# Date 2008-01-16 Time 02:26:02 PST -0800 (1200479162.62 s)
#phil __OFF__

Command line arguments: "../827.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26182
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 827

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97143
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933476

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9714

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97143
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933476

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2187 [2202/2230]  1983   219   9.9%
  bin  2:  4.2187 -  3.3609 [2098/2121]  1889   209  10.0%
  bin  3:  3.3609 -  2.9397 [2084/2109]  1871   213  10.2%
  bin  4:  2.9397 -  2.6726 [2065/2081]  1864   201   9.7%
  bin  5:  2.6726 -  2.4820 [2042/2086]  1834   208  10.2%
  bin  6:  2.4820 -  2.3362 [2056/2084]  1854   202   9.8%
  bin  7:  2.3362 -  2.2196 [2007/2043]  1806   201  10.0%
  bin  8:  2.2196 -  2.1233 [2014/2056]  1813   201  10.0%
  bin  9:  2.1233 -  2.0417 [2017/2062]  1814   203  10.1%
  bin 10:  2.0417 -  1.9714 [1004/2049]   902   102  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/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:
        1.66 -     2.31: 19
        2.31 -     2.96: 1680
        2.96 -     3.60: 4504
        3.60 -     4.25: 9134
        4.25 -     4.90: 12880
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.662 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.669 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.775 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.881 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28212 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_827/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4864   r_free= 0.4816   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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: 6.289820                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.4017 0.4056       6.608      6.6167|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.4122 0.4323      6.8206      6.8378|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.4547 0.4086      6.6845      6.6638|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.4734 0.4516      6.5214      6.4998|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.5185 0.5344      6.3817      6.3751|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.5116 0.4927       6.282       6.189|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.5091 0.4548       6.258      6.1652|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.5243 0.5331      6.1543       6.193|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.5553 0.5483      6.1351      6.1398|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.5111 0.5480      6.1067      6.1477|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.5220 0.5148       6.034      6.0021|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.5354 0.5502      5.9549      5.9982|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.5358 0.5373      5.8811      5.8438|
| 14:  2.0206 -  1.9714 0.33    434   46 0.5771 0.5255      5.8316       5.725|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7055  1425   161  0.68  36.46   0.79     0.70      78845.72|
|  2:  4.7055 -  3.7542  1371   148  0.68  36.90   0.87     0.74     110665.17|
|  3:  3.7542 -  3.2853  1345   153  0.58  45.57   0.82     0.69     117902.80|
|  4:  3.2853 -  2.9876  1336   147  0.49  52.66   0.80     0.58     103586.90|
|  5:  2.9876 -  2.7749  1331   148  0.41  59.16   0.73     0.49      84993.62|
|  6:  2.7749 -  2.6122  1325   146  0.41  59.37   0.73     0.47      69907.62|
|  7:  2.6122 -  2.4820  1308   147  0.42  58.67   0.73     0.47      61731.79|
|  8:  2.4820 -  2.3744  1309   145  0.36  62.96   0.71     0.42      59060.10|
|  9:  2.3744 -  2.2833  1315   146  0.28  69.22   0.70     0.34      58835.88|
| 10:  2.2833 -  2.2048  1303   144  0.25  71.63   0.77     0.29      56791.28|
| 11:  2.2048 -  2.1360  1282   138  0.23  72.83   0.76     0.29      52114.76|
| 12:  2.1360 -  2.0751  1290   153  0.23  72.68   0.74     0.30      47700.34|
| 13:  2.0751 -  2.0206  1256   137  0.22  73.65   0.73     0.28      40595.79|
| 14:  2.0206 -  1.9714   434    46  0.20  75.15   0.69     0.24      34375.91|
|alpha:            min =        0.24 max =            0.74 mean =         0.47|
|beta:             min =    34375.91 max =       117902.80 mean =     72063.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.97 mean =        59.41|
|phase err.(test): min =        0.00 max =           89.96 mean =        59.65|
|-----------------------------------------------------------------------------|

============================== 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 = 15.320997             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.835   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.462634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.844   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.016 -  1.404:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.404 -  1.793:        8 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.793 -  2.181:       96 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.181 -  2.570:      512 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.570 -  2.958:     1302 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.958 -  3.346:     2423 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.346 -  3.735:     3936 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.735 -  4.123:     5150 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.123 -  4.512:     6735 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.512 -  4.900:     8067 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.873 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.016 |       1.973 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4919   r_free= 0.4885   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.290877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4790   r_free= 0.4713   ksol= 0.30   Bsol= 20.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.16,11.08,7.31,0.00,0.00,0.00); trace/3= 8.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.286427                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.577669             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.744   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.235583              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.998   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4790      final r-factor (work) = 0.4119          |
| start r-factor (free) = 0.4713      final r-factor (free) = 0.4318          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.5563 = 13.58 * 0.50 * 6.2873 + 1.00 * 53.8731                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.3355 = 13.58 * 0.50 * 6.2146 + 1.00 * 0.1457                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4119      final r-factor (work) = 0.3677          |
| start r-factor (free) = 0.4318      final r-factor (free) = 0.4169          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6934 = 1.24 * 1.00 * 6.2146 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6141 = 1.24 * 1.00 * 6.1483 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.48  14.14    None  None   None       |
|    all(noH): 2823   0      0.00    105.48  14.14    None  None   None       |
|    Sol.    : 438    0      0.00    105.48  26.99    None  None   None       |
|    Mac.    : 2385   0      0.00    80.24   11.79    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 -  10.548: 1398   |   5:    52.738 -  63.286:   26        |
|      1:    10.548 -  21.095:  810   |   6:    63.286 -  73.833:   13        |
|      2:    21.095 -  31.643:  343   |   7:    73.833 -  84.381:    5        |
|      3:    31.643 -  42.191:  158   |   8:    84.381 -  94.929:    3        |
|      4:    42.191 -  52.738:   66   |   9:    94.929 - 105.476:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3677 r_free = 0.4169             target_work(ml) = 6.132         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3675 r_free = 0.4173             target_work(ml) = 6.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3675   r_free= 0.4173   ksol= 0.30   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.16,11.08,7.31,0.00,0.00,0.00); trace/3= 8.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.131978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3657   r_free= 0.4127   ksol= 0.29   Bsol= 30.22   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,7.13,4.64,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.133716                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.368559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.958   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.552  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3657      final r-factor (work) = 0.2965          |
