        |
|      4:    32.380 -  40.475:  114   |   9:    72.855 -  80.950:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1385 r_free = 0.1819             target_work(ml) = 5.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1382 r_free = 0.1815             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1382   r_free= 0.1815   ksol= 0.32   Bsol= 32.14   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,1.25,1.97,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.297424                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1803   ksol= 0.33   Bsol= 32.14   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,0.83,1.44,0.00,0.00,0.00); trace/3= 0.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.295691                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.936312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.856  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2295 = 1.94 * 0.50 * 5.3308 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1449 = 1.94 * 0.50 * 5.2515 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3720 = 0.26 * 1.00 * 5.2515 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3911 = 0.26 * 1.00 * 5.2079 + 1.00 * 0.0385                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.61   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    90.61   13.80    None  None   None       |
|    Sol.    : 438    0      3.72    81.27   36.08    None  None   None       |
|    Mac.    : 2385   0      0.00    90.61   9.71     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 -   9.062: 1508   |   5:    45.308 -  54.369:   95        |
|      1:     9.062 -  18.123:  744   |   6:    54.369 -  63.430:   35        |
|      2:    18.123 -  27.185:  167   |   7:    63.430 -  72.492:    9        |
|      3:    27.185 -  36.246:  146   |   8:    72.492 -  81.553:   10        |
|      4:    36.246 -  45.308:  108   |   9:    81.553 -  90.615:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1661             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1659             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1659   ksol= 0.33   Bsol= 32.14   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,0.83,1.44,0.00,0.00,0.00); trace/3= 0.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204093                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.1125 0.1388      5.4796       5.607|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.0986 0.1268      5.5485      5.7744|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.1195 0.1507       5.568      5.8251|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.1357 0.1730       5.531      5.6842|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.1371 0.1665       5.365      5.4949|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.1339 0.1866      5.2674      5.4845|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.1263 0.1678      5.1771      5.3732|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.1258 0.1757      5.1263      5.3747|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.1262 0.1821      5.0571      5.2886|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.1232 0.1741      5.0272      5.2191|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.1217 0.1881      4.9768      5.3783|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.1222 0.1741      4.9521      5.1888|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.1243 0.1930      4.8688      5.1408|
| 14:  1.9991 -  1.9505 0.78    993  118 0.1108 0.1921      4.7455      5.0128|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.93  10.17   0.99     0.97       8370.17|
|  2:  4.6535 -  3.7135  1322   146  0.95   8.89   1.04     1.02      10425.85|
|  3:  3.7135 -  3.2500  1299   146  0.92  12.61   1.05     1.04      11911.33|
|  4:  3.2500 -  2.9555  1287   139  0.92  14.08   1.02     1.02      11052.34|
|  5:  2.9555 -  2.7452  1274   142  0.90  15.90   1.00     0.95       8468.54|
|  6:  2.7452 -  2.5843  1279   146  0.90  16.21   0.99     0.96       7410.98|
|  7:  2.5843 -  2.4555  1268   139  0.90  16.02   1.00     0.97       6403.25|
|  8:  2.4555 -  2.3491  1267   143  0.90  15.76   1.01     0.98       5729.61|
|  9:  2.3491 -  2.2590  1264   139  0.91  15.71   1.02     1.00       5046.40|
| 10:  2.2590 -  2.1813  1244   135  0.90  16.05   1.03     0.99       4829.86|
| 11:  2.1813 -  2.1133  1266   147  0.90  16.47   1.01     0.98       4596.88|
| 12:  2.1133 -  2.0530  1253   128  0.90  16.67   1.03     1.01       4569.84|
| 13:  2.0530 -  1.9991  1240   138  0.89  17.07   1.02     1.01       3860.04|
| 14:  1.9991 -  1.9505   993   118  0.90  16.19   1.02     0.99       3045.58|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3045.58 max =        11911.33 mean =      6941.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.77|
|phase err.(test): min =        0.00 max =           88.53 mean =        14.29|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1659   ksol= 0.33   Bsol= 32.94   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.03,0.59,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1659   ksol= 0.33   Bsol= 32.94   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.03,0.59,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204055                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.1125 0.1388      5.4794      5.6068|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.0986 0.1268      5.5484      5.7745|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.1195 0.1507       5.568       5.825|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.1357 0.1731       5.531      5.6844|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.1371 0.1665      5.3651       5.495|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.1339 0.1867      5.2675      5.4849|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.1264 0.1678      5.1772      5.3731|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.1258 0.1757      5.1262      5.3746|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.1262 0.1821      5.0571      5.2884|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.1231 0.1741      5.0271      5.2189|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.1217 0.1881      4.9767       5.378|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.1222 0.1741       4.952      5.1884|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.1243 0.1929      4.8688      5.1405|
