# Date 2008-01-16 Time 00:51:32 PST -0800 (1200473492.50 s)
#phil __OFF__

Command line arguments: "../176.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9936
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 176

-------------------------------------------------------------------------------
  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: (68.845, 46.93, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95127
Completeness in resolution range: 0.958741
Completeness with d_max=infinity: 0.955747

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             d_min =   1.9513

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: (68.845, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95127
Completeness in resolution range: 0.958741
Completeness with d_max=infinity: 0.955747

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1746 [2148/2176]  1933   215  10.0%
  bin  2:  4.1746 -  3.3262 [2050/2073]  1846   204  10.0%
  bin  3:  3.3262 -  2.9095 [2040/2062]  1834   206  10.1%
  bin  4:  2.9095 -  2.6452 [2010/2029]  1816   194   9.7%
  bin  5:  2.6452 -  2.4565 [2010/2039]  1800   210  10.4%
  bin  6:  2.4565 -  2.3123 [1970/2011]  1780   190   9.6%
  bin  7:  2.3123 -  2.1969 [1984/2020]  1782   202  10.2%
  bin  8:  2.1969 -  2.1015 [1981/2019]  1781   200  10.1%
  bin  9:  2.1015 -  2.0208 [1953/1985]  1762   191   9.8%
  bin 10:  2.0208 -  1.9513 [1443/2018]  1296   147  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.05 -     1.82: 12
        1.82 -     2.59: 89
        2.59 -     3.36: 4215
        3.36 -     4.13: 9636
        4.13 -     4.90: 15063
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.053 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.273 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.409 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.566 3.040 -x+1/2,-y+1,z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.580 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 29010 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_176/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 68.845 46.93 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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4884   r_free= 0.4852   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.287365                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6559 0.99   1388  156 0.4036 0.3973      6.6027      6.6382|
|  2:  4.6559 -  3.7153 0.99   1350  146 0.4196 0.4099      6.7983      6.8062|
|  3:  3.7153 -  3.2514 0.99   1312  153 0.4457 0.4460      6.6958      6.7751|
|  4:  3.2514 -  2.9568 0.99   1313  137 0.4604 0.4963      6.5256      6.5221|
|  5:  2.9568 -  2.7464 0.98   1278  143 0.5141 0.5102      6.3997      6.3838|
|  6:  2.7464 -  2.5854 0.98   1292  145 0.5081 0.5482      6.2799       6.221|
|  7:  2.5854 -  2.4565 0.99   1296  149 0.5289 0.4759      6.2629      6.1649|
|  8:  2.4565 -  2.3500 0.99   1281  135 0.5230 0.5202      6.1824      6.1727|
|  9:  2.3500 -  2.2599 0.98   1288  146 0.5341 0.5293      6.1277      6.1606|
| 10:  2.2599 -  2.1822 0.97   1248  143 0.5443 0.5172      6.1192      6.1042|
| 11:  2.1822 -  2.1142 0.98   1268  142 0.5497 0.5534      6.0467      6.0635|
| 12:  2.1142 -  2.0539 0.99   1273  135 0.5255 0.5294       5.988      6.0086|
| 13:  2.0539 -  1.9999 0.97   1259  138 0.5506 0.5287      5.8931      5.8855|
| 14:  1.9999 -  1.9513 0.61    784   91 0.5344 0.5181      5.8461      5.7342|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6559  1388   156  0.65  38.21   0.80     0.68      83342.69|
|  2:  4.6559 -  3.7153  1350   146  0.65  39.51   0.87     0.73     125048.00|
|  3:  3.7153 -  3.2514  1312   153  0.55  47.90   0.85     0.68     134058.35|
|  4:  3.2514 -  2.9568  1313   137  0.47  54.21   0.82     0.59     113939.70|
|  5:  2.9568 -  2.7464  1278   143  0.40  59.61   0.74     0.50      89310.44|
|  6:  2.7464 -  2.5854  1292   145  0.39  60.75   0.74     0.46      72210.54|
|  7:  2.5854 -  2.4565  1296   149  0.38  61.50   0.73     0.43      65384.91|
|  8:  2.4565 -  2.3500  1281   135  0.37  62.20   0.74     0.44      58372.59|
|  9:  2.3500 -  2.2599  1288   146  0.34  64.43   0.74     0.42      54905.86|
| 10:  2.2599 -  2.1822  1248   143  0.35  64.06   0.76     0.42      50266.09|
| 11:  2.1822 -  2.1142  1268   142  0.29  68.00   0.76     0.38      48988.89|
| 12:  2.1142 -  2.0539  1273   135  0.29  68.19   0.76     0.37      45956.00|
| 13:  2.0539 -  1.9999  1259   138  0.27  69.85   0.74     0.36      39650.22|
| 14:  1.9999 -  1.9513   784    91  0.33  65.62   0.73     0.38      30477.25|
|alpha:            min =        0.36 max =            0.73 mean =         0.50|
|beta:             min =    30477.25 max =       134058.35 mean =     74011.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.41|
|phase err.(test): min =        0.00 max =           90.00 mean =        59.01|
|-----------------------------------------------------------------------------|

============================== 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 = 16.742470             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.323016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.190   (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 |  0.553 -  0.988:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.988 -  1.422:        3 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.422 -  1.857:       26 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.857 -  2.292:      196 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.292 -  2.727:      896 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.727 -  3.161:     2120 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.161 -  3.596:     3754 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.596 -  4.031:     5534 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.031 -  4.465:     7420 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.465 -  4.900:     9088 |
|-----------------------------------------------------------------------------|
|-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 |       52.750 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.553 |       3.007 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    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 = 11.329)------------------------------------------|
|    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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4941   r_free= 0.4899   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.288908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4748   ksol= 0.37   Bsol= 5.11   scale= 0.998    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,7.53,9.60,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.282405                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.849877             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.395   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.299557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.058   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4797      final r-factor (work) = 0.4077          |
| start r-factor (free) = 0.4748      final r-factor (free) = 0.4284          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.2832 = 13.85 * 0.50 * 6.2864 + 1.00 * 52.7504                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.1486 = 13.85 * 0.50 * 6.2083 + 1.00 * 0.1563                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4077      final r-factor (work) = 0.3612          |
| start r-factor (free) = 0.4284      final r-factor (free) = 0.4151          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0824 = 1.30 * 1.00 * 6.2083 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9918 = 1.30 * 1.00 * 6.1357 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.38   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    83.38   14.08    None  None   None       |
|    Sol.    : 438    0      0.00    83.38   26.30    None  None   None       |
|    Mac.    : 2385   0      0.00    80.84   11.84    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 -   8.338: 1172   |   5:    41.688 -  50.026:   60        |
|      1:     8.338 -  16.675:  741   |   6:    50.026 -  58.363:   28        |
|      2:    16.675 -  25.013:  424   |   7:    58.363 -  66.701:   18        |
|      3:    25.013 -  33.351:  238   |   8:    66.701 -  75.039:    6        |