| start r-factor (free) = 0.4127      final r-factor (free) = 0.3622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7840 = 7.37 * 0.50 * 6.1447 + 1.00 * 0.1452                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3339 = 7.37 * 0.50 * 6.0382 + 1.00 * 0.0876                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2965      final r-factor (work) = 0.2807          |
| start r-factor (free) = 0.3622      final r-factor (free) = 0.3470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3546 = 0.55 * 1.00 * 6.0382 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3047 = 0.55 * 1.00 * 5.9579 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.29   13.96    None  None   None       |
|    all(noH): 2823   0      0.00    99.29   13.96    None  None   None       |
|    Sol.    : 438    0      0.00    99.29   30.12    None  None   None       |
|    Mac.    : 2385   0      0.00    74.92   10.99    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 -   9.929: 1390   |   5:    49.646 -  59.575:   36        |
|      1:     9.929 -  19.858:  779   |   6:    59.575 -  69.504:   14        |
|      2:    19.858 -  29.788:  331   |   7:    69.504 -  79.433:    4        |
|      3:    29.788 -  39.717:  185   |   8:    79.433 -  89.363:    3        |
|      4:    39.717 -  49.646:   80   |   9:    89.363 -  99.292:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2807 r_free = 0.3470             target_work(ml) = 5.943         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2804 r_free = 0.3467             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2804   r_free= 0.3467   ksol= 0.29   Bsol= 30.22   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.04,7.13,4.64,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.942208                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2791   r_free= 0.3450   ksol= 0.30   Bsol= 48.74   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,4.51,2.57,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.942007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.669257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.750  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415402              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.765  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2791      final r-factor (work) = 0.2188          |
| start r-factor (free) = 0.3450      final r-factor (free) = 0.2748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0004 = 4.67 * 0.50 * 5.9593 + 1.00 * 0.0876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7158 = 4.67 * 0.50 * 5.8437 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2188      final r-factor (work) = 0.2037          |
| start r-factor (free) = 0.2748      final r-factor (free) = 0.2606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4392 = 0.42 * 1.00 * 5.8437 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3832 = 0.42 * 1.00 * 5.6929 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.60  13.93    None  None   None       |
|    all(noH): 2823   0      0.00    121.60  13.93    None  None   None       |
|    Sol.    : 438    0      2.15    98.78   33.54    None  None   None       |
|    Mac.    : 2385   0      0.00    121.60  10.33    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 -  12.160: 1729   |   5:    60.800 -  72.960:   13        |
|      1:    12.160 -  24.320:  599   |   6:    72.960 -  85.120:    6        |
|      2:    24.320 -  36.480:  254   |   7:    85.120 -  97.280:    0        |
|      3:    36.480 -  48.640:  165   |   8:    97.280 - 109.439:    1        |
|      4:    48.640 -  60.800:   55   |   9:   109.439 - 121.599:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2037 r_free = 0.2606             target_work(ml) = 5.671         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2034 r_free = 0.2604             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2034   r_free= 0.2604   ksol= 0.30   Bsol= 48.74   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,4.51,2.57,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.670209                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2030   r_free= 0.2600   ksol= 0.31   Bsol= 48.74   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,3.12,1.93,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.670339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.521318              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.902  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.175660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.582  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2030      final r-factor (work) = 0.1646          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.2098          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2524 = 2.52 * 0.50 * 5.6948 + 1.00 * 0.0732                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0943 = 2.52 * 0.50 * 5.5795 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1646      final r-factor (work) = 0.1515          |
| start r-factor (free) = 0.2098      final r-factor (free) = 0.1986          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5841 = 1.18 * 1.00 * 5.5795 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3986 = 1.18 * 1.00 * 5.4294 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.27  15.15    None  None   None       |
|    all(noH): 2823   0      0.00    101.27  15.15    None  None   None       |
|    Sol.    : 438    0      2.74    97.85   41.76    None  None   None       |
|    Mac.    : 2385   0      0.00    101.27  10.26    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 -  10.127: 1591   |   5:    50.634 -  60.761:   79        |
|      1:    10.127 -  20.254:  641   |   6:    60.761 -  70.888:   65        |
|      2:    20.254 -  30.381:  183   |   7:    70.888 -  81.015:   18        |
|      3:    30.381 -  40.507:  116   |   8:    81.015 -  91.142:   14        |
|      4:    40.507 -  50.634:  107   |   9:    91.142 - 101.269:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1515 r_free = 0.1986             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1514 r_free = 0.1985             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1514   r_free= 0.1985   ksol= 0.31   Bsol= 48.74   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,3.12,1.93,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.405705                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1513   r_free= 0.1987   ksol= 0.31   Bsol= 48.74   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.94,2.29,1.80,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.406591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.790142              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.661  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.853949              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.889  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1513      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1987      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0664 = 4.79 * 0.50 * 5.4303 + 1.00 * 0.0604                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8437 = 4.79 * 0.50 * 5.3284 + 1.00 * 0.0818                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1707          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5656 = 0.85 * 1.00 * 5.3284 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4857 = 0.85 * 1.00 * 5.2367 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.92  14.68    None  None   None       |
|    all(noH): 2823   0      0.00    103.92  14.68    None  None   None       |
|    Sol.    : 438    0      2.39    99.34   40.97    None  None   None       |
|    Mac.    : 2385   0      0.00    103.92  9.85     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 -  10.392: 1702   |   5:    51.961 -  62.354:   85        |
|      1:    10.392 -  20.785:  584   |   6:    62.354 -  72.746:   44        |
|      2:    20.785 -  31.177:  167   |   7:    72.746 -  83.138:   21        |
|      3:    31.177 -  41.569:  114   |   8:    83.138 -  93.530:    8        |
