# Date 2008-01-16 Time 00:39:34 PST -0800 (1200472774.85 s)
#phil __OFF__

Command line arguments: "../102.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15951
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 102

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.8686, 85.5261, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.95075
Completeness in resolution range: 0.929887
Completeness with d_max=infinity: 0.927114

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9494
                             d_min =   1.9507

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9494 1.95075
Completeness in resolution range: 0.929887
Completeness with d_max=infinity: 0.927114

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9499 -  4.1751 [2216/2245]  1989   227  10.2%
  bin  2:  4.1751 -  3.3259 [2117/2140]  1908   209   9.9%
  bin  3:  3.3259 -  2.9090 [2094/2119]  1888   206   9.8%
  bin  4:  2.9090 -  2.6446 [2065/2092]  1857   208  10.1%
  bin  5:  2.6446 -  2.4560 [2054/2087]  1846   208  10.1%
  bin  6:  2.4560 -  2.3117 [2063/2091]  1865   198   9.6%
  bin  7:  2.3117 -  2.1963 [2042/2078]  1837   205  10.0%
  bin  8:  2.1963 -  2.1010 [2019/2061]  1818   201  10.0%
  bin  9:  2.1010 -  2.0203 [1994/2077]  1792   202  10.1%
  bin 10:  2.0203 -  1.9507 [ 925/2076]   830    95  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.87 -     1.67: 10
        1.67 -     2.48: 64
        2.48 -     3.29: 3682
        3.29 -     4.09: 9531
        4.09 -     4.90: 15379
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  0.866 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.363 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.410 3.270 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.475 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.503 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28661 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_102/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.8686 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5120   r_free= 0.4971   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.306948                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9499 -  4.6572 0.99   1436  159 0.4283 0.4190      6.6482      6.6882|
|  2:  4.6572 -  3.7152 0.99   1380  154 0.4467 0.4352      6.8535       6.854|
|  3:  3.7152 -  3.2511 0.99   1364  150 0.4946 0.4512      6.7195      6.7538|
|  4:  3.2511 -  2.9563 0.98   1331  144 0.4974 0.4779      6.5359      6.4958|
|  5:  2.9563 -  2.7458 0.99   1333  152 0.5436 0.5463      6.3894      6.3984|
|  6:  2.7458 -  2.5848 0.99   1350  151 0.5367 0.5210      6.2947      6.1899|
|  7:  2.5848 -  2.4560 0.98   1294  148 0.5450 0.4948       6.251      6.2035|
|  8:  2.4560 -  2.3495 0.98   1332  136 0.5447 0.5137      6.1873      6.2083|
|  9:  2.3495 -  2.2594 0.99   1307  149 0.5498 0.5818       6.125       6.178|
| 10:  2.2594 -  2.1816 0.99   1319  143 0.5435 0.5808      6.1157      6.1252|
| 11:  2.1816 -  2.1136 0.97   1322  148 0.5641 0.5529      6.0283      6.0408|
| 12:  2.1136 -  2.0533 0.98   1280  152 0.5513 0.5121      5.9572      5.9688|
| 13:  2.0533 -  1.9994 0.87   1148  125 0.5533 0.5398      5.8836      5.8517|
| 14:  1.9994 -  1.9507 0.32    434   48 0.5756 0.4867      5.8888       5.714|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9499 -  4.6572  1436   159  0.61  41.63   0.78     0.63      95939.29|
|  2:  4.6572 -  3.7152  1380   154  0.62  41.70   0.86     0.68     136376.06|
|  3:  3.7152 -  3.2511  1364   150  0.51  51.32   0.82     0.64     141502.96|
|  4:  3.2511 -  2.9563  1331   144  0.43  57.60   0.78     0.53     116986.41|
|  5:  2.9563 -  2.7458  1333   152  0.32  66.08   0.71     0.40      96618.01|
|  6:  2.7458 -  2.5848  1350   151  0.27  69.74   0.70     0.32      81944.86|
|  7:  2.5848 -  2.4560  1294   148  0.24  72.17   0.71     0.28      75503.42|
|  8:  2.4560 -  2.3495  1332   136  0.25  71.23   0.72     0.30      65838.52|
|  9:  2.3495 -  2.2594  1307   149  0.26  70.76   0.71     0.32      61594.90|
| 10:  2.2594 -  2.1816  1319   143  0.23  73.02   0.75     0.27      55547.52|
| 11:  2.1816 -  2.1136  1322   148  0.18  76.43   0.72     0.25      54782.60|
| 12:  2.1136 -  2.0533  1280   152  0.17  77.47   0.73     0.24      51249.22|
| 13:  2.0533 -  1.9994  1148   125  0.22  74.03   0.73     0.29      42236.11|
| 14:  1.9994 -  1.9507   434    48  0.32  65.91   0.70     0.35      28147.64|
|alpha:            min =        0.24 max =            0.68 mean =         0.40|
|beta:             min =    28147.64 max =       141502.96 mean =     82359.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.50|
|phase err.(test): min =        0.00 max =           89.97 mean =        64.51|
|-----------------------------------------------------------------------------|

============================== 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 = 18.831796             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.156   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.053659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.986   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.653 -  1.078:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.078 -  1.503:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.503 -  1.927:       29 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.927 -  2.352:      255 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.352 -  2.777:      972 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.777 -  3.201:     2187 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.201 -  3.626:     3793 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.626 -  4.051:     5426 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.051 -  4.475:     7204 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.475 -  4.900:     8786 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.327 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.653 |       3.361 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5159   r_free= 0.5026   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.307287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5044   r_free= 0.4919   ksol= 0.34   Bsol= 0.08   scale= 0.974    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.67,11.14,7.47,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.301731                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.896379             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.683   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.989836              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.643   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5044      final r-factor (work) = 0.4516          |
| start r-factor (free) = 0.4919      final r-factor (free) = 0.4679          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.5993 = 16.90 * 0.50 * 6.3057 + 1.00 * 53.3274                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.0345 = 16.90 * 0.50 * 6.2599 + 1.00 * 0.1495                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4516      final r-factor (work) = 0.4113          |
| start r-factor (free) = 0.4679      final r-factor (free) = 0.4647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4710 = 1.99 * 1.00 * 6.2599 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1089 = 1.99 * 1.00 * 6.0737 + 1.00 * 0.0233                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.56  17.20    None  None   None       |
|    all(noH): 2823   0      0.00    105.56  17.20    None  None   None       |
|    Sol.    : 438    0      0.00    105.56  26.44    None  None   None       |
|    Mac.    : 2385   0      0.00    80.59   15.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.556: 1099   |   5:    52.782 -  63.339:   39        |
|      1:    10.556 -  21.113:  857   |   6:    63.339 -  73.895:   17        |
|      2:    21.113 -  31.669:  461   |   7:    73.895 -  84.451:   13        |
|      3:    31.669 -  42.226:  235   |   8:    84.451 -  95.008:    2        |
|      4:    42.226 -  52.782:   99   |   9:    95.008 - 105.564:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4113 r_free = 0.4647             target_work(ml) = 6.207         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4107 r_free = 0.4637             target_work(ml) = 6.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4107   r_free= 0.4637   ksol= 0.34   Bsol= 0.08   scale= 1.129    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.67,11.14,7.47,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.205872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4090   r_free= 0.4550   ksol= 0.30   Bsol= 20.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,6.36,4.22,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.205995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.540412             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.039  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.729278              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.668  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4090      final r-factor (work) = 0.3466          |
| start r-factor (free) = 0.4550      final r-factor (free) = 0.4025          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.1414 = 10.54 * 0.50 * 6.0704 + 1.00 * 0.1489                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4676 = 10.54 * 0.50 * 6.1418 + 1.00 * 0.0988                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3466      final r-factor (work) = 0.3296          |
| start r-factor (free) = 0.4025      final r-factor (free) = 0.3926          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5023 = 0.73 * 1.00 * 6.1418 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4391 = 0.73 * 1.00 * 6.0690 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.80  16.81    None  None   None       |
|    all(noH): 2823   0      0.00    108.80  16.81    None  None   None       |
|    Sol.    : 438    0      0.00    108.80  30.38    None  None   None       |
|    Mac.    : 2385   0      0.00    87.16   14.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.880: 1203   |   5:    54.399 -  65.279:   23        |
|      1:    10.880 -  21.760:  856   |   6:    65.279 -  76.159:   21        |
|      2:    21.760 -  32.639:  397   |   7:    76.159 -  87.038:    5        |
|      3:    32.639 -  43.519:  233   |   8:    87.038 -  97.918:    3        |
|      4:    43.519 -  54.399:   81   |   9:    97.918 - 108.798:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3296 r_free = 0.3926             target_work(ml) = 6.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3295 r_free = 0.3921             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3295   r_free= 0.3921   ksol= 0.30   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.76,6.36,4.22,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.055988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3271   r_free= 0.3897   ksol= 0.32   Bsol= 44.45   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,3.32,2.09,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.055499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.612775              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.574  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.337241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.822  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3271      final r-factor (work) = 0.2565          |
