# Date 2008-01-16 Time 01:46:30 PST -0800 (1200476790.34 s)
#phil __OFF__

Command line arguments: "../560.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28633
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 560

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.1647, 88.5498, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99078
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.945963

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0370
                             d_min =   1.9908

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99078
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.945963

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0375 -  4.2595 [2175/2202]  1955   220  10.1%
  bin  2:  4.2595 -  3.3937 [2068/2084]  1862   206  10.0%
  bin  3:  3.3937 -  2.9685 [2060/2079]  1856   204   9.9%
  bin  4:  2.9685 -  2.6988 [2042/2072]  1835   207  10.1%
  bin  5:  2.6988 -  2.5063 [2006/2025]  1807   199   9.9%
  bin  6:  2.5063 -  2.3591 [2026/2051]  1822   204  10.1%
  bin  7:  2.3591 -  2.2414 [2012/2045]  1816   196   9.7%
  bin  8:  2.2414 -  2.1441 [1985/2016]  1778   207  10.4%
  bin  9:  2.1441 -  2.0618 [1978/2020]  1788   190   9.6%
  bin 10:  2.0618 -  1.9908 [1237/2050]  1111   126  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/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:
        1.37 -     2.08: 7
        2.08 -     2.78: 573
        2.78 -     3.49: 4434
        3.49 -     4.19: 9219
        4.19 -     4.90: 13728
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.369 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.563 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.604 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.692 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.692 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27956 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_560/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/model_refine_001.geo

CPU time processing inputs: 8.94


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.16465 88.54975 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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4699   r_free= 0.4568   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.273486                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1411  156 0.3838 0.3579      6.5937       6.521|
|  2:  4.7508 -  3.7907 0.99   1353  152 0.3798 0.4385      6.7503      6.9109|
|  3:  3.7907 -  3.3174 0.99   1324  147 0.4342 0.3994       6.668      6.6205|
|  4:  3.3174 -  3.0168 0.99   1329  141 0.4570 0.4287      6.5091      6.4531|
|  5:  3.0168 -  2.8020 0.99   1308  152 0.4932 0.4678      6.3528      6.3644|
|  6:  2.8020 -  2.6378 0.99   1307  141 0.4959 0.5737      6.2709      6.2404|
|  7:  2.6378 -  2.5063 0.99   1283  147 0.5020 0.4553      6.2222      6.1211|
|  8:  2.5063 -  2.3976 0.98   1291  144 0.5296 0.4324      6.2008       6.137|
|  9:  2.3976 -  2.3057 0.98   1305  140 0.5099 0.5166      6.1013      6.1476|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.5301 0.4541      6.1178       6.045|
| 11:  2.2264 -  2.1570 0.99   1270  149 0.5092 0.5472      6.0206      6.0696|
| 12:  2.1570 -  2.0955 0.97   1275  137 0.5228 0.4967      5.9526      6.0129|
| 13:  2.0955 -  2.0404 0.98   1282  137 0.5271 0.5348      5.8933       5.833|
| 14:  2.0404 -  1.9908 0.46    592   74 0.5064 0.4395      5.8876      5.7071|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.7508  1411   156  0.72  32.17   0.80     0.74      63769.75|
|  2:  4.7508 -  3.7907  1353   152  0.72  33.49   0.88     0.77      98465.78|
|  3:  3.7907 -  3.3174  1324   147  0.63  41.49   0.82     0.73     104225.99|
|  4:  3.3174 -  3.0168  1329   141  0.54  48.71   0.80     0.61      92800.39|
|  5:  3.0168 -  2.8020  1308   152  0.44  56.66   0.74     0.51      77880.39|
|  6:  2.8020 -  2.6378  1307   141  0.39  60.22   0.72     0.45      71178.47|
|  7:  2.6378 -  2.5063  1283   147  0.41  59.15   0.74     0.46      61509.58|
|  8:  2.5063 -  2.3976  1291   144  0.45  56.21   0.72     0.51      51049.45|
|  9:  2.3976 -  2.3057  1305   140  0.45  55.72   0.71     0.53      46797.52|
| 10:  2.3057 -  2.2264  1300   142  0.42  58.62   0.74     0.48      44621.38|
| 11:  2.2264 -  2.1570  1270   149  0.36  63.13   0.75     0.44      46097.98|
| 12:  2.1570 -  2.0955  1275   137  0.35  63.61   0.74     0.44      41555.47|
| 13:  2.0955 -  2.0404  1282   137  0.38  61.93   0.73     0.46      34719.89|
| 14:  2.0404 -  1.9908   592    74  0.47  54.66   0.75     0.48      24409.29|
|alpha:            min =        0.44 max =            0.77 mean =         0.55|
|beta:             min =    24409.29 max =       104225.99 mean =     63177.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.96|
|phase err.(test): min =        0.00 max =           89.96 mean =        53.29|
|-----------------------------------------------------------------------------|