|      4:    41.569 -  51.961:   90   |   9:    93.530 - 103.923:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1211 r_free = 0.1707             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1210 r_free = 0.1706             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1706   ksol= 0.31   Bsol= 48.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.94,2.29,1.80,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223637                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.0939 0.1239       5.363      5.5434|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.0867 0.1169      5.4526      5.6705|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.1122 0.1714      5.5305      5.9277|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.1360 0.1726      5.5305      5.7339|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.1459 0.1800      5.4191      5.5711|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.1369 0.2184      5.3131      5.5984|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.1373 0.1840      5.2527      5.4436|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.1272 0.1792      5.1366       5.359|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.1302 0.1884      5.1017      5.3375|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.1253 0.1979       5.059      5.3938|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.1284 0.1924      5.0168      5.2911|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.1244 0.1854      4.9527      5.1695|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.1308 0.1946      4.8725      5.1178|
| 14:  2.0206 -  1.9714 0.33    434   46 0.1222 0.1774      4.7462      5.0344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7055  1425   161  0.94   9.43   0.97     0.95       7628.98|
|  2:  4.7055 -  3.7542  1371   148  0.95   8.77   1.02     1.00       9777.02|
|  3:  3.7542 -  3.2853  1345   153  0.92  12.78   1.03     1.03      12063.07|
|  4:  3.2853 -  2.9876  1336   147  0.90  15.70   1.01     0.98      12146.15|
|  5:  2.9876 -  2.7749  1331   148  0.88  18.51   1.01     0.98      10413.36|
|  6:  2.7749 -  2.6122  1325   146  0.88  18.09   0.99     0.97       8781.48|
|  7:  2.6122 -  2.4820  1308   147  0.89  17.58   0.99     0.96       7496.51|
|  8:  2.4820 -  2.3744  1309   145  0.89  17.33   1.01     0.98       6403.14|
|  9:  2.3744 -  2.2833  1315   146  0.88  18.11   1.00     0.96       5842.81|
| 10:  2.2833 -  2.2048  1303   144  0.89  16.88   0.99     0.96       5395.48|
| 11:  2.2048 -  2.1360  1282   138  0.88  18.55   0.99     0.95       5187.59|
| 12:  2.1360 -  2.0751  1290   153  0.90  17.12   1.00     0.99       4639.13|
| 13:  2.0751 -  2.0206  1256   137  0.88  18.43   1.00     0.99       3953.83|
| 14:  2.0206 -  1.9714   434    46  0.88  17.78   0.97     0.95       3096.58|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3096.58 max =        12146.15 mean =      7604.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.91|
|phase err.(test): min =        0.00 max =           89.80 mean =        15.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1706   ksol= 0.32   Bsol= 56.44   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,0.43,0.19,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1706   ksol= 0.32   Bsol= 56.44   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,0.43,0.19,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.0960 0.1258      5.3822      5.5592|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.0884 0.1164      5.4643      5.6807|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.1127 0.1716      5.5362      5.9258|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.1362 0.1725      5.5302      5.7348|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.1458 0.1795      5.4189       5.568|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.1367 0.2177       5.311       5.597|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.1371 0.1838      5.2503      5.4429|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.1269 0.1784       5.135      5.3554|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.1298 0.1890         5.1      5.3377|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.1250 0.1976      5.0575      5.3928|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.1281 0.1920      5.0147      5.2882|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.1244 0.1863       4.952       5.172|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.1309 0.1939      4.8721      5.1156|
| 14:  2.0206 -  1.9714 0.33    434   46 0.1221 0.1760      4.7442      5.0289|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9863 -  4.7055  1425   161  0.94   9.69   0.97     0.94       7879.80|
|  2:  4.7055 -  3.7542  1371   148  0.95   8.96   1.01     1.00       9988.60|
|  3:  3.7542 -  3.2853  1345   153  0.92  12.88   1.03     1.03      12228.10|
|  4:  3.2853 -  2.9876  1336   147  0.90  15.68   1.01     0.98      12094.03|
|  5:  2.9876 -  2.7749  1331   148  0.88  18.52   1.01     0.98      10417.55|
|  6:  2.7749 -  2.6122  1325   146  0.88  18.06   0.99     0.96       8740.13|
|  7:  2.6122 -  2.4820  1308   147  0.89  17.55   0.99     0.96       7469.86|
|  8:  2.4820 -  2.3744  1309   145  0.89  17.29   1.00     0.98       6380.12|
|  9:  2.3744 -  2.2833  1315   146  0.88  18.09   1.00     0.96       5836.95|
| 10:  2.2833 -  2.2048  1303   144  0.89  16.85   0.99     0.96       5381.67|
| 11:  2.2048 -  2.1360  1282   138  0.88  18.52   0.99     0.95       5167.54|
| 12:  2.1360 -  2.0751  1290   153  0.90  17.10   1.00     0.98       4633.08|
| 13:  2.0751 -  2.0206  1256   137  0.88  18.40   0.99     0.99       3942.57|
| 14:  2.0206 -  1.9714   434    46  0.88  17.74   0.97     0.94       3077.18|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3077.18 max =        12228.10 mean =      7638.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.93|
|phase err.(test): min =        0.00 max =           89.38 mean =        15.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    105.51  16.27    None  None   None       |
|    all(noH): 2823   0      1.59    105.51  16.27    None  None   None       |
|    Sol.    : 438    0      3.98    100.93  42.56    None  None   None       |
|    Mac.    : 2385   0      1.59    105.51  11.45    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:     1.592 -  11.984: 1702   |   5:    53.553 -  63.946:   85        |
|      1:    11.984 -  22.377:  584   |   6:    63.946 -  74.338:   44        |
|      2:    22.377 -  32.769:  167   |   7:    74.338 -  84.730:   21        |
|      3:    32.769 -  43.161:  114   |   8:    84.730 -  95.122:    8        |
|      4:    43.161 -  53.553:   90   |   9:    95.122 - 105.515:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.422 - 5.190
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 342
   mapped sites are within: 0.708 - 5.190

peak=    8.399 closest distance to " CG2 VAL A 230 " =    1.297
peak=    8.268 closest distance to " O   HOH Z 120 " =    1.565
peak=    6.864 closest distance to " CG2 VAL A 296 " =    1.138
peak=    6.603 closest distance to " CD1AILE A 234 " =    1.429
peak=    6.436 closest distance to " CG  LEU A   5 " =    1.256
peak=    5.927 closest distance to " O   HOH Z 210 " =    1.316
peak=    5.818 closest distance to " NH2 ARG A  56 " =    2.338
peak=    5.616 closest distance to " O   HOH Z 247 " =    1.703
peak=    5.389 closest distance to " O   HOH Z 279 " =    1.223
peak=    5.183 closest distance to " O   HOH Z 433 " =    1.776
peak=    5.055 closest distance to " CB  SER A  63 " =    1.301
peak=    4.818 closest distance to " O   HOH Z 124 " =    1.568
peak=    4.778 closest distance to " CB  VAL A 230 " =    1.273
peak=    4.739 closest distance to " CG  PRO A  54 " =    1.122
peak=    4.739 closest distance to " O   HOH Z  48 " =    2.102
peak=    4.647 closest distance to " O   HOH Z  80 " =    2.076
peak=    4.559 closest distance to " CA  TYR A  30 " =    0.975
peak=    4.544 closest distance to " O   HOH Z 134 " =    2.223
peak=    4.507 closest distance to " O   HOH Z 130 " =    2.812
peak=    4.501 closest distance to " O   HOH Z 394 " =    1.785
peak=    4.493 closest distance to " O   HOH Z  49 " =    1.140
peak=    4.460 closest distance to " O   HOH Z 402 " =    1.554
peak=    4.459 closest distance to " CB  GLN A 223 " =    1.423
peak=    4.458 closest distance to " O   HOH Z  40 " =    1.976
peak=    4.452 closest distance to " C   PRO A 198 " =    1.528
peak=    4.431 closest distance to " O   HOH Z  43 " =    1.713
peak=    4.424 closest distance to " CB  GLN A 183 " =    1.328
peak=    4.419 closest distance to " O   HOH Z 193 " =    1.780
peak=    4.414 closest distance to " O   HOH Z 412 " =    3.391
peak=    4.410 closest distance to " O   HOH Z 403 " =    1.802
peak=    4.395 closest distance to " CG2 THR A 221 " =    1.174
peak=    4.381 closest distance to " O   HOH Z 431 " =    1.349