|      4:    33.351 -  41.688:  132   |   9:    75.039 -  83.376:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3612 r_free = 0.4151             target_work(ml) = 6.120         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3608 r_free = 0.4151             target_work(ml) = 6.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3608   r_free= 0.4151   ksol= 0.37   Bsol= 5.11   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,7.53,9.60,0.00,0.00,0.00); trace/3= 8.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.118819                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3568   r_free= 0.4112   ksol= 0.34   Bsol= 22.29   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.94,3.78,6.24,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.117347                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.899164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.062   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.540847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.238  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3568      final r-factor (work) = 0.2732          |
| start r-factor (free) = 0.4112      final r-factor (free) = 0.3304          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4947 = 9.90 * 0.50 * 6.1295 + 1.00 * 0.1563                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8600 = 9.90 * 0.50 * 6.0144 + 1.00 * 0.0911                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2732      final r-factor (work) = 0.2503          |
| start r-factor (free) = 0.3304      final r-factor (free) = 0.3075          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2765 = 0.54 * 1.00 * 6.0144 + 1.00 * 0.0236                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1803 = 0.54 * 1.00 * 5.8580 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.03   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    86.03   14.09    None  None   None       |
|    Sol.    : 438    0      0.00    86.03   31.24    None  None   None       |
|    Mac.    : 2385   0      0.00    81.98   10.94    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 -   8.603: 1299   |   5:    43.014 -  51.616:   75        |
|      1:     8.603 -  17.205:  708   |   6:    51.616 -  60.219:   28        |
|      2:    17.205 -  25.808:  337   |   7:    60.219 -  68.822:    7        |
|      3:    25.808 -  34.411:  217   |   8:    68.822 -  77.424:    6        |
|      4:    34.411 -  43.014:  143   |   9:    77.424 -  86.027:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2503 r_free = 0.3075             target_work(ml) = 5.831         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2500 r_free = 0.3076             target_work(ml) = 5.830         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2500   r_free= 0.3076   ksol= 0.34   Bsol= 22.29   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.94,3.78,6.24,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.830495                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2476   r_free= 0.3065   ksol= 0.33   Bsol= 32.24   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.25,3.44,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.827880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.943091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.514  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.532754              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.798  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2476      final r-factor (work) = 0.1874          |
| start r-factor (free) = 0.3065      final r-factor (free) = 0.2438          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6480 = 3.94 * 0.50 * 5.8617 + 1.00 * 0.0914                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3395 = 3.94 * 0.50 * 5.7172 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1874      final r-factor (work) = 0.1668          |
| start r-factor (free) = 0.2438      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0580 = 0.53 * 1.00 * 5.7172 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9649 = 0.53 * 1.00 * 5.5442 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.64   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    95.64   14.08    None  None   None       |
|    Sol.    : 438    0      2.33    95.64   36.90    None  None   None       |
|    Mac.    : 2385   0      0.00    84.09   9.89     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 -   9.564: 1563   |   5:    47.821 -  57.385:   89        |
|      1:     9.564 -  19.128:  652   |   6:    57.385 -  66.949:   35        |
|      2:    19.128 -  28.692:  195   |   7:    66.949 -  76.513:    9        |
|      3:    28.692 -  38.256:  151   |   8:    76.513 -  86.077:    5        |
|      4:    38.256 -  47.821:  123   |   9:    86.077 -  95.641:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1668 r_free = 0.2187             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1665 r_free = 0.2186             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2186   ksol= 0.33   Bsol= 32.24   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.25,3.44,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.484885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2166   ksol= 0.32   Bsol= 30.47   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,1.59,2.19,0.00,0.00,0.00); trace/3= 1.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.480463                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.518086              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.095  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198595              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.687  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1659      final r-factor (work) = 0.1360          |
| start r-factor (free) = 0.2166      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0518 = 2.52 * 0.50 * 5.5471 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8549 = 2.52 * 0.50 * 5.3961 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1311          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0829 = 0.20 * 1.00 * 5.3961 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0604 = 0.20 * 1.00 * 5.2860 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.56   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    90.56   13.62    None  None   None       |
|    Sol.    : 438    0      3.26    90.56   36.23    None  None   None       |
|    Mac.    : 2385   0      0.00    87.38   9.47     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 -   9.056: 1555   |   5:    45.278 -  54.334:   86        |
|      1:     9.056 -  18.111:  695   |   6:    54.334 -  63.389:   42        |
|      2:    18.111 -  27.167:  171   |   7:    63.389 -  72.445:   10        |
|      3:    27.167 -  36.222:  134   |   8:    72.445 -  81.500:    8        |
|      4:    36.222 -  45.278:  119   |   9:    81.500 -  90.556:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1311 r_free = 0.1729             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1308 r_free = 0.1728             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1308   r_free= 0.1728   ksol= 0.32   Bsol= 30.47   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.86,1.59,2.19,0.00,0.00,0.00); trace/3= 1.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.256287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1725   ksol= 0.32   Bsol= 30.47   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.58,1.40,1.72,0.00,0.00,0.00); trace/3= 1.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.256406                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.018242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.708  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.430814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1725      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0386 = 3.02 * 0.50 * 5.2863 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9273 = 3.02 * 0.50 * 5.2062 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2527 = 0.43 * 1.00 * 5.2062 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2314 = 0.43 * 1.00 * 5.1572 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.09   13.68    None  None   None       |
|    all(noH): 2823   0      0.00    90.09   13.68    None  None   None       |
|    Sol.    : 438    0      2.44    87.23   36.94    None  None   None       |