============================== 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 = 12.298897             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.383   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.005127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.692   (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 |  1.174 -  1.547:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.547 -  1.919:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.919 -  2.292:      156 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.292 -  2.665:      660 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.665 -  3.037:     1456 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.037 -  3.410:     2545 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.410 -  3.782:     3886 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.782 -  4.155:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.155 -  4.527:     6567 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.527 -  4.900:     7642 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.265 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.174 |       1.883 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    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 = 12.115)------------------------------------------|
|    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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4758   r_free= 0.4574   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.278122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4600   r_free= 0.4439   ksol= 0.32   Bsol= 11.93   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.60,7.71,12.49,0.00,0.00,0.00); trace/3= 8.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.266660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.792910             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.367   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.937866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.237   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4600      final r-factor (work) = 0.3703          |
| start r-factor (free) = 0.4439      final r-factor (free) = 0.3942          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.1213 = 10.79 * 0.50 * 6.2739 + 1.00 * 54.2645                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.3915 = 10.79 * 0.50 * 6.1619 + 1.00 * 0.1393                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3703      final r-factor (work) = 0.3233          |
| start r-factor (free) = 0.3942      final r-factor (free) = 0.3687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7934 = 0.94 * 1.00 * 6.1619 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7001 = 0.94 * 1.00 * 6.0621 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.86   12.70    None  None   None       |
|    all(noH): 2823   0      0.00    67.86   12.70    None  None   None       |
|    Sol.    : 438    0      0.00    67.86   26.44    None  None   None       |
|    Mac.    : 2385   0      0.00    59.05   10.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.786: 1068   |   5:    33.929 -  40.714:   90        |
|      1:     6.786 -  13.572:  775   |   6:    40.714 -  47.500:   49        |
|      2:    13.572 -  20.357:  422   |   7:    47.500 -  54.286:   37        |
|      3:    20.357 -  27.143:  222   |   8:    54.286 -  61.072:    9        |
|      4:    27.143 -  33.929:  143   |   9:    61.072 -  67.857:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3233 r_free = 0.3687             target_work(ml) = 6.036         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3227 r_free = 0.3700             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3227   r_free= 0.3700   ksol= 0.32   Bsol= 11.93   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.60,7.71,12.49,0.00,0.00,0.00); trace/3= 8.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.035029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3189   r_free= 0.3674   ksol= 0.33   Bsol= 44.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,3.99,8.39,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.035292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.882896              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.393   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.470692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.772  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3189      final r-factor (work) = 0.2463          |
| start r-factor (free) = 0.3674      final r-factor (free) = 0.2988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9322 = 4.88 * 0.50 * 6.0591 + 1.00 * 0.1393                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5187 = 4.88 * 0.50 * 5.9159 + 1.00 * 0.0754                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2463      final r-factor (work) = 0.2270          |
| start r-factor (free) = 0.2988      final r-factor (free) = 0.2801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7994 = 0.47 * 1.00 * 5.9159 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7317 = 0.47 * 1.00 * 5.7787 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.42   12.67    None  None   None       |
|    all(noH): 2823   0      0.00    68.42   12.67    None  None   None       |
|    Sol.    : 438    0      0.00    68.42   31.87    None  None   None       |
|    Mac.    : 2385   0      0.00    64.09   9.15     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.842: 1190   |   5:    34.209 -  41.051:  110        |
|      1:     6.842 -  13.684:  768   |   6:    41.051 -  47.893:   75        |
|      2:    13.684 -  20.525:  333   |   7:    47.893 -  54.734:   39        |
|      3:    20.525 -  27.367:  170   |   8:    54.734 -  61.576:   14        |
|      4:    27.367 -  34.209:  115   |   9:    61.576 -  68.418:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2270 r_free = 0.2801             target_work(ml) = 5.754         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2269 r_free = 0.2802             target_work(ml) = 5.754         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2269   r_free= 0.2802   ksol= 0.33   Bsol= 44.51   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.93,3.99,8.39,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.754002                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2258   r_free= 0.2810   ksol= 0.31   Bsol= 57.13   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.91,2.95,5.78,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.755537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.527740              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.389  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.735934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.595  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2258      final r-factor (work) = 0.1687          |
| start r-factor (free) = 0.2810      final r-factor (free) = 0.2204          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2733 = 3.53 * 0.50 * 5.7815 + 1.00 * 0.0755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0051 = 3.53 * 0.50 * 5.6324 + 1.00 * 0.0703                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1687      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2204      final r-factor (free) = 0.2049          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1567 = 0.74 * 1.00 * 5.6324 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0218 = 0.74 * 1.00 * 5.4454 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.04   13.22    None  None   None       |
|    all(noH): 2823   0      0.00    85.04   13.22    None  None   None       |
|    Sol.    : 438    0      1.34    85.04   37.58    None  None   None       |
|    Mac.    : 2385   0      0.00    74.34   8.75     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.504: 1554   |   5:    42.520 -  51.024:  112        |
|      1:     8.504 -  17.008:  655   |   6:    51.024 -  59.528:   69        |
|      2:    17.008 -  25.512:  188   |   7:    59.528 -  68.032:   29        |
|      3:    25.512 -  34.016:  100   |   8:    68.032 -  76.536:   12        |
|      4:    34.016 -  42.520:  101   |   9:    76.536 -  85.040:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1527 r_free = 0.2049             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1525 r_free = 0.2046             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1525   r_free= 0.2046   ksol= 0.31   Bsol= 57.13   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.91,2.95,5.78,0.00,0.00,0.00); trace/3= 3.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1522   r_free= 0.2039   ksol= 0.32   Bsol= 66.99   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.51,2.33,4.41,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.409083                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.968007              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.942  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.553642              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.990  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1522      final r-factor (work) = 0.1353          |
| start r-factor (free) = 0.2039      final r-factor (free) = 0.1812          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4324 = 1.97 * 0.50 * 5.4493 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3341 = 1.97 * 0.50 * 5.3595 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1320          |