peak=    4.376 closest distance to " CB  VAL A 296 " =    1.084
peak=    4.373 closest distance to " O   HOH Z 126 " =    1.689
peak=    4.305 closest distance to " CB  TRP A 179 " =    1.249
peak=    4.283 closest distance to " O   HOH Z 389 " =    1.976
peak=    4.247 closest distance to " CG  LEU A 228 " =    1.256
peak=    4.236 closest distance to " CE  LYS A 119 " =    1.161
peak=    4.232 closest distance to " O   HOH Z 137 " =    1.967
peak=    4.226 closest distance to " O   HOH Z 163 " =    1.702
peak=    4.224 closest distance to " O   HOH Z 234 " =    3.697
peak=    4.217 closest distance to " NE2 GLN A  11 " =    1.102
peak=    4.208 closest distance to " O   HOH Z  44 " =    2.375
peak=    4.190 closest distance to " O   HOH Z  68 " =    1.961
peak=    4.185 closest distance to " CB BVAL A  41 " =    1.138
peak=    4.175 closest distance to " O   HOH Z  15 " =    2.282
peak=    4.170 closest distance to " O   HOH Z 272 " =    2.042
peak=    4.163 closest distance to " O   HOH Z  11 " =    1.297
peak=    4.139 closest distance to " CB  ARG A 275 " =    0.906
peak=    4.131 closest distance to " CG  PRO A 213 " =    1.248
peak=    4.130 closest distance to " CG  PRO A 198 " =    1.176
peak=    4.101 closest distance to " O   HOH Z  97 " =    1.885
peak=    4.089 closest distance to " O   HOH Z 156 " =    3.301
peak=    4.059 closest distance to " CB  PRO A  54 " =    0.790
peak=    4.058 closest distance to " CG1 ILE A  33 " =    1.261
peak=    4.024 closest distance to " O   HOH Z   4 " =    1.503
peak=    4.023 closest distance to " CD2 LEU A 228 " =    1.233
peak=    4.017 closest distance to " O   HOH Z 102 " =    1.363
peak=    4.005 closest distance to " O   HOH Z 155 " =    1.562
peak=    3.994 closest distance to " O   GLY A  91 " =    1.230
peak=    3.983 closest distance to " O   HOH Z 369 " =    2.156
peak=    3.976 closest distance to " O   HOH Z 112 " =    1.526
peak=    3.973 closest distance to " O   HOH Z 136 " =    1.384
peak=    3.964 closest distance to " O   HOH Z 316 " =    2.686
peak=    3.960 closest distance to " CG  GLN A  77 " =    0.708
peak=    3.953 closest distance to " O   HOH Z 232 " =    2.316
peak=    3.945 closest distance to " O   HOH Z 133 " =    1.917
peak=    3.936 closest distance to " O   HOH Z 395 " =    1.472
peak=    3.930 closest distance to " O   HOH Z  88 " =    3.357
peak=    3.929 closest distance to " O   ASP A 124 " =    1.710
peak=    3.910 closest distance to " O   HOH Z 128 " =    1.510
peak=    3.903 closest distance to " NZ  LYS A 117 " =    2.960
peak=    3.903 closest distance to " O   ALA A 165 " =    1.240
peak=    3.897 closest distance to " O   SER A  87 " =    2.341
peak=    3.894 closest distance to " O   HOH Z 263 " =    1.564
peak=    3.883 closest distance to " O   HOH Z 221 " =    1.153
peak=    3.880 closest distance to " O   HOH Z 345 " =    2.992
peak=    3.872 closest distance to " CG  PRO A 280 " =    0.785
peak=    3.869 closest distance to " CB  ASN A 148 " =    1.226
peak=    3.865 closest distance to " O   HOH Z 130 " =    1.198
peak=    3.865 closest distance to " CB  LEU A 228 " =    1.415
peak=    3.857 closest distance to " CA  ARG A  66 " =    0.913
peak=    3.841 closest distance to " OE1 GLN A  11 " =    1.976
peak=    3.819 closest distance to " O   HOH Z 359 " =    1.953
peak=    3.813 closest distance to " O   HOH Z 423 " =    1.784
peak=    3.809 closest distance to " O   HOH Z 189 " =    2.792
peak=    3.809 closest distance to " O   HOH Z 151 " =    1.924
peak=    3.800 closest distance to " O   HOH Z 128 " =    1.984
peak=    3.786 closest distance to " CA  ALA A  21 " =    1.374
peak=    3.779 closest distance to " O   HOH Z 425 " =    1.412
peak=    3.777 closest distance to " CD  LYS A 166 " =    1.520
peak=    3.774 closest distance to " O   HOH Z 303 " =    2.233
peak=    3.773 closest distance to " O   HOH Z 142 " =    1.525
peak=    3.772 closest distance to " OE1 GLU A   2 " =    2.069
peak=    3.764 closest distance to " CD  PRO A  54 " =    1.098
peak=    3.762 closest distance to " O   HOH Z 132 " =    2.544
peak=    3.759 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.752 closest distance to " CB  ALA A 100 " =    1.434
peak=    3.748 closest distance to " O   HOH Z 146 " =    1.440
peak=    3.741 closest distance to " CB  SER A  62 " =    0.794
peak=    3.739 closest distance to " O   GLY A  23 " =    2.403
peak=    3.736 closest distance to " O   HOH Z 403 " =    1.497
peak=    3.724 closest distance to " O   HOH Z  44 " =    1.863
peak=    3.723 closest distance to " O   HOH Z 149 " =    2.169
peak=    3.709 closest distance to " CD  ARG A 159 " =    0.842
peak=    3.709 closest distance to " O   HOH Z 408 " =    1.530
peak=    3.708 closest distance to " CB  ALA A  71 " =    1.275
peak=    3.708 closest distance to " NH1 ARG A 138 " =    1.091
peak=    3.706 closest distance to " CG1BVAL A  72 " =    1.808
peak=    3.694 closest distance to " CB  TYR A 169 " =    0.896
peak=    3.694 closest distance to " O   HOH Z 196 " =    1.366
peak=    3.692 closest distance to " O   HOH Z 133 " =    2.006
peak=    3.685 closest distance to " O   HOH Z 377 " =    1.296
peak=    3.684 closest distance to " O   HOH Z 426 " =    1.426
peak=    3.682 closest distance to " O   HOH Z  63 " =    1.819
peak=    3.671 closest distance to " O   HOH Z 131 " =    2.505
peak=    3.667 closest distance to " O   HOH Z  78 " =    2.169
peak=    3.651 closest distance to " C   ILE A 106 " =    1.905
peak=    3.649 closest distance to " O   HOH Z  30 " =    1.262
peak=    3.645 closest distance to " O   HOH Z 387 " =    2.642
peak=    3.642 closest distance to " O   HOH Z 280 " =    3.038
peak=    3.641 closest distance to " O   HOH Z 386 " =    2.229
peak=    3.638 closest distance to " CG1BVAL A 121 " =    1.359
peak=    3.635 closest distance to " O   HOH Z 214 " =    1.230
peak=    3.634 closest distance to " CB  GLU A 128 " =    1.220
peak=    3.630 closest distance to " CZ3 TRP A  92 " =    1.013
peak=    3.629 closest distance to " O   HOH Z 373 " =    1.615
peak=    3.628 closest distance to " O   HOH Z 126 " =    2.438
peak=    3.627 closest distance to " O   HOH Z  20 " =    1.921
peak=    3.627 closest distance to " O   HOH Z  37 " =    1.057
peak=    3.626 closest distance to " O   HOH Z 146 " =    1.260
peak=    3.623 closest distance to " CA  VAL A  41 " =    0.878
peak=    3.620 closest distance to " O   HOH Z 414 " =    1.556
peak=    3.618 closest distance to " O   HOH Z  21 " =    1.872
peak=    3.611 closest distance to " N   ASN A  39 " =    1.342
peak=    3.607 closest distance to " CB  SER A 141 " =    1.072
peak=    3.602 closest distance to " CA  SER A  12 " =    1.497
peak=    3.602 closest distance to " CG2 ILE A 234 " =    0.970
peak=    3.597 closest distance to " CB  GLU A 152 " =    1.110
peak=    3.596 closest distance to " CD  ARG A 269 " =    1.019
peak=    3.587 closest distance to " CD2 LEU A   5 " =    1.132
peak=    3.584 closest distance to " C   SER A  32 " =    1.116
peak=    3.583 closest distance to " CB  GLN A  88 " =    1.213
peak=    3.579 closest distance to " OD1 ASN A 217 " =    1.793
peak=    3.578 closest distance to " CG2 VAL A 257 " =    1.841
peak=    3.574 closest distance to " CG AARG A 275 " =    1.063
peak=    3.571 closest distance to " O   HOH Z  47 " =    1.343
peak=    3.569 closest distance to " O   HOH Z 118 " =    1.459
peak=    3.568 closest distance to " O   HOH Z  61 " =    1.530
peak=    3.566 closest distance to " O   HOH Z 189 " =    3.054
peak=    3.563 closest distance to " O   HOH Z  66 " =    2.268
peak=    3.563 closest distance to " O   HOH Z 437 " =    2.240
peak=    3.560 closest distance to " O  BHOH Z 338 " =    0.983
peak=    3.560 closest distance to " OG1 THR A 294 " =    2.297
peak=    3.559 closest distance to " O   HOH Z 301 " =    1.906
peak=    3.554 closest distance to " O   HOH Z 273 " =    2.734
peak=    3.552 closest distance to " O   HOH Z 404 " =    1.460
peak=    3.551 closest distance to " CB  ASN A 187 " =    1.072
peak=    3.549 closest distance to " NE2 HIS A 115 " =    0.912
peak=    3.549 closest distance to " CB  TRP A 266 " =    1.025
peak=    3.547 closest distance to " O   HOH Z 244 " =    1.621
peak=    3.546 closest distance to " CB  TYR A  30 " =    1.016
peak=    3.545 closest distance to " O   HOH Z  48 " =    1.884
peak=    3.537 closest distance to " CG  ARG A 138 " =    1.076
peak=    3.521 closest distance to " CA  ASP A 191 " =    0.870
peak=    3.517 closest distance to " O   HOH Z 203 " =    1.696
peak=    3.515 closest distance to " O   HOH Z 352 " =    1.318
peak=    3.510 closest distance to " O   HOH Z 427 " =    3.069
peak=    3.501 closest distance to " CG1 VAL A 153 " =    1.072