| start r-factor (free) = 0.3897      final r-factor (free) = 0.3146          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1708 = 6.61 * 0.50 * 6.0707 + 1.00 * 0.0988                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8217 = 6.61 * 0.50 * 5.9672 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2565      final r-factor (work) = 0.2353          |
| start r-factor (free) = 0.3146      final r-factor (free) = 0.2918          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0255 = 0.34 * 1.00 * 5.9672 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9706 = 0.34 * 1.00 * 5.8167 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.14  16.03    None  None   None       |
|    all(noH): 2823   0      0.00    101.14  16.03    None  None   None       |
|    Sol.    : 438    0      3.26    101.14  34.33    None  None   None       |
|    Mac.    : 2385   0      0.00    88.76   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.115: 1225   |   5:    50.572 -  60.687:   46        |
|      1:    10.115 -  20.229:  881   |   6:    60.687 -  70.801:   14        |
|      2:    20.229 -  30.344:  325   |   7:    70.801 -  80.916:   10        |
|      3:    30.344 -  40.458:  191   |   8:    80.916 -  91.030:    5        |
|      4:    40.458 -  50.572:  125   |   9:    91.030 - 101.145:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2353 r_free = 0.2918             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2349 r_free = 0.2915             target_work(ml) = 5.786         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2349   r_free= 0.2915   ksol= 0.32   Bsol= 44.45   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,3.32,2.09,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.785935                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2336   r_free= 0.2904   ksol= 0.31   Bsol= 40.68   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,1.65,0.70,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.784481                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.622833              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.078   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.295981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.959  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2336      final r-factor (work) = 0.1747          |
| start r-factor (free) = 0.2904      final r-factor (free) = 0.2184          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5448 = 4.62 * 0.50 * 5.8202 + 1.00 * 0.0919                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1779 = 4.62 * 0.50 * 5.6687 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1747      final r-factor (work) = 0.1584          |
| start r-factor (free) = 0.2184      final r-factor (free) = 0.2020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6868 = 0.30 * 1.00 * 5.6687 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6281 = 0.30 * 1.00 * 5.4696 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.87   16.11    None  None   None       |
|    all(noH): 2823   0      0.00    93.87   16.11    None  None   None       |
|    Sol.    : 438    0      3.33    93.87   38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    90.97   11.91    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 -   9.387: 1161   |   5:    46.936 -  56.324:  101        |
|      1:     9.387 -  18.775:  988   |   6:    56.324 -  65.711:   49        |
|      2:    18.775 -  28.162:  228   |   7:    65.711 -  75.098:   18        |
|      3:    28.162 -  37.549:  132   |   8:    75.098 -  84.486:    3        |
|      4:    37.549 -  46.936:  138   |   9:    84.486 -  93.873:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1584 r_free = 0.2020             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1581 r_free = 0.2020             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1581   r_free= 0.2020   ksol= 0.31   Bsol= 40.68   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,1.65,0.70,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.428679                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1576   r_free= 0.2020   ksol= 0.32   Bsol= 45.18   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,0.34,0.03,0.00,0.00,0.00); trace/3= -0.45                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.431194                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.109839              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.498  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.217  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1576      final r-factor (work) = 0.1365          |
| start r-factor (free) = 0.2020      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8531 = 2.11 * 0.50 * 5.4771 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7234 = 2.11 * 0.50 * 5.3677 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1365      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2675 = 0.42 * 1.00 * 5.3677 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2374 = 0.42 * 1.00 * 5.2938 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.48   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    94.48   16.32    None  None   None       |
|    Sol.    : 438    0      4.93    85.46   41.21    None  None   None       |
|    Mac.    : 2385   0      0.00    94.48   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.448: 1203   |   5:    47.239 -  56.686:   94        |
|      1:     9.448 -  18.896:  987   |   6:    56.686 -  66.134:   64        |
|      2:    18.896 -  28.343:  194   |   7:    66.134 -  75.582:   32        |
|      3:    28.343 -  37.791:  124   |   8:    75.582 -  85.030:    7        |