| start r-factor (free) = 0.1812      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9842 = 0.55 * 1.00 * 5.3595 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9445 = 0.55 * 1.00 * 5.2940 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.39   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    86.39   13.05    None  None   None       |
|    Sol.    : 438    0      1.11    86.39   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    75.06   8.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.639: 1602   |   5:    43.196 -  51.835:  112        |
|      1:     8.639 -  17.278:  626   |   6:    51.835 -  60.474:   65        |
|      2:    17.278 -  25.917:  172   |   7:    60.474 -  69.113:   25        |
|      3:    25.917 -  34.556:  107   |   8:    69.113 -  77.752:   12        |
|      4:    34.556 -  43.196:  100   |   9:    77.752 -  86.391:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1320 r_free = 0.1779             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1319 r_free = 0.1778             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1778   ksol= 0.32   Bsol= 66.99   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.51,2.33,4.41,0.00,0.00,0.00); trace/3= 2.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.283966                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1318   r_free= 0.1778   ksol= 0.33   Bsol= 63.29   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.40,4.19,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.283747                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.163759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.928  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.812666              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.491  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7877 = 2.16 * 0.50 * 5.2939 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7501 = 2.16 * 0.50 * 5.2527 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7875 = 2.81 * 1.00 * 5.2527 + 1.00 * 0.0134                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6989 = 2.81 * 1.00 * 5.2204 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.20   13.17    None  None   None       |
|    all(noH): 2823   0      0.00    97.20   13.17    None  None   None       |
|    Sol.    : 438    0      0.70    97.20   38.52    None  None   None       |
|    Mac.    : 2385   0      0.00    83.95   8.52     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 -   9.720: 1763   |   5:    48.600 -  58.320:   96        |
|      1:     9.720 -  19.440:  514   |   6:    58.320 -  68.040:   46        |
|      2:    19.440 -  29.160:  169   |   7:    68.040 -  77.760:   23        |
|      3:    29.160 -  38.880:  113   |   8:    77.760 -  87.479:    8        |
|      4:    38.880 -  48.600:   90   |   9:    87.479 -  97.199:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1683             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1683             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1683   ksol= 0.33   Bsol= 63.29   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.40,4.19,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.222067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1411  156 0.1026 0.1339      5.4326      5.5844|
|  2:  4.7508 -  3.7907 0.99   1353  152 0.0869 0.1128      5.4706      5.6838|
|  3:  3.7907 -  3.3174 0.99   1324  147 0.1141 0.1581      5.5354      5.8703|
|  4:  3.3174 -  3.0168 0.99   1329  141 0.1290 0.1732      5.4995      5.6836|
|  5:  3.0168 -  2.8020 0.99   1308  152 0.1459 0.1651      5.4096      5.5544|
|  6:  2.8020 -  2.6378 0.99   1307  141 0.1361 0.2281      5.2941       5.625|
|  7:  2.6378 -  2.5063 0.99   1283  147 0.1388 0.1755      5.2716      5.4072|
|  8:  2.5063 -  2.3976 0.98   1291  144 0.1261 0.1762      5.1641      5.4047|
|  9:  2.3976 -  2.3057 0.98   1305  140 0.1300 0.2143      5.1089      5.4676|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.1222 0.1644       5.034      5.1908|
| 11:  2.2264 -  2.1570 0.99   1270  149 0.1251 0.2091      5.0197      5.3817|
| 12:  2.1570 -  2.0955 0.97   1275  137 0.1272 0.1685      4.9678      5.2085|
| 13:  2.0955 -  2.0404 0.98   1282  137 0.1205 0.1904      4.8524       5.087|
| 14:  2.0404 -  1.9908 0.46    592   74 0.1038 0.1788       4.719      4.9938|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.7508  1411   156  0.94   9.84   0.97     0.95       8352.47|
|  2:  4.7508 -  3.7907  1353   152  0.95   8.59   1.01     0.98       9931.91|
|  3:  3.7907 -  3.3174  1324   147  0.93  12.18   1.02     1.02      11450.93|
|  4:  3.3174 -  3.0168  1329   141  0.91  14.32   1.01     1.00      11175.18|
|  5:  3.0168 -  2.8020  1308   152  0.89  17.23   1.00     0.97       9649.56|
|  6:  2.8020 -  2.6378  1307   141  0.88  18.27   0.97     0.94       8509.63|
|  7:  2.6378 -  2.5063  1283   147  0.89  17.47   0.98     0.94       7665.77|
|  8:  2.5063 -  2.3976  1291   144  0.89  16.98   0.99     0.96       6596.20|
|  9:  2.3976 -  2.3057  1305   140  0.89  17.31   0.99     0.95       5909.51|
| 10:  2.3057 -  2.2264  1300   142  0.89  17.39   0.99     0.94       5151.79|
| 11:  2.2264 -  2.1570  1270   149  0.88  18.33   0.98     0.94       5294.64|
| 12:  2.1570 -  2.0955  1275   137  0.89  17.31   0.99     0.98       4731.78|
| 13:  2.0955 -  2.0404  1282   137  0.89  17.78   0.98     0.95       3860.89|
| 14:  2.0404 -  1.9908   592    74  0.91  14.91   0.96     0.92       2840.08|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2840.08 max =        11450.93 mean =      7437.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.52|
|phase err.(test): min =        0.00 max =           88.87 mean =        14.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1683   ksol= 0.33   Bsol= 66.18   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-0.37,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.221979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1683   ksol= 0.33   Bsol= 66.18   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,-0.37,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.221979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7508 0.99   1411  156 0.1011 0.1338      5.4256      5.5774|
|  2:  4.7508 -  3.7907 0.99   1353  152 0.0877 0.1131      5.4776      5.6881|
|  3:  3.7907 -  3.3174 0.99   1324  147 0.1141 0.1583      5.5371       5.871|
|  4:  3.3174 -  3.0168 0.99   1329  141 0.1289 0.1740      5.4995      5.6868|
|  5:  3.0168 -  2.8020 0.99   1308  152 0.1456 0.1646      5.4094      5.5517|
|  6:  2.8020 -  2.6378 0.99   1307  141 0.1359 0.2277      5.2922      5.6227|
|  7:  2.6378 -  2.5063 0.99   1283  147 0.1386 0.1756      5.2712      5.4064|
|  8:  2.5063 -  2.3976 0.98   1291  144 0.1261 0.1765      5.1641      5.4053|
|  9:  2.3976 -  2.3057 0.98   1305  140 0.1299 0.2143       5.109      5.4682|
| 10:  2.3057 -  2.2264 0.98   1300  142 0.1221 0.1644      5.0341       5.191|
| 11:  2.2264 -  2.1570 0.99   1270  149 0.1251 0.2089      5.0194      5.3814|
| 12:  2.1570 -  2.0955 0.97   1275  137 0.1272 0.1683      4.9677      5.2076|
| 13:  2.0955 -  2.0404 0.98   1282  137 0.1204 0.1907      4.8522      5.0877|
| 14:  2.0404 -  1.9908 0.46    592   74 0.1039 0.1785      4.7195       4.993|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.7508  1411   156  0.93  10.01   0.97     0.94       8381.73|
|  2:  4.7508 -  3.7907  1353   152  0.95   8.61   1.01     0.98       9961.83|
|  3:  3.7907 -  3.3174  1324   147  0.93  12.21   1.02     1.02      11521.89|
|  4:  3.3174 -  3.0168  1329   141  0.91  14.34   1.01     1.00      11192.37|
|  5:  3.0168 -  2.8020  1308   152  0.89  17.21   1.00     0.97       9645.05|
|  6:  2.8020 -  2.6378  1307   141  0.88  18.21   0.98     0.95       8472.70|
|  7:  2.6378 -  2.5063  1283   147  0.89  17.45   0.99     0.94       7654.71|
|  8:  2.5063 -  2.3976  1291   144  0.89  16.98   0.99     0.96       6594.42|
|  9:  2.3976 -  2.3057  1305   140  0.89  17.32   1.00     0.96       5917.98|
| 10:  2.3057 -  2.2264  1300   142  0.89  17.38   1.00     0.94       5151.99|
| 11:  2.2264 -  2.1570  1270   149  0.88  18.32   0.99     0.94       5292.07|
| 12:  2.1570 -  2.0955  1275   137  0.89  17.31   0.99     0.98       4730.81|
| 13:  2.0955 -  2.0404  1282   137  0.89  17.78   0.99     0.96       3859.15|
| 14:  2.0404 -  1.9908   592    74  0.91  14.91   0.97     0.92       2838.65|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2838.65 max =        11521.89 mean =      7445.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.53|
|phase err.(test): min =        0.00 max =           87.38 mean =        14.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.115)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.89    100.09  16.06    None  None   None       |
|    all(noH): 2823   0      2.89    100.09  16.06    None  None   None       |
|    Sol.    : 438    0      3.59    100.09  41.41    None  None   None       |
|    Mac.    : 2385   0      2.89    86.84   11.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.891 -  12.611: 1763   |   5:    51.491 -  61.211:   96        |
|      1:    12.611 -  22.331:  514   |   6:    61.211 -  70.931:   46        |
|      2:    22.331 -  32.051:  169   |   7:    70.931 -  80.650:   23        |
|      3:    32.051 -  41.771:  113   |   8:    80.650 -  90.370:    8        |
|      4:    41.771 -  51.491:   90   |   9:    90.370 - 100.090:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.172 - 4.460
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 295
   mapped sites are within: 0.704 - 4.460