peak=    3.501 closest distance to " CD1 LEU A 222 " =    0.861
peak=    3.500 closest distance to " O   HOH Z 261 " =    1.722
peak=    3.495 closest distance to " O   HOH Z  54 " =    1.176
peak=    3.484 closest distance to " O   HOH Z  54 " =    2.351
peak=    3.479 closest distance to " CB  MET A  40 " =    0.720
peak=    3.477 closest distance to " CA  ALA A 291 " =    0.989
peak=    3.477 closest distance to " O   HOH Z 271 " =    2.495
peak=    3.475 closest distance to " O   HOH Z 346 " =    1.542
peak=    3.474 closest distance to " O   ALA A 158 " =    1.212
peak=    3.472 closest distance to " O   HOH Z 132 " =    0.919
peak=    3.469 closest distance to " CA  THR A 246 " =    1.031
peak=    3.469 closest distance to " O   HOH Z 368 " =    3.258
peak=    3.464 closest distance to " O   HOH Z 214 " =    2.558
peak=    3.460 closest distance to " O   HOH Z 336 " =    1.738
peak=    3.457 closest distance to " CD2 HIS A  81 " =    1.426
peak=    3.457 closest distance to " O   HOH Z 185 " =    1.802
peak=    3.456 closest distance to " CA  ALA A 160 " =    0.856
peak=    3.452 closest distance to " O   HOH Z 261 " =    1.837
peak=    3.450 closest distance to " OD2 ASP A 286 " =    2.852
peak=    3.450 closest distance to " CG2 THR A 294 " =    1.536
peak=    3.445 closest distance to " CB  GLN A  58 " =    0.961
peak=    3.440 closest distance to " O   HOH Z  97 " =    2.581
peak=    3.438 closest distance to " O   HOH Z 374 " =    2.673
peak=    3.435 closest distance to " O   GLN A 278 " =    1.250
peak=    3.434 closest distance to " O   HOH Z 365 " =    3.065
peak=    3.432 closest distance to " O   HOH Z 420 " =    2.443
peak=    3.432 closest distance to " CA  LEU A 282 " =    1.102
peak=    3.424 closest distance to " CD BLYS A 290 " =    1.128
peak=    3.422 closest distance to " CG2 VAL A 296 " =    1.671
peak=    3.421 closest distance to " O   HOH Z 423 " =    3.047
peak=    3.419 closest distance to " CD2 LEU A 255 " =    1.253
peak=    3.417 closest distance to " O   HOH Z   9 " =    2.326
peak=    3.417 closest distance to " CA  ALA A  51 " =    1.108
peak=    3.414 closest distance to " CB  VAL A 202 " =    1.508
peak=    3.409 closest distance to " CB  ARG A 139 " =    0.866
peak=    3.404 closest distance to " O   HOH Z 128 " =    1.700
peak=    3.400 closest distance to " CB  ALA A 256 " =    1.084
peak=    3.399 closest distance to " CB  GLU A 277 " =    3.669
peak=    3.397 closest distance to " O   HOH Z 298 " =    5.190
peak=    3.397 closest distance to " CA  GLY A 196 " =    1.114
peak=    3.391 closest distance to " NH1 ARG A  14 " =    1.226
peak=    3.390 closest distance to " O   HOH Z 166 " =    1.601
peak=    3.384 closest distance to " O   HOH Z 326 " =    1.435
peak=    3.382 closest distance to " OG  SER A  97 " =    2.645
peak=    3.377 closest distance to " O   HOH Z 406 " =    1.897
peak=    3.376 closest distance to " CD2 TRP A 179 " =    1.398
peak=    3.371 closest distance to " O   HOH Z 344 " =    2.849
peak=    3.368 closest distance to " CG1 ILE A  49 " =    1.730
peak=    3.368 closest distance to " O   HOH Z 123 " =    2.162
peak=    3.367 closest distance to " O   HOH Z 227 " =    1.953
peak=    3.365 closest distance to " CB  SER A   3 " =    1.459
peak=    3.364 closest distance to " CG2 THR A 220 " =    0.719
peak=    3.361 closest distance to " CB  SER A  26 " =    1.676
peak=    3.359 closest distance to " O   HOH Z 383 " =    2.027
peak=    3.355 closest distance to " CD  ARG A 195 " =    0.979
peak=    3.353 closest distance to " OD1 ASN A  69 " =    2.451
peak=    3.352 closest distance to " O   HOH Z 298 " =    1.947
peak=    3.345 closest distance to " CD1 LEU A 300 " =    1.139
peak=    3.344 closest distance to " O   HOH Z 295 " =    1.595
peak=    3.344 closest distance to " O   HOH Z 355 " =    1.791
peak=    3.343 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.343 closest distance to " CE1 HIS A 108 " =    1.093
peak=    3.338 closest distance to " OG ASER A 134 " =    1.499
peak=    3.333 closest distance to " O   HOH Z 433 " =    2.004
peak=    3.329 closest distance to " CA  ALA A 295 " =    1.044
peak=    3.328 closest distance to " O   HOH Z 114 " =    1.365
peak=    3.327 closest distance to " O   HOH Z 427 " =    3.015
peak=    3.325 closest distance to " NH2 ARG A 156 " =    1.243
peak=    3.325 closest distance to " ND1 HIS A  81 " =    1.478
peak=    3.319 closest distance to " O   HOH Z 183 " =    1.707
peak=    3.318 closest distance to " O   HOH Z 154 " =    1.236
peak=    3.312 closest distance to " O   HOH Z  57 " =    1.413
peak=    3.312 closest distance to " CG  LYS A 166 " =    1.407
peak=    3.296 closest distance to " N   TYR A 247 " =    1.303
peak=    3.294 closest distance to " CA  MET A  40 " =    1.135
peak=    3.294 closest distance to " O   HOH Z 279 " =    2.161
peak=    3.292 closest distance to " CB  ILE A 199 " =    1.132
peak=    3.288 closest distance to " O   HOH Z 278 " =    1.087
peak=    3.284 closest distance to " O   HOH Z 291 " =    1.510
peak=    3.283 closest distance to " O   HOH Z  22 " =    2.762
peak=    3.282 closest distance to " CG1 VAL A 174 " =    1.253
peak=    3.281 closest distance to " O   HOH Z 174 " =    2.073
peak=    3.279 closest distance to " OG  SER A  62 " =    3.072
peak=    3.278 closest distance to " O   HOH Z 126 " =    1.877
peak=    3.275 closest distance to " CE BMET A  47 " =    1.372
peak=    3.275 closest distance to " O   HOH Z  39 " =    1.145
peak=    3.275 closest distance to " CB  ARG A 190 " =    1.711
peak=    3.273 closest distance to " CA  ILE A  33 " =    1.595
peak=    3.268 closest distance to " CB  VAL A 265 " =    1.266
peak=    3.264 closest distance to " O   VAL A  72 " =    3.367
peak=    3.261 closest distance to " CG2AVAL A 121 " =    1.941
peak=    3.253 closest distance to " O   HOH Z 417 " =    3.326
peak=    3.250 closest distance to " O   HOH Z 248 " =    1.607
peak=    3.248 closest distance to " CB  LEU A 261 " =    1.192
peak=    3.242 closest distance to " CB  ALA A   9 " =    1.562
peak=    3.241 closest distance to " NH2AARG A 275 " =    3.816
peak=    3.241 closest distance to " CA  GLY A  80 " =    1.095
peak=    3.240 closest distance to " CB  ASN A 285 " =    0.861
peak=    3.240 closest distance to " O   HOH Z 409 " =    3.909
peak=    3.237 closest distance to " CG  PRO A 243 " =    1.164
peak=    3.232 closest distance to " CB  PHE A  16 " =    1.188
peak=    3.232 closest distance to " O   HOH Z  66 " =    1.582
peak=    3.226 closest distance to " CB  ALA A 114 " =    1.177
peak=    3.224 closest distance to " O   HOH Z  69 " =    1.109
peak=    3.221 closest distance to " O   HOH Z  85 " =    1.172
peak=    3.220 closest distance to " C   VAL A 265 " =    1.134
peak=    3.219 closest distance to " NE  ARG A  14 " =    1.328
peak=    3.212 closest distance to " O   HOH Z  54 " =    1.396
peak=    3.210 closest distance to " CG2 THR A 251 " =    1.167
peak=    3.208 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.202 closest distance to " NZ  LYS A 193 " =    1.250
peak=    3.200 closest distance to " O   HOH Z 236 " =    1.612
peak=    3.200 closest distance to " CB  ALA A   1 " =    1.259
peak=    3.199 closest distance to " O   HOH Z 358 " =    2.098
peak=    3.196 closest distance to " CA  ASN A 127 " =    1.058
peak=    3.192 closest distance to " O   HOH Z 155 " =    2.689
peak=    3.187 closest distance to " O   HOH Z 145 " =    2.446
peak=    3.184 closest distance to " O   HOH Z 180 " =    2.132
peak=    3.182 closest distance to " O   HOH Z 260 " =    1.260
peak=    3.180 closest distance to " NZ  LYS A 166 " =    3.056
peak=    3.179 closest distance to " O   HOH Z 234 " =    1.850
peak=    3.179 closest distance to " O   HOH Z 104 " =    3.072
peak=    3.178 closest distance to " OG BSER A 258 " =    3.025
peak=    3.176 closest distance to " O   HOH Z  94 " =    1.940
peak=    3.176 closest distance to " CA  GLU A  46 " =    0.814
peak=    3.173 closest distance to " CE1 TYR A 186 " =    1.299
peak=    3.170 closest distance to " O   HOH Z 290 " =    1.021
peak=    3.169 closest distance to " O   HOH Z  62 " =    1.796
peak=    3.165 closest distance to " O   HOH Z 368 " =    4.171
peak=    3.161 closest distance to " CG2 VAL A 197 " =    1.200
peak=    3.157 closest distance to " CB  THR A 235 " =    0.962
peak=    3.157 closest distance to " CB  THR A  31 " =    1.686
peak=    3.156 closest distance to " CA  ASP A 162 " =    1.173
peak=    3.153 closest distance to " CA  LYS A 117 " =    1.289
peak=    3.152 closest distance to " CG BARG A 102 " =    1.872
peak=    3.150 closest distance to " O   HOH Z 207 " =    2.698
peak=    3.149 closest distance to " CG AARG A 275 " =    1.090