|    Mac.    : 2385   0      0.00    90.09   9.41     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 -   9.009: 1584   |   5:    45.044 -  54.052:   88        |
|      1:     9.009 -  18.017:  672   |   6:    54.052 -  63.061:   50        |
|      2:    18.017 -  27.026:  160   |   7:    63.061 -  72.070:   20        |
|      3:    27.026 -  36.035:  123   |   8:    72.070 -  81.078:    5        |
|      4:    36.035 -  45.044:  116   |   9:    81.078 -  90.087:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1607             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1606             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1606   ksol= 0.32   Bsol= 30.47   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.58,1.40,1.72,0.00,0.00,0.00); trace/3= 1.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155159                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6559 0.99   1388  156 0.1040 0.1340      5.4235      5.5787|
|  2:  4.6559 -  3.7153 0.99   1350  146 0.0891 0.1146      5.4575      5.6584|
|  3:  3.7153 -  3.2514 0.99   1312  153 0.1068 0.1531       5.476      5.8106|
|  4:  3.2514 -  2.9568 0.99   1313  137 0.1254 0.1576      5.4649      5.6293|
|  5:  2.9568 -  2.7464 0.98   1278  143 0.1305 0.1578      5.3244      5.4629|
|  6:  2.7464 -  2.5854 0.98   1292  145 0.1257 0.2021      5.2216        5.49|
|  7:  2.5854 -  2.4565 0.99   1296  149 0.1187 0.1582      5.1386      5.3636|
|  8:  2.4565 -  2.3500 0.99   1281  135 0.1158 0.1766      5.0722      5.3364|
|  9:  2.3500 -  2.2599 0.98   1288  146 0.1193 0.1783      5.0239      5.3002|
| 10:  2.2599 -  2.1822 0.97   1248  143 0.1151 0.1745      4.9858      5.2014|
| 11:  2.1822 -  2.1142 0.98   1268  142 0.1153 0.1842      4.9417      5.3102|
| 12:  2.1142 -  2.0539 0.99   1273  135 0.1118 0.1860       4.886      5.1763|
| 13:  2.0539 -  1.9999 0.97   1259  138 0.1159 0.1739      4.8087      5.0487|
| 14:  1.9999 -  1.9513 0.61    784   91 0.1090 0.1798      4.7052       4.909|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6559  1388   156  0.94   9.36   0.99     0.97       7605.91|
|  2:  4.6559 -  3.7153  1350   146  0.95   8.40   1.03     1.02       9371.84|
|  3:  3.7153 -  3.2514  1312   153  0.93  11.44   1.04     1.03      10461.30|
|  4:  3.2514 -  2.9568  1313   137  0.92  13.67   1.02     1.02      10197.10|
|  5:  2.9568 -  2.7464  1278   143  0.90  15.53   1.00     0.96       8059.18|
|  6:  2.7464 -  2.5854  1292   145  0.90  16.26   0.99     0.96       7178.10|
|  7:  2.5854 -  2.4565  1296   149  0.91  15.20   0.99     0.96       5919.43|
|  8:  2.4565 -  2.3500  1281   135  0.91  15.19   1.01     0.99       5451.29|
|  9:  2.3500 -  2.2599  1288   146  0.90  15.65   1.02     1.00       4909.30|
| 10:  2.2599 -  2.1822  1248   143  0.90  15.79   1.02     0.99       4677.04|
| 11:  2.1822 -  2.1142  1268   142  0.90  16.29   1.01     0.97       4349.20|
| 12:  2.1142 -  2.0539  1273   135  0.91  15.68   1.02     1.00       4087.72|
| 13:  2.0539 -  1.9999  1259   138  0.90  16.49   1.02     1.01       3504.99|
| 14:  1.9999 -  1.9513   784    91  0.91  15.42   1.01     0.98       2767.27|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2767.27 max =        10461.30 mean =      6466.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.22|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1606   ksol= 0.32   Bsol= 33.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,0.17,0.49,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154970                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1606   ksol= 0.32   Bsol= 33.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,0.17,0.49,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154970                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6559 0.99   1388  156 0.1040 0.1341      5.4232      5.5792|
|  2:  4.6559 -  3.7153 0.99   1350  146 0.0893 0.1149       5.459      5.6612|
|  3:  3.7153 -  3.2514 0.99   1312  153 0.1069 0.1533      5.4772      5.8115|
|  4:  3.2514 -  2.9568 0.99   1313  137 0.1254 0.1574      5.4652      5.6289|
|  5:  2.9568 -  2.7464 0.98   1278  143 0.1305 0.1578      5.3241      5.4628|
|  6:  2.7464 -  2.5854 0.98   1292  145 0.1256 0.2020      5.2212      5.4895|
|  7:  2.5854 -  2.4565 0.99   1296  149 0.1186 0.1582      5.1378      5.3636|
|  8:  2.4565 -  2.3500 0.99   1281  135 0.1157 0.1763      5.0716       5.335|
|  9:  2.3500 -  2.2599 0.98   1288  146 0.1193 0.1783      5.0232         5.3|
| 10:  2.2599 -  2.1822 0.97   1248  143 0.1150 0.1744      4.9852      5.2002|
| 11:  2.1822 -  2.1142 0.98   1268  142 0.1152 0.1841      4.9412      5.3107|
| 12:  2.1142 -  2.0539 0.99   1273  135 0.1116 0.1860      4.8856      5.1759|
| 13:  2.0539 -  1.9999 0.97   1259  138 0.1159 0.1738      4.8082      5.0479|
| 14:  1.9999 -  1.9513 0.61    784   91 0.1091 0.1796      4.7042      4.9076|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6559  1388   156  0.94   9.36   0.99     0.97       7609.55|
|  2:  4.6559 -  3.7153  1350   146  0.95   8.43   1.03     1.02       9397.35|
|  3:  3.7153 -  3.2514  1312   153  0.93  11.46   1.04     1.03      10491.96|
|  4:  3.2514 -  2.9568  1313   137  0.92  13.67   1.02     1.02      10203.17|
|  5:  2.9568 -  2.7464  1278   143  0.90  15.53   1.00     0.96       8056.33|
|  6:  2.7464 -  2.5854  1292   145  0.90  16.26   0.99     0.96       7174.41|
|  7:  2.5854 -  2.4565  1296   149  0.91  15.19   0.99     0.96       5913.51|
|  8:  2.4565 -  2.3500  1281   135  0.91  15.18   1.01     0.99       5442.51|
|  9:  2.3500 -  2.2599  1288   146  0.90  15.63   1.02     1.01       4900.93|
| 10:  2.2599 -  2.1822  1248   143  0.90  15.79   1.02     0.99       4671.59|
| 11:  2.1822 -  2.1142  1268   142  0.90  16.29   1.01     0.97       4346.38|
| 12:  2.1142 -  2.0539  1273   135  0.91  15.67   1.02     1.00       4084.53|
| 13:  2.0539 -  1.9999  1259   138  0.90  16.47   1.02     1.01       3499.67|
| 14:  1.9999 -  1.9513   784    91  0.91  15.40   1.01     0.99       2759.71|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2759.71 max =        10491.96 mean =      6468.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.21|
|phase err.(test): min =        0.00 max =           89.21 mean =        13.80|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.329)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    91.32   14.92    None  None   None       |
|    all(noH): 2823   0      1.23    91.32   14.92    None  None   None       |
|    Sol.    : 438    0      3.68    88.47   38.17    None  None   None       |
|    Mac.    : 2385   0      1.23    91.32   10.65    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:     1.234 -  10.243: 1584   |   5:    46.278 -  55.286:   88        |
|      1:    10.243 -  19.252:  672   |   6:    55.286 -  64.295:   50        |
|      2:    19.252 -  28.260:  160   |   7:    64.295 -  73.304:   20        |
|      3:    28.260 -  37.269:  123   |   8:    73.304 -  82.312:    5        |
|      4:    37.269 -  46.278:  116   |   9:    82.312 -  91.321:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.404 - 5.972
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 323
   mapped sites are within: 0.762 - 5.972

peak=   10.922 closest distance to " CB  VAL A 230 " =    1.450
peak=    9.482 closest distance to " CG2 VAL A 296 " =    1.358
peak=    7.852 closest distance to " O   HOH Z 199 " =    1.784
peak=    6.206 closest distance to " O   HOH Z 278 " =    1.788
peak=    6.144 closest distance to " O   HOH Z 279 " =    1.207
peak=    5.869 closest distance to " CG  LEU A   5 " =    1.248
peak=    5.830 closest distance to " O   HOH Z 142 " =    1.812
peak=    5.735 closest distance to " O   HOH Z 193 " =    1.739
peak=    5.591 closest distance to " NE2 GLN A  11 " =    1.116
peak=    5.377 closest distance to " O   HOH Z 124 " =    1.521
peak=    5.321 closest distance to " CD2 LEU A   5 " =    1.219
peak=    5.214 closest distance to " NH2 ARG A  56 " =    2.095
peak=    4.963 closest distance to " O   HOH Z 236 " =    1.590
peak=    4.870 closest distance to " O   HOH Z 411 " =    3.755
peak=    4.834 closest distance to " O   HOH Z 126 " =    2.040
peak=    4.792 closest distance to " O   HOH Z 132 " =    1.463
peak=    4.766 closest distance to " O   HOH Z 120 " =    1.060
peak=    4.738 closest distance to " O   HOH Z 232 " =    2.139
peak=    4.707 closest distance to " CB  ARG A 275 " =    0.965