| 14:  1.9991 -  1.9505 0.78    993  118 0.1108 0.1922      4.7457      5.0131|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.93  10.17   0.99     0.97       8366.18|
|  2:  4.6535 -  3.7135  1322   146  0.95   8.89   1.04     1.02      10423.90|
|  3:  3.7135 -  3.2500  1299   146  0.92  12.61   1.05     1.04      11911.29|
|  4:  3.2500 -  2.9555  1287   139  0.92  14.08   1.02     1.02      11054.26|
|  5:  2.9555 -  2.7452  1274   142  0.90  15.90   1.00     0.95       8473.03|
|  6:  2.7452 -  2.5843  1279   146  0.90  16.21   0.99     0.95       7412.59|
|  7:  2.5843 -  2.4555  1268   139  0.90  16.03   0.99     0.97       6404.52|
|  8:  2.4555 -  2.3491  1267   143  0.90  15.76   1.01     0.98       5726.88|
|  9:  2.3491 -  2.2590  1264   139  0.91  15.71   1.02     1.00       5044.79|
| 10:  2.2590 -  2.1813  1244   135  0.90  16.04   1.02     0.99       4826.87|
| 11:  2.1813 -  2.1133  1266   147  0.90  16.46   1.01     0.98       4595.03|
| 12:  2.1133 -  2.0530  1253   128  0.90  16.67   1.03     1.01       4567.79|
| 13:  2.0530 -  1.9991  1240   138  0.89  17.07   1.02     1.01       3860.06|
| 14:  1.9991 -  1.9505   993   118  0.90  16.20   1.02     0.98       3047.31|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3047.31 max =        11911.29 mean =      6940.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.76|
|phase err.(test): min =        0.00 max =           88.53 mean =        14.29|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    91.41   14.59    None  None   None       |
|    all(noH): 2823   0      0.79    91.41   14.59    None  None   None       |
|    Sol.    : 438    0      4.51    82.07   36.87    None  None   None       |
|    Mac.    : 2385   0      0.79    91.41   10.50    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:     0.791 -   9.853: 1508   |   5:    46.099 -  55.160:   95        |
|      1:     9.853 -  18.914:  744   |   6:    55.160 -  64.222:   35        |
|      2:    18.914 -  27.976:  167   |   7:    64.222 -  73.283:    9        |
|      3:    27.976 -  37.037:  146   |   8:    73.283 -  82.345:   10        |
|      4:    37.037 -  46.099:  108   |   9:    82.345 -  91.406:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.574 - 5.797
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 329
   mapped sites are within: 0.755 - 5.797

peak=   10.925 closest distance to " CB  VAL A 230 " =    1.418
peak=   10.858 closest distance to " CB  VAL A 296 " =    1.555
peak=    9.756 closest distance to " O   HOH Z 403 " =    2.472
peak=    7.007 closest distance to " O   HOH Z 199 " =    1.987
peak=    6.204 closest distance to " O   HOH Z 278 " =    2.115
peak=    6.137 closest distance to " O   HOH Z 138 " =    0.756
peak=    6.130 closest distance to " O   HOH Z 193 " =    1.938
peak=    6.059 closest distance to " O   HOH Z 236 " =    1.908
peak=    5.854 closest distance to " O   HOH Z 142 " =    1.958
peak=    5.762 closest distance to " CD2 LEU A   5 " =    1.257
peak=    5.670 closest distance to " NE2 GLN A  11 " =    1.194
peak=    5.434 closest distance to " O   HOH Z 263 " =    1.638
peak=    5.417 closest distance to " O   HOH Z 124 " =    1.561
peak=    5.329 closest distance to " O   HOH Z  69 " =    1.738
peak=    5.278 closest distance to " CG  LEU A   5 " =    1.278
peak=    5.182 closest distance to " O   HOH Z 188 " =    1.394
peak=    5.079 closest distance to " O   HOH Z  78 " =    1.581
peak=    4.984 closest distance to " O   HOH Z  97 " =    1.670
peak=    4.971 closest distance to " O   HOH Z 132 " =    1.512
peak=    4.878 closest distance to " O   HOH Z 126 " =    2.164
peak=    4.870 closest distance to " NE2 GLN A  55 " =    1.584
peak=    4.770 closest distance to " CG  PRO A 213 " =    1.322
peak=    4.769 closest distance to " CG  GLN A  11 " =    2.100
peak=    4.764 closest distance to " CB  ARG A 275 " =    1.036
peak=    4.747 closest distance to " O   HOH Z 357 " =    1.832
peak=    4.681 closest distance to " O   HOH Z 249 " =    1.313
peak=    4.653 closest distance to " CG AARG A 275 " =    1.258
peak=    4.616 closest distance to " O   HOH Z   9 " =    1.224
peak=    4.508 closest distance to " O   SER A  87 " =    2.375
peak=    4.482 closest distance to " NH2 ARG A  56 " =    1.931
peak=    4.462 closest distance to " CD2 LEU A 228 " =    1.269
peak=    4.447 closest distance to " CB  GLN A 223 " =    1.606
peak=    4.433 closest distance to " O   HOH Z 217 " =    1.546
peak=    4.432 closest distance to " NZ  LYS A 117 " =    3.363
peak=    4.394 closest distance to " O   HOH Z  85 " =    1.286
peak=    4.379 closest distance to " CD1AILE A 234 " =    0.918
peak=    4.378 closest distance to " O   HOH Z 192 " =    1.915
peak=    4.377 closest distance to " O   HOH Z   5 " =    1.500
peak=    4.349 closest distance to " O   HOH Z 213 " =    1.820
peak=    4.347 closest distance to " O   HOH Z 322 " =    1.992
peak=    4.322 closest distance to " CB  ARG A 102 " =    0.785
peak=    4.319 closest distance to " O   HOH Z 414 " =    1.371
peak=    4.309 closest distance to " CA  GLY A 241 " =    3.675
peak=    4.308 closest distance to " O   HOH Z 427 " =    2.624
peak=    4.292 closest distance to " O   HOH Z 232 " =    2.113
peak=    4.274 closest distance to " O   HOH Z  28 " =    1.295
peak=    4.270 closest distance to " O   HOH Z 227 " =    1.947
peak=    4.255 closest distance to " O   HOH Z 423 " =    1.334
peak=    4.228 closest distance to " CB  ASN A 148 " =    1.882
peak=    4.208 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.191 closest distance to " O   HOH Z 234 " =    3.296
peak=    4.179 closest distance to " O   HOH Z 406 " =    1.344
peak=    4.175 closest distance to " O   HOH Z 276 " =    1.464
peak=    4.173 closest distance to " O   HOH Z 316 " =    2.456
peak=    4.172 closest distance to " CB  VAL A 230 " =    1.145
peak=    4.170 closest distance to " O   HOH Z 214 " =    1.448
peak=    4.170 closest distance to " O   HOH Z 134 " =    1.610
peak=    4.165 closest distance to " O   HOH Z 260 " =    1.678
peak=    4.153 closest distance to " O   HOH Z 108 " =    1.169
peak=    4.139 closest distance to " O   HOH Z 303 " =    2.196
peak=    4.138 closest distance to " NH1 ARG A  14 " =    0.957
peak=    4.131 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.098 closest distance to " O   HOH Z 289 " =    1.577
peak=    4.096 closest distance to " O   HOH Z  97 " =    2.002