peak=   10.269 closest distance to " CB  VAL A 230 " =    1.444
peak=    6.116 closest distance to " CD1AILE A 234 " =    1.113
peak=    5.832 closest distance to " CD2 LEU A   5 " =    1.144
peak=    5.655 closest distance to " O   HOH Z 248 " =    1.340
peak=    5.521 closest distance to " NH1 ARG A 138 " =    0.978
peak=    5.464 closest distance to " CG  LEU A   5 " =    1.226
peak=    5.329 closest distance to " CB  GLN A 223 " =    1.510
peak=    5.298 closest distance to " NH2 ARG A  56 " =    2.117
peak=    5.260 closest distance to " CG  PRO A  54 " =    1.328
peak=    5.141 closest distance to " CG  LEU A 228 " =    1.242
peak=    5.132 closest distance to " NE2 GLN A  11 " =    1.062
peak=    5.082 closest distance to " O   HOH Z 142 " =    1.796
peak=    5.025 closest distance to " CG1 VAL A 296 " =    1.201
peak=    4.971 closest distance to " CB  VAL A 296 " =    1.058
peak=    4.825 closest distance to " CG2 VAL A 296 " =    1.051
peak=    4.698 closest distance to " O   HOH Z 265 " =    2.072
peak=    4.671 closest distance to " O   HOH Z 232 " =    2.236
peak=    4.621 closest distance to " CB  ARG A 275 " =    0.946
peak=    4.621 closest distance to " O   HOH Z 126 " =    1.640
peak=    4.590 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.585 closest distance to " CZ  PHE A 218 " =    1.178
peak=    4.549 closest distance to " CB  ASN A 148 " =    1.436
peak=    4.472 closest distance to " O   HOH Z 425 " =    1.526
peak=    4.421 closest distance to " O   HOH Z 369 " =    2.207
peak=    4.402 closest distance to " O   HOH Z 128 " =    1.286
peak=    4.381 closest distance to " CA  TYR A  30 " =    0.961
peak=    4.376 closest distance to " O   HOH Z 368 " =    2.385
peak=    4.371 closest distance to " CB  ASN A 142 " =    1.226
peak=    4.355 closest distance to " O   HOH Z 251 " =    1.693
peak=    4.345 closest distance to " CB  ARG A 190 " =    1.662
peak=    4.335 closest distance to " CD2 LEU A 228 " =    1.200
peak=    4.335 closest distance to " O   PRO A 198 " =    1.581
peak=    4.284 closest distance to " O   HOH Z 214 " =    1.300
peak=    4.282 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.271 closest distance to " CB  GLU A 277 " =    3.768
peak=    4.260 closest distance to " CB  PRO A  54 " =    0.976
peak=    4.239 closest distance to " O   SER A  87 " =    2.477
peak=    4.236 closest distance to " O   HOH Z 313 " =    1.921
peak=    4.168 closest distance to " O   HOH Z   4 " =    1.597
peak=    4.167 closest distance to " CD2 TRP A 179 " =    1.292
peak=    4.159 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.152 closest distance to " O   HOH Z   9 " =    1.297
peak=    4.118 closest distance to " CZ3 TRP A 266 " =    1.131
peak=    4.104 closest distance to " O   HOH Z 427 " =    3.022
peak=    4.102 closest distance to " O   HOH Z 346 " =    1.495
peak=    4.096 closest distance to " CB  ASP A 124 " =    0.843
peak=    4.085 closest distance to " O   HOH Z 261 " =    2.307
peak=    4.068 closest distance to " O   HOH Z 411 " =    3.915
peak=    4.059 closest distance to " CA  ARG A 195 " =    1.212
peak=    4.056 closest distance to " NH2AARG A 145 " =    1.139
peak=    4.050 closest distance to " CB  VAL A 230 " =    1.170
peak=    4.044 closest distance to " O   HOH Z 207 " =    1.162
peak=    4.041 closest distance to " O   HOH Z 422 " =    2.628
peak=    4.036 closest distance to " O   HOH Z 402 " =    1.378
peak=    4.028 closest distance to " CG2 ILE A 234 " =    1.034
peak=    4.004 closest distance to " CE  LYS A  76 " =    0.900
peak=    4.000 closest distance to " CA  ALA A  51 " =    0.943
peak=    3.994 closest distance to " O  BHOH Z 338 " =    2.195
peak=    3.980 closest distance to " CB  VAL A 265 " =    1.222
peak=    3.969 closest distance to " O  BHOH Z  74 " =    1.223
peak=    3.961 closest distance to " CB  SER A  63 " =    1.121
peak=    3.946 closest distance to " CD  ARG A 269 " =    0.984
peak=    3.946 closest distance to " O   HOH Z  76 " =    1.169
peak=    3.942 closest distance to " CB  TYR A 169 " =    0.704
peak=    3.941 closest distance to " O   HOH Z 406 " =    1.547
peak=    3.936 closest distance to " O   HOH Z 365 " =    2.709
peak=    3.927 closest distance to " CZ  PHE A  38 " =    1.166
peak=    3.924 closest distance to " CG  GLN A  58 " =    0.901
peak=    3.921 closest distance to " NH1AARG A 145 " =    1.259
peak=    3.919 closest distance to " O   HOH Z 287 " =    1.938
peak=    3.912 closest distance to " O   HOH Z 353 " =    2.665
peak=    3.909 closest distance to " O   HOH Z 303 " =    2.085
peak=    3.906 closest distance to " ND2 ASN A 249 " =    0.897
peak=    3.903 closest distance to " O   HOH Z 403 " =    1.576
peak=    3.897 closest distance to " O   HOH Z  78 " =    1.631
peak=    3.896 closest distance to " O   HOH Z 247 " =    1.370
peak=    3.876 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.875 closest distance to " CB  PRO A  90 " =    1.146
peak=    3.872 closest distance to " CB  SER A  26 " =    1.825
peak=    3.868 closest distance to " CB  ARG A  79 " =    1.401
peak=    3.851 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.850 closest distance to " O   HOH Z 214 " =    2.420
peak=    3.827 closest distance to " O   HOH Z 127 " =    0.945
peak=    3.818 closest distance to " CA  ARG A  36 " =    1.036
peak=    3.814 closest distance to " O   HOH Z 199 " =    1.552
peak=    3.810 closest distance to " CA  VAL A 125 " =    1.201
peak=    3.795 closest distance to " CB  VAL A 202 " =    1.579
peak=    3.779 closest distance to " O   HOH Z 359 " =    1.813
peak=    3.771 closest distance to " O   HOH Z  40 " =    1.724
peak=    3.770 closest distance to " CB  TRP A 179 " =    1.452
peak=    3.762 closest distance to " O   HOH Z 188 " =    2.852
peak=    3.760 closest distance to " N   ASN A  39 " =    1.267
peak=    3.757 closest distance to " CG  GLU A  37 " =    0.961
peak=    3.749 closest distance to " CG AARG A 275 " =    1.237
peak=    3.747 closest distance to " O   HOH Z 263 " =    1.696
peak=    3.740 closest distance to " O   HOH Z 290 " =    1.022
peak=    3.739 closest distance to " O   HOH Z 126 " =    2.060
peak=    3.738 closest distance to " O   HOH Z 298 " =    1.860
peak=    3.737 closest distance to " O   HOH Z 193 " =    1.639
peak=    3.735 closest distance to " CG1 ILE A  49 " =    1.611
peak=    3.728 closest distance to " O   HOH Z  43 " =    2.056
peak=    3.725 closest distance to " N   GLY A 133 " =    3.736
peak=    3.716 closest distance to " CB  THR A  52 " =    0.827
peak=    3.713 closest distance to " CG2AVAL A 121 " =    2.329
peak=    3.709 closest distance to " O   HOH Z 193 " =    1.400
peak=    3.708 closest distance to " CG1 VAL A 153 " =    1.051
peak=    3.701 closest distance to " O   HOH Z  80 " =    1.893
peak=    3.683 closest distance to " CB BVAL A  41 " =    1.250
peak=    3.679 closest distance to " CG  PRO A 213 " =    1.156
peak=    3.676 closest distance to " CD  ARG A 159 " =    0.732
peak=    3.667 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.654 closest distance to " NH2 ARG A  56 " =    1.177
peak=    3.646 closest distance to " CD1 LEU A  96 " =    0.763
peak=    3.642 closest distance to " SD AMET A  47 " =    0.722
peak=    3.638 closest distance to " O   HOH Z  49 " =    1.122
peak=    3.632 closest distance to " O   HOH Z 154 " =    2.283
peak=    3.620 closest distance to " O   HOH Z 162 " =    1.379
peak=    3.614 closest distance to " CB  GLN A  89 " =    1.203
peak=    3.610 closest distance to " O   ALA A 165 " =    1.436
peak=    3.608 closest distance to " O   HOH Z 234 " =    3.582
peak=    3.600 closest distance to " CB  GLU A 128 " =    1.066
peak=    3.596 closest distance to " O   THR A 182 " =    1.403
peak=    3.595 closest distance to " O   HOH Z 203 " =    1.732
peak=    3.594 closest distance to " O   HOH Z 258 " =    1.970
peak=    3.592 closest distance to " O   HOH Z 299 " =    4.311
peak=    3.591 closest distance to " O   HOH Z 112 " =    0.933
peak=    3.588 closest distance to " CG  MET A 185 " =    1.235
peak=    3.587 closest distance to " CG  ARG A  66 " =    2.697
peak=    3.586 closest distance to " O   ASP A 124 " =    1.175
peak=    3.586 closest distance to " ND2 ASN A 187 " =    1.669
peak=    3.580 closest distance to " CB  GLU A 152 " =    1.160
peak=    3.576 closest distance to " OG BSER A 164 " =    2.368
peak=    3.572 closest distance to " O   HOH Z 193 " =    1.798
peak=    3.571 closest distance to " NE2 HIS A 207 " =    1.142
peak=    3.568 closest distance to " CB  PHE A 204 " =    0.996
peak=    3.567 closest distance to " O   HOH Z 438 " =    2.799
peak=    3.565 closest distance to " CA  MET A 105 " =    1.016
peak=    3.564 closest distance to " CG2 ILE A  20 " =    1.338
peak=    3.563 closest distance to " O   HOH Z 329 " =    4.238
peak=    3.561 closest distance to " O   ASN A  74 " =    1.374
peak=    3.559 closest distance to " O   HOH Z 280 " =    2.968
peak=    3.557 closest distance to " CA  ALA A 160 " =    0.985
peak=    3.553 closest distance to " CG AARG A 102 " =    1.207
peak=    3.549 closest distance to " O   HOH Z  83 " =    1.428