peak=    4.700 closest distance to " O   SER A  87 " =    2.255
peak=    4.606 closest distance to " O   HOH Z 427 " =    2.612
peak=    4.558 closest distance to " CB  GLN A 223 " =    1.500
peak=    4.554 closest distance to " O   HOH Z 188 " =    1.234
peak=    4.547 closest distance to " O   HOH Z  78 " =    1.684
peak=    4.532 closest distance to " CD2 LEU A 228 " =    1.185
peak=    4.498 closest distance to " O   HOH Z 249 " =    1.095
peak=    4.485 closest distance to " CB  GLU A 152 " =    1.133
peak=    4.464 closest distance to " CG  LEU A 228 " =    1.176
peak=    4.464 closest distance to " O   HOH Z  85 " =    1.542
peak=    4.448 closest distance to " CD1AILE A 234 " =    0.906
peak=    4.442 closest distance to " O   HOH Z 402 " =    1.482
peak=    4.441 closest distance to " O   HOH Z 263 " =    1.367
peak=    4.424 closest distance to " O   HOH Z 134 " =    1.709
peak=    4.413 closest distance to " O   HOH Z 128 " =    2.161
peak=    4.413 closest distance to " O   HOH Z  97 " =    1.733
peak=    4.412 closest distance to " O   HOH Z 346 " =    1.548
peak=    4.397 closest distance to " CG1BVAL A  72 " =    1.493
peak=    4.395 closest distance to " CG  PRO A 213 " =    1.242
peak=    4.389 closest distance to " O   HOH Z 368 " =    2.155
peak=    4.362 closest distance to " O   HOH Z  59 " =    1.920
peak=    4.359 closest distance to " C   PRO A 198 " =    1.498
peak=    4.347 closest distance to " CB  GLN A 183 " =    1.333
peak=    4.346 closest distance to " O   HOH Z  97 " =    2.326
peak=    4.325 closest distance to " NZ  LYS A 119 " =    1.972
peak=    4.324 closest distance to " CB  SER A  63 " =    1.188
peak=    4.317 closest distance to " O   HOH Z 322 " =    2.013
peak=    4.310 closest distance to " O   HOH Z  20 " =    1.773
peak=    4.304 closest distance to " O   HOH Z 203 " =    1.494
peak=    4.263 closest distance to " O   HOH Z 234 " =    3.650
peak=    4.255 closest distance to " O   HOH Z 108 " =    1.281
peak=    4.252 closest distance to " CB  SER A   3 " =    1.257
peak=    4.249 closest distance to " CB  VAL A 296 " =    0.967
peak=    4.246 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.226 closest distance to " O   HOH Z 260 " =    1.445
peak=    4.218 closest distance to " O   HOH Z 202 " =    1.161
peak=    4.210 closest distance to " O   HOH Z 191 " =    1.601
peak=    4.206 closest distance to " O   HOH Z 303 " =    2.059
peak=    4.181 closest distance to " O   HOH Z 334 " =    1.588
peak=    4.171 closest distance to " CG AARG A 275 " =    1.128
peak=    4.164 closest distance to " O   HOH Z 392 " =    2.425
peak=    4.148 closest distance to " O   HOH Z 209 " =    2.171
peak=    4.147 closest distance to " OE1 GLU A   2 " =    2.176
peak=    4.138 closest distance to " CA  VAL A  41 " =    0.855
peak=    4.136 closest distance to " CA  TYR A  30 " =    1.021
peak=    4.129 closest distance to " O   HOH Z 192 " =    1.889
peak=    4.116 closest distance to " O   HOH Z 118 " =    1.813
peak=    4.106 closest distance to " O   HOH Z 128 " =    1.913
peak=    4.103 closest distance to " O   HOH Z 406 " =    1.109
peak=    4.098 closest distance to " O   HOH Z 214 " =    2.428
peak=    4.089 closest distance to " CB  VAL A 230 " =    1.080
peak=    4.089 closest distance to " O   HOH Z 327 " =    1.776
peak=    4.081 closest distance to " O   HOH Z 156 " =    3.280
peak=    4.080 closest distance to " O   HOH Z 403 " =    1.948
peak=    4.076 closest distance to " O   HOH Z 227 " =    1.714
peak=    4.065 closest distance to " CA  ALA A  21 " =    1.097
peak=    4.058 closest distance to " CB  ASN A 148 " =    1.453
peak=    4.057 closest distance to " O   HOH Z 316 " =    2.710
peak=    4.051 closest distance to " O   HOH Z 250 " =    1.378
peak=    4.040 closest distance to " O   HOH Z   3 " =    1.858
peak=    4.016 closest distance to " O   HOH Z 276 " =    1.339
peak=    3.988 closest distance to " CG  GLN A  77 " =    2.297
peak=    3.964 closest distance to " O   HOH Z  43 " =    2.235
peak=    3.959 closest distance to " CB  VAL A 265 " =    1.183
peak=    3.949 closest distance to " NZ  LYS A 117 " =    3.287
peak=    3.946 closest distance to " O   HOH Z 345 " =    2.738
peak=    3.925 closest distance to " CD2 TRP A 179 " =    1.396
peak=    3.922 closest distance to " O   HOH Z 209 " =    2.383
peak=    3.897 closest distance to " CB  ALA A   9 " =    1.592
peak=    3.886 closest distance to " O   HOH Z 261 " =    2.139
peak=    3.882 closest distance to " O   HOH Z 407 " =    2.399
peak=    3.878 closest distance to " CD  GLN A 194 " =    1.486
peak=    3.863 closest distance to " O   LYS A 290 " =    2.336
peak=    3.847 closest distance to " O   HOH Z 299 " =    4.141
peak=    3.844 closest distance to " CB  VAL A 202 " =    1.640
peak=    3.834 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.821 closest distance to " CB  SER A  26 " =    1.633
peak=    3.810 closest distance to " O   HOH Z  54 " =    1.520
peak=    3.809 closest distance to " CD  ARG A 269 " =    1.025
peak=    3.804 closest distance to " O   HOH Z 423 " =    1.952
peak=    3.803 closest distance to " O   HOH Z 291 " =    1.463
peak=    3.802 closest distance to " CB  SER A  62 " =    1.245
peak=    3.795 closest distance to " O   HOH Z 217 " =    1.443
peak=    3.795 closest distance to " NE2 GLN A  58 " =    5.757
peak=    3.791 closest distance to " O   HOH Z 189 " =    2.259
peak=    3.783 closest distance to " O   HOH Z 155 " =    1.722
peak=    3.773 closest distance to " CD1 ILE A 106 " =    1.235
peak=    3.772 closest distance to " O   HOH Z 344 " =    2.595
peak=    3.770 closest distance to " O   HOH Z  80 " =    1.702
peak=    3.767 closest distance to " CB  ASN A 148 " =    2.033
peak=    3.764 closest distance to " O   HOH Z 214 " =    1.219
peak=    3.755 closest distance to " O   HOH Z 326 " =    1.411
peak=    3.731 closest distance to " CB  TYR A 169 " =    1.137
peak=    3.718 closest distance to " O   HOH Z 366 " =    2.787
peak=    3.702 closest distance to " O   HOH Z 298 " =    1.890
peak=    3.700 closest distance to " O   HOH Z  19 " =    1.807
peak=    3.683 closest distance to " O   HOH Z  61 " =    1.577
peak=    3.680 closest distance to " O   HOH Z 148 " =    3.078
peak=    3.664 closest distance to " NH1 ARG A  14 " =    1.017
peak=    3.663 closest distance to " O   HOH Z  39 " =    2.644
peak=    3.661 closest distance to " O   HOH Z  50 " =    1.605
peak=    3.653 closest distance to " O   HOH Z 374 " =    2.363
peak=    3.653 closest distance to " O   HOH Z 136 " =    1.181
peak=    3.651 closest distance to " CB  GLN A  88 " =    1.261
peak=    3.642 closest distance to " O   HOH Z 334 " =    2.933
peak=    3.637 closest distance to " O   HOH Z  15 " =    2.178
peak=    3.626 closest distance to " O   HOH Z 247 " =    1.169
peak=    3.623 closest distance to " O   HOH Z 108 " =    1.900
peak=    3.620 closest distance to " O   HOH Z 369 " =    2.090
peak=    3.617 closest distance to " CB  THR A  31 " =    1.653
peak=    3.609 closest distance to " CG2 ILE A  20 " =    1.565
peak=    3.602 closest distance to " O   HOH Z 406 " =    1.028
peak=    3.601 closest distance to " O   HOH Z  13 " =    1.656
peak=    3.599 closest distance to " O   HOH Z 113 " =    1.799
peak=    3.598 closest distance to " O   HOH Z 343 " =    1.472
peak=    3.591 closest distance to " CB  TRP A 179 " =    1.192
peak=    3.583 closest distance to " CB  GLU A 277 " =    3.472
peak=    3.575 closest distance to " CB  GLU A 128 " =    1.195
peak=    3.574 closest distance to " ND2 ASN A 187 " =    1.621
peak=    3.573 closest distance to " OG BSER A 164 " =    2.202
peak=    3.568 closest distance to " O   HOH Z 137 " =    1.580
peak=    3.568 closest distance to " CB  ARG A  79 " =    1.370
peak=    3.559 closest distance to " O   HOH Z 425 " =    2.106
peak=    3.558 closest distance to " CZ AARG A 102 " =    1.541
peak=    3.556 closest distance to " O   HOH Z 283 " =    1.896
peak=    3.555 closest distance to " O   HOH Z 287 " =    1.624
peak=    3.552 closest distance to " O   HOH Z  63 " =    2.592
peak=    3.550 closest distance to " ND1 HIS A  81 " =    1.431
peak=    3.543 closest distance to " O   HOH Z 109 " =    2.396
peak=    3.541 closest distance to " O   HOH Z 280 " =    1.365
peak=    3.538 closest distance to " O   HOH Z 172 " =    3.816
peak=    3.536 closest distance to " O   HOH Z 380 " =    2.004
peak=    3.531 closest distance to " O   HOH Z  66 " =    2.156