peak=    4.089 closest distance to " CB  SER A  26 " =    1.579
peak=    4.053 closest distance to " O   HOH Z 344 " =    1.408
peak=    4.045 closest distance to " CB  SER A   3 " =    1.257
peak=    4.044 closest distance to " O   HOH Z 291 " =    1.481
peak=    4.038 closest distance to " O   HOH Z  43 " =    1.314
peak=    4.036 closest distance to " O   HOH Z 148 " =    1.819
peak=    4.035 closest distance to " CG2 VAL A 257 " =    0.954
peak=    4.032 closest distance to " O   HOH Z  59 " =    1.717
peak=    3.994 closest distance to " O   HOH Z 365 " =    1.687
peak=    3.987 closest distance to " CG  LEU A 228 " =    1.185
peak=    3.976 closest distance to " CG1BVAL A  72 " =    1.271
peak=    3.976 closest distance to " CB  SER A  63 " =    1.275
peak=    3.972 closest distance to " O   HOH Z 196 " =    1.502
peak=    3.963 closest distance to " CB  TRP A 179 " =    1.152
peak=    3.962 closest distance to " O   HOH Z 272 " =    1.796
peak=    3.946 closest distance to " O   HOH Z 380 " =    1.816
peak=    3.942 closest distance to " O   HOH Z 191 " =    1.788
peak=    3.934 closest distance to " O   HOH Z 203 " =    1.543
peak=    3.872 closest distance to " O   HOH Z 279 " =    0.884
peak=    3.872 closest distance to " OD2 ASP A 286 " =    2.409
peak=    3.857 closest distance to " CB  VAL A 265 " =    1.294
peak=    3.847 closest distance to " CD  GLN A 194 " =    1.497
peak=    3.844 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.841 closest distance to " O   HOH Z 284 " =    1.361
peak=    3.833 closest distance to " SD BMET A  47 " =    1.528
peak=    3.830 closest distance to " CE BMET A  47 " =    1.363
peak=    3.827 closest distance to " O   HOH Z 137 " =    1.492
peak=    3.826 closest distance to " CB  GLU A 152 " =    1.218
peak=    3.812 closest distance to " CA  VAL A  41 " =    0.883
peak=    3.810 closest distance to " O   HOH Z  96 " =    1.674
peak=    3.810 closest distance to " O   HOH Z 156 " =    2.658
peak=    3.807 closest distance to " CA  ASN A 284 " =    0.970
peak=    3.804 closest distance to " O   HOH Z 117 " =    1.758
peak=    3.804 closest distance to " O   HOH Z  20 " =    1.895
peak=    3.802 closest distance to " O   HOH Z 425 " =    2.223
peak=    3.795 closest distance to " O   HOH Z 345 " =    2.974
peak=    3.792 closest distance to " C   PRO A 198 " =    1.522
peak=    3.781 closest distance to " CB  GLN A 183 " =    1.240
peak=    3.779 closest distance to " O   HOH Z 368 " =    2.049
peak=    3.779 closest distance to " O   HOH Z  13 " =    1.808
peak=    3.775 closest distance to " O   HOH Z  95 " =    1.717
peak=    3.772 closest distance to " O   HOH Z 251 " =    1.679
peak=    3.764 closest distance to " O   HOH Z 280 " =    1.547
peak=    3.752 closest distance to " CG  GLN A  77 " =    2.213
peak=    3.750 closest distance to " O   HOH Z  44 " =    1.929
peak=    3.746 closest distance to " O   HOH Z 143 " =    1.312
peak=    3.739 closest distance to " O   HOH Z 326 " =    1.372
peak=    3.734 closest distance to " O   LYS A 290 " =    2.346
peak=    3.734 closest distance to " O   HOH Z 118 " =    2.049
peak=    3.727 closest distance to " O   HOH Z   7 " =    1.452
peak=    3.725 closest distance to " O   HOH Z  54 " =    1.566
peak=    3.712 closest distance to " CB  TYR A  30 " =    1.690
peak=    3.712 closest distance to " O   HOH Z 113 " =    1.960
peak=    3.712 closest distance to " O   HOH Z 112 " =    1.032
peak=    3.709 closest distance to " O   HOH Z 250 " =    1.509
peak=    3.706 closest distance to " O   HOH Z 126 " =    2.323
peak=    3.706 closest distance to " NH2BARG A 190 " =    1.463
peak=    3.699 closest distance to " O   HOH Z 142 " =    1.781
peak=    3.686 closest distance to " CA  ALA A  21 " =    1.076
peak=    3.679 closest distance to " OD1 ASN A  60 " =    1.856
peak=    3.678 closest distance to " OE1 GLU A   2 " =    2.160
peak=    3.677 closest distance to " O   HOH Z 247 " =    1.304
peak=    3.675 closest distance to " CA  GLN A 194 " =    1.118
peak=    3.672 closest distance to " NH2BARG A 145 " =    1.524
peak=    3.670 closest distance to " O   HOH Z 214 " =    2.185
peak=    3.667 closest distance to " O   HOH Z 108 " =    1.818
peak=    3.661 closest distance to " O   HOH Z  10 " =    1.762
peak=    3.660 closest distance to " O   HOH Z 176 " =    1.634
peak=    3.652 closest distance to " O   HOH Z 392 " =    2.912
peak=    3.649 closest distance to " CB  ALA A   9 " =    1.521
peak=    3.639 closest distance to " O   HOH Z 113 " =    1.835
peak=    3.638 closest distance to " O   HOH Z 286 " =    2.201
peak=    3.638 closest distance to " O   HOH Z 130 " =    2.542
peak=    3.634 closest distance to " O   HOH Z 423 " =    2.077
peak=    3.633 closest distance to " O   HOH Z 298 " =    1.824
peak=    3.624 closest distance to " O   SER A 164 " =    1.137
peak=    3.624 closest distance to " O   HOH Z  80 " =    1.846
peak=    3.623 closest distance to " O   HOH Z  66 " =    2.030
peak=    3.620 closest distance to " O   HOH Z 147 " =    1.263
peak=    3.608 closest distance to " CB  VAL A 202 " =    1.618
peak=    3.599 closest distance to " CA  TYR A  30 " =    1.071
peak=    3.597 closest distance to " NH2BARG A 145 " =    2.370
peak=    3.594 closest distance to " CG  GLN A  77 " =    2.126
peak=    3.574 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.573 closest distance to " O   HOH Z   9 " =    2.152
peak=    3.570 closest distance to " O   HOH Z 327 " =    1.756
peak=    3.565 closest distance to " CD1 ILE A 106 " =    1.229
peak=    3.564 closest distance to " O   HOH Z 144 " =    2.030
peak=    3.544 closest distance to " O   HOH Z  68 " =    2.794
peak=    3.540 closest distance to " N   PHE A 130 " =    1.394
peak=    3.537 closest distance to " O   HOH Z  56 " =    1.794
peak=    3.537 closest distance to " CB  ARG A 275 " =    1.066
peak=    3.534 closest distance to " O   HOH Z 245 " =    1.432
peak=    3.529 closest distance to " O   HOH Z 215 " =    1.487
peak=    3.527 closest distance to " O   HOH Z 344 " =    2.763
peak=    3.525 closest distance to " O   HOH Z 234 " =    2.159
peak=    3.523 closest distance to " O   HOH Z 395 " =    1.452
peak=    3.523 closest distance to " O   HOH Z 374 " =    2.385
peak=    3.520 closest distance to " O   HOH Z 150 " =    2.784
peak=    3.519 closest distance to " OD1 ASP A 253 " =    1.946
peak=    3.512 closest distance to " O   HOH Z 407 " =    2.282