|      4:    37.791 -  47.239:  113   |   9:    85.030 -  94.477:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1779             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1314 r_free = 0.1779             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1779   ksol= 0.32   Bsol= 45.18   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,0.34,0.03,0.00,0.00,0.00); trace/3= -0.45                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282083                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9499 -  4.6572 0.99   1436  159 0.1045 0.1429      5.4505      5.6254|
|  2:  4.6572 -  3.7152 0.99   1380  154 0.0940 0.1135      5.5233      5.7218|
|  3:  3.7152 -  3.2511 0.99   1364  150 0.1259 0.1720      5.6034      5.9351|
|  4:  3.2511 -  2.9563 0.98   1331  144 0.1487 0.1902      5.6011      5.7883|
|  5:  2.9563 -  2.7458 0.99   1333  152 0.1567 0.1894      5.4785      5.6068|
|  6:  2.7458 -  2.5848 0.99   1350  151 0.1512 0.2334        5.37      5.6138|
|  7:  2.5848 -  2.4560 0.98   1294  148 0.1460 0.1674      5.2787      5.4027|
|  8:  2.4560 -  2.3495 0.98   1332  136 0.1418 0.1837      5.2119      5.4112|
|  9:  2.3495 -  2.2594 0.99   1307  149 0.1391 0.2174      5.1409      5.4555|
| 10:  2.2594 -  2.1816 0.99   1319  143 0.1373 0.1874      5.1267      5.2969|
| 11:  2.1816 -  2.1136 0.97   1322  148 0.1321 0.2018      5.0299      5.3089|
| 12:  2.1136 -  2.0533 0.98   1280  152 0.1371 0.1883      4.9851      5.2425|
| 13:  2.0533 -  1.9994 0.87   1148  125 0.1330 0.2023      4.9087      5.1872|
| 14:  1.9994 -  1.9507 0.32    434   48 0.1271 0.1864      4.8475      5.0029|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9499 -  4.6572  1436   159  0.93  10.34   0.98     0.95       8630.94|
|  2:  4.6572 -  3.7152  1380   154  0.94   9.32   1.03     1.02      10953.61|
|  3:  3.7152 -  3.2511  1364   150  0.92  13.31   1.03     1.02      13025.71|
|  4:  3.2511 -  2.9563  1331   144  0.89  16.79   1.02     1.03      13700.57|
|  5:  2.9563 -  2.7458  1333   152  0.87  19.02   1.01     0.98      11424.55|
|  6:  2.7458 -  2.5848  1350   151  0.87  19.18   0.98     0.93       9203.26|
|  7:  2.5848 -  2.4560  1294   148  0.89  17.77   0.99     0.95       7495.10|
|  8:  2.4560 -  2.3495  1332   136  0.88  18.07   1.01     0.99       7011.56|
|  9:  2.3495 -  2.2594  1307   149  0.88  18.37   1.01     0.97       6267.36|
| 10:  2.2594 -  2.1816  1319   143  0.88  18.80   1.01     0.98       6219.06|
| 11:  2.1816 -  2.1136  1322   148  0.88  18.50   1.01     0.97       5282.08|
| 12:  2.1136 -  2.0533  1280   152  0.88  18.29   1.01     0.99       4822.07|
| 13:  2.0533 -  1.9994  1148   125  0.88  18.89   1.01     1.00       4252.55|
| 14:  1.9994 -  1.9507   434    48  0.88  17.95   0.98     0.92       3536.20|
|alpha:            min =        0.92 max =            1.03 mean =         0.98|
|beta:             min =     3536.20 max =        13700.57 mean =      8290.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        16.60|
|phase err.(test): min =        0.00 max =           89.01 mean =        16.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1779   ksol= 0.32   Bsol= 47.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.06,-0.03,0.00,-0.00,-0.00); trace/3= -0.59                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1779   ksol= 0.32   Bsol= 47.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,0.06,-0.03,0.00,-0.00,-0.00); trace/3= -0.59                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.282013                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9499 -  4.6572 0.99   1436  159 0.1046 0.1430      5.4505      5.6259|
|  2:  4.6572 -  3.7152 0.99   1380  154 0.0942 0.1138      5.5248      5.7237|
|  3:  3.7152 -  3.2511 0.99   1364  150 0.1260 0.1722      5.6045      5.9367|
|  4:  3.2511 -  2.9563 0.98   1331  144 0.1487 0.1903       5.601      5.7886|
|  5:  2.9563 -  2.7458 0.99   1333  152 0.1566 0.1890      5.4779       5.606|
|  6:  2.7458 -  2.5848 0.99   1350  151 0.1510 0.2329      5.3692      5.6127|
|  7:  2.5848 -  2.4560 0.98   1294  148 0.1459 0.1676      5.2777      5.4028|
|  8:  2.4560 -  2.3495 0.98   1332  136 0.1416 0.1836      5.2115      5.4117|
|  9:  2.3495 -  2.2594 0.99   1307  149 0.1389 0.2176      5.1404      5.4543|
| 10:  2.2594 -  2.1816 0.99   1319  143 0.1370 0.1877      5.1261      5.2983|
| 11:  2.1816 -  2.1136 0.97   1322  148 0.1320 0.2018      5.0297      5.3083|
| 12:  2.1136 -  2.0533 0.98   1280  152 0.1372 0.1884      4.9858      5.2439|
| 13:  2.0533 -  1.9994 0.87   1148  125 0.1331 0.2018      4.9087      5.1851|
| 14:  1.9994 -  1.9507 0.32    434   48 0.1268 0.1865      4.8467      5.0025|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9499 -  4.6572  1436   159  0.93  10.35   0.97     0.95       8639.68|
|  2:  4.6572 -  3.7152  1380   154  0.94   9.34   1.03     1.01      10979.96|
|  3:  3.7152 -  3.2511  1364   150  0.92  13.35   1.03     1.02      13071.47|
|  4:  3.2511 -  2.9563  1331   144  0.89  16.80   1.02     1.02      13714.50|
|  5:  2.9563 -  2.7458  1333   152  0.87  19.00   1.00     0.97      11406.10|
|  6:  2.7458 -  2.5848  1350   151  0.87  19.16   0.98     0.93       9193.45|
|  7:  2.5848 -  2.4560  1294   148  0.89  17.75   0.99     0.94       7484.81|
|  8:  2.4560 -  2.3495  1332   136  0.88  18.06   1.01     0.98       7011.29|
|  9:  2.3495 -  2.2594  1307   149  0.88  18.37   1.01     0.97       6267.15|
| 10:  2.2594 -  2.1816  1319   143  0.88  18.80   1.01     0.97       6215.48|
| 11:  2.1816 -  2.1136  1322   148  0.88  18.49   1.01     0.97       5281.46|
| 12:  2.1136 -  2.0533  1280   152  0.88  18.30   1.00     0.98       4829.81|
| 13:  2.0533 -  1.9994  1148   125  0.88  18.88   1.00     0.99       4248.81|
| 14:  1.9994 -  1.9507   434    48  0.88  17.92   0.98     0.92       3518.05|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3518.05 max =        13714.50 mean =      8294.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        16.60|