peak=    3.530 closest distance to " O   HOH Z  88 " =    3.090
peak=    3.530 closest distance to " CA  ASN A 176 " =    0.986
peak=    3.527 closest distance to " CB BVAL A  41 " =    1.154
peak=    3.526 closest distance to " O   HOH Z 233 " =    1.489
peak=    3.519 closest distance to " NZ  LYS A  76 " =    1.402
peak=    3.518 closest distance to " O   HOH Z  61 " =    1.531
peak=    3.517 closest distance to " O   HOH Z 380 " =    1.959
peak=    3.513 closest distance to " O   TRP A 274 " =    1.924
peak=    3.509 closest distance to " O   HOH Z  10 " =    1.664
peak=    3.501 closest distance to " OD2 ASP A 286 " =    2.417
peak=    3.495 closest distance to " O   HOH Z 193 " =    2.059
peak=    3.493 closest distance to " NH2BARG A 145 " =    1.263
peak=    3.492 closest distance to " CD1 ILE A  33 " =    1.701
peak=    3.489 closest distance to " O   SER A 164 " =    1.299
peak=    3.489 closest distance to " O   HOH Z 251 " =    1.617
peak=    3.487 closest distance to " O   HOH Z 426 " =    1.405
peak=    3.486 closest distance to " O   HOH Z 422 " =    2.524
peak=    3.484 closest distance to " CG  MET A 185 " =    1.226
peak=    3.484 closest distance to " O   HOH Z 357 " =    1.891
peak=    3.483 closest distance to " O   HOH Z 408 " =    1.518
peak=    3.482 closest distance to " O   HOH Z 419 " =    1.582
peak=    3.480 closest distance to " O   HOH Z  47 " =    1.707
peak=    3.476 closest distance to " CB  ASN A 110 " =    1.251
peak=    3.476 closest distance to " CG2 THR A 294 " =    1.547
peak=    3.472 closest distance to " OD1 ASN A  69 " =    2.713
peak=    3.469 closest distance to " O   HOH Z 389 " =    1.577
peak=    3.467 closest distance to " CE2 TRP A 179 " =    1.738
peak=    3.454 closest distance to " O   HOH Z 102 " =    1.168
peak=    3.453 closest distance to " O   HOH Z 113 " =    1.790
peak=    3.453 closest distance to " N   ASN A  39 " =    1.222
peak=    3.452 closest distance to " C   ALA A   1 " =    1.653
peak=    3.449 closest distance to " O   HOH Z 303 " =    1.666
peak=    3.449 closest distance to " O   HOH Z 173 " =    2.145
peak=    3.439 closest distance to " O   HOH Z 344 " =    1.310
peak=    3.430 closest distance to " O   HOH Z 180 " =    2.209
peak=    3.419 closest distance to " CA  ALA A  51 " =    1.079
peak=    3.418 closest distance to " C   ILE A 106 " =    1.861
peak=    3.416 closest distance to " O   HOH Z 274 " =    1.923
peak=    3.411 closest distance to " O   HOH Z 425 " =    1.372
peak=    3.408 closest distance to " CZ2 TRP A 274 " =    1.665
peak=    3.407 closest distance to " O   HOH Z 343 " =    2.262
peak=    3.405 closest distance to " CB  ARG A 102 " =    0.771
peak=    3.384 closest distance to " O   HOH Z 345 " =    1.662
peak=    3.381 closest distance to " CG  PRO A 198 " =    1.182
peak=    3.381 closest distance to " CG  GLN A  77 " =    2.207
peak=    3.369 closest distance to " O   HOH Z 261 " =    1.826
peak=    3.368 closest distance to " O   HOH Z  21 " =    1.847
peak=    3.358 closest distance to " OG  SER A  22 " =    2.661
peak=    3.356 closest distance to " O   HOH Z 116 " =    2.350
peak=    3.356 closest distance to " CG  ARG A  66 " =    1.039
peak=    3.355 closest distance to " OD1 ASP A 286 " =    1.625
peak=    3.355 closest distance to " O   HOH Z  68 " =    1.666
peak=    3.353 closest distance to " CG  MET A 188 " =    1.415
peak=    3.351 closest distance to " CG  MET A  93 " =    1.013
peak=    3.345 closest distance to " CA  ASN A 215 " =    1.147
peak=    3.339 closest distance to " SD BMET A  47 " =    1.265
peak=    3.338 closest distance to " O   HOH Z 164 " =    1.982
peak=    3.336 closest distance to " NH2BARG A 145 " =    2.228
peak=    3.332 closest distance to " CB  TYR A  30 " =    1.647
peak=    3.325 closest distance to " CB  ALA A 248 " =    1.348
peak=    3.324 closest distance to " CB  ALA A  10 " =    1.455
peak=    3.322 closest distance to " O   HOH Z 329 " =    3.160
peak=    3.322 closest distance to " O   HOH Z 215 " =    1.377
peak=    3.321 closest distance to " O   HOH Z 435 " =    1.975
peak=    3.321 closest distance to " CA  ARG A  36 " =    0.985
peak=    3.318 closest distance to " CG  GLN A  88 " =    1.031
peak=    3.314 closest distance to " CA  GLN A 194 " =    1.192
peak=    3.301 closest distance to " N   TRP A 177 " =    1.659
peak=    3.301 closest distance to " CB  SER A 216 " =    0.847
peak=    3.299 closest distance to " O   HOH Z 248 " =    1.790
peak=    3.299 closest distance to " O   HOH Z 361 " =    3.125
peak=    3.299 closest distance to " O   HOH Z 155 " =    2.455
peak=    3.298 closest distance to " CB  LEU A 228 " =    1.426
peak=    3.297 closest distance to " NE  ARG A 269 " =    1.061
peak=    3.295 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.294 closest distance to " N   ARG A 156 " =    1.280
peak=    3.294 closest distance to " CH2 TRP A 274 " =    2.167
peak=    3.292 closest distance to " CB  ARG A 190 " =    1.802
peak=    3.290 closest distance to " C   ALA A 299 " =    0.959
peak=    3.289 closest distance to " O   HOH Z 273 " =    2.844
peak=    3.289 closest distance to " O   HOH Z  49 " =    2.213
peak=    3.289 closest distance to " CG2 VAL A 257 " =    0.806
peak=    3.288 closest distance to " O   HOH Z 421 " =    1.337
peak=    3.286 closest distance to " O   HOH Z 118 " =    5.972
peak=    3.284 closest distance to " O   HOH Z 143 " =    1.077
peak=    3.282 closest distance to " OG  SER A  62 " =    2.913
peak=    3.277 closest distance to " O   HOH Z 253 " =    1.512
peak=    3.276 closest distance to " O   HOH Z 438 " =    2.154
peak=    3.274 closest distance to " O   HOH Z 244 " =    1.588
peak=    3.267 closest distance to " CB  ASN A  39 " =    0.762
peak=    3.264 closest distance to " CA  THR A 221 " =    0.897
peak=    3.263 closest distance to " O   GLY A  91 " =    1.654
peak=    3.263 closest distance to " CD2 HIS A  81 " =    1.317
peak=    3.259 closest distance to " O   HOH Z 112 " =    1.692
peak=    3.255 closest distance to " CG2AVAL A 121 " =    2.184
peak=    3.248 closest distance to " O   HOH Z 280 " =    2.334
peak=    3.247 closest distance to " O   HOH Z 302 " =    1.609
peak=    3.246 closest distance to " O   HOH Z 271 " =    1.766
peak=    3.245 closest distance to " CG1 VAL A 153 " =    0.986
peak=    3.241 closest distance to " CB  ALA A   1 " =    1.184
peak=    3.240 closest distance to " CD1 LEU A 228 " =    1.532
peak=    3.239 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.238 closest distance to " O   HOH Z 420 " =    1.872
peak=    3.233 closest distance to " CA  LEU A 237 " =    1.152
peak=    3.231 closest distance to " CD  LYS A 119 " =    1.960
peak=    3.230 closest distance to " O   HOH Z   4 " =    1.475
peak=    3.228 closest distance to " O   HOH Z 265 " =    2.257
peak=    3.227 closest distance to " CG2 VAL A  67 " =    1.110
peak=    3.227 closest distance to " CB  THR A 279 " =    1.535
peak=    3.223 closest distance to " O   HOH Z 417 " =    3.175
peak=    3.223 closest distance to " O   HOH Z 130 " =    2.945
peak=    3.220 closest distance to " OG BSER A 210 " =    1.493
peak=    3.219 closest distance to " O   HOH Z 150 " =    1.731
peak=    3.219 closest distance to " CA  ALA A 158 " =    1.169
peak=    3.212 closest distance to " CA  ALA A 295 " =    1.106
peak=    3.206 closest distance to " CG  GLN A  77 " =    0.944
peak=    3.205 closest distance to " NH2BARG A 190 " =    1.897
peak=    3.204 closest distance to " OE1 GLN A  11 " =    1.768
peak=    3.202 closest distance to " O   HOH Z  89 " =    1.692
peak=    3.199 closest distance to " CB  THR A  52 " =    1.274
peak=    3.198 closest distance to " CD2 TYR A  30 " =    0.963
peak=    3.197 closest distance to " NE2 GLN A  58 " =    2.279
peak=    3.195 closest distance to " CD  LYS A 166 " =    1.348
peak=    3.195 closest distance to " CB  PRO A  90 " =    1.377
peak=    3.194 closest distance to " CB  ALA A 295 " =    1.303
peak=    3.192 closest distance to " CB  GLN A 278 " =    0.804
peak=    3.189 closest distance to " O   HOH Z  63 " =    2.079
peak=    3.188 closest distance to " CB  SER A 141 " =    1.058
peak=    3.185 closest distance to " CG  LEU A 167 " =    1.148
peak=    3.182 closest distance to " CA  LYS A 117 " =    1.270
peak=    3.181 closest distance to " O   HOH Z   9 " =    1.980
peak=    3.180 closest distance to " O   HOH Z  30 " =    2.200
peak=    3.173 closest distance to " CD2 LEU A 255 " =    1.171