peak=    3.509 closest distance to " O   HOH Z 189 " =    2.015
peak=    3.508 closest distance to " O   HOH Z  78 " =    2.251
peak=    3.505 closest distance to " O   HOH Z 148 " =    3.267
peak=    3.501 closest distance to " O   HOH Z 170 " =    1.957
peak=    3.497 closest distance to " O   HOH Z 375 " =    1.126
peak=    3.493 closest distance to " O   HOH Z 100 " =    1.064
peak=    3.492 closest distance to " O   HOH Z  59 " =    2.162
peak=    3.489 closest distance to " O   HOH Z 209 " =    2.316
peak=    3.488 closest distance to " O   HOH Z 392 " =    1.498
peak=    3.488 closest distance to " O   HOH Z  88 " =    2.287
peak=    3.484 closest distance to " OG ASER A 134 " =    1.883
peak=    3.484 closest distance to " O   HOH Z 145 " =    2.121
peak=    3.479 closest distance to " O   HOH Z 233 " =    1.592
peak=    3.476 closest distance to " O   HOH Z 343 " =    1.604
peak=    3.471 closest distance to " OD1 ASN A  69 " =    2.819
peak=    3.466 closest distance to " O   HOH Z  89 " =    1.796
peak=    3.464 closest distance to " CD AARG A 145 " =    0.924
peak=    3.460 closest distance to " CG  ARG A  66 " =    1.046
peak=    3.459 closest distance to " O   HOH Z 172 " =    5.797
peak=    3.458 closest distance to " O   HOH Z 284 " =    2.654
peak=    3.458 closest distance to " O   HOH Z 366 " =    2.723
peak=    3.455 closest distance to " O   HOH Z  47 " =    1.731
peak=    3.454 closest distance to " CA  ALA A  51 " =    1.052
peak=    3.451 closest distance to " O   HOH Z 193 " =    2.137
peak=    3.451 closest distance to " O   HOH Z 302 " =    1.721
peak=    3.444 closest distance to " O   HOH Z 412 " =    2.084
peak=    3.440 closest distance to " O   HOH Z 244 " =    1.619
peak=    3.436 closest distance to " CG2 THR A 221 " =    1.245
peak=    3.433 closest distance to " CE  LYS A 119 " =    1.041
peak=    3.431 closest distance to " C   ALA A 299 " =    0.917
peak=    3.427 closest distance to " CD  ARG A 269 " =    1.088
peak=    3.427 closest distance to " N   TRP A 177 " =    1.499
peak=    3.425 closest distance to " O   HOH Z 281 " =    1.781
peak=    3.423 closest distance to " O   HOH Z 207 " =    1.803
peak=    3.417 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.415 closest distance to " CA  ASN A 215 " =    1.053
peak=    3.415 closest distance to " O   GLY A  91 " =    1.780
peak=    3.413 closest distance to " O   HOH Z 238 " =    0.966
peak=    3.412 closest distance to " O   HOH Z 356 " =    1.466
peak=    3.409 closest distance to " CB  ALA A   1 " =    1.114
peak=    3.406 closest distance to " O   HOH Z  45 " =    0.845
peak=    3.404 closest distance to " CB  GLU A 128 " =    1.147
peak=    3.402 closest distance to " O   HOH Z 202 " =    1.175
peak=    3.400 closest distance to " NE2 GLN A  58 " =    5.600
peak=    3.398 closest distance to " O   HOH Z  88 " =    3.020
peak=    3.392 closest distance to " ND1 HIS A  81 " =    1.332
peak=    3.391 closest distance to " CD2 TYR A  30 " =    0.755
peak=    3.391 closest distance to " CD2 TRP A 179 " =    1.339
peak=    3.388 closest distance to " CB  GLN A  88 " =    1.283
peak=    3.382 closest distance to " O   HOH Z 435 " =    1.954
peak=    3.381 closest distance to " O   HOH Z 269 " =    2.956
peak=    3.378 closest distance to " CG2 ILE A  20 " =    1.746
peak=    3.376 closest distance to " CG  ASN A  60 " =    1.238
peak=    3.372 closest distance to " CB  SER A  62 " =    1.114
peak=    3.370 closest distance to " O   HOH Z 156 " =    2.288
peak=    3.368 closest distance to " ND2 ASN A 187 " =    1.629
peak=    3.364 closest distance to " N   ASN A  39 " =    1.144
peak=    3.362 closest distance to " O   HOH Z 438 " =    2.557
peak=    3.358 closest distance to " CB  THR A  31 " =    1.619
peak=    3.356 closest distance to " CA  ARG A 275 " =    1.961
peak=    3.356 closest distance to " CE1 PHE A  61 " =    1.248
peak=    3.355 closest distance to " CD1 LEU A 228 " =    1.587
peak=    3.351 closest distance to " CB  SER A 216 " =    0.805
peak=    3.349 closest distance to " O   HOH Z 269 " =    1.110
peak=    3.342 closest distance to " CZ AARG A 102 " =    1.465
peak=    3.342 closest distance to " CB  ALA A 248 " =    1.315
peak=    3.341 closest distance to " O   HOH Z  19 " =    1.891
peak=    3.336 closest distance to " O   HOH Z 285 " =    1.722
peak=    3.332 closest distance to " O   HOH Z 383 " =    1.660
peak=    3.331 closest distance to " O   HOH Z 109 " =    2.010
peak=    3.330 closest distance to " OG BSER A 164 " =    2.365
peak=    3.329 closest distance to " N   GLU A 236 " =    0.957
peak=    3.324 closest distance to " O   HOH Z  61 " =    1.624
peak=    3.318 closest distance to " O   HOH Z 366 " =    1.791
peak=    3.314 closest distance to " O   HOH Z  11 " =    1.439
peak=    3.314 closest distance to " CA  THR A 221 " =    0.870
peak=    3.301 closest distance to " CD  LYS A 119 " =    2.129
peak=    3.299 closest distance to " CG1 VAL A 153 " =    1.003
peak=    3.298 closest distance to " CB  THR A  52 " =    1.230
peak=    3.297 closest distance to " CD AARG A 190 " =    1.874
peak=    3.296 closest distance to " O   HOH Z 361 " =    1.527
peak=    3.295 closest distance to " O   HOH Z 389 " =    1.391
peak=    3.294 closest distance to " CG  PRO A  54 " =    1.684
peak=    3.294 closest distance to " CB  GLN A 205 " =    1.292
peak=    3.294 closest distance to " O  BHOH Z 338 " =    2.398
peak=    3.291 closest distance to " O   HOH Z 422 " =    2.406
peak=    3.288 closest distance to " CD1 LEU A   5 " =    1.781
peak=    3.287 closest distance to " O   HOH Z 380 " =    2.711
peak=    3.286 closest distance to " CB  PRO A 198 " =    1.294
peak=    3.285 closest distance to " N   TYR A  15 " =    1.052
peak=    3.278 closest distance to " CB  LEU A 255 " =    0.827
peak=    3.278 closest distance to " CA  LEU A 282 " =    1.206
peak=    3.275 closest distance to " O   HOH Z 145 " =    1.636
peak=    3.273 closest distance to " CG  PRO A 280 " =    0.961
peak=    3.273 closest distance to " OG BSER A 258 " =    2.300
peak=    3.261 closest distance to " NH1AARG A 145 " =    0.820
peak=    3.259 closest distance to " CZ2 TRP A 274 " =    1.657
peak=    3.250 closest distance to " O   HOH Z 423 " =    1.432
peak=    3.245 closest distance to " O   PHE A 155 " =    1.444
peak=    3.243 closest distance to " CB  PRO A  90 " =    1.295
peak=    3.238 closest distance to " CE1 HIS A 108 " =    1.179
peak=    3.237 closest distance to " CG2 ILE A 120 " =    1.299