|phase err.(test): min =        0.00 max =           89.10 mean =        16.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.584)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.48   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    94.48   16.32    None  None   None       |
|    Sol.    : 438    0      4.93    85.46   41.21    None  None   None       |
|    Mac.    : 2385   0      0.00    94.48   11.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.451: 1203   |   5:    47.242 -  56.689:   94        |
|      1:     9.451 -  18.898:  987   |   6:    56.689 -  66.137:   64        |
|      2:    18.898 -  28.346:  194   |   7:    66.137 -  75.585:   32        |
|      3:    28.346 -  37.794:  124   |   8:    75.585 -  85.033:    7        |
|      4:    37.794 -  47.242:  113   |   9:    85.033 -  94.480:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.769 - 4.914
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 321
   mapped sites are within: 0.769 - 4.914

peak=    9.939 closest distance to " CB  VAL A 230 " =    1.424
peak=    7.313 closest distance to " O   HOH Z 120 " =    1.456
peak=    7.040 closest distance to " CG2 VAL A 296 " =    1.255
peak=    6.653 closest distance to " CG1 ILE A 234 " =    1.456
peak=    6.072 closest distance to " O   HOH Z 403 " =    2.176
peak=    6.009 closest distance to " O   HOH Z 178 " =    1.021
peak=    5.813 closest distance to " O   HOH Z  46 " =    1.259
peak=    5.377 closest distance to " O   HOH Z 249 " =    1.406
peak=    5.271 closest distance to " O   HOH Z 116 " =    1.534
peak=    5.238 closest distance to " CG  LEU A   5 " =    1.365
peak=    5.216 closest distance to " O   HOH Z 193 " =    1.750
peak=    5.165 closest distance to " O   HOH Z 236 " =    1.672
peak=    5.142 closest distance to " CB  ARG A 275 " =    0.992
peak=    5.104 closest distance to " O   HOH Z 128 " =    1.691
peak=    5.082 closest distance to " CD2 LEU A   5 " =    1.200
peak=    5.049 closest distance to " O   HOH Z 124 " =    1.747
peak=    5.043 closest distance to " CG  ARG A  66 " =    1.158
peak=    4.944 closest distance to " CG AARG A 275 " =    1.222
peak=    4.940 closest distance to " O   HOH Z 102 " =    1.536
peak=    4.841 closest distance to " CB  VAL A 296 " =    1.037
peak=    4.820 closest distance to " O   HOH Z  80 " =    2.237
peak=    4.793 closest distance to " O   HOH Z 247 " =    1.421
peak=    4.774 closest distance to " O   HOH Z 142 " =    1.566
peak=    4.628 closest distance to " O   HOH Z 406 " =    1.321
peak=    4.612 closest distance to " CD2 LEU A 228 " =    1.315
peak=    4.606 closest distance to " O   HOH Z 400 " =    0.844
peak=    4.557 closest distance to " O   HOH Z  49 " =    1.553
peak=    4.541 closest distance to " O   HOH Z 402 " =    1.543
peak=    4.525 closest distance to " CB  GLN A 223 " =    1.417
peak=    4.519 closest distance to " O   HOH Z 433 " =    1.619
peak=    4.495 closest distance to " O   HOH Z 357 " =    1.804
peak=    4.479 closest distance to " O   HOH Z 248 " =    1.667
peak=    4.428 closest distance to " O   HOH Z 137 " =    1.029
peak=    4.419 closest distance to " O   HOH Z  85 " =    1.980
peak=    4.414 closest distance to " CA  TYR A  30 " =    0.987
peak=    4.384 closest distance to " O   HOH Z 404 " =    1.307
peak=    4.377 closest distance to " O   HOH Z 156 " =    2.973
peak=    4.365 closest distance to " O   HOH Z  68 " =    1.945
peak=    4.354 closest distance to " O   HOH Z 411 " =    3.420
peak=    4.353 closest distance to " O   HOH Z 263 " =    1.539
peak=    4.349 closest distance to " CB  SER A  26 " =    1.738
peak=    4.347 closest distance to " NH1AARG A 275 " =    1.254
peak=    4.335 closest distance to " CB  VAL A 230 " =    1.153
peak=    4.316 closest distance to " CD2 TRP A 179 " =    1.372
peak=    4.310 closest distance to " O   HOH Z 327 " =    1.797
peak=    4.309 closest distance to " O   HOH Z 130 " =    2.393
peak=    4.296 closest distance to " O   HOH Z  78 " =    1.467
peak=    4.293 closest distance to " CG  GLN A  77 " =    0.941
peak=    4.288 closest distance to " O   HOH Z  43 " =    2.018
peak=    4.279 closest distance to " O   HOH Z 414 " =    2.607
peak=    4.262 closest distance to " CB  ASN A 187 " =    1.419
peak=    4.248 closest distance to " O   HOH Z 394 " =    1.712
peak=    4.242 closest distance to " O   HOH Z 425 " =    1.525
peak=    4.240 closest distance to " OE1 GLU A   2 " =    1.902
peak=    4.234 closest distance to " O   ASN A 285 " =    0.937
peak=    4.217 closest distance to " O   HOH Z 389 " =    1.777
peak=    4.194 closest distance to " O   HOH Z 154 " =    1.834
peak=    4.186 closest distance to " CB  SER A  63 " =    1.223
peak=    4.179 closest distance to " O   HOH Z 250 " =    2.313
peak=    4.175 closest distance to " O   HOH Z  44 " =    2.072
peak=    4.165 closest distance to " CE BMET A  47 " =    1.045
peak=    4.161 closest distance to " O   HOH Z 126 " =    1.423
peak=    4.160 closest distance to " O   HOH Z  40 " =    1.936
peak=    4.147 closest distance to " O   PRO A 198 " =    1.575
peak=    4.142 closest distance to " O   HOH Z 134 " =    2.152
peak=    4.117 closest distance to " O   HOH Z 278 " =    1.218
peak=    4.116 closest distance to " CD  ARG A 269 " =    1.146
peak=    4.103 closest distance to " CB  ASN A 148 " =    1.156
peak=    4.085 closest distance to " O   HOH Z 126 " =    2.464
peak=    4.077 closest distance to " NZ  LYS A  76 " =    0.970
peak=    4.074 closest distance to " OE1 GLN A  11 " =    1.894
peak=    4.071 closest distance to " O   HOH Z 130 " =    1.105
peak=    4.067 closest distance to " O   HOH Z 261 " =    2.299
peak=    4.064 closest distance to " O   HOH Z 361 " =    2.618
peak=    4.058 closest distance to " O   HOH Z  39 " =    1.520