peak=    3.172 closest distance to " O   HOH Z 414 " =    1.298
peak=    3.166 closest distance to " CB  THR A 235 " =    1.009
peak=    3.164 closest distance to " O   HOH Z 281 " =    4.623
peak=    3.163 closest distance to " CB  ARG A 139 " =    1.026
peak=    3.162 closest distance to " N   PHE A 130 " =    1.364
peak=    3.161 closest distance to " O   HOH Z 430 " =    5.639
peak=    3.151 closest distance to " CG2 VAL A 126 " =    1.752
peak=    3.150 closest distance to " OD1 ASN A  60 " =    1.518
peak=    3.148 closest distance to " CB  LEU A 255 " =    0.769
peak=    3.146 closest distance to " N   ASP A 162 " =    1.331
peak=    3.146 closest distance to " O   HOH Z  88 " =    2.403
peak=    3.143 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.142 closest distance to " NE2 GLN A 223 " =    1.513
peak=    3.137 closest distance to " O   GLN A  58 " =    1.518
peak=    3.134 closest distance to " O   HOH Z 394 " =    1.577
peak=    3.134 closest distance to " O   HOH Z 227 " =    1.481
peak=    3.127 closest distance to " CE BLYS A 290 " =    1.013
peak=    3.126 closest distance to " O   HOH Z  13 " =    1.925
peak=    3.119 closest distance to " O   HOH Z 426 " =    2.950
peak=    3.106 closest distance to " O   HOH Z 148 " =    1.465
peak=    3.105 closest distance to " CE BMET A  47 " =    1.128
peak=    3.094 closest distance to " O   HOH Z 211 " =    2.297
peak=    3.091 closest distance to " OG BSER A 258 " =    2.366
peak=    3.087 closest distance to " O   THR A  31 " =    1.752
peak=    3.082 closest distance to " CE  LYS A 119 " =    1.049
peak=    3.078 closest distance to " O   HOH Z 313 " =    1.908
peak=    3.078 closest distance to " O   HOH Z 342 " =    0.831
peak=    3.078 closest distance to " O   HOH Z 367 " =    3.521
peak=    3.070 closest distance to " CA  LYS A 290 " =    1.329
peak=    3.067 closest distance to " O   HOH Z   1 " =    1.573
peak=    3.058 closest distance to " CB  TRP A  85 " =    1.813
peak=    3.047 closest distance to " CB  GLU A  46 " =    1.128
peak=    3.046 closest distance to " CD1BILE A 234 " =    0.924
peak=    3.045 closest distance to " CB  TRP A 266 " =    1.033
peak=    3.033 closest distance to " O   HOH Z 214 " =    1.407
peak=    3.028 closest distance to " O   HOH Z 172 " =    3.490
peak=    2.848 closest distance to " OG  SER A  97 " =    2.592

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.744 - 5.693
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.744 - 5.693

peak=   -4.893 closest distance to " CG2 VAL A 230 " =    0.744
peak=   -4.663 closest distance to " SG  CYS A 254 " =    3.196
peak=   -4.590 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.325 closest distance to " O   PRO A 163 " =    2.029
peak=   -4.323 closest distance to " O   HOH Z  11 " =    1.689
peak=   -4.274 closest distance to " N   HIS A 115 " =    1.978
peak=   -4.190 closest distance to " OXT GLY A 302 " =    2.697
peak=   -4.148 closest distance to " CD1 LEU A 101 " =    2.419
peak=   -4.134 closest distance to " O   HOH Z 266 " =    4.238
peak=   -4.131 closest distance to " CE2 TYR A  30 " =    2.855
peak=   -4.107 closest distance to " O   HOH Z  98 " =    1.426
peak=   -4.094 closest distance to " CB  ALA A 161 " =    2.457
peak=   -4.040 closest distance to " N   ALA A 248 " =    1.667
peak=   -4.034 closest distance to " ND2 ASN A  45 " =    1.126
peak=   -4.034 closest distance to " O   HOH Z 290 " =    0.955
peak=   -4.016 closest distance to " C   HIS A 108 " =    1.152
peak=   -3.996 closest distance to " CG2BVAL A  41 " =    2.684
peak=   -3.964 closest distance to " O   HOH Z 423 " =    2.192
peak=   -3.938 closest distance to " O   HOH Z 166 " =    1.490
peak=   -3.912 closest distance to " O   HOH Z 362 " =    5.693
peak=   -3.879 closest distance to " O   ALA A 161 " =    1.434
peak=   -3.877 closest distance to " CB  ALA A  51 " =    1.859
peak=   -3.858 closest distance to " O   ALA A   8 " =    1.721
peak=   -3.851 closest distance to " C   ASP A 231 " =    2.410
peak=   -3.820 closest distance to " O   HOH Z  56 " =    1.961
peak=   -3.820 closest distance to " CB  ALA A  43 " =    2.160
peak=   -3.810 closest distance to " O   VAL A  67 " =    2.751
peak=   -3.804 closest distance to " CA  GLY A  23 " =    1.887
peak=   -3.795 closest distance to " O   HOH Z 191 " =    4.793
peak=   -3.768 closest distance to " O   ALA A  51 " =    1.278
peak=   -3.762 closest distance to " OG ASER A 134 " =    1.254
peak=   -3.754 closest distance to " N   GLN A 122 " =    1.426
peak=   -3.733 closest distance to " OD1 ASN A 249 " =    1.168
peak=   -3.722 closest distance to " NH2 ARG A  79 " =    1.896
peak=   -3.683 closest distance to " O   HOH Z 166 " =    2.038
peak=   -3.682 closest distance to " CD  ARG A 139 " =    1.687
peak=   -3.680 closest distance to " CD2 LEU A 300 " =    2.897
peak=   -3.677 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.676 closest distance to " O   HOH Z   3 " =    1.858
peak=   -3.673 closest distance to " O   HOH Z 427 " =    1.566
peak=   -3.668 closest distance to " CG  LYS A 193 " =    2.068
peak=   -3.667 closest distance to " O   HOH Z  37 " =    1.835
peak=   -3.666 closest distance to " O   MET A  40 " =    2.758
peak=   -3.666 closest distance to " CG  LEU A 228 " =    1.104
peak=   -3.660 closest distance to " OD2 ASP A  50 " =    1.259
peak=   -3.646 closest distance to " CD1 LEU A 255 " =    2.737
peak=   -3.643 closest distance to " CD  GLN A  88 " =    1.077
peak=   -3.631 closest distance to " CG  GLU A 152 " =    2.561
peak=   -3.630 closest distance to " O   HOH Z 407 " =    2.846
peak=   -3.629 closest distance to " O   HOH Z 250 " =    1.449
peak=   -3.620 closest distance to " CB  ASP A 132 " =    2.164
peak=   -3.607 closest distance to " N   SER A 276 " =    1.260
peak=   -3.603 closest distance to " CB  ASP A 132 " =    2.051
peak=   -3.584 closest distance to " CZ  TYR A 169 " =    1.844
peak=   -3.584 closest distance to " O   HOH Z 102 " =    1.756
peak=   -3.582 closest distance to " CG  ASP A  50 " =    2.378
peak=   -3.580 closest distance to " OG BSER A 134 " =    1.331
peak=   -3.574 closest distance to " N   THR A 157 " =    1.510
peak=   -3.573 closest distance to " O   HOH Z 165 " =    2.071
peak=   -3.569 closest distance to " O   HOH Z 292 " =    4.228
peak=   -3.568 closest distance to " O   PRO A 198 " =    1.283
peak=   -3.566 closest distance to " OG  SER A   3 " =    1.168
peak=   -3.556 closest distance to " O   HOH Z 313 " =    1.759
peak=   -3.550 closest distance to " CB  ALA A 291 " =    2.356
peak=   -3.547 closest distance to " OG1 THR A  82 " =    1.299
peak=   -3.544 closest distance to " OD1 ASP A 200 " =    1.195
peak=   -3.529 closest distance to " OG  SER A  97 " =    2.078
peak=   -3.522 closest distance to " N   GLN A  58 " =    1.794
peak=   -3.522 closest distance to " CG  ARG A 219 " =    2.266
peak=   -3.519 closest distance to " CB  TYR A  15 " =    2.149
peak=   -3.515 closest distance to " ND2 ASN A 187 " =    1.523
peak=   -3.509 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.499 closest distance to " O   SER A 273 " =    1.452
peak=   -3.496 closest distance to " O   HOH Z 231 " =    1.861
peak=   -3.493 closest distance to " CE  LYS A  76 " =    2.983
peak=   -3.493 closest distance to " ND2 ASN A  39 " =    1.117
peak=   -3.484 closest distance to " O   HOH Z  11 " =    1.875
peak=   -3.474 closest distance to " O   ASN A 187 " =    1.465
peak=   -3.470 closest distance to " O   HOH Z 188 " =    4.313
peak=   -3.467 closest distance to " C   ASN A 187 " =    1.871
peak=   -3.455 closest distance to " NH2AARG A 275 " =    4.880
peak=   -3.447 closest distance to " OG BSER A 134 " =    1.565
peak=   -3.445 closest distance to " CG2 VAL A 296 " =    1.743
peak=   -3.445 closest distance to " CG  ASP A 231 " =    0.814
peak=   -3.436 closest distance to " O   HOH Z 175 " =    4.381
peak=   -3.419 closest distance to " OG1 THR A 246 " =    1.048
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.045
peak=   -3.402 closest distance to " O   HOH Z  63 " =    0.914
peak=   -3.395 closest distance to " O   HOH Z 346 " =    1.849
peak=   -3.393 closest distance to " CB  ALA A 100 " =    2.533
peak=   -3.377 closest distance to " O   HOH Z 211 " =    1.418
peak=   -3.372 closest distance to " CA  GLY A 133 " =    1.812
peak=   -3.371 closest distance to " CD1 PHE A  59 " =    2.167
peak=   -3.369 closest distance to " O   HOH Z 350 " =    2.129