peak=    3.235 closest distance to " O  BHOH Z  74 " =    1.388
peak=    3.233 closest distance to " C   GLU A 277 " =    1.411
peak=    3.233 closest distance to " CD1 ILE A  33 " =    1.632
peak=    3.224 closest distance to " O   HOH Z 151 " =    1.784
peak=    3.220 closest distance to " O   HOH Z 313 " =    1.681
peak=    3.217 closest distance to " CA  SER A 210 " =    1.549
peak=    3.215 closest distance to " O   HOH Z 345 " =    1.631
peak=    3.210 closest distance to " O   HOH Z 116 " =    2.317
peak=    3.208 closest distance to " O   HOH Z   1 " =    1.568
peak=    3.205 closest distance to " NZ  LYS A 119 " =    2.382
peak=    3.205 closest distance to " O   HOH Z  63 " =    2.418
peak=    3.204 closest distance to " CE ALYS A 290 " =    1.176
peak=    3.201 closest distance to " O   HOH Z  89 " =    2.202
peak=    3.197 closest distance to " CB  ASN A 110 " =    1.149
peak=    3.196 closest distance to " O   HOH Z 257 " =    1.994
peak=    3.194 closest distance to " O   HOH Z 303 " =    1.703
peak=    3.192 closest distance to " CB  ASN A 142 " =    1.128
peak=    3.192 closest distance to " CB  PRO A 198 " =    0.951
peak=    3.191 closest distance to " CG  LEU A 281 " =    0.924
peak=    3.187 closest distance to " CG  LYS A  76 " =    1.397
peak=    3.180 closest distance to " NH1AARG A 275 " =    1.107
peak=    3.180 closest distance to " CB  TRP A 266 " =    1.129
peak=    3.178 closest distance to " NE2 GLN A  58 " =    1.874
peak=    3.178 closest distance to " O   HOH Z 130 " =    0.798
peak=    3.176 closest distance to " CB  ARG A  79 " =    1.347
peak=    3.175 closest distance to " CB  ASP A 200 " =    1.070
peak=    3.171 closest distance to " CB  ARG A 138 " =    0.826
peak=    3.168 closest distance to " O   HOH Z 222 " =    1.991
peak=    3.167 closest distance to " O   HOH Z 271 " =    1.744
peak=    3.158 closest distance to " NH1 ARG A 138 " =    1.515
peak=    3.157 closest distance to " CG AARG A 190 " =    1.344
peak=    3.152 closest distance to " O   HOH Z 183 " =    1.828
peak=    3.151 closest distance to " CB  MET A 188 " =    1.712
peak=    3.151 closest distance to " O   HOH Z 402 " =    1.458
peak=    3.139 closest distance to " O   HOH Z 396 " =    1.393
peak=    3.139 closest distance to " CD2 HIS A  81 " =    1.339
peak=    3.138 closest distance to " OH  TYR A 116 " =    1.096
peak=    3.131 closest distance to " O   HOH Z 274 " =    3.062
peak=    3.129 closest distance to " N   GLN A 278 " =    0.990
peak=    3.128 closest distance to " O   HOH Z 269 " =    1.897
peak=    3.122 closest distance to " O   HOH Z 409 " =    1.832
peak=    3.121 closest distance to " CB  TYR A 169 " =    0.840
peak=    3.113 closest distance to " CA  PRO A 163 " =    0.981
peak=    3.113 closest distance to " O   HOH Z 421 " =    1.622
peak=    3.113 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.106 closest distance to " OG  SER A  62 " =    2.840
peak=    3.105 closest distance to " CG2 THR A 220 " =    0.944
peak=    3.103 closest distance to " N   ASP A 162 " =    1.181
peak=    3.100 closest distance to " CB  GLN A  73 " =    1.544
peak=    3.097 closest distance to " NE1 TRP A 274 " =    0.986
peak=    3.084 closest distance to " O   HOH Z 287 " =    1.459
peak=    3.077 closest distance to " CB  ILE A  20 " =    1.497
peak=    3.068 closest distance to " O   HOH Z 389 " =    1.478
peak=    3.062 closest distance to " N   SER A 135 " =    1.156
peak=    3.059 closest distance to " O   HOH Z 257 " =    1.114
peak=    3.059 closest distance to " CB  ALA A   1 " =    4.346
peak=    3.052 closest distance to " CG  LYS A  76 " =    0.953
peak=    3.048 closest distance to " O   HOH Z 250 " =    1.963
peak=    3.013 closest distance to " O   HOH Z 284 " =    1.042

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.427 - 5.536
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 179 from: 188
   mapped sites are within: 0.729 - 5.536

peak=   -4.623 closest distance to " O   HOH Z 290 " =    0.901
peak=   -4.606 closest distance to " SG  CYS A 254 " =    3.182
peak=   -4.348 closest distance to " C   HIS A 108 " =    1.184
peak=   -4.320 closest distance to " O   HOH Z  69 " =    1.030
peak=   -4.209 closest distance to " O   HOH Z 164 " =    5.536
peak=   -4.103 closest distance to " N   HIS A 115 " =    2.057
peak=   -4.085 closest distance to " O   ALA A 161 " =    1.410
peak=   -4.041 closest distance to " NH2 ARG A  79 " =    1.933
peak=   -4.016 closest distance to " CE2 TYR A  30 " =    2.935
peak=   -4.002 closest distance to " O   HOH Z  11 " =    1.702
peak=   -3.943 closest distance to " N   GLN A  58 " =    1.974
peak=   -3.938 closest distance to " O   SER A  22 " =    2.399
peak=   -3.919 closest distance to " ND2 ASN A  45 " =    1.098
peak=   -3.913 closest distance to " O   HOH Z  37 " =    1.650
peak=   -3.903 closest distance to " O   HOH Z 423 " =    2.240
peak=   -3.888 closest distance to " O   ALA A   8 " =    1.644
peak=   -3.877 closest distance to " C   ASN A 285 " =    1.900
peak=   -3.871 closest distance to " CA  GLY A  23 " =    1.715
peak=   -3.860 closest distance to " O   HOH Z 175 " =    4.288
peak=   -3.801 closest distance to " O   ALA A  51 " =    1.217
peak=   -3.780 closest distance to " O   ILE A  49 " =    1.721
peak=   -3.777 closest distance to " O   PRO A 163 " =    1.832
peak=   -3.761 closest distance to " CG  PHE A 283 " =    2.566
peak=   -3.744 closest distance to " CD  ARG A 156 " =    2.066
peak=   -3.740 closest distance to " O   HOH Z 220 " =    1.159
peak=   -3.729 closest distance to " CB  ALA A 244 " =    1.972
peak=   -3.720 closest distance to " OD1 ASN A 249 " =    1.165
peak=   -3.706 closest distance to " O   HOH Z 126 " =    1.735
peak=   -3.699 closest distance to " CD  GLN A  88 " =    1.024
peak=   -3.684 closest distance to " O   VAL A  67 " =    2.718
peak=   -3.683 closest distance to " O   HOH Z  60 " =    2.248
peak=   -3.677 closest distance to " OG  SER A   3 " =    1.172
peak=   -3.673 closest distance to " O   HOH Z  56 " =    1.916
peak=   -3.669 closest distance to " O   HOH Z 351 " =    1.402
peak=   -3.656 closest distance to " OD1 ASP A 191 " =    1.564
peak=   -3.650 closest distance to " CD1 LEU A 255 " =    2.765
peak=   -3.650 closest distance to " OXT GLY A 302 " =    2.670
peak=   -3.633 closest distance to " O   HOH Z 344 " =    2.410
peak=   -3.632 closest distance to " ND2 ASN A 187 " =    1.476