peak=    4.057 closest distance to " CA  VAL A  41 " =    0.903
peak=    4.051 closest distance to " O   HOH Z 245 " =    1.395
peak=    4.039 closest distance to " ND1 HIS A  81 " =    1.156
peak=    4.010 closest distance to " NH2 ARG A 156 " =    1.151
peak=    4.007 closest distance to " O   HOH Z 144 " =    1.604
peak=    3.979 closest distance to " O   HOH Z  11 " =    1.364
peak=    3.975 closest distance to " OG  SER A  62 " =    2.754
peak=    3.973 closest distance to " O   HOH Z 234 " =    3.513
peak=    3.973 closest distance to " O   HOH Z 146 " =    1.401
peak=    3.958 closest distance to " NE2 GLN A  11 " =    0.959
peak=    3.952 closest distance to " CE  LYS A 119 " =    1.150
peak=    3.951 closest distance to " O   HOH Z  54 " =    1.258
peak=    3.941 closest distance to " O   HOH Z 203 " =    0.928
peak=    3.940 closest distance to " CB  ASN A 285 " =    0.982
peak=    3.938 closest distance to " O   HOH Z  38 " =    1.613
peak=    3.929 closest distance to " CG2 VAL A 296 " =    1.619
peak=    3.925 closest distance to " O   HOH Z 188 " =    0.958
peak=    3.917 closest distance to " O   HOH Z 255 " =    1.375
peak=    3.892 closest distance to " O   HOH Z 250 " =    1.423
peak=    3.885 closest distance to " NE BARG A 190 " =    1.546
peak=    3.874 closest distance to " CB  SER A 141 " =    1.029
peak=    3.872 closest distance to " OG BSER A 210 " =    1.257
peak=    3.857 closest distance to " O   HOH Z 136 " =    1.321
peak=    3.848 closest distance to " NH1 ARG A 138 " =    1.007
peak=    3.825 closest distance to " CD  PRO A  54 " =    0.880
peak=    3.819 closest distance to " O   HOH Z 189 " =    2.523
peak=    3.813 closest distance to " O   HOH Z 146 " =    1.519
peak=    3.801 closest distance to " O   HOH Z 316 " =    2.431
peak=    3.795 closest distance to " CE1 HIS A 108 " =    1.225
peak=    3.787 closest distance to " CA  SER A  12 " =    1.399
peak=    3.786 closest distance to " O   HOH Z 289 " =    1.671
peak=    3.783 closest distance to " O   SER A  87 " =    2.256
peak=    3.769 closest distance to " O   HOH Z  97 " =    1.728
peak=    3.766 closest distance to " O   HOH Z  42 " =    2.202
peak=    3.766 closest distance to " CB  PRO A 198 " =    1.228
peak=    3.765 closest distance to " O   HOH Z 238 " =    1.335
peak=    3.765 closest distance to " CG2 ILE A  20 " =    1.187
peak=    3.763 closest distance to " O   HOH Z   4 " =    1.668
peak=    3.757 closest distance to " O   HOH Z 423 " =    1.907
peak=    3.757 closest distance to " NZ  LYS A 117 " =    3.020
peak=    3.751 closest distance to " CB  GLN A 183 " =    1.328
peak=    3.741 closest distance to " CB  THR A  31 " =    1.429
peak=    3.733 closest distance to " CB  GLU A 277 " =    0.983
peak=    3.728 closest distance to " O   HOH Z 345 " =    2.208
peak=    3.728 closest distance to " NH2BARG A 145 " =    2.401
peak=    3.721 closest distance to " CG2 THR A 221 " =    1.259
peak=    3.720 closest distance to " NH2 ARG A  56 " =    2.064
peak=    3.713 closest distance to " O   HOH Z 279 " =    1.280
peak=    3.707 closest distance to " O   HOH Z 132 " =    2.681
peak=    3.703 closest distance to " CG  PRO A 198 " =    1.321
peak=    3.696 closest distance to " CB BVAL A  41 " =    1.151
peak=    3.688 closest distance to " CB  GLU A 175 " =    1.210
peak=    3.685 closest distance to " CG1 ILE A  33 " =    1.294
peak=    3.683 closest distance to " O   HOH Z 132 " =    2.478
peak=    3.681 closest distance to " NH1 ARG A  14 " =    1.111
peak=    3.676 closest distance to " O   HOH Z  92 " =    1.142
peak=    3.671 closest distance to " O   HOH Z 405 " =    1.346
peak=    3.670 closest distance to " CG  PRO A 243 " =    1.194
peak=    3.667 closest distance to " N   ASN A  39 " =    1.316
peak=    3.666 closest distance to " CB  PHE A  16 " =    1.098
peak=    3.660 closest distance to " O   HOH Z 409 " =    3.211
peak=    3.658 closest distance to " O   HOH Z  45 " =    1.184
peak=    3.658 closest distance to " CD BLYS A 290 " =    0.942
peak=    3.649 closest distance to " O   HOH Z 214 " =    1.503
peak=    3.644 closest distance to " O   HOH Z 163 " =    1.509
peak=    3.641 closest distance to " CG2 ILE A 234 " =    1.019
peak=    3.639 closest distance to " O   HOH Z 403 " =    1.379
peak=    3.637 closest distance to " O   HOH Z 367 " =    3.220
peak=    3.627 closest distance to " CB  VAL A 265 " =    1.350
peak=    3.624 closest distance to " CB  PRO A  54 " =    0.876
peak=    3.614 closest distance to " O   HOH Z 209 " =    2.365
peak=    3.613 closest distance to " CA  TRP A  85 " =    1.151
peak=    3.612 closest distance to " CB  LEU A 237 " =    0.823
peak=    3.611 closest distance to " O   GLY A  91 " =    1.346
peak=    3.601 closest distance to " O   HOH Z 272 " =    1.860
peak=    3.599 closest distance to " O   HOH Z  48 " =    1.619
peak=    3.592 closest distance to " O   HOH Z 352 " =    1.794
peak=    3.591 closest distance to " OD1 ASN A  60 " =    1.166
peak=    3.577 closest distance to " CG  PRO A 213 " =    1.305
peak=    3.575 closest distance to " CA  ALA A  51 " =    1.162
peak=    3.575 closest distance to " O   HOH Z 337 " =    1.548
peak=    3.574 closest distance to " O   HOH Z  97 " =    1.924
peak=    3.573 closest distance to " O   HOH Z 291 " =    1.095
peak=    3.567 closest distance to " O   HOH Z 315 " =    1.793
peak=    3.564 closest distance to " O   HOH Z  88 " =    3.565
peak=    3.561 closest distance to " CB  ALA A 100 " =    1.102
peak=    3.555 closest distance to " N   THR A  42 " =    1.559
peak=    3.549 closest distance to " CA  ARG A  66 " =    1.107
peak=    3.545 closest distance to " O   HOH Z 183 " =    1.923
peak=    3.544 closest distance to " CG2 THR A 220 " =    0.833
peak=    3.538 closest distance to " CG  MET A 185 " =    1.486