peak=    3.145 closest distance to " O   HOH Z 192 " =    1.630
peak=    3.136 closest distance to " CB  GLU A 175 " =    1.385
peak=    3.135 closest distance to " CB  LEU A 143 " =    1.084
peak=    3.133 closest distance to " O   HOH Z  44 " =    3.019
peak=    3.130 closest distance to " O   HOH Z 329 " =    3.565
peak=    3.130 closest distance to " CZ3 TRP A  85 " =    0.956
peak=    3.126 closest distance to " CB  SER A  28 " =    1.103
peak=    3.126 closest distance to " CA  LEU A  83 " =    1.465
peak=    3.121 closest distance to " O   THR A 251 " =    1.385
peak=    3.120 closest distance to " CB  ARG A 219 " =    1.662
peak=    3.116 closest distance to " CG ALYS A 290 " =    1.039
peak=    3.113 closest distance to " CA  ASN A 110 " =    1.079
peak=    3.113 closest distance to " O   HOH Z 380 " =    1.861
peak=    3.111 closest distance to " OG  SER A  22 " =    2.915
peak=    3.108 closest distance to " O   HOH Z 402 " =    3.029
peak=    3.105 closest distance to " CD2 TYR A 186 " =    1.037
peak=    3.104 closest distance to " CA  ALA A 100 " =    1.140
peak=    3.095 closest distance to " O   GLY A  57 " =    2.361
peak=    3.093 closest distance to " O   HOH Z 236 " =    1.837
peak=    3.092 closest distance to " CB  GLN A 194 " =    0.819
peak=    3.086 closest distance to " CA  VAL A 126 " =    1.009
peak=    3.086 closest distance to " O   HOH Z 211 " =    2.626
peak=    3.073 closest distance to " O   HOH Z 334 " =    1.485
peak=    3.073 closest distance to " O   HOH Z 416 " =    1.072
peak=    3.073 closest distance to " CA  LEU A 101 " =    1.556
peak=    3.065 closest distance to " O   HOH Z 250 " =    1.341
peak=    3.062 closest distance to " CB  TRP A 179 " =    1.959
peak=    3.054 closest distance to " CE AMET A  47 " =    1.382
peak=    3.050 closest distance to " CG2 VAL A 112 " =    1.577
peak=    3.044 closest distance to " O   HOH Z 367 " =    1.757
peak=    3.042 closest distance to " O   HOH Z 275 " =    1.376
peak=    3.017 closest distance to " O   HOH Z 116 " =    1.683

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.615 - 5.658
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 214
   mapped sites are within: 0.839 - 5.658

peak=   -5.112 closest distance to " CG2 VAL A 230 " =    0.925
peak=   -4.551 closest distance to " O   HOH Z 166 " =    1.727
peak=   -4.543 closest distance to " O   HOH Z  13 " =    1.522
peak=   -4.430 closest distance to " NH2 ARG A  66 " =    1.196
peak=   -4.372 closest distance to " CG2BVAL A  41 " =    2.670
peak=   -4.286 closest distance to " OXT GLY A 302 " =    2.936
peak=   -4.256 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.244 closest distance to " CA  SER A 164 " =    2.025
peak=   -4.213 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -4.200 closest distance to " O   HOH Z 151 " =    1.268
peak=   -4.160 closest distance to " OG ASER A 134 " =    1.231
peak=   -4.122 closest distance to " CE2 TYR A  30 " =    2.721
peak=   -4.108 closest distance to " CD2 LEU A 237 " =    2.665
peak=   -4.097 closest distance to " O   HOH Z 266 " =    4.586
peak=   -4.072 closest distance to " CA  SER A 276 " =    1.441
peak=   -4.042 closest distance to " N   ALA A 226 " =    2.069
peak=   -3.981 closest distance to " O   ILE A 109 " =    2.639
peak=   -3.976 closest distance to " O   HOH Z 426 " =    1.834
peak=   -3.960 closest distance to " CG  PRO A 243 " =    1.641
peak=   -3.930 closest distance to " O   HOH Z  19 " =    2.410
peak=   -3.927 closest distance to " N   GLN A  58 " =    1.751
peak=   -3.919 closest distance to " ND2 ASN A  60 " =    1.526
peak=   -3.888 closest distance to " CG2 THR A 182 " =    2.337
peak=   -3.875 closest distance to " N   THR A 235 " =    1.327
peak=   -3.855 closest distance to " O   HOH Z 120 " =    0.958
peak=   -3.829 closest distance to " O   VAL A  67 " =    2.824
peak=   -3.828 closest distance to " O   HOH Z 234 " =    4.259
peak=   -3.824 closest distance to " O   HOH Z  71 " =    1.213
peak=   -3.821 closest distance to " O   HOH Z 221 " =    1.337
peak=   -3.817 closest distance to " O   HOH Z  52 " =    2.187
peak=   -3.815 closest distance to " CG  ARG A 269 " =    2.402
peak=   -3.789 closest distance to " OG  SER A  97 " =    2.208
peak=   -3.789 closest distance to " O   HOH Z 423 " =    1.042
peak=   -3.781 closest distance to " O   HOH Z  10 " =    1.646
peak=   -3.767 closest distance to " CD2 PHE A  59 " =    2.485
peak=   -3.767 closest distance to " C   ASN A 285 " =    2.451
peak=   -3.764 closest distance to " CD2 LEU A 300 " =    2.762
peak=   -3.745 closest distance to " O   HOH Z 103 " =    1.909
peak=   -3.739 closest distance to " O   HOH Z  37 " =    1.326
peak=   -3.739 closest distance to " O   HOH Z 208 " =    1.495
peak=   -3.729 closest distance to " OD1 ASN A  39 " =    2.277
peak=   -3.718 closest distance to " O   HOH Z 423 " =    2.269
peak=   -3.701 closest distance to " O   HOH Z 407 " =    3.338
peak=   -3.697 closest distance to " OD1 ASN A 148 " =    1.566
peak=   -3.689 closest distance to " CA  VAL A 197 " =    0.983
peak=   -3.682 closest distance to " C   GLY A  91 " =    1.594
peak=   -3.680 closest distance to " O   HOH Z 377 " =    0.909
peak=   -3.670 closest distance to " CG  ASP A 231 " =    0.859
peak=   -3.669 closest distance to " O   HOH Z 210 " =    2.649
peak=   -3.665 closest distance to " NH1 ARG A 195 " =    2.666
peak=   -3.657 closest distance to " O   HOH Z 396 " =    1.548
peak=   -3.652 closest distance to " O   HOH Z  49 " =    0.995
peak=   -3.641 closest distance to " O   HOH Z 252 " =    1.295
peak=   -3.636 closest distance to " CA  GLY A 203 " =    2.178
peak=   -3.634 closest distance to " O   HOH Z 385 " =    3.850
peak=   -3.626 closest distance to " CB  SER A 146 " =    2.143
peak=   -3.611 closest distance to " O   HOH Z 290 " =    1.033
peak=   -3.604 closest distance to " O   HOH Z 132 " =    1.165
peak=   -3.597 closest distance to " SG  CYS A 254 " =    3.279
peak=   -3.596 closest distance to " OG BSER A 210 " =    1.175
peak=   -3.593 closest distance to " CD1 LEU A 228 " =    2.434
peak=   -3.589 closest distance to " C   THR A 279 " =    1.093
peak=   -3.584 closest distance to " O   HOH Z 292 " =    4.385
peak=   -3.581 closest distance to " O   HOH Z 351 " =    1.576
peak=   -3.578 closest distance to " O   HOH Z 184 " =    1.294
peak=   -3.574 closest distance to " O   HOH Z 275 " =    1.467
peak=   -3.572 closest distance to " O   ALA A  34 " =    2.129
peak=   -3.567 closest distance to " O   HOH Z 407 " =    1.442
peak=   -3.562 closest distance to " O   HOH Z  39 " =    1.773
peak=   -3.561 closest distance to " CG  ARG A 219 " =    2.463
peak=   -3.557 closest distance to " ND2 ASN A  60 " =    1.525
peak=   -3.554 closest distance to " O   HOH Z  92 " =    1.313
peak=   -3.552 closest distance to " O   HOH Z 412 " =    5.605
peak=   -3.550 closest distance to " O   ALA A   1 " =    1.887
peak=   -3.546 closest distance to " CB  ALA A 291 " =    2.490
peak=   -3.540 closest distance to " OG1 THR A  82 " =    1.592
peak=   -3.538 closest distance to " O   HOH Z 384 " =    2.010
peak=   -3.538 closest distance to " O   SER A 271 " =    2.127
peak=   -3.536 closest distance to " OD1 ASN A 249 " =    2.304
peak=   -3.520 closest distance to " CD2 LEU A 167 " =    1.718
peak=   -3.513 closest distance to " CG1 VAL A  78 " =    2.692
peak=   -3.510 closest distance to " O   HOH Z 136 " =    2.314
peak=   -3.505 closest distance to " O   HOH Z 380 " =    4.486
peak=   -3.504 closest distance to " O   PHE A 218 " =    1.373
peak=   -3.503 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.494 closest distance to " CD  GLN A  88 " =    0.839
peak=   -3.493 closest distance to " O   HOH Z  15 " =    1.500
peak=   -3.489 closest distance to " O   ASN A 187 " =    1.563
peak=   -3.487 closest distance to " NE2 GLN A 194 " =    2.390
peak=   -3.479 closest distance to " OG BSER A 134 " =    1.365
peak=   -3.478 closest distance to " C   ASN A 187 " =    1.939
peak=   -3.477 closest distance to " NE2 GLN A  88 " =    1.127
peak=   -3.477 closest distance to " O   HOH Z 166 " =    2.206
peak=   -3.474 closest distance to " O   HOH Z 171 " =    2.398
peak=   -3.473 closest distance to " CB  PRO A 280 " =    2.270
peak=   -3.473 closest distance to " O   HOH Z  38 " =    1.431
peak=   -3.469 closest distance to " O   HOH Z 150 " =    1.315
peak=   -3.469 closest distance to " O   HOH Z  93 " =    1.731
peak=   -3.466 closest distance to " O   HOH Z 200 " =    1.321
peak=   -3.460 closest distance to " CD  ARG A 195 " =    5.075
peak=   -3.459 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.451 closest distance to " O   THR A  18 " =    1.433
peak=   -3.449 closest distance to " CG  GLU A   2 " =    1.687