peak=   -3.632 closest distance to " O   HOH Z  93 " =    1.311
peak=   -3.627 closest distance to " CB  ALA A 161 " =    2.341
peak=   -3.609 closest distance to " O   HOH Z  88 " =    2.253
peak=   -3.603 closest distance to " O   HOH Z 419 " =    0.963
peak=   -3.602 closest distance to " OG1 THR A 246 " =    1.189
peak=   -3.602 closest distance to " CB  ALA A  64 " =    2.745
peak=   -3.601 closest distance to " O   PRO A 198 " =    1.173
peak=   -3.600 closest distance to " O   HOH Z  98 " =    1.604
peak=   -3.597 closest distance to " CD1 PHE A  59 " =    2.271
peak=   -3.587 closest distance to " CB  ALA A 100 " =    2.535
peak=   -3.580 closest distance to " CB  ALA A 248 " =    1.915
peak=   -3.574 closest distance to " O   HOH Z 427 " =    1.633
peak=   -3.562 closest distance to " CD1 LEU A 101 " =    2.252
peak=   -3.561 closest distance to " N   GLN A 122 " =    1.400
peak=   -3.555 closest distance to " O   HOH Z 313 " =    1.468
peak=   -3.543 closest distance to " CB  ALA A  43 " =    2.112
peak=   -3.528 closest distance to " O   HOH Z 407 " =    2.514
peak=   -3.528 closest distance to " O   HOH Z 404 " =    1.527
peak=   -3.516 closest distance to " O   THR A 182 " =    1.162
peak=   -3.512 closest distance to " O   HOH Z 429 " =    1.920
peak=   -3.509 closest distance to " O   HOH Z 426 " =    2.184
peak=   -3.498 closest distance to " CG  ASP A  50 " =    2.138
peak=   -3.495 closest distance to " C   ASN A  69 " =    1.374
peak=   -3.495 closest distance to " O   HOH Z 388 " =    2.064
peak=   -3.494 closest distance to " CD  LYS A 289 " =    2.599
peak=   -3.494 closest distance to " CZ  PHE A 130 " =    0.893
peak=   -3.492 closest distance to " N   GLN A  77 " =    1.462
peak=   -3.483 closest distance to " C   ASP A 231 " =    2.351
peak=   -3.479 closest distance to " CE2 PHE A 218 " =    2.602
peak=   -3.477 closest distance to " CD  GLU A 152 " =    2.242
peak=   -3.476 closest distance to " N   ALA A 248 " =    1.706
peak=   -3.471 closest distance to " OG BSER A 134 " =    1.262
peak=   -3.466 closest distance to " O   HOH Z 410 " =    2.391
peak=   -3.459 closest distance to " O   HOH Z 137 " =    1.534
peak=   -3.447 closest distance to " NE1 TRP A 274 " =    1.195
peak=   -3.443 closest distance to " CD  GLU A 277 " =    0.881
peak=   -3.441 closest distance to " CD2 LEU A 237 " =    2.812
peak=   -3.441 closest distance to " O   HOH Z 266 " =    4.278
peak=   -3.439 closest distance to " O   SER A 146 " =    0.903
peak=   -3.435 closest distance to " OD1 ASN A  39 " =    2.031
peak=   -3.432 closest distance to " CG  PRO A 198 " =    1.835
peak=   -3.424 closest distance to " O   HOH Z  11 " =    2.086
peak=   -3.422 closest distance to " O   HOH Z 188 " =    4.118
peak=   -3.420 closest distance to " N   THR A 157 " =    1.512
peak=   -3.418 closest distance to " O   ASN A 215 " =    1.368
peak=   -3.418 closest distance to " OG ASER A 134 " =    1.300
peak=   -3.418 closest distance to " ND2 ASN A 209 " =    1.827
peak=   -3.418 closest distance to " O   MET A  40 " =    2.663
peak=   -3.399 closest distance to " O   HOH Z 414 " =    2.546
peak=   -3.395 closest distance to " OG BSER A  99 " =    0.918
peak=   -3.395 closest distance to " O   HOH Z  97 " =    1.342
peak=   -3.395 closest distance to " OE1 GLN A  88 " =    0.984
peak=   -3.394 closest distance to " CD1 ILE A 199 " =    2.177
peak=   -3.393 closest distance to " CB  ALA A  51 " =    1.756
peak=   -3.390 closest distance to " CG1 VAL A 296 " =    1.984
peak=   -3.383 closest distance to " O   HOH Z 250 " =    1.354
peak=   -3.382 closest distance to " O   SER A 135 " =    1.595
peak=   -3.378 closest distance to " O   HOH Z  35 " =    2.371
peak=   -3.375 closest distance to " O   HOH Z 211 " =    1.313
peak=   -3.374 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.367 closest distance to " O   HOH Z 165 " =    2.155
peak=   -3.365 closest distance to " CG  LYS A 193 " =    2.217
peak=   -3.361 closest distance to " O   HOH Z 191 " =    4.687
peak=   -3.358 closest distance to " O   HOH Z   9 " =    1.445
peak=   -3.357 closest distance to " CE  LYS A  76 " =    2.922
peak=   -3.352 closest distance to " C   LEU A 143 " =    1.099
peak=   -3.350 closest distance to " O   HOH Z 192 " =    0.770
peak=   -3.346 closest distance to " CG  ARG A 219 " =    2.670
peak=   -3.342 closest distance to " CG  ARG A 219 " =    2.228
peak=   -3.332 closest distance to " O   HOH Z 171 " =    1.377
peak=   -3.332 closest distance to " O   GLN A 183 " =    1.570
peak=   -3.326 closest distance to " CG  LEU A 228 " =    0.997
peak=   -3.319 closest distance to " C   LEU A 282 " =    1.210
peak=   -3.319 closest distance to " OD2 ASP A 191 " =    1.420
peak=   -3.315 closest distance to " CZ2 TRP A  92 " =    2.093
peak=   -3.312 closest distance to " O   HOH Z 197 " =    4.983
peak=   -3.310 closest distance to " OD1 ASP A 200 " =    1.159
peak=   -3.307 closest distance to " OG  SER A  97 " =    2.050
peak=   -3.306 closest distance to " O   HOH Z 313 " =    1.150
peak=   -3.306 closest distance to " OG  SER A  63 " =    1.379
peak=   -3.305 closest distance to " CD  PRO A 198 " =    1.336
peak=   -3.294 closest distance to " OG BSER A  99 " =    1.637
peak=   -3.293 closest distance to " O   HOH Z 421 " =    3.096
peak=   -3.292 closest distance to " N   SER A 210 " =    1.327
peak=   -3.287 closest distance to " O   HOH Z 148 " =    2.688
peak=   -3.285 closest distance to " O   HOH Z 249 " =    1.105
peak=   -3.284 closest distance to " O   HOH Z 377 " =    0.729
peak=   -3.282 closest distance to " OD2 ASP A  50 " =    1.396
peak=   -3.277 closest distance to " ND2 ASN A  39 " =    1.099
peak=   -3.274 closest distance to " O   HOH Z 153 " =    1.445
peak=   -3.274 closest distance to " CB  ALA A 248 " =    1.857
peak=   -3.274 closest distance to " CG  GLN A  58 " =    1.116
peak=   -3.274 closest distance to " O   LYS A 117 " =    1.726
peak=   -3.273 closest distance to " OG  SER A 206 " =    1.369
peak=   -3.271 closest distance to " CD1 TYR A  30 " =    1.986
peak=   -3.268 closest distance to " C   GLY A  91 " =    1.434
peak=   -3.263 closest distance to " CB  ASP A 132 " =    2.001
peak=   -3.259 closest distance to " CB  TRP A 274 " =    2.748
peak=   -3.251 closest distance to " O   HOH Z 210 " =    0.759
peak=   -3.247 closest distance to " O   HOH Z 397 " =    1.256
peak=   -3.239 closest distance to " O   ALA A   1 " =    1.695