peak=    3.546 closest distance to " CD1 ILE A 199 " =    0.971
peak=    3.538 closest distance to " CD  LYS A  76 " =    1.995
peak=    3.535 closest distance to " O   HOH Z  63 " =    1.746
peak=    3.531 closest distance to " O   HOH Z 337 " =    1.976
peak=    3.530 closest distance to " CG2 VAL A 257 " =    0.791
peak=    3.529 closest distance to " CG  PHE A 204 " =    0.919
peak=    3.529 closest distance to " O   HOH Z   3 " =    1.835
peak=    3.528 closest distance to " CA  TYR A 116 " =    1.441
peak=    3.522 closest distance to " CE3 TRP A 150 " =    1.171
peak=    3.504 closest distance to " CG  LEU A 167 " =    1.219
peak=    3.497 closest distance to " OG  SER A 276 " =    1.311
peak=    3.494 closest distance to " CE1 TYR A 186 " =    1.230
peak=    3.492 closest distance to " O   HOH Z 368 " =    3.328
peak=    3.489 closest distance to " CD1 ILE A  33 " =    1.762
peak=    3.488 closest distance to " CB  GLU A  46 " =    0.926
peak=    3.481 closest distance to " CA  SER A  87 " =    1.029
peak=    3.478 closest distance to " O   HOH Z  92 " =    2.090
peak=    3.478 closest distance to " O   HOH Z 148 " =    3.475
peak=    3.477 closest distance to " CD1 LEU A 101 " =    1.200
peak=    3.468 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.468 closest distance to " CB  LYS A 117 " =    1.270
peak=    3.466 closest distance to " CB  THR A  31 " =    1.587
peak=    3.462 closest distance to " CB  ASP A 298 " =    1.165
peak=    3.460 closest distance to " O   HOH Z 213 " =    1.944
peak=    3.459 closest distance to " O   HOH Z 154 " =    1.534
peak=    3.453 closest distance to " O   HOH Z  61 " =    1.786
peak=    3.447 closest distance to " O   ASP A 200 " =    1.674
peak=    3.435 closest distance to " CA  ASP A 191 " =    1.314
peak=    3.435 closest distance to " O   HOH Z 133 " =    1.229
peak=    3.414 closest distance to " O   HOH Z  68 " =    2.201
peak=    3.406 closest distance to " CA  ALA A 291 " =    0.859
peak=    3.405 closest distance to " CA  ALA A 154 " =    1.034
peak=    3.403 closest distance to " OD1 ASN A  69 " =    2.516
peak=    3.402 closest distance to " CZ3 TRP A 274 " =    4.460
peak=    3.394 closest distance to " O   HOH Z 407 " =    2.384
peak=    3.394 closest distance to " O   PHE A 192 " =    1.409
peak=    3.394 closest distance to " N   ALA A 256 " =    1.098
peak=    3.392 closest distance to " O   HOH Z 371 " =    2.873
peak=    3.382 closest distance to " O   HOH Z 305 " =    3.353
peak=    3.382 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.375 closest distance to " O   HOH Z 158 " =    3.059
peak=    3.375 closest distance to " O   HOH Z 316 " =    3.029
peak=    3.375 closest distance to " CA  ASN A 127 " =    1.101
peak=    3.374 closest distance to " CA  LEU A 282 " =    1.168
peak=    3.374 closest distance to " O   LEU A 228 " =    1.809
peak=    3.368 closest distance to " O   HOH Z 272 " =    1.815
peak=    3.361 closest distance to " CB  ASN A 215 " =    1.202
peak=    3.360 closest distance to " OG  SER A 245 " =    1.570
peak=    3.357 closest distance to " CB  ASN A 110 " =    1.180
peak=    3.355 closest distance to " CA  ARG A 139 " =    1.117
peak=    3.354 closest distance to " CA  GLY A 267 " =    0.909
peak=    3.348 closest distance to " O   HOH Z 172 " =    3.848
peak=    3.336 closest distance to " CD  LYS A 119 " =    2.000
peak=    3.327 closest distance to " CB  SER A  62 " =    1.023
peak=    3.322 closest distance to " O   HOH Z 133 " =    2.773
peak=    3.316 closest distance to " CG BARG A 102 " =    1.840
peak=    3.316 closest distance to " O   HOH Z 189 " =    2.956
peak=    3.315 closest distance to " N   ASP A 162 " =    1.269
peak=    3.315 closest distance to " CA  ILE A 106 " =    0.769
peak=    3.314 closest distance to " CB  PRO A 243 " =    1.131
peak=    3.312 closest distance to " O   HOH Z 417 " =    3.204
peak=    3.309 closest distance to " O   GLN A  88 " =    1.656
peak=    3.307 closest distance to " CE1 HIS A  81 " =    1.673
peak=    3.306 closest distance to " O   HOH Z  44 " =    2.703
peak=    3.302 closest distance to " O   HOH Z 421 " =    3.038
peak=    3.301 closest distance to " O   HOH Z 171 " =    3.987
peak=    3.293 closest distance to " CE  LYS A  48 " =    1.140
peak=    3.290 closest distance to " CA  GLN A  94 " =    0.799
peak=    3.289 closest distance to " CZ3 TRP A  92 " =    1.356
peak=    3.287 closest distance to " CB  ARG A 219 " =    1.115
peak=    3.286 closest distance to " CB  SER A 273 " =    0.952
peak=    3.283 closest distance to " O   HOH Z 394 " =    3.744
peak=    3.282 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.281 closest distance to " CB  SER A 212 " =    1.240
peak=    3.279 closest distance to " CB  ALA A 242 " =    0.894
peak=    3.276 closest distance to " NE2 GLN A  77 " =    3.263
peak=    3.275 closest distance to " CD BLYS A 290 " =    0.997
peak=    3.270 closest distance to " CA  ASN A 215 " =    1.050
peak=    3.263 closest distance to " CG2AVAL A  72 " =    1.812
peak=    3.262 closest distance to " CB  GLN A  88 " =    1.246
peak=    3.261 closest distance to " CA  LYS A 290 " =    1.143
peak=    3.249 closest distance to " O   HOH Z  21 " =    1.714
peak=    3.248 closest distance to " O   HOH Z  47 " =    1.877
peak=    3.245 closest distance to " O   HOH Z 392 " =    2.870
peak=    3.242 closest distance to " CB  SER A   3 " =    1.356
peak=    3.238 closest distance to " CD1 LEU A  96 " =    1.277
peak=    3.238 closest distance to " OE2 GLU A  53 " =    1.951
peak=    3.230 closest distance to " N   PHE A 130 " =    1.249
peak=    3.227 closest distance to " CA  ALA A 158 " =    1.332
peak=    3.226 closest distance to " O   HOH Z 258 " =    1.225
peak=    3.224 closest distance to " CD2 TYR A 186 " =    1.057
peak=    3.220 closest distance to " CG2 THR A 220 " =    0.784
peak=    3.216 closest distance to " O   HOH Z 258 " =    1.485
peak=    3.215 closest distance to " O   HOH Z 285 " =    2.221
peak=    3.206 closest distance to " CA  ASN A  74 " =    1.149
peak=    3.202 closest distance to " CA  LYS A 117 " =    1.282
peak=    3.198 closest distance to " OE1 GLN A  55 " =    1.399
peak=    3.196 closest distance to " CA  ASP A 162 " =    0.979
peak=    3.194 closest distance to " CE3 TRP A  85 " =    1.205
peak=    3.193 closest distance to " OG BSER A 134 " =    2.875
peak=    3.191 closest distance to " OG  SER A 135 " =    1.275
peak=    3.191 closest distance to " OD2 ASP A  50 " =    2.863
peak=    3.191 closest distance to " CA  THR A 264 " =    0.764
peak=    3.190 closest distance to " O   HOH Z 371 " =    3.369
peak=    3.189 closest distance to " CB  ASN A 173 " =    1.103
peak=    3.185 closest distance to " CG2BVAL A 121 " =    0.748
peak=    3.184 closest distance to " CE  LYS A 119 " =    1.092
peak=    3.181 closest distance to " O   HOH Z 132 " =    2.653
peak=    3.177 closest distance to " CB  SER A 288 " =    1.534
peak=    3.172 closest distance to " O   HOH Z 200 " =    2.307
peak=    3.172 closest distance to " O   HOH Z 368 " =    4.018
peak=    3.160 closest distance to " O   HOH Z 383 " =    1.841
peak=    3.159 closest distance to " O   HOH Z 116 " =    1.733
peak=    3.152 closest distance to " NZ  LYS A  48 " =    1.122
peak=    3.148 closest distance to " O   MET A 105 " =    1.878
peak=    3.142 closest distance to " CG  PRO A 280 " =    1.008
peak=    3.141 closest distance to " CG2 ILE A 120 " =    1.280
peak=    3.140 closest distance to " CB  SER A 216 " =    0.920
peak=    3.138 closest distance to " CG2 VAL A 197 " =    1.041
peak=    3.137 closest distance to " O   HOH Z 345 " =    3.461
peak=    3.136 closest distance to " CA  ALA A  21 " =    1.113
peak=    3.134 closest distance to " N   TYR A 247 " =    1.309
peak=    3.134 closest distance to " O   HOH Z 350 " =    1.526
peak=    3.130 closest distance to " OG  SER A  62 " =    2.860
peak=    3.123 closest distance to " OH  TYR A 169 " =    0.966
peak=    3.123 closest distance to " O   HOH Z   1 " =    2.028
peak=    3.121 closest distance to " O   HOH Z 371 " =    2.326
peak=    3.118 closest distance to " O   HOH Z 421 " =    2.231
peak=    3.116 closest distance to " O   ASN A 284 " =    1.754
peak=    3.109 closest distance to " CG  LEU A 281 " =    1.024
peak=    3.101 closest distance to " CG1 ILE A  20 " =    1.296
peak=    3.100 closest distance to " CG  MET A 185 " =    1.004
peak=    3.099 closest distance to " O   SER A 164 " =    1.325
peak=    3.089 closest distance to " O   HOH Z 117 " =    2.032
peak=    3.072 closest distance to " O   HOH Z 391 " =    2.913
peak=    3.061 closest distance to " CB  HIS A 108 " =    0.835
peak=    3.057 closest distance to " CG  LEU A 101 " =    1.208
peak=    3.051 closest distance to " O   HOH Z 145 " =    2.412
peak=    3.047 closest distance to " OE2 GLU A   2 " =    1.939
peak=    3.045 closest distance to " CB  ASN A 187 " =    1.446
peak=    3.042 closest distance to " CB  LEU A 300 " =    0.899
peak=    3.038 closest distance to " CB  ASN A  74 " =    1.471
peak=    3.027 closest distance to " CB  ALA A  43 " =    0.832
peak=    3.020 closest distance to " O   HOH Z   3 " =    2.069