peak=   -3.365 closest distance to " OG1 THR A 251 " =    2.824
peak=   -3.362 closest distance to " O   HOH Z  97 " =    1.184
peak=   -3.354 closest distance to " O   SER A  22 " =    2.353
peak=   -3.354 closest distance to " C   ASN A  69 " =    1.280
peak=   -3.353 closest distance to " CB  ASN A  39 " =    2.017
peak=   -3.349 closest distance to " CG  GLN A  58 " =    1.333
peak=   -3.344 closest distance to " CG2 VAL A 189 " =    2.033
peak=   -3.338 closest distance to " OG  SER A  63 " =    1.144
peak=   -3.336 closest distance to " O   SER A 146 " =    0.832
peak=   -3.334 closest distance to " O   HOH Z  17 " =    1.439
peak=   -3.329 closest distance to " O   HOH Z 198 " =    2.078
peak=   -3.328 closest distance to " C   GLN A 205 " =    1.829
peak=   -3.324 closest distance to " ND2 ASN A 209 " =    1.830
peak=   -3.323 closest distance to " N   VAL A 230 " =    1.265
peak=   -3.322 closest distance to " OE2 GLU A  44 " =    1.133
peak=   -3.321 closest distance to " CD2 TYR A 293 " =    2.138
peak=   -3.316 closest distance to " O   MET A 188 " =    1.773
peak=   -3.315 closest distance to " O   HOH Z 116 " =    1.048
peak=   -3.300 closest distance to " O   HOH Z 131 " =    3.935
peak=   -3.292 closest distance to " O   ILE A  49 " =    1.743
peak=   -3.290 closest distance to " OD1 ASP A 191 " =    1.617
peak=   -3.289 closest distance to " O   ASN A 249 " =    1.635
peak=   -3.288 closest distance to " O   PHE A 218 " =    1.581
peak=   -3.284 closest distance to " O   HOH Z 281 " =    3.349
peak=   -3.283 closest distance to " O   GLU A  44 " =    1.815
peak=   -3.283 closest distance to " O   HOH Z 197 " =    5.018
peak=   -3.280 closest distance to " OG  SER A 206 " =    1.460
peak=   -3.279 closest distance to " CE  MET A 105 " =    1.786
peak=   -3.271 closest distance to " CB  ALA A  64 " =    2.681
peak=   -3.271 closest distance to " C   ALA A 158 " =    1.164
peak=   -3.265 closest distance to " O   HOH Z 423 " =    1.208
peak=   -3.264 closest distance to " C   ASN A 285 " =    2.090
peak=   -3.262 closest distance to " CG  ASN A 110 " =    1.158
peak=   -3.261 closest distance to " O   VAL A 197 " =    1.155
peak=   -3.258 closest distance to " O   HOH Z 234 " =    4.081
peak=   -3.252 closest distance to " CD  LYS A 289 " =    2.513
peak=   -3.251 closest distance to " O   HOH Z  93 " =    1.486
peak=   -3.243 closest distance to " CE1 TYR A 169 " =    2.221
peak=   -3.243 closest distance to " N   ARG A  66 " =    1.706
peak=   -3.243 closest distance to " O   ALA A 160 " =    1.285
peak=   -3.242 closest distance to " O   HOH Z 310 " =    3.529
peak=   -3.241 closest distance to " C   ARG A 269 " =    1.422
peak=   -3.236 closest distance to " N   GLN A  77 " =    1.485
peak=   -3.236 closest distance to " CB  PRO A 163 " =    2.627
peak=   -3.234 closest distance to " CG  ASN A  45 " =    1.721
peak=   -3.229 closest distance to " ND2 ASN A 142 " =    1.909
peak=   -3.228 closest distance to " CG  PHE A 283 " =    2.674
peak=   -3.227 closest distance to " O   HOH Z 406 " =    0.840
peak=   -3.225 closest distance to " O   HOH Z 145 " =    2.804
peak=   -3.225 closest distance to " O   VAL A 174 " =    1.868
peak=   -3.211 closest distance to " O   HOH Z 388 " =    2.071
peak=   -3.204 closest distance to " CG1 VAL A 112 " =    2.983
peak=   -3.202 closest distance to " OD1 ASP A 191 " =    1.441
peak=   -3.197 closest distance to " O   HOH Z 134 " =    2.610
peak=   -3.196 closest distance to " NE2 GLN A  88 " =    2.245
peak=   -3.195 closest distance to " O   HOH Z 431 " =    1.641
peak=   -3.188 closest distance to " O   HOH Z 429 " =    2.134
peak=   -3.184 closest distance to " CE2 TRP A 179 " =    1.253
peak=   -3.182 closest distance to " CE1 HIS A  81 " =    1.446
peak=   -3.180 closest distance to " O   LEU A 228 " =    2.271
peak=   -3.180 closest distance to " O   HOH Z 351 " =    1.465
peak=   -3.176 closest distance to " O   SER A 135 " =    1.528
peak=   -3.172 closest distance to " O   HOH Z 344 " =    2.477
peak=   -3.172 closest distance to " O   HOH Z 193 " =    1.913
peak=   -3.171 closest distance to " O   HOH Z 360 " =    2.364
peak=   -3.171 closest distance to " N   ALA A 226 " =    1.930
peak=   -3.165 closest distance to " O   HOH Z  60 " =    2.056
peak=   -3.160 closest distance to " CD2 LEU A 167 " =    1.747
peak=   -3.159 closest distance to " O   HOH Z 397 " =    1.287
peak=   -3.159 closest distance to " O   HOH Z  88 " =    1.739
peak=   -3.155 closest distance to " CB  ALA A 131 " =    1.980
peak=   -3.148 closest distance to " OXT GLY A 302 " =    3.549
peak=   -3.144 closest distance to " O   HOH Z 295 " =    1.341
peak=   -3.141 closest distance to " O   HOH Z  44 " =    2.207
peak=   -3.141 closest distance to " CE BMET A  47 " =    1.392
peak=   -3.140 closest distance to " O   HOH Z 138 " =    1.117
peak=   -3.139 closest distance to " OD1 ASN A  45 " =    1.213
peak=   -3.133 closest distance to " OE1 GLN A  88 " =    1.148
peak=   -3.129 closest distance to " CG  GLU A 152 " =    1.194
peak=   -3.125 closest distance to " O   GLY A 196 " =    1.059
peak=   -3.125 closest distance to " N   THR A 220 " =    2.147
peak=   -3.125 closest distance to " OE1 GLN A  73 " =    2.479
peak=   -3.121 closest distance to " CZ3 TRP A 274 " =    2.227
peak=   -3.120 closest distance to " CD2 LEU A  25 " =    2.850
peak=   -3.116 closest distance to " C   THR A 279 " =    1.203
peak=   -3.114 closest distance to " OG  SER A  62 " =    1.284
peak=   -3.104 closest distance to " OG1 THR A 178 " =    1.167
peak=   -3.103 closest distance to " O   TRP A  92 " =    1.860
peak=   -3.094 closest distance to " O   HOH Z 222 " =    3.020
peak=   -3.085 closest distance to " CD2 TRP A 274 " =    1.010
peak=   -3.084 closest distance to " O   HOH Z 137 " =    1.526
peak=   -3.083 closest distance to " N   ALA A 248 " =    2.202
peak=   -3.082 closest distance to " O   HOH Z  13 " =    1.636
peak=   -3.075 closest distance to " OH  TYR A 214 " =    1.342
peak=   -3.074 closest distance to " OG ASER A 210 " =    2.088
peak=   -3.073 closest distance to " CB  PHE A 208 " =    2.199
peak=   -3.066 closest distance to " CB  PRO A 280 " =    2.087
peak=   -3.063 closest distance to " O   ASN A 215 " =    1.520
peak=   -3.039 closest distance to " O   HOH Z  47 " =    1.457
peak=   -3.037 closest distance to " O   ASP A 270 " =    1.839
peak=   -3.037 closest distance to " CB  ALA A 227 " =    2.165
peak=   -3.007 closest distance to " N   ALA A  43 " =    2.608

================= 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    :  0.4884 0.4852   6.287365e+00   6.281127e+00
   1_bss:  0.4797 0.4748   6.282405e+00   6.269977e+00
   1_xyz:  0.4077 0.4284   6.189270e+00   6.220083e+00
   1_adp:  0.3612 0.4151   6.119588e+00   6.200490e+00
   1_occ:  0.3608 0.4151   6.118819e+00   6.200402e+00
   2_bss:  0.3568 0.4112   6.117347e+00   6.198452e+00
   2_xyz:  0.2732 0.3304   5.897970e+00   6.035986e+00
   2_adp:  0.2503 0.3075   5.830560e+00   5.985494e+00
   2_occ:  0.2500 0.3076   5.830495e+00   5.986053e+00
   3_bss:  0.2476 0.3065   5.827880e+00   5.983190e+00
   3_xyz:  0.1874 0.2438   5.596715e+00   5.799371e+00
   3_adp:  0.1668 0.2187   5.485423e+00   5.698385e+00
   3_occ:  0.1665 0.2186   5.484885e+00   5.697505e+00
   4_bss:  0.1659 0.2166   5.480463e+00   5.692478e+00
   4_xyz:  0.1360 0.1817   5.301431e+00   5.522161e+00
   4_adp:  0.1311 0.1729   5.257897e+00   5.468884e+00
   4_occ:  0.1308 0.1728   5.256287e+00   5.467191e+00
   5_bss:  0.1309 0.1725   5.256406e+00   5.466470e+00
   5_xyz:  0.1167 0.1613   5.168925e+00   5.398670e+00
   5_adp:  0.1138 0.1607   5.155459e+00   5.394465e+00
   5_occ:  0.1138 0.1606   5.155159e+00   5.394283e+00
   5_bss:  0.1138 0.1606   5.154970e+00   5.394219e+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:  0.366   5.108   7.632   7.531   9.597   0.000   0.000   0.000
   1_xyz:  0.366   5.108   7.632   7.531   9.597   0.000   0.000   0.000
   1_adp:  0.366   5.108   7.632   7.531   9.597   0.000   0.000   0.000
   1_occ:  0.366   5.108   7.632   7.531   9.597   0.000   0.000   0.000
   2_bss:  0.345  22.287   3.943   3.778   6.235   0.000   0.000   0.000
   2_xyz:  0.345  22.287   3.943   3.778   6.235   0.000   0.000   0.000
   2_adp:  0.345  22.287   3.943   3.778   6.235   0.000   0.000   0.000
   2_occ:  0.345  22.287   3.943   3.778   6.235   0.000   0.000   0.000
   3_bss:  0.332  32.241   1.707   2.249   3.443   0.000   0.000   0.000