peak=   -3.236 closest distance to " C   TYR A  30 " =    1.030
peak=   -3.233 closest distance to " O   ASN A 187 " =    1.378
peak=   -3.232 closest distance to " O   GLU A 152 " =    1.468
peak=   -3.230 closest distance to " CG  GLU A 152 " =    1.233
peak=   -3.229 closest distance to " OD1 ASP A 171 " =    1.601
peak=   -3.228 closest distance to " O   HOH Z 436 " =    1.417
peak=   -3.227 closest distance to " O   HOH Z 166 " =    1.737
peak=   -3.226 closest distance to " ND2 ASN A 127 " =    1.542
peak=   -3.226 closest distance to " O   HOH Z  63 " =    0.933
peak=   -3.218 closest distance to " O   HOH Z  24 " =    1.429
peak=   -3.215 closest distance to " O   PHE A  59 " =    2.048
peak=   -3.205 closest distance to " CA  ASP A 298 " =    1.130
peak=   -3.203 closest distance to " O   HOH Z  79 " =    1.625
peak=   -3.190 closest distance to " CD  ARG A 219 " =    2.422
peak=   -3.190 closest distance to " OD1 ASN A 301 " =    1.784
peak=   -3.188 closest distance to " CG  GLN A 223 " =    2.009
peak=   -3.185 closest distance to " O   HOH Z  15 " =    1.577
peak=   -3.185 closest distance to " O   HOH Z 385 " =    1.884
peak=   -3.185 closest distance to " O   GLY A  80 " =    2.198
peak=   -3.163 closest distance to " OE2 GLU A   2 " =    1.086
peak=   -3.140 closest distance to " CB  ASP A 132 " =    2.048
peak=   -3.139 closest distance to " NH2AARG A 275 " =    4.644
peak=   -3.129 closest distance to " O   GLY A 118 " =    1.394
peak=   -3.128 closest distance to " CA  GLY A 133 " =    1.842
peak=   -3.115 closest distance to " O   HOH Z 389 " =    1.842
peak=   -3.106 closest distance to " CD2 LEU A 143 " =    2.669
peak=   -3.104 closest distance to " CG BARG A 275 " =    1.020
peak=   -3.099 closest distance to " N   GLN A 223 " =    1.511
peak=   -3.099 closest distance to " O   HOH Z 235 " =    1.116
peak=   -3.096 closest distance to " N   ALA A 226 " =    1.938
peak=   -3.094 closest distance to " OG1 THR A 178 " =    1.146
peak=   -3.089 closest distance to " C   THR A 279 " =    1.240
peak=   -3.074 closest distance to " OG  SER A  26 " =    0.789
peak=   -3.073 closest distance to " CA  ALA A 291 " =    2.615
peak=   -3.072 closest distance to " N   SER A 206 " =    1.942
peak=   -3.062 closest distance to " O   HOH Z 423 " =    2.637
peak=   -3.050 closest distance to " O   ASP A 107 " =    1.129
peak=   -3.046 closest distance to " O   HOH Z 234 " =    3.906
peak=   -3.009 closest distance to " O   ASP A 231 " =    2.344

================= 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    :  0.5127 0.5008   6.304288e+00   6.296020e+00
   1_bss:  0.5043 0.4933   6.298470e+00   6.287316e+00
   1_xyz:  0.4382 0.4537   6.228439e+00   6.251471e+00
   1_adp:  0.3986 0.4522   6.178454e+00   6.241698e+00
   1_occ:  0.3979 0.4516   6.178037e+00   6.242007e+00
   2_bss:  0.3951 0.4487   6.178238e+00   6.240460e+00
   2_xyz:  0.3120 0.3719   5.998432e+00   6.122303e+00
   2_adp:  0.2844 0.3498   5.934688e+00   6.078716e+00
   2_occ:  0.2840 0.3498   5.934721e+00   6.079289e+00
   3_bss:  0.2818 0.3491   5.931772e+00   6.077249e+00
   3_xyz:  0.2086 0.2660   5.676977e+00   5.870750e+00
   3_adp:  0.1871 0.2394   5.576377e+00   5.773936e+00
   3_occ:  0.1867 0.2388   5.575024e+00   5.772206e+00
   4_bss:  0.1860 0.2362   5.569792e+00   5.765010e+00
   4_xyz:  0.1457 0.1909   5.354361e+00   5.568783e+00
   4_adp:  0.1385 0.1819   5.299285e+00   5.511789e+00
   4_occ:  0.1382 0.1815   5.297424e+00   5.508948e+00
   5_bss:  0.1381 0.1803   5.295691e+00   5.505898e+00
   5_xyz:  0.1250 0.1659   5.216525e+00   5.433719e+00
   5_adp:  0.1230 0.1661   5.206930e+00   5.430249e+00
   5_occ:  0.1226 0.1659   5.204093e+00   5.427966e+00
   5_bss:  0.1226 0.1659   5.204055e+00   5.427917e+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:  0.378   0.000   7.341   8.135   8.925   0.000   0.000   0.000
   1_xyz:  0.378   0.000   7.341   8.135   8.925   0.000   0.000   0.000
   1_adp:  0.378   0.000   7.341   8.135   8.925   0.000   0.000   0.000
   1_occ:  0.378   0.000   7.341   8.135   8.925   0.000   0.000   0.000
   2_bss:  0.355  24.112   3.565   4.210   5.484   0.000   0.000   0.000
   2_xyz:  0.355  24.112   3.565   4.210   5.484   0.000   0.000   0.000
   2_adp:  0.355  24.112   3.565   4.210   5.484   0.000   0.000   0.000
   2_occ:  0.355  24.112   3.565   4.210   5.484   0.000   0.000   0.000
   3_bss:  0.336  34.195   1.796   2.246   3.194   0.000   0.000   0.000
   3_xyz:  0.336  34.195   1.796   2.246   3.194   0.000   0.000   0.000
   3_adp:  0.336  34.195   1.796   2.246   3.194   0.000   0.000   0.000
   3_occ:  0.336  34.195   1.796   2.246   3.194   0.000   0.000   0.000
   4_bss:  0.319  32.144   0.704   1.249   1.969   0.000   0.000   0.000
   4_xyz:  0.319  32.144   0.704   1.249   1.969   0.000   0.000   0.000
   4_adp:  0.319  32.144   0.704   1.249   1.969   0.000   0.000   0.000
   4_occ:  0.319  32.144   0.704   1.249   1.969   0.000   0.000   0.000
   5_bss:  0.326  32.144   0.214   0.833   1.437   0.000   0.000   0.000
   5_xyz:  0.326  32.144   0.214   0.833   1.437   0.000   0.000   0.000
   5_adp:  0.326  32.144   0.214   0.833   1.437   0.000   0.000   0.000
   5_occ:  0.326  32.144   0.214   0.833   1.437   0.000   0.000   0.000
   5_bss:  0.326  32.936  -0.613   0.028   0.585   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.621 0.3608  0.4372    81218.908
   1_bss:  62.837 0.3561  0.5379    78098.282
   1_xyz:  55.090 0.4557  0.6802    64529.944
   1_adp:  52.887 0.4838  0.7900    61860.522
   1_occ:  53.029 0.4819  0.7850    61886.806
   2_bss:  52.785 0.4848  0.6991    61479.549
   2_xyz:  40.664 0.6342  0.9025    38407.577
   2_adp:  36.903 0.6792  0.9533    32938.452
   2_occ:  36.905 0.6792  0.9534    33013.432
   3_bss:  36.764 0.6807  0.8884    32743.268
   3_xyz:  27.054 0.7895  0.9894    18525.594
   3_adp:  23.227 0.8307  1.0155    14866.258
   3_occ:  23.171 0.8313  1.0160    14812.836
   4_bss:  22.940 0.8333  0.9757    14394.422
   4_xyz:  17.883 0.8819  1.0016     9287.507
   4_adp:  16.467 0.8948  1.0071     8323.479
   4_occ:  16.407 0.8953  1.0073     8272.361
   5_bss:  16.325 0.8960  0.9895     8179.825
   5_xyz:  14.846 0.9083  0.9943     7000.457
   5_adp:  14.756 0.9093  0.9918     6961.742
   5_occ:  14.718 0.9096  0.9922     6940.054
   5_bss:  14.716 0.9096  0.9908     6939.565
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2436e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2436e+01