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.772 - 5.642
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 218
   mapped sites are within: 0.772 - 5.642

peak=   -4.620 closest distance to " CG2 VAL A 230 " =    0.783
peak=   -4.582 closest distance to " SG  CYS A 254 " =    3.354
peak=   -4.443 closest distance to " CG1 VAL A 296 " =    1.074
peak=   -4.432 closest distance to " CG  GLN A  58 " =    1.068
peak=   -4.354 closest distance to " O   HOH Z 211 " =    1.055
peak=   -4.308 closest distance to " O   HOH Z 193 " =    0.891
peak=   -4.304 closest distance to " C   HIS A 108 " =    1.150
peak=   -4.280 closest distance to " CB  PRO A 243 " =    2.797
peak=   -4.279 closest distance to " CA  ASP A 298 " =    1.106
peak=   -4.258 closest distance to " O   VAL A  67 " =    2.682
peak=   -4.221 closest distance to " CD  ARG A 156 " =    2.118
peak=   -4.213 closest distance to " CZ2 TRP A  92 " =    2.827
peak=   -4.164 closest distance to " OG BSER A 134 " =    1.493
peak=   -4.138 closest distance to " O   HOH Z 411 " =    5.629
peak=   -4.097 closest distance to " O   HOH Z 216 " =    1.103
peak=   -4.071 closest distance to " CE3 TRP A 150 " =    2.300
peak=   -4.054 closest distance to " O   HOH Z 127 " =    1.102
peak=   -4.031 closest distance to " O   HOH Z 166 " =    2.322
peak=   -4.027 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.991 closest distance to " CG1 VAL A 112 " =    2.742
peak=   -3.974 closest distance to " O   HOH Z 359 " =    2.825
peak=   -3.954 closest distance to " OE1 GLN A 223 " =    2.353
peak=   -3.952 closest distance to " CG1 VAL A 250 " =    2.773
peak=   -3.942 closest distance to " CD1 LEU A 101 " =    2.395
peak=   -3.898 closest distance to " O   HOH Z 133 " =    1.087
peak=   -3.891 closest distance to " CD2 TYR A 293 " =    1.975
peak=   -3.886 closest distance to " O   HOH Z 166 " =    1.809
peak=   -3.848 closest distance to " CE2 PHE A  61 " =    2.696
peak=   -3.831 closest distance to " O   PRO A 163 " =    2.172
peak=   -3.814 closest distance to " O   SER A 271 " =    2.096
peak=   -3.811 closest distance to " CB  HIS A  86 " =    1.167
peak=   -3.810 closest distance to " NE2 GLN A  11 " =    1.672
peak=   -3.809 closest distance to " CE2 TYR A  30 " =    2.690
peak=   -3.795 closest distance to " CA  GLY A 241 " =    2.364
peak=   -3.792 closest distance to " O   HOH Z 394 " =    1.637
peak=   -3.773 closest distance to " O   HOH Z 131 " =    4.062
peak=   -3.772 closest distance to " O   HOH Z  69 " =    1.775
peak=   -3.760 closest distance to " CG2 VAL A 189 " =    1.992
peak=   -3.759 closest distance to " CG1 VAL A 112 " =    2.686
peak=   -3.750 closest distance to " CG  ARG A 269 " =    2.279
peak=   -3.750 closest distance to " O   HOH Z 231 " =    2.176
peak=   -3.747 closest distance to " CB  VAL A 230 " =    1.189
peak=   -3.736 closest distance to " O   HOH Z 103 " =    1.723
peak=   -3.730 closest distance to " O   HOH Z 154 " =    1.575
peak=   -3.719 closest distance to " OG  SER A  97 " =    2.336
peak=   -3.710 closest distance to " O   HOH Z 100 " =    0.949
peak=   -3.696 closest distance to " CD  PRO A 243 " =    1.892
peak=   -3.693 closest distance to " O   HOH Z 285 " =    1.971
peak=   -3.687 closest distance to " O   HOH Z 149 " =    1.946
peak=   -3.672 closest distance to " O   HOH Z 295 " =    1.597
peak=   -3.665 closest distance to " O   HOH Z  73 " =    2.433
peak=   -3.662 closest distance to " OXT GLY A 302 " =    3.062
peak=   -3.661 closest distance to " O   HOH Z 252 " =    3.694
peak=   -3.660 closest distance to " CB  ALA A 161 " =    2.586
peak=   -3.656 closest distance to " O   HOH Z 110 " =    1.328
peak=   -3.653 closest distance to " CE2 TRP A  70 " =    2.111
peak=   -3.645 closest distance to " CB  PHE A 192 " =    2.054
peak=   -3.618 closest distance to " O   HOH Z 210 " =    0.940
peak=   -3.611 closest distance to " CG2 ILE A  20 " =    3.004
peak=   -3.609 closest distance to " CG  GLU A 277 " =    1.254
peak=   -3.579 closest distance to " O   ALA A 227 " =    1.255
peak=   -3.575 closest distance to " OE1 GLN A  88 " =    0.943
peak=   -3.567 closest distance to " O   GLY A  17 " =    1.140
peak=   -3.565 closest distance to " CG2 THR A 178 " =    2.305
peak=   -3.563 closest distance to " NE  ARG A  66 " =    4.268
peak=   -3.562 closest distance to " O   HOH Z 106 " =    1.831
peak=   -3.544 closest distance to " O   HOH Z 198 " =    1.783
peak=   -3.542 closest distance to " O   HOH Z 128 " =    1.023
peak=   -3.541 closest distance to " O   HOH Z 431 " =    1.982
peak=   -3.540 closest distance to " CB  PRO A 280 " =    2.111
peak=   -3.530 closest distance to " O   HOH Z 191 " =    5.642
peak=   -3.522 closest distance to " CE BMET A  47 " =    1.354
peak=   -3.518 closest distance to " CD1 ILE A 199 " =    2.468
peak=   -3.516 closest distance to " O   HOH Z   6 " =    2.234
peak=   -3.514 closest distance to " N   THR A  52 " =    1.633
peak=   -3.509 closest distance to " OD1 ASN A 249 " =    2.511
peak=   -3.507 closest distance to " CB  ALA A 248 " =    2.223
peak=   -3.486 closest distance to " O   HOH Z 107 " =    1.094
peak=   -3.484 closest distance to " O   HOH Z 128 " =    2.431
peak=   -3.482 closest distance to " O   HOH Z 275 " =    1.865
peak=   -3.475 closest distance to " O   HOH Z  68 " =    1.274
peak=   -3.465 closest distance to " CB  ALA A  43 " =    2.641
peak=   -3.464 closest distance to " OD1 ASN A 148 " =    1.356
peak=   -3.460 closest distance to " CG2 VAL A 296 " =    1.183
peak=   -3.457 closest distance to " O   HOH Z  19 " =    2.313
peak=   -3.449 closest distance to " O   HOH Z 165 " =    1.915
peak=   -3.443 closest distance to " ND2 ASN A  45 " =    1.236
peak=   -3.438 closest distance to " NE2 GLN A  88 " =    1.136
peak=   -3.436 closest distance to " O   HOH Z 115 " =    1.783
peak=   -3.432 closest distance to " CE3 TRP A  70 " =    1.780
peak=   -3.430 closest distance to " O   HOH Z  43 " =    1.657
peak=   -3.418 closest distance to " O   HOH Z  64 " =    1.540
peak=   -3.418 closest distance to " CG2AVAL A  41 " =    2.853
peak=   -3.414 closest distance to " O   HOH Z 251 " =    4.956
peak=   -3.409 closest distance to " CG  PRO A 243 " =    1.623
peak=   -3.403 closest distance to " O   HOH Z 174 " =    2.464
peak=   -3.400 closest distance to " CD2 PHE A 225 " =    1.087
peak=   -3.396 closest distance to " O   HOH Z  52 " =    1.755
peak=   -3.393 closest distance to " O   HOH Z 286 " =    1.880
peak=   -3.391 closest distance to " O   HOH Z 290 " =    1.137
peak=   -3.386 closest distance to " O   TRP A  70 " =    1.604
peak=   -3.380 closest distance to " O   HOH Z 119 " =    2.117
peak=   -3.380 closest distance to " OD1 ASN A  39 " =    2.147
peak=   -3.372 closest distance to " O   HOH Z 177 " =    1.764
peak=   -3.371 closest distance to " N   ALA A 226 " =    2.004
peak=   -3.370 closest distance to " O   HOH Z 275 " =    1.547
peak=   -3.363 closest distance to " O   HOH Z 111 " =    1.566
peak=   -3.362 closest distance to " O   HOH Z 236 " =    1.424