peak=   -3.445 closest distance to " CA  ASP A 298 " =    1.012
peak=   -3.439 closest distance to " O   HOH Z 210 " =    0.865
peak=   -3.438 closest distance to " O   HOH Z 189 " =    1.762
peak=   -3.434 closest distance to " O   HOH Z 422 " =    1.551
peak=   -3.428 closest distance to " CG1 VAL A 265 " =    2.384
peak=   -3.424 closest distance to " CD1 TYR A 247 " =    2.109
peak=   -3.416 closest distance to " CG1 VAL A 112 " =    2.349
peak=   -3.408 closest distance to " O   GLY A  80 " =    2.244
peak=   -3.404 closest distance to " CG2 VAL A 189 " =    2.085
peak=   -3.403 closest distance to " O   HOH Z 283 " =    2.083
peak=   -3.401 closest distance to " O   HOH Z  17 " =    1.214
peak=   -3.396 closest distance to " O   HOH Z 227 " =    1.133
peak=   -3.393 closest distance to " CD1 TRP A 179 " =    1.109
peak=   -3.376 closest distance to " CH2 TRP A 179 " =    1.191
peak=   -3.369 closest distance to " CE  MET A 105 " =    2.248
peak=   -3.366 closest distance to " OG  SER A  26 " =    1.407
peak=   -3.360 closest distance to " O   GLY A 118 " =    2.182
peak=   -3.358 closest distance to " ND2 ASN A  39 " =    1.271
peak=   -3.357 closest distance to " O   ALA A 100 " =    2.217
peak=   -3.353 closest distance to " O   HOH Z 185 " =    1.931
peak=   -3.352 closest distance to " O   LEU A 228 " =    2.476
peak=   -3.352 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.347 closest distance to " OG  SER A  62 " =    1.411
peak=   -3.344 closest distance to " OG1 THR A   4 " =    1.883
peak=   -3.338 closest distance to " NH2AARG A 275 " =    5.034
peak=   -3.338 closest distance to " O   HOH Z 427 " =    1.323
peak=   -3.337 closest distance to " CD  LYS A 289 " =    2.385
peak=   -3.336 closest distance to " CA  ARG A  66 " =    1.999
peak=   -3.330 closest distance to " CB  PRO A 163 " =    2.818
peak=   -3.329 closest distance to " O   HOH Z 418 " =    1.502
peak=   -3.320 closest distance to " CB  ALA A 100 " =    1.851
peak=   -3.317 closest distance to " C   ALA A 165 " =    1.866
peak=   -3.316 closest distance to " CG2 ILE A  49 " =    2.666
peak=   -3.309 closest distance to " C   SER A 206 " =    1.593
peak=   -3.309 closest distance to " O   HOH Z  56 " =    1.943
peak=   -3.308 closest distance to " O   HOH Z 313 " =    1.234
peak=   -3.304 closest distance to " CB  PHE A 208 " =    2.376
peak=   -3.302 closest distance to " O   HOH Z  94 " =    2.440
peak=   -3.297 closest distance to " O   HOH Z 137 " =    1.406
peak=   -3.296 closest distance to " O   HOH Z 231 " =    2.217
peak=   -3.296 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.290 closest distance to " O   HOH Z 252 " =    4.129
peak=   -3.284 closest distance to " OD2 ASP A 171 " =    1.880
peak=   -3.277 closest distance to " O   HOH Z 222 " =    1.304
peak=   -3.274 closest distance to " N   GLY A  17 " =    1.670
peak=   -3.274 closest distance to " O  BHOH Z 338 " =    1.479
peak=   -3.273 closest distance to " O   HOH Z  11 " =    1.442
peak=   -3.269 closest distance to " CA  LYS A 166 " =    2.270
peak=   -3.262 closest distance to " O   TYR A  15 " =    1.534
peak=   -3.262 closest distance to " C   GLY A 133 " =    1.293
peak=   -3.261 closest distance to " CB  CYS A 254 " =    2.420
peak=   -3.247 closest distance to " O   ALA A 161 " =    1.629
peak=   -3.242 closest distance to " NE2 GLN A 103 " =    1.588
peak=   -3.240 closest distance to " OD2 ASP A 171 " =    2.141
peak=   -3.238 closest distance to " O   HOH Z 191 " =    5.658
peak=   -3.236 closest distance to " O   VAL A 197 " =    1.348
peak=   -3.235 closest distance to " OD1 ASN A 187 " =    1.694
peak=   -3.220 closest distance to " O   HOH Z 156 " =    1.507
peak=   -3.219 closest distance to " O   HOH Z  20 " =    1.408
peak=   -3.217 closest distance to " O   HOH Z 139 " =    3.138
peak=   -3.217 closest distance to " OD1 ASP A 191 " =    1.708
peak=   -3.213 closest distance to " CG  MET A  93 " =    2.524
peak=   -3.212 closest distance to " O   HOH Z 292 " =    2.913
peak=   -3.208 closest distance to " CG  ASN A 301 " =    1.818
peak=   -3.207 closest distance to " CB  ARG A 219 " =    2.526
peak=   -3.205 closest distance to " O   HOH Z 246 " =    1.286
peak=   -3.201 closest distance to " O   HOH Z 111 " =    1.120
peak=   -3.200 closest distance to " ND2BASN A 224 " =    1.969
peak=   -3.192 closest distance to " CE3 TRP A 150 " =    2.255
peak=   -3.192 closest distance to " OG  SER A  87 " =    1.583
peak=   -3.188 closest distance to " O   TRP A  92 " =    1.968
peak=   -3.187 closest distance to " NH2 ARG A  79 " =    1.924
peak=   -3.184 closest distance to " CG  GLU A  53 " =    1.448
peak=   -3.184 closest distance to " O   HOH Z 435 " =    2.878
peak=   -3.184 closest distance to " NE2 GLN A 223 " =    1.785
peak=   -3.179 closest distance to " CB  LEU A 167 " =    2.085
peak=   -3.178 closest distance to " CD  PRO A 213 " =    2.214
peak=   -3.176 closest distance to " CD2 LEU A 237 " =    2.785
peak=   -3.175 closest distance to " O   HOH Z  22 " =    2.601
peak=   -3.174 closest distance to " O   LEU A 101 " =    1.956
peak=   -3.172 closest distance to " CB  SER A  63 " =    3.140
peak=   -3.171 closest distance to " CD1 LEU A 222 " =    2.573
peak=   -3.168 closest distance to " OG BSER A 134 " =    1.767
peak=   -3.166 closest distance to " O   ALA A   8 " =    1.854
peak=   -3.163 closest distance to " CD1 ILE A 109 " =    2.169
peak=   -3.159 closest distance to " OG  SER A  32 " =    1.340
peak=   -3.156 closest distance to " CG1 VAL A 197 " =    2.345
peak=   -3.149 closest distance to " CB  ALA A 248 " =    2.233
peak=   -3.144 closest distance to " O   HOH Z 174 " =    2.018
peak=   -3.140 closest distance to " O   HOH Z 298 " =    2.922
peak=   -3.133 closest distance to " O   HOH Z 165 " =    2.063
peak=   -3.131 closest distance to " O   HOH Z 297 " =    2.764
peak=   -3.130 closest distance to " NH2 ARG A  66 " =    5.093
peak=   -3.128 closest distance to " O   HOH Z  43 " =    1.879
peak=   -3.114 closest distance to " O   HOH Z 389 " =    1.148
peak=   -3.112 closest distance to " O   HOH Z 198 " =    2.407
peak=   -3.112 closest distance to " CG2 VAL A 296 " =    0.919
peak=   -3.111 closest distance to " C   HIS A 108 " =    1.203
peak=   -3.110 closest distance to " CE3 TRP A  70 " =    1.842
peak=   -3.107 closest distance to " O   HOH Z 100 " =    1.115
peak=   -3.100 closest distance to " O   HOH Z 193 " =    1.612
peak=   -3.096 closest distance to " O   HOH Z 402 " =    1.279
peak=   -3.094 closest distance to " C   LEU A 255 " =    1.768
peak=   -3.089 closest distance to " CE  MET A 105 " =    2.247
peak=   -3.085 closest distance to " O   HOH Z   6 " =    2.063
peak=   -3.076 closest distance to " O   HOH Z  12 " =    3.428
peak=   -3.065 closest distance to " O   HOH Z 366 " =    1.676
peak=   -3.043 closest distance to " OG BSER A  99 " =    1.152
peak=   -3.027 closest distance to " O   HOH Z 150 " =    1.400

================= 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    :  0.4864 0.4816   6.289820e+00   6.276335e+00
   1_bss:  0.4790 0.4713   6.286427e+00   6.269338e+00
   1_xyz:  0.4119 0.4318   6.198635e+00   6.222334e+00
   1_adp:  0.3677 0.4169   6.132477e+00   6.202548e+00
   1_occ:  0.3675 0.4173   6.131978e+00   6.203162e+00
   2_bss:  0.3657 0.4127   6.133716e+00   6.203045e+00
   2_xyz:  0.2965 0.3622   5.979277e+00   6.110795e+00
   2_adp:  0.2807 0.3470   5.942782e+00   6.083291e+00
   2_occ:  0.2804 0.3467   5.942208e+00   6.082826e+00
   3_bss:  0.2791 0.3450   5.942007e+00   6.081605e+00
   3_xyz:  0.2188 0.2748   5.724780e+00   5.893647e+00
   3_adp:  0.2037 0.2606   5.670621e+00   5.850708e+00
   3_occ:  0.2034 0.2604   5.670209e+00   5.850633e+00
   4_bss:  0.2030 0.2600   5.670339e+00   5.849483e+00
   4_xyz:  0.1646 0.2098   5.468833e+00   5.668139e+00
   4_adp:  0.1515 0.1986   5.405914e+00   5.616614e+00
   4_occ:  0.1514 0.1985   5.405705e+00   5.616622e+00
   5_bss:  0.1513 0.1987   5.406591e+00   5.617601e+00
   5_xyz:  0.1259 0.1757   5.251943e+00   5.491133e+00
   5_adp:  0.1211 0.1707   5.224033e+00   5.467603e+00
   5_occ:  0.1210 0.1706   5.223637e+00   5.467328e+00
   5_bss:  0.1214 0.1706   5.225538e+00   5.468302e+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:  0.300  20.000   6.157  11.081   7.309   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.157  11.081   7.309   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.157  11.081   7.309   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.157  11.081   7.309   0.000   0.000   0.000
   2_bss:  0.292  30.217   3.038   7.125   4.636   0.000   0.000   0.000
   2_xyz:  0.292  30.217   3.038   7.125   4.636   0.000   0.000   0.000