   1_xyz:   1.880  0.015  0.116 18.653  0.007  4.103   1.7726e-01
   1_adp:   1.880  0.015  0.116 18.653  0.007  4.103   1.7726e-01
   1_occ:   1.880  0.015  0.116 18.653  0.007  4.103   1.7726e-01
   2_bss:   1.880  0.015  0.116 18.653  0.007  4.103   1.7726e-01
   2_xyz:   1.439  0.011  0.095 17.822  0.006  4.099   1.2261e-01
   2_adp:   1.439  0.011  0.095 17.822  0.006  4.099   1.2261e-01
   2_occ:   1.439  0.011  0.095 17.822  0.006  4.099   1.2261e-01
   3_bss:   1.439  0.011  0.095 17.822  0.006  4.099   1.2261e-01
   3_xyz:   1.212  0.009  0.081 16.671  0.005  4.112   8.8030e-02
   3_adp:   1.212  0.009  0.081 16.671  0.005  4.112   8.8030e-02
   3_occ:   1.212  0.009  0.081 16.671  0.005  4.112   8.8030e-02
   4_bss:   1.212  0.009  0.081 16.671  0.005  4.112   8.8030e-02
   4_xyz:   1.062  0.007  0.072 16.045  0.004  4.107   6.8693e-02
   4_adp:   1.062  0.007  0.072 16.045  0.004  4.107   6.8693e-02
   4_occ:   1.062  0.007  0.072 16.045  0.004  4.107   6.8693e-02
   5_bss:   1.062  0.007  0.072 16.045  0.004  4.107   6.8693e-02
   5_xyz:   0.984  0.006  0.068 15.879  0.004  4.104   6.0592e-02
   5_adp:   0.984  0.006  0.068 15.879  0.004  4.104   6.0592e-02
   5_occ:   0.984  0.006  0.068 15.879  0.004  4.104   6.0592e-02
   5_bss:   0.984  0.006  0.068 15.879  0.004  4.104   6.0592e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.589   6.7814e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.589   6.7814e+00
   1_xyz:  15.821  0.183  0.548 83.886  0.049  2.085   1.1565e-01
   1_adp:  15.821  0.183  0.548 83.886  0.049  2.085   1.1565e-01
   1_occ:  15.821  0.183  0.548 83.886  0.049  2.085   1.1565e-01
   2_bss:  15.821  0.183  0.548 83.886  0.049  2.085   1.1565e-01
   2_xyz:  10.694  0.088  0.373 75.722  0.056  2.099   8.1867e-02
   2_adp:  10.694  0.088  0.373 75.722  0.056  2.099   8.1867e-02
   2_occ:  10.694  0.088  0.373 75.722  0.056  2.099   8.1867e-02
   3_bss:  10.694  0.088  0.373 75.722  0.056  2.099   8.1867e-02
   3_xyz:   9.291  0.046  0.312 86.570  0.029  2.312   1.0436e-01
   3_adp:   9.291  0.046  0.312 86.570  0.029  2.312   1.0436e-01
   3_occ:   9.291  0.046  0.312 86.570  0.029  2.312   1.0436e-01
   4_bss:   9.291  0.046  0.312 86.570  0.029  2.312   1.0436e-01
   4_xyz:   7.888  0.043  0.293 84.506  0.028  2.271   4.4961e-02
   4_adp:   7.888  0.043  0.293 84.506  0.028  2.271   4.4961e-02
   4_occ:   7.888  0.043  0.293 84.506  0.028  2.271   4.4961e-02
   5_bss:   7.888  0.043  0.293 84.506  0.028  2.271   4.4961e-02
   5_xyz:   7.217  0.041  0.272 85.204  0.028  2.303   3.8131e-02
   5_adp:   7.217  0.041  0.272 85.204  0.028  2.303   3.8131e-02
   5_occ:   7.217  0.041  0.272 85.204  0.028  2.303   3.8131e-02
   5_bss:   7.217  0.041  0.272 85.204  0.028  2.303   3.8131e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.14   0.00  15.42  76.28   0.00  13.65  79.14   0.00  25.05
   1_occ:  79.14   0.00  15.42  76.28   0.00  13.65  79.14   0.00  25.05
   2_bss:  79.14   0.00  15.42  76.28   0.00  13.65  79.14   0.00  25.05
   2_xyz:  79.14   0.00  15.42  76.28   0.00  13.65  79.14   0.00  25.05
   2_adp:  85.04   0.00  14.88  85.04   0.00  11.83  84.12   0.00  31.48
   2_occ:  85.04   0.00  14.88  85.04   0.00  11.83  84.12   0.00  31.48
   3_bss:  85.04   0.00  14.88  85.04   0.00  11.83  84.12   0.00  31.48
   3_xyz:  85.04   0.00  14.88  85.04   0.00  11.83  84.12   0.00  31.48
   3_adp:  86.85   0.00  14.07  86.85   0.00  10.17  79.55   2.50  35.34
   3_occ:  86.85   0.00  14.07  86.85   0.00  10.17  79.55   2.50  35.34
   4_bss:  86.85   0.00  14.07  86.85   0.00  10.17  79.55   2.50  35.34
   4_xyz:  86.85   0.00  14.07  86.85   0.00  10.17  79.55   2.50  35.34
   4_adp:  80.95   0.00  13.80  80.47   0.00   9.75  80.95   3.43  35.85
   4_occ:  80.95   0.00  13.80  80.47   0.00   9.75  80.95   3.43  35.85
   5_bss:  80.95   0.00  13.80  80.47   0.00   9.75  80.95   3.43  35.85
   5_xyz:  80.95   0.00  13.80  80.47   0.00   9.75  80.95   3.43  35.85
   5_adp:  90.61   0.00  13.80  90.61   0.00   9.71  81.27   3.72  36.08
   5_occ:  90.61   0.00  13.80  90.61   0.00   9.71  81.27   3.72  36.08
   5_bss:  91.41   0.79  14.59  91.41   0.79  10.50  82.07   4.51  36.87
------------------------------------------------------------------------
 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:    1.282    0.034    0.432
   1_adp:    1.282    0.034    0.432
   1_occ:    1.282    0.034    0.432
   2_bss:    1.282    0.034    0.432
   2_xyz:    1.638    0.043    0.642
   2_adp:    1.638    0.043    0.642
   2_occ:    1.638    0.043    0.642
   3_bss:    1.638    0.043    0.642
   3_xyz:    1.732    0.014    0.768
   3_adp:    1.732    0.014    0.768
   3_occ:    1.732    0.014    0.768
   4_bss:    1.732    0.014    0.768
   4_xyz:    1.831    0.083    0.833
   4_adp:    1.831    0.083    0.833
   4_occ:    1.831    0.083    0.833
   5_bss:    1.831    0.083    0.833
   5_xyz:    1.903    0.056    0.860
   5_adp:    1.903    0.056    0.860
   5_occ:    1.903    0.056    0.860
   5_bss:    1.903    0.056    0.860
------------------------------------------------------------------------

CPU time actual refinement: 341.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/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_33/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_33/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.29 
  Macro-tasks:
    bulk solvent and scale       = 47.77  
    individual site refinement   = 139.27 
    weights calculation          = 32.96  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.65 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 103.69 
    alpha_beta                      = 8.55   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 113.59 
    fmodel                         = 7.59   
    r_factors                      = 0.22   
    phase_errors                   = 10.11  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 247.67 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.866 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    626 calls, 103.43 s
gradients_fft:          570 calls, 100.81 s

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

# Date 2008-01-16 Time 00:33:19 PST -0800 (1200472399.83 s)
Start R-work = 0.5127, R-free = 0.5008 (no bulk solvent and anisotropic scale)
Final R-work = 0.1397, R-free = 0.1833 (no bulk solvent and anisotropic scale)

Start R-work = 0.5043, R-free = 0.4933
Final R-work = 0.1226, R-free = 0.1659