peak=   -3.362 closest distance to " CE  MET A 105 " =    2.376
peak=   -3.358 closest distance to " NE2 GLN A 103 " =    1.679
peak=   -3.355 closest distance to " O   HOH Z  44 " =    0.772
peak=   -3.354 closest distance to " O   SER A 210 " =    1.765
peak=   -3.351 closest distance to " C   ALA A 158 " =    1.227
peak=   -3.350 closest distance to " O   HOH Z 434 " =    1.629
peak=   -3.350 closest distance to " O   ASP A  27 " =    1.903
peak=   -3.348 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.346 closest distance to " CD  LYS A 289 " =    2.416
peak=   -3.343 closest distance to " NE2 GLN A 194 " =    1.973
peak=   -3.338 closest distance to " OG  SER A  62 " =    4.336
peak=   -3.337 closest distance to " CD2 LEU A  96 " =    2.046
peak=   -3.334 closest distance to " CD1 LEU A 255 " =    2.835
peak=   -3.320 closest distance to " O   HOH Z 351 " =    1.720
peak=   -3.318 closest distance to " OD2 ASP A  50 " =    2.228
peak=   -3.316 closest distance to " O   HOH Z 102 " =    1.606
peak=   -3.309 closest distance to " CB  ALA A 129 " =    2.459
peak=   -3.307 closest distance to " CG  LYS A 193 " =    2.751
peak=   -3.304 closest distance to " CH2 TRP A 179 " =    1.247
peak=   -3.301 closest distance to " N   SER A 276 " =    1.447
peak=   -3.301 closest distance to " O   HOH Z 238 " =    0.872
peak=   -3.298 closest distance to " NE2 GLN A 278 " =    1.864
peak=   -3.294 closest distance to " CZ  TYR A 169 " =    1.823
peak=   -3.283 closest distance to " CG  GLU A  53 " =    1.564
peak=   -3.280 closest distance to " CG1 VAL A 125 " =    1.920
peak=   -3.280 closest distance to " OD1 ASN A 173 " =    1.438
peak=   -3.273 closest distance to " CD2 HIS A 207 " =    2.134
peak=   -3.268 closest distance to " N   PHE A  59 " =    2.071
peak=   -3.268 closest distance to " CZ  PHE A  38 " =    2.534
peak=   -3.262 closest distance to " CE3 TRP A 274 " =    2.343
peak=   -3.259 closest distance to " O   HOH Z 244 " =    2.019
peak=   -3.255 closest distance to " CB  ALA A 248 " =    2.268
peak=   -3.253 closest distance to " CE1 TYR A 247 " =    2.622
peak=   -3.250 closest distance to " O   ILE A 263 " =    2.210
peak=   -3.249 closest distance to " C   MET A 188 " =    1.474
peak=   -3.248 closest distance to " O   ILE A 106 " =    1.922
peak=   -3.247 closest distance to " OD1 ASP A 171 " =    1.621
peak=   -3.241 closest distance to " O   ALA A 180 " =    1.437
peak=   -3.240 closest distance to " O   HOH Z 348 " =    2.208
peak=   -3.239 closest distance to " O   HOH Z   6 " =    1.524
peak=   -3.236 closest distance to " CD1 TRP A  70 " =    1.820
peak=   -3.234 closest distance to " O   HOH Z 372 " =    0.984
peak=   -3.226 closest distance to " OG  SER A  87 " =    1.616
peak=   -3.218 closest distance to " ND2 ASN A 249 " =    2.429
peak=   -3.218 closest distance to " O   HOH Z 411 " =    1.604
peak=   -3.215 closest distance to " CA  GLY A 241 " =    3.162
peak=   -3.215 closest distance to " CA  GLY A 203 " =    2.501
peak=   -3.214 closest distance to " CG2 VAL A 202 " =    2.675
peak=   -3.209 closest distance to " O   TYR A 186 " =    1.776
peak=   -3.200 closest distance to " CA  GLY A 133 " =    2.316
peak=   -3.194 closest distance to " ND2 ASN A  45 " =    1.610
peak=   -3.193 closest distance to " O   SER A 276 " =    1.674
peak=   -3.192 closest distance to " O   HOH Z 301 " =    2.486
peak=   -3.192 closest distance to " O   HOH Z 265 " =    2.427
peak=   -3.190 closest distance to " O   HOH Z 423 " =    2.228
peak=   -3.187 closest distance to " O   HOH Z 260 " =    1.887
peak=   -3.186 closest distance to " CB  ALA A  10 " =    2.281
peak=   -3.186 closest distance to " CD  GLN A 223 " =    1.614
peak=   -3.185 closest distance to " O   HOH Z  10 " =    1.502
peak=   -3.183 closest distance to " NH1 ARG A  66 " =    3.728
peak=   -3.182 closest distance to " CB  ASP A 171 " =    2.237
peak=   -3.177 closest distance to " CD1 ILE A 239 " =    2.174
peak=   -3.174 closest distance to " CG  ASP A 231 " =    0.966
peak=   -3.174 closest distance to " O   HOH Z 421 " =    3.235
peak=   -3.170 closest distance to " CB  TRP A  85 " =    2.606
peak=   -3.169 closest distance to " O   HOH Z 368 " =    1.442
peak=   -3.169 closest distance to " O   HOH Z 357 " =    2.230
peak=   -3.165 closest distance to " O   HOH Z 278 " =    1.186
peak=   -3.164 closest distance to " O   HOH Z 139 " =    5.289
peak=   -3.152 closest distance to " O   HOH Z 244 " =    1.504
peak=   -3.152 closest distance to " O   HOH Z  60 " =    1.639
peak=   -3.151 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.150 closest distance to " OG  SER A  28 " =    2.099
peak=   -3.150 closest distance to " O   HOH Z 292 " =    1.778
peak=   -3.149 closest distance to " O   ASN A 187 " =    1.613
peak=   -3.146 closest distance to " O   HOH Z   9 " =    2.923
peak=   -3.146 closest distance to " CB  ALA A   9 " =    2.418
peak=   -3.145 closest distance to " OG ASER A 134 " =    1.345
peak=   -3.144 closest distance to " CD1 TYR A 247 " =    2.394
peak=   -3.143 closest distance to " CG2 THR A  29 " =    2.567
peak=   -3.141 closest distance to " CG  MET A 105 " =    1.005
peak=   -3.139 closest distance to " O   HOH Z 246 " =    0.864
peak=   -3.138 closest distance to " O   HOH Z 162 " =    2.795
peak=   -3.137 closest distance to " CG2 VAL A 125 " =    1.456
peak=   -3.132 closest distance to " O   HOH Z 371 " =    2.496
peak=   -3.130 closest distance to " O   HOH Z 371 " =    1.225
peak=   -3.123 closest distance to " NH2AARG A 275 " =    5.088
peak=   -3.123 closest distance to " O   HOH Z  17 " =    1.516
peak=   -3.122 closest distance to " O   ASN A 252 " =    1.423
peak=   -3.118 closest distance to " O   HOH Z 155 " =    2.343
peak=   -3.114 closest distance to " CA  HIS A 207 " =    1.195
peak=   -3.112 closest distance to " CH2 TRP A 150 " =    1.177
peak=   -3.112 closest distance to " ND2 ASN A  69 " =    1.990
peak=   -3.110 closest distance to " OXT GLY A 302 " =    3.333
peak=   -3.107 closest distance to " O   HOH Z 346 " =    1.824
peak=   -3.104 closest distance to " CD  GLN A  73 " =    0.891
peak=   -3.104 closest distance to " O   HOH Z 323 " =    1.384
peak=   -3.100 closest distance to " CB  ALA A 291 " =    2.203
peak=   -3.100 closest distance to " N   ASP A 286 " =    2.328
peak=   -3.092 closest distance to " OG  SER A  63 " =    1.190
peak=   -3.092 closest distance to " C   ASP A 270 " =    1.227
peak=   -3.088 closest distance to " OH  TYR A 247 " =    1.866
peak=   -3.086 closest distance to " N   ALA A 248 " =    1.918
peak=   -3.084 closest distance to " O   HOH Z 185 " =    2.437
peak=   -3.081 closest distance to " N   ALA A 248 " =    2.343
peak=   -3.072 closest distance to " OG  SER A 141 " =    1.776
peak=   -3.055 closest distance to " ND2BASN A 224 " =    1.849
peak=   -3.047 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.046 closest distance to " C   ARG A  79 " =    2.637
peak=   -3.013 closest distance to " CA  SER A  62 " =    2.543