   2_adp:  0.292  30.217   3.038   7.125   4.636   0.000   0.000   0.000
   2_occ:  0.292  30.217   3.038   7.125   4.636   0.000   0.000   0.000
   3_bss:  0.297  48.744   1.757   4.511   2.571   0.000   0.000   0.000
   3_xyz:  0.297  48.744   1.757   4.511   2.571   0.000   0.000   0.000
   3_adp:  0.297  48.744   1.757   4.511   2.571   0.000   0.000   0.000
   3_occ:  0.297  48.744   1.757   4.511   2.571   0.000   0.000   0.000
   4_bss:  0.315  48.744   1.133   3.123   1.935   0.000   0.000   0.000
   4_xyz:  0.315  48.744   1.133   3.123   1.935   0.000   0.000   0.000
   4_adp:  0.315  48.744   1.133   3.123   1.935   0.000   0.000   0.000
   4_occ:  0.315  48.744   1.133   3.123   1.935   0.000   0.000   0.000
   5_bss:  0.308  48.744   0.943   2.288   1.800   0.000   0.000   0.000
   5_xyz:  0.308  48.744   0.943   2.288   1.800   0.000   0.000   0.000
   5_adp:  0.308  48.744   0.943   2.288   1.800   0.000   0.000   0.000
   5_occ:  0.308  48.744   0.943   2.288   1.800   0.000   0.000   0.000
   5_bss:  0.321  56.444  -0.618   0.427   0.191   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.431 0.4008  0.4661    72062.965
   1_bss:  59.667 0.3956  0.5748    69699.191
   1_xyz:  51.318 0.5019  0.7222    55239.143
   1_adp:  47.464 0.5507  0.8492    49707.059
   1_occ:  47.501 0.5502  0.8480    49754.241
   2_bss:  47.287 0.5529  0.7639    49568.504
   2_xyz:  39.317 0.6501  0.8927    36454.473
   2_adp:  37.101 0.6769  0.9214    33408.721
   2_occ:  37.082 0.6771  0.9213    33374.164
   3_bss:  36.855 0.6798  0.8630    33103.290
   3_xyz:  28.073 0.7786  0.9530    20066.666
   3_adp:  26.151 0.7998  0.9607    18054.821
   3_occ:  26.158 0.7997  0.9604    18055.754
   4_bss:  26.109 0.8002  0.9319    17981.641
   4_xyz:  20.449 0.8572  0.9737    11502.728
   4_adp:  19.151 0.8698  0.9764    10334.127
   4_occ:  19.146 0.8699  0.9763    10330.394
   5_bss:  19.141 0.8699  0.9634    10347.063
   5_xyz:  16.440 0.8940  0.9776     7938.467
   5_adp:  15.847 0.8995  0.9760     7607.584
   5_occ:  15.836 0.8996  0.9759     7604.719
   5_bss:  15.853 0.8995  0.9730     7639.001
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3873e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3873e+01
   1_xyz:   1.723  0.013  0.108 18.201  0.007  4.123   1.4573e-01
   1_adp:   1.723  0.013  0.108 18.201  0.007  4.123   1.4573e-01
   1_occ:   1.723  0.013  0.108 18.201  0.007  4.123   1.4573e-01
   2_bss:   1.723  0.013  0.108 18.201  0.007  4.123   1.4573e-01
   2_xyz:   1.230  0.009  0.083 16.429  0.005  4.114   8.7586e-02
   2_adp:   1.230  0.009  0.083 16.429  0.005  4.114   8.7586e-02
   2_occ:   1.230  0.009  0.083 16.429  0.005  4.114   8.7586e-02
   3_bss:   1.230  0.009  0.083 16.429  0.005  4.114   8.7586e-02
   3_xyz:   1.151  0.008  0.083 15.473  0.004  4.132   7.2935e-02
   3_adp:   1.151  0.008  0.083 15.473  0.004  4.132   7.2935e-02
   3_occ:   1.151  0.008  0.083 15.473  0.004  4.132   7.2935e-02
   4_bss:   1.151  0.008  0.083 15.473  0.004  4.132   7.2935e-02
   4_xyz:   0.967  0.007  0.073 15.406  0.004  4.125   6.0391e-02
   4_adp:   0.967  0.007  0.073 15.406  0.004  4.125   6.0391e-02
   4_occ:   0.967  0.007  0.073 15.406  0.004  4.125   6.0391e-02
   5_bss:   0.967  0.007  0.073 15.406  0.004  4.125   6.0391e-02
   5_xyz:   1.176  0.010  0.091 15.603  0.004  4.114   8.1823e-02
   5_adp:   1.176  0.010  0.091 15.603  0.004  4.114   8.1823e-02
   5_occ:   1.176  0.010  0.091 15.603  0.004  4.114   8.1823e-02
   5_bss:   1.176  0.010  0.091 15.603  0.004  4.114   8.1823e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.016   6.9829e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.016   6.9829e+00
   1_xyz:  15.157  0.165  0.508 88.128  0.053  2.214   1.0193e-01
   1_adp:  15.157  0.165  0.508 88.128  0.053  2.214   1.0193e-01
   1_occ:  15.157  0.165  0.508 88.128  0.053  2.214   1.0193e-01
   2_bss:  15.157  0.165  0.508 88.128  0.053  2.214   1.0193e-01
   2_xyz:   8.679  0.098  0.284 84.809  0.040  2.044   6.3656e-02
   2_adp:   8.679  0.098  0.284 84.809  0.040  2.044   6.3656e-02
   2_occ:   8.679  0.098  0.284 84.809  0.040  2.044   6.3656e-02
   3_bss:   8.679  0.098  0.284 84.809  0.040  2.044   6.3656e-02
   3_xyz:   7.738  0.080  0.259 78.855  0.048  2.255   6.6157e-02
   3_adp:   7.738  0.080  0.259 78.855  0.048  2.255   6.6157e-02
   3_occ:   7.738  0.080  0.259 78.855  0.048  2.255   6.6157e-02
   4_bss:   7.738  0.080  0.259 78.855  0.048  2.255   6.6157e-02
   4_xyz:   7.693  0.045  0.281 88.430  0.032  2.324   6.1749e-02
   4_adp:   7.693  0.045  0.281 88.430  0.032  2.324   6.1749e-02
   4_occ:   7.693  0.045  0.281 88.430  0.032  2.324   6.1749e-02
   5_bss:   7.693  0.045  0.281 88.430  0.032  2.324   6.1749e-02
   5_xyz:   7.784  0.058  0.661 81.867  0.030  2.259   8.3268e-02
   5_adp:   7.784  0.058  0.661 81.867  0.030  2.259   8.3268e-02
   5_occ:   7.784  0.058  0.661 81.867  0.030  2.259   8.3268e-02
   5_bss:   7.784  0.058  0.661 81.867  0.030  2.259   8.3268e-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: 105.48   0.00  14.14  80.24   0.00  11.79 105.48   0.00  26.99
   1_occ: 105.48   0.00  14.14  80.24   0.00  11.79 105.48   0.00  26.99
   2_bss: 105.48   0.00  14.14  80.24   0.00  11.79 105.48   0.00  26.99
   2_xyz: 105.48   0.00  14.14  80.24   0.00  11.79 105.48   0.00  26.99
   2_adp:  99.29   0.00  13.96  74.92   0.00  10.99  99.29   0.00  30.12
   2_occ:  99.29   0.00  13.96  74.92   0.00  10.99  99.29   0.00  30.12
   3_bss:  99.29   0.00  13.96  74.92   0.00  10.99  99.29   0.00  30.12
   3_xyz:  99.29   0.00  13.96  74.92   0.00  10.99  99.29   0.00  30.12
   3_adp: 121.60   0.00  13.93 121.60   0.00  10.33  98.78   2.15  33.54
   3_occ: 121.60   0.00  13.93 121.60   0.00  10.33  98.78   2.15  33.54
   4_bss: 121.60   0.00  13.93 121.60   0.00  10.33  98.78   2.15  33.54
   4_xyz: 121.60   0.00  13.93 121.60   0.00  10.33  98.78   2.15  33.54
   4_adp: 101.27   0.00  15.15 101.27   0.00  10.26  97.85   2.74  41.76
   4_occ: 101.27   0.00  15.15 101.27   0.00  10.26  97.85   2.74  41.76
   5_bss: 101.27   0.00  15.15 101.27   0.00  10.26  97.85   2.74  41.76
   5_xyz: 101.27   0.00  15.15 101.27   0.00  10.26  97.85   2.74  41.76
   5_adp: 103.92   0.00  14.68 103.92   0.00   9.85  99.34   2.39  40.97
   5_occ: 103.92   0.00  14.68 103.92   0.00   9.85  99.34   2.39  40.97
   5_bss: 105.51   1.59  16.27 105.51   1.59  11.45 100.93   3.98  42.56
------------------------------------------------------------------------
 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:    1.127    0.020    0.411
   1_adp:    1.127    0.020    0.411
   1_occ:    1.127    0.020    0.411
   2_bss:    1.127    0.020    0.411
   2_xyz:    1.931    0.021    0.569
   2_adp:    1.931    0.021    0.569
   2_occ:    1.931    0.021    0.569
   3_bss:    1.931    0.021    0.569
   3_xyz:    1.553    0.027    0.673
   3_adp:    1.553    0.027    0.673
   3_occ:    1.553    0.027    0.673
   4_bss:    1.553    0.027    0.673
   4_xyz:    1.797    0.027    0.758
   4_adp:    1.797    0.027    0.758
   4_occ:    1.797    0.027    0.758
   5_bss:    1.797    0.027    0.758
   5_xyz:    1.841    0.033    0.810
   5_adp:    1.841    0.033    0.810
   5_occ:    1.841    0.033    0.810
   5_bss:    1.841    0.033    0.810
------------------------------------------------------------------------

CPU time actual refinement: 337.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/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_827/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_827/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.47 
  Macro-tasks:
    bulk solvent and scale       = 41.95  
    individual site refinement   = 141.93 
    weights calculation          = 32.25  
    collect and process          = 6.34   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.59 
  Micro-tasks:
    mask                            = 3.01   
    f_calc                          = 103.81 
    alpha_beta                      = 8.36   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.79 
    fmodel                         = 7.30   
    r_factors                      = 0.19   
    phase_errors                   = 10.24  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 249.09 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.719 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    641 calls, 103.51 s
gradients_fft:          586 calls, 101.29 s

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

# Date 2008-01-16 Time 02:31:53 PST -0800 (1200479513.03 s)
Start R-work = 0.4864, R-free = 0.4816 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1864 (no bulk solvent and anisotropic scale)

Start R-work = 0.4790, R-free = 0.4713
Final R-work = 0.1214, R-free = 0.1706