   3_xyz:  0.332  32.241   1.707   2.249   3.443   0.000   0.000   0.000
   3_adp:  0.332  32.241   1.707   2.249   3.443   0.000   0.000   0.000
   3_occ:  0.332  32.241   1.707   2.249   3.443   0.000   0.000   0.000
   4_bss:  0.317  30.465   0.855   1.592   2.195   0.000   0.000   0.000
   4_xyz:  0.317  30.465   0.855   1.592   2.195   0.000   0.000   0.000
   4_adp:  0.317  30.465   0.855   1.592   2.195   0.000   0.000   0.000
   4_occ:  0.317  30.465   0.855   1.592   2.195   0.000   0.000   0.000
   5_bss:  0.317  30.465   0.577   1.401   1.724   0.000   0.000   0.000
   5_xyz:  0.317  30.465   0.577   1.401   1.724   0.000   0.000   0.000
   5_adp:  0.317  30.465   0.577   1.401   1.724   0.000   0.000   0.000
   5_occ:  0.317  30.465   0.577   1.401   1.724   0.000   0.000   0.000
   5_bss:  0.318  33.561  -0.657   0.167   0.490   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.472 0.4145  0.4958    74004.230
   1_bss:  58.485 0.4119  0.6199    69916.821
   1_xyz:  50.644 0.5112  0.7595    55193.268
   1_adp:  47.469 0.5516  0.8703    51515.301
   1_occ:  47.436 0.5520  0.8701    51392.493
   2_bss:  46.980 0.5575  0.7756    50755.553
   2_xyz:  35.003 0.7003  0.9557    29244.027
   2_adp:  31.849 0.7369  1.0067    25206.647
   2_occ:  31.865 0.7368  1.0063    25252.826
   3_bss:  31.623 0.7393  0.9313    24906.961
   3_xyz:  24.208 0.8195  0.9935    15424.475
   3_adp:  20.987 0.8527  1.0112    12344.294
   3_occ:  20.982 0.8528  1.0111    12347.669
   4_bss:  20.784 0.8545  0.9774    12071.897
   4_xyz:  16.940 0.8900  0.9949     8401.353
   4_adp:  15.688 0.9013  0.9995     7584.925
   4_occ:  15.659 0.9016  0.9994     7564.301
   5_bss:  15.648 0.9016  0.9877     7551.120
   5_xyz:  14.282 0.9126  0.9930     6521.386
   5_adp:  14.180 0.9136  0.9916     6471.460
   5_occ:  14.175 0.9137  0.9915     6466.203
   5_bss:  14.172 0.9137  0.9916     6467.483
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2750e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2750e+01
   1_xyz:   1.755  0.014  0.111 18.504  0.007  4.106   1.5632e-01
   1_adp:   1.755  0.014  0.111 18.504  0.007  4.106   1.5632e-01
   1_occ:   1.755  0.014  0.111 18.504  0.007  4.106   1.5632e-01
   2_bss:   1.755  0.014  0.111 18.504  0.007  4.106   1.5632e-01
   2_xyz:   1.207  0.009  0.084 16.982  0.006  4.106   9.1128e-02
   2_adp:   1.207  0.009  0.084 16.982  0.006  4.106   9.1128e-02
   2_occ:   1.207  0.009  0.084 16.982  0.006  4.106   9.1128e-02
   3_bss:   1.207  0.009  0.084 16.982  0.006  4.106   9.1128e-02
   3_xyz:   1.074  0.007  0.076 16.033  0.004  4.113   6.7787e-02
   3_adp:   1.074  0.007  0.076 16.033  0.004  4.113   6.7787e-02
   3_occ:   1.074  0.007  0.076 16.033  0.004  4.113   6.7787e-02
   4_bss:   1.074  0.007  0.076 16.033  0.004  4.113   6.7787e-02
   4_xyz:   0.988  0.006  0.071 15.879  0.003  4.114   6.0998e-02
   4_adp:   0.988  0.006  0.071 15.879  0.003  4.114   6.0998e-02
   4_occ:   0.988  0.006  0.071 15.879  0.003  4.114   6.0998e-02
   5_bss:   0.988  0.006  0.071 15.879  0.003  4.114   6.0998e-02
   5_xyz:   1.110  0.007  0.082 16.038  0.004  4.105   7.0512e-02
   5_adp:   1.110  0.007  0.082 16.038  0.004  4.105   7.0512e-02
   5_occ:   1.110  0.007  0.082 16.038  0.004  4.105   7.0512e-02
   5_bss:   1.110  0.007  0.082 16.038  0.004  4.105   7.0512e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.553   6.8294e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.553   6.8294e+00
   1_xyz:  15.725  0.180  0.522 87.144  0.049  2.172   1.0554e-01
   1_adp:  15.725  0.180  0.522 87.144  0.049  2.172   1.0554e-01
   1_occ:  15.725  0.180  0.522 87.144  0.049  2.172   1.0554e-01
   2_bss:  15.725  0.180  0.522 87.144  0.049  2.172   1.0554e-01
   2_xyz:   7.230  0.091  0.364 81.882  0.066  2.219   7.3624e-02
   2_adp:   7.230  0.091  0.364 81.882  0.066  2.219   7.3624e-02
   2_occ:   7.230  0.091  0.364 81.882  0.066  2.219   7.3624e-02
   3_bss:   7.230  0.091  0.364 81.882  0.066  2.219   7.3624e-02
   3_xyz:   7.770  0.045  0.392 82.969  0.027  2.276   4.5441e-02
   3_adp:   7.770  0.045  0.392 82.969  0.027  2.276   4.5441e-02
   3_occ:   7.770  0.045  0.392 82.969  0.027  2.276   4.5441e-02
   4_bss:   7.770  0.045  0.392 82.969  0.027  2.276   4.5441e-02
   4_xyz:   6.828  0.036  0.387 83.137  0.029  2.317   4.1241e-02
   4_adp:   6.828  0.036  0.387 83.137  0.029  2.317   4.1241e-02
   4_occ:   6.828  0.036  0.387 83.137  0.029  2.317   4.1241e-02
   5_bss:   6.828  0.036  0.387 83.137  0.029  2.317   4.1241e-02
   5_xyz:   7.053  0.044  0.510 83.096  0.036  2.280   5.1645e-02
   5_adp:   7.053  0.044  0.510 83.096  0.036  2.280   5.1645e-02
   5_occ:   7.053  0.044  0.510 83.096  0.036  2.280   5.1645e-02
   5_bss:   7.053  0.044  0.510 83.096  0.036  2.280   5.1645e-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:  83.38   0.00  14.08  80.84   0.00  11.84  83.38   0.00  26.30
   1_occ:  83.38   0.00  14.08  80.84   0.00  11.84  83.38   0.00  26.30
   2_bss:  83.38   0.00  14.08  80.84   0.00  11.84  83.38   0.00  26.30
   2_xyz:  83.38   0.00  14.08  80.84   0.00  11.84  83.38   0.00  26.30
   2_adp:  86.03   0.00  14.09  81.98   0.00  10.94  86.03   0.00  31.24
   2_occ:  86.03   0.00  14.09  81.98   0.00  10.94  86.03   0.00  31.24
   3_bss:  86.03   0.00  14.09  81.98   0.00  10.94  86.03   0.00  31.24
   3_xyz:  86.03   0.00  14.09  81.98   0.00  10.94  86.03   0.00  31.24
   3_adp:  95.64   0.00  14.08  84.09   0.00   9.89  95.64   2.33  36.90
   3_occ:  95.64   0.00  14.08  84.09   0.00   9.89  95.64   2.33  36.90
   4_bss:  95.64   0.00  14.08  84.09   0.00   9.89  95.64   2.33  36.90
   4_xyz:  95.64   0.00  14.08  84.09   0.00   9.89  95.64   2.33  36.90
   4_adp:  90.56   0.00  13.62  87.38   0.00   9.47  90.56   3.26  36.23
   4_occ:  90.56   0.00  13.62  87.38   0.00   9.47  90.56   3.26  36.23
   5_bss:  90.56   0.00  13.62  87.38   0.00   9.47  90.56   3.26  36.23
   5_xyz:  90.56   0.00  13.62  87.38   0.00   9.47  90.56   3.26  36.23
   5_adp:  90.09   0.00  13.68  90.09   0.00   9.41  87.23   2.44  36.94
   5_occ:  90.09   0.00  13.68  90.09   0.00   9.41  87.23   2.44  36.94
   5_bss:  91.32   1.23  14.92  91.32   1.23  10.65  88.47   3.68  38.17
------------------------------------------------------------------------
 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:    1.280    0.025    0.420
   1_adp:    1.280    0.025    0.420
   1_occ:    1.280    0.025    0.420
   2_bss:    1.280    0.025    0.420
   2_xyz:    1.700    0.026    0.599
   2_adp:    1.700    0.026    0.599
   2_occ:    1.700    0.026    0.599
   3_bss:    1.700    0.026    0.599
   3_xyz:    1.622    0.069    0.689
   3_adp:    1.622    0.069    0.689
   3_occ:    1.622    0.069    0.689
   4_bss:    1.622    0.069    0.689
   4_xyz:    1.772    0.068    0.740
   4_adp:    1.772    0.068    0.740
   4_occ:    1.772    0.068    0.740
   5_bss:    1.772    0.068    0.740
   5_xyz:    1.786    0.052    0.764
   5_adp:    1.786    0.052    0.764
   5_occ:    1.786    0.052    0.764
   5_bss:    1.786    0.052    0.764
------------------------------------------------------------------------

CPU time actual refinement: 351.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/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_176/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_176/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.51 
  Macro-tasks:
    bulk solvent and scale       = 47.76  
    individual site refinement   = 138.45 
    weights calculation          = 32.77  
    collect and process          = 6.55   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 225.66 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 109.32 
    alpha_beta                      = 8.56   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 117.34 
    fmodel                         = 7.86   
    r_factors                      = 0.25   
    phase_errors                   = 10.32  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 257.50 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.991 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    642 calls, 108.91 s
gradients_fft:          586 calls, 104.71 s

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

# Date 2008-01-16 Time 00:57:38 PST -0800 (1200473858.71 s)
Start R-work = 0.4884, R-free = 0.4852 (no bulk solvent and anisotropic scale)
Final R-work = 0.1315, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.4797, R-free = 0.4748
Final R-work = 0.1138, R-free = 0.1606