================= 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    :  0.4699 0.4568   6.273486e+00   6.253351e+00
   1_bss:  0.4600 0.4439   6.266660e+00   6.240185e+00
   1_xyz:  0.3703 0.3942   6.133811e+00   6.169488e+00
   1_adp:  0.3233 0.3687   6.035696e+00   6.121953e+00
   1_occ:  0.3227 0.3700   6.035029e+00   6.123858e+00
   2_bss:  0.3189 0.3674   6.035292e+00   6.123650e+00
   2_xyz:  0.2463 0.2988   5.814443e+00   5.960538e+00
   2_adp:  0.2270 0.2801   5.754019e+00   5.916950e+00
   2_occ:  0.2269 0.2802   5.754002e+00   5.917485e+00
   3_bss:  0.2258 0.2810   5.755537e+00   5.919140e+00
   3_xyz:  0.1687 0.2204   5.492054e+00   5.689325e+00
   3_adp:  0.1527 0.2049   5.410797e+00   5.622856e+00
   3_occ:  0.1525 0.2046   5.410812e+00   5.623378e+00
   4_bss:  0.1522 0.2039   5.409083e+00   5.620165e+00
   4_xyz:  0.1353 0.1812   5.304557e+00   5.522713e+00
   4_adp:  0.1320 0.1779   5.284371e+00   5.502802e+00
   4_occ:  0.1319 0.1778   5.283966e+00   5.502444e+00
   5_bss:  0.1318 0.1778   5.283747e+00   5.502337e+00
   5_xyz:  0.1228 0.1680   5.228810e+00   5.459634e+00
   5_adp:  0.1206 0.1683   5.222210e+00   5.459191e+00
   5_occ:  0.1206 0.1683   5.222067e+00   5.459113e+00
   5_bss:  0.1204 0.1683   5.221979e+00   5.458781e+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:  0.322  11.932   6.596   7.710  12.490   0.000   0.000   0.000
   1_xyz:  0.322  11.932   6.596   7.710  12.490   0.000   0.000   0.000
   1_adp:  0.322  11.932   6.596   7.710  12.490   0.000   0.000   0.000
   1_occ:  0.322  11.932   6.596   7.710  12.490   0.000   0.000   0.000
   2_bss:  0.328  44.506   2.928   3.991   8.391   0.000   0.000   0.000
   2_xyz:  0.328  44.506   2.928   3.991   8.391   0.000   0.000   0.000
   2_adp:  0.328  44.506   2.928   3.991   8.391   0.000   0.000   0.000
   2_occ:  0.328  44.506   2.928   3.991   8.391   0.000   0.000   0.000
   3_bss:  0.314  57.130   1.911   2.952   5.779   0.000   0.000   0.000
   3_xyz:  0.314  57.130   1.911   2.952   5.779   0.000   0.000   0.000
   3_adp:  0.314  57.130   1.911   2.952   5.779   0.000   0.000   0.000
   3_occ:  0.314  57.130   1.911   2.952   5.779   0.000   0.000   0.000
   4_bss:  0.320  66.991   1.514   2.332   4.405   0.000   0.000   0.000
   4_xyz:  0.320  66.991   1.514   2.332   4.405   0.000   0.000   0.000
   4_adp:  0.320  66.991   1.514   2.332   4.405   0.000   0.000   0.000
   4_occ:  0.320  66.991   1.514   2.332   4.405   0.000   0.000   0.000
   5_bss:  0.328  63.292   1.707   2.402   4.187   0.000   0.000   0.000
   5_xyz:  0.328  63.292   1.707   2.402   4.187   0.000   0.000   0.000
   5_adp:  0.328  63.292   1.707   2.402   4.187   0.000   0.000   0.000
   5_occ:  0.328  63.292   1.707   2.402   4.187   0.000   0.000   0.000
   5_bss:  0.328  66.183  -0.987  -0.368   1.355   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.988 0.4841  0.5506    63169.003
   1_bss:  51.716 0.4994  0.7412    60544.179
   1_xyz:  44.315 0.5900  0.8503    44818.389
   1_adp:  40.017 0.6427  0.9533    38476.357
   1_occ:  40.099 0.6417  0.9507    38634.746
   2_bss:  39.815 0.6452  0.8385    38480.323
   2_xyz:  31.040 0.7461  0.9503    24098.923
   2_adp:  28.539 0.7742  0.9737    21337.691
   2_occ:  28.576 0.7738  0.9732    21373.461
   3_bss:  28.514 0.7746  0.9216    21446.235
   3_xyz:  21.351 0.8486  0.9771    12420.024
   3_adp:  19.465 0.8672  0.9813    10806.717
   3_occ:  19.480 0.8670  0.9812    10806.085
   4_bss:  19.346 0.8682  0.9552    10693.142
   4_xyz:  16.974 0.8899  0.9652     8538.836
   4_adp:  16.451 0.8948  0.9604     8240.295
   4_occ:  16.441 0.8949  0.9605     8235.585
   5_bss:  16.434 0.8950  0.9614     8229.008
   5_xyz:  15.487 0.9031  0.9673     7462.409
   5_adp:  15.459 0.9035  0.9602     7439.607
   5_occ:  15.457 0.9035  0.9602     7436.733
   5_bss:  15.472 0.9034  0.9642     7444.197
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4265e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4265e+01
   1_xyz:   1.680  0.014  0.106 18.119  0.007  4.112   1.3932e-01
   1_adp:   1.680  0.014  0.106 18.119  0.007  4.112   1.3932e-01
   1_occ:   1.680  0.014  0.106 18.119  0.007  4.112   1.3932e-01
   2_bss:   1.680  0.014  0.106 18.119  0.007  4.112   1.3932e-01
   2_xyz:   1.136  0.008  0.077 16.058  0.004  4.127   7.5419e-02
   2_adp:   1.136  0.008  0.077 16.058  0.004  4.127   7.5419e-02
   2_occ:   1.136  0.008  0.077 16.058  0.004  4.127   7.5419e-02
   3_bss:   1.136  0.008  0.077 16.058  0.004  4.127   7.5419e-02
   3_xyz:   1.106  0.008  0.082 15.980  0.004  4.131   7.0283e-02
   3_adp:   1.106  0.008  0.082 15.980  0.004  4.131   7.0283e-02
   3_occ:   1.106  0.008  0.082 15.980  0.004  4.131   7.0283e-02
   4_bss:   1.106  0.008  0.082 15.980  0.004  4.131   7.0283e-02
   4_xyz:   0.978  0.007  0.075 15.631  0.003  4.115   6.0331e-02
   4_adp:   0.978  0.007  0.075 15.631  0.003  4.115   6.0331e-02
   4_occ:   0.978  0.007  0.075 15.631  0.003  4.115   6.0331e-02
   5_bss:   0.978  0.007  0.075 15.631  0.003  4.115   6.0331e-02
   5_xyz:   1.057  0.009  0.083 15.441  0.004  4.120   6.7323e-02
   5_adp:   1.057  0.009  0.083 15.441  0.004  4.120   6.7323e-02
   5_occ:   1.057  0.009  0.083 15.441  0.004  4.120   6.7323e-02
   5_bss:   1.057  0.009  0.083 15.441  0.004  4.120   6.7323e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.174   7.0341e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.174   7.0341e+00
   1_xyz:  14.086  0.160  0.439 86.921  0.045  2.172   1.0430e-01
   1_adp:  14.086  0.160  0.439 86.921  0.045  2.172   1.0430e-01
   1_occ:  14.086  0.160  0.439 86.921  0.045  2.172   1.0430e-01
   2_bss:  14.086  0.160  0.439 86.921  0.045  2.172   1.0430e-01
   2_xyz:   7.145  0.067  0.262 85.581  0.031  2.285   6.8038e-02
   2_adp:   7.145  0.067  0.262 85.581  0.031  2.285   6.8038e-02
   2_occ:   7.145  0.067  0.262 85.581  0.031  2.285   6.8038e-02
   3_bss:   7.145  0.067  0.262 85.581  0.031  2.285   6.8038e-02
   3_xyz:   7.437  0.059  0.287 85.972  0.044  2.275   5.3317e-02
   3_adp:   7.437  0.059  0.287 85.972  0.044  2.275   5.3317e-02
   3_occ:   7.437  0.059  0.287 85.972  0.044  2.275   5.3317e-02
   4_bss:   7.437  0.059  0.287 85.972  0.044  2.275   5.3317e-02
   4_xyz:   7.486  0.043  0.294 82.573  0.038  2.364   3.5630e-02
   4_adp:   7.486  0.043  0.294 82.573  0.038  2.364   3.5630e-02
   4_occ:   7.486  0.043  0.294 82.573  0.038  2.364   3.5630e-02
   5_bss:   7.486  0.043  0.294 82.573  0.038  2.364   3.5630e-02
   5_xyz:   7.181  0.055  0.400 81.792  0.038  2.342   4.3487e-02
   5_adp:   7.181  0.055  0.400 81.792  0.038  2.342   4.3487e-02
   5_occ:   7.181  0.055  0.400 81.792  0.038  2.342   4.3487e-02
   5_bss:   7.181  0.055  0.400 81.792  0.038  2.342   4.3487e-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:  67.86   0.00  12.70  59.05   0.00  10.17  67.86   0.00  26.44
   1_occ:  67.86   0.00  12.70  59.05   0.00  10.17  67.86   0.00  26.44
   2_bss:  67.86   0.00  12.70  59.05   0.00  10.17  67.86   0.00  26.44
   2_xyz:  67.86   0.00  12.70  59.05   0.00  10.17  67.86   0.00  26.44
   2_adp:  68.42   0.00  12.67  64.09   0.00   9.15  68.42   0.00  31.87
   2_occ:  68.42   0.00  12.67  64.09   0.00   9.15  68.42   0.00  31.87
   3_bss:  68.42   0.00  12.67  64.09   0.00   9.15  68.42   0.00  31.87
   3_xyz:  68.42   0.00  12.67  64.09   0.00   9.15  68.42   0.00  31.87
   3_adp:  85.04   0.00  13.22  74.34   0.00   8.75  85.04   1.34  37.58
   3_occ:  85.04   0.00  13.22  74.34   0.00   8.75  85.04   1.34  37.58
   4_bss:  85.04   0.00  13.22  74.34   0.00   8.75  85.04   1.34  37.58
   4_xyz:  85.04   0.00  13.22  74.34   0.00   8.75  85.04   1.34  37.58
   4_adp:  86.39   0.00  13.05  75.06   0.00   8.53  86.39   1.11  37.66
   4_occ:  86.39   0.00  13.05  75.06   0.00   8.53  86.39   1.11  37.66
   5_bss:  86.39   0.00  13.05  75.06   0.00   8.53  86.39   1.11  37.66
   5_xyz:  86.39   0.00  13.05  75.06   0.00   8.53  86.39   1.11  37.66
   5_adp:  97.20   0.00  13.17  83.95   0.00   8.52  97.20   0.70  38.52
   5_occ:  97.20   0.00  13.17  83.95   0.00   8.52  97.20   0.70  38.52
   5_bss: 100.09   2.89  16.06  86.84   2.89  11.41 100.09   3.59  41.41
------------------------------------------------------------------------
 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:    1.263    0.012    0.412
   1_adp:    1.263    0.012    0.412
   1_occ:    1.263    0.012    0.412
   2_bss:    1.263    0.012    0.412
   2_xyz:    1.910    0.020    0.547
   2_adp:    1.910    0.020    0.547
   2_occ:    1.910    0.020    0.547
   3_bss:    1.910    0.020    0.547
   3_xyz:    1.791    0.035    0.635
   3_adp:    1.791    0.035    0.635
   3_occ:    1.791    0.035    0.635
   4_bss:    1.791    0.035    0.635
   4_xyz:    2.001    0.042    0.670
   4_adp:    2.001    0.042    0.670
   4_occ:    2.001    0.042    0.670
   5_bss:    2.001    0.042    0.670
   5_xyz:    1.991    0.028    0.689
   5_adp:    1.991    0.028    0.689
   5_occ:    1.991    0.028    0.689
   5_bss:    1.991    0.028    0.689
------------------------------------------------------------------------

CPU time actual refinement: 336.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/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_560/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_560/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.18 
  Macro-tasks:
    bulk solvent and scale       = 41.95  
    individual site refinement   = 130.02 
    weights calculation          = 31.72  
    collect and process          = 6.64   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 210.43 
  Micro-tasks:
    mask                            = 2.14   
    f_calc                          = 105.95 
    alpha_beta                      = 8.80   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 109.96 
    fmodel                         = 7.61   
    r_factors                      = 0.15   
    phase_errors                   = 11.43  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 247.49 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.776 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    662 calls, 105.35 s
gradients_fft:          607 calls,  99.09 s

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

# Date 2008-01-16 Time 01:52:19 PST -0800 (1200477139.98 s)
Start R-work = 0.4699, R-free = 0.4568 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4600, R-free = 0.4439
Final R-work = 0.1204, R-free = 0.1683