peak=    3.534 closest distance to " OG1 THR A 221 " =    1.202
peak=    3.531 closest distance to " O   HOH Z 155 " =    1.645
peak=    3.529 closest distance to " CB  SER A  62 " =    1.031
peak=    3.527 closest distance to " CA  ALA A 295 " =    1.056
peak=    3.524 closest distance to " OD1 ASN A 301 " =    1.161
peak=    3.519 closest distance to " ND1 HIS A  81 " =    1.452
peak=    3.509 closest distance to " O   HOH Z  47 " =    1.578
peak=    3.502 closest distance to " O   HOH Z 316 " =    1.195
peak=    3.501 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.497 closest distance to " CB  ASP A 286 " =    1.074
peak=    3.495 closest distance to " O   HOH Z 383 " =    2.221
peak=    3.493 closest distance to " O   HOH Z 431 " =    1.584
peak=    3.492 closest distance to " O   HOH Z 395 " =    1.370
peak=    3.491 closest distance to " O   HOH Z 380 " =    1.813
peak=    3.490 closest distance to " CA  ALA A 248 " =    1.367
peak=    3.483 closest distance to " O   VAL A  72 " =    1.361
peak=    3.479 closest distance to " CB  TRP A 179 " =    1.031
peak=    3.478 closest distance to " O   HOH Z 257 " =    2.223
peak=    3.475 closest distance to " O   HOH Z 381 " =    1.409
peak=    3.472 closest distance to " O   HOH Z 435 " =    1.794
peak=    3.458 closest distance to " CB  VAL A 202 " =    1.468
peak=    3.453 closest distance to " CB  PRO A 280 " =    1.106
peak=    3.452 closest distance to " O   HOH Z 345 " =    1.848
peak=    3.449 closest distance to " CA  ILE A 263 " =    0.997
peak=    3.443 closest distance to " CB  GLU A 128 " =    1.311
peak=    3.441 closest distance to " O   HOH Z 322 " =    2.119
peak=    3.438 closest distance to " O   HOH Z  35 " =    1.995
peak=    3.438 closest distance to " CD  ARG A  36 " =    1.125
peak=    3.436 closest distance to " O   HOH Z 334 " =    1.671
peak=    3.431 closest distance to " O   HOH Z 427 " =    2.732
peak=    3.431 closest distance to " O   HOH Z 412 " =    3.561
peak=    3.431 closest distance to " CG  LEU A 228 " =    1.297
peak=    3.431 closest distance to " O   HOH Z 303 " =    2.441
peak=    3.429 closest distance to " N   GLU A  44 " =    1.496
peak=    3.426 closest distance to " O   HOH Z 408 " =    1.831
peak=    3.425 closest distance to " CD  LYS A 119 " =    1.804
peak=    3.424 closest distance to " O   HOH Z 418 " =    3.189
peak=    3.420 closest distance to " O   HOH Z 417 " =    1.261
peak=    3.415 closest distance to " O   HOH Z 423 " =    1.963
peak=    3.414 closest distance to " CG2 VAL A 197 " =    1.312
peak=    3.411 closest distance to " O   HOH Z 253 " =    2.025
peak=    3.410 closest distance to " CE1 TYR A 186 " =    1.397
peak=    3.405 closest distance to " O   HOH Z 155 " =    2.666
peak=    3.396 closest distance to " CB  ASP A 191 " =    1.138
peak=    3.395 closest distance to " O   HOH Z  22 " =    2.653
peak=    3.383 closest distance to " CB  LYS A 289 " =    1.074
peak=    3.383 closest distance to " CZ  PHE A 218 " =    1.227
peak=    3.382 closest distance to " CA  ARG A 195 " =    1.150
peak=    3.381 closest distance to " O   HOH Z 128 " =    1.714
peak=    3.381 closest distance to " CZ AARG A 102 " =    1.623
peak=    3.373 closest distance to " CB  GLN A  73 " =    1.193
peak=    3.372 closest distance to " CG  MET A  93 " =    1.113
peak=    3.372 closest distance to " O   ASP A 124 " =    1.703
peak=    3.364 closest distance to " CA  ARG A  36 " =    0.963
peak=    3.363 closest distance to " O   HOH Z 423 " =    2.970
peak=    3.363 closest distance to " O   HOH Z 359 " =    1.544
peak=    3.357 closest distance to " NZ  LYS A  76 " =    1.404
peak=    3.345 closest distance to " O   HOH Z 109 " =    1.453
peak=    3.344 closest distance to " CB  GLN A  58 " =    1.188
peak=    3.341 closest distance to " O   HOH Z   6 " =    2.403
peak=    3.340 closest distance to " NE1 TRP A  92 " =    1.114
peak=    3.327 closest distance to " O   HOH Z 126 " =    1.864
peak=    3.322 closest distance to " OG BSER A 258 " =    2.859
peak=    3.314 closest distance to " O   HOH Z  66 " =    2.078
peak=    3.311 closest distance to " OH  TYR A  30 " =    1.067
peak=    3.305 closest distance to " O   HOH Z 162 " =    2.024
peak=    3.300 closest distance to " CD  LYS A 166 " =    1.510
peak=    3.299 closest distance to " O   HOH Z 387 " =    2.254
peak=    3.288 closest distance to " O   HOH Z 111 " =    1.496
peak=    3.287 closest distance to " O   HOH Z 271 " =    2.240
peak=    3.282 closest distance to " O   HOH Z 284 " =    1.229
peak=    3.279 closest distance to " O   HOH Z 369 " =    1.930
peak=    3.269 closest distance to " O   HOH Z 166 " =    1.693
peak=    3.264 closest distance to " O   HOH Z 298 " =    1.859
peak=    3.264 closest distance to " CB  PRO A 243 " =    1.105
peak=    3.264 closest distance to " O   HOH Z 281 " =    4.104
peak=    3.263 closest distance to " O   HOH Z 158 " =    3.320
peak=    3.262 closest distance to " O   HOH Z  85 " =    1.394
peak=    3.259 closest distance to " O   HOH Z 244 " =    1.516
peak=    3.251 closest distance to " O   HOH Z 343 " =    2.459
peak=    3.248 closest distance to " CB  GLU A   2 " =    1.004
peak=    3.248 closest distance to " O   HOH Z 358 " =    2.228
peak=    3.245 closest distance to " O   HOH Z  63 " =    1.779
peak=    3.242 closest distance to " NH2BARG A 190 " =    1.543
peak=    3.242 closest distance to " O   HOH Z 234 " =    1.850
peak=    3.241 closest distance to " O   THR A  82 " =    2.017
peak=    3.240 closest distance to " CE  MET A  93 " =    1.321
peak=    3.233 closest distance to " O   HOH Z 112 " =    1.645
peak=    3.232 closest distance to " O   HOH Z 388 " =    2.118
peak=    3.231 closest distance to " OD1 ASP A 171 " =    1.159
peak=    3.229 closest distance to " O   HOH Z 265 " =    1.947
peak=    3.229 closest distance to " CB  THR A 235 " =    1.192
peak=    3.221 closest distance to " CB  PRO A 163 " =    3.890
peak=    3.213 closest distance to " O   HOH Z 273 " =    2.864
peak=    3.211 closest distance to " CB  SER A   3 " =    1.304
peak=    3.210 closest distance to " CB  ARG A  79 " =    0.812
peak=    3.206 closest distance to " CB  ARG A 269 " =    1.546
peak=    3.205 closest distance to " O   HOH Z 438 " =    2.549
peak=    3.202 closest distance to " CA  ALA A  21 " =    1.248
peak=    3.202 closest distance to " CZ  PHE A  38 " =    1.131
peak=    3.198 closest distance to " CA  SER A 210 " =    1.484
peak=    3.195 closest distance to " CG  ARG A 138 " =    1.045
peak=    3.189 closest distance to " C   ALA A 299 " =    0.973
peak=    3.187 closest distance to " O   HOH Z 298 " =    4.914
peak=    3.183 closest distance to " OG BSER A 212 " =    2.563
peak=    3.182 closest distance to " O   HOH Z 425 " =    2.117
peak=    3.181 closest distance to " O   HOH Z 156 " =    1.874
peak=    3.181 closest distance to " CD  ARG A 195 " =    1.088
peak=    3.178 closest distance to " CD2 LEU A 255 " =    1.296
peak=    3.177 closest distance to " CB  GLU A 152 " =    1.075
peak=    3.176 closest distance to " O   HOH Z  95 " =    1.791
peak=    3.163 closest distance to " O   HOH Z 301 " =    1.824
peak=    3.160 closest distance to " OE1 GLN A  88 " =    2.384
peak=    3.157 closest distance to " CG2 VAL A 268 " =    1.049
peak=    3.154 closest distance to " O   HOH Z 426 " =    1.392
peak=    3.153 closest distance to " CD2 LEU A 297 " =    0.847
peak=    3.150 closest distance to " O   HOH Z 227 " =    1.680
peak=    3.147 closest distance to " O   ASP A 200 " =    1.625
peak=    3.145 closest distance to " O   ILE A 234 " =    1.898
peak=    3.144 closest distance to " O   THR A 251 " =    1.272
peak=    3.143 closest distance to " CB  SER A  62 " =    3.772
peak=    3.143 closest distance to " CB  TYR A 169 " =    0.810
peak=    3.143 closest distance to " N   CYS A 260 " =    0.769
peak=    3.139 closest distance to " ND1 HIS A 207 " =    0.806
peak=    3.139 closest distance to " O   HOH Z 435 " =    2.112
peak=    3.138 closest distance to " O   HOH Z 194 " =    1.804
peak=    3.135 closest distance to " CA  GLU A 152 " =    0.927
peak=    3.135 closest distance to " CB  TRP A 266 " =    1.228
peak=    3.134 closest distance to " O   HOH Z  59 " =    1.927
peak=    3.130 closest distance to " CA  ARG A 156 " =    1.130
peak=    3.128 closest distance to " O   HOH Z  54 " =    1.460
peak=    3.126 closest distance to " CA  THR A 246 " =    1.065
peak=    3.126 closest distance to " CA  VAL A 126 " =    1.139
peak=    3.126 closest distance to " O   HOH Z 366 " =    2.679
peak=    3.125 closest distance to " CG1 VAL A 296 " =    1.183
peak=    3.121 closest distance to " CG2 THR A 294 " =    1.371
peak=    3.120 closest distance to " O   PHE A  61 " =    1.294
peak=    3.118 closest distance to " CA  THR A 294 " =    2.118
peak=    3.116 closest distance to " O   HOH Z 267 " =    1.922
peak=    3.116 closest distance to " CA  PHE A  59 " =    0.961
peak=    3.099 closest distance to " CB  GLN A 278 " =    0.913
peak=    3.097 closest distance to " O   HOH Z  29 " =    1.324
peak=    3.095 closest distance to " O   HOH Z  89 " =    1.839
peak=    3.093 closest distance to " CD1 LEU A 300 " =    0.921
peak=    3.083 closest distance to " NH1 ARG A 269 " =    0.951
peak=    3.082 closest distance to " O   GLN A  11 " =    0.878
peak=    3.078 closest distance to " OH  TYR A 116 " =    1.170
peak=    3.074 closest distance to " CD  ARG A  24 " =    1.342
peak=    3.068 closest distance to " N   TYR A  15 " =    0.851
peak=    3.035 closest distance to " O   HOH Z  95 " =    1.397
peak=    3.032 closest distance to " CD2 LEU A  25 " =    1.235
peak=    3.031 closest distance to " CB  ARG A 259 " =    1.932
peak=    3.031 closest distance to " CA  ILE A 120 " =    1.195
peak=    3.017 closest distance to " O   LYS A 289 " =    0.966

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.616 - 5.773
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.714 - 5.773

peak=   -5.131 closest distance to " CG2 VAL A 230 " =    0.794
peak=   -4.874 closest distance to " O   HOH Z 210 " =    0.786
peak=   -4.696 closest distance to " O   HOH Z  13 " =    1.558
peak=   -4.692 closest distance to " O   HOH Z 422 " =    1.024
peak=   -4.446 closest distance to " C   HIS A 108 " =    1.137
peak=   -4.326 closest distance to " O   GLN A  11 " =    0.995
peak=   -4.212 closest distance to " O   HOH Z 400 " =    1.090
peak=   -4.187 closest distance to " C   THR A 279 " =    1.160
peak=   -4.181 closest distance to " CG  GLN A  58 " =    1.187
peak=   -4.107 closest distance to " CD1 PHE A  59 " =    1.873
peak=   -4.073 closest distance to " O   TYR A  15 " =    1.748
peak=   -4.039 closest distance to " O   HOH Z 109 " =    5.773
peak=   -4.004 closest distance to " CG2BVAL A  41 " =    2.265
peak=   -3.985 closest distance to " CD  ARG A  14 " =    3.103
peak=   -3.976 closest distance to " CD1 TRP A 179 " =    1.126
peak=   -3.964 closest distance to " O   HOH Z  56 " =    1.576
peak=   -3.955 closest distance to " O   HOH Z  92 " =    1.618
peak=   -3.954 closest distance to " O   HOH Z 137 " =    1.800
peak=   -3.928 closest distance to " ND2 ASN A  39 " =    1.115
peak=   -3.918 closest distance to " O   HOH Z 166 " =    1.756
peak=   -3.906 closest distance to " O   HOH Z 266 " =    4.625
peak=   -3.901 closest distance to " O   HOH Z 174 " =    1.634
peak=   -3.869 closest distance to " O   HOH Z  52 " =    2.392
peak=   -3.866 closest distance to " CG  ARG A 219 " =    2.306
peak=   -3.864 closest distance to " CA  VAL A  67 " =    2.669
peak=   -3.861 closest distance to " CB  ALA A 161 " =    2.371
peak=   -3.839 closest distance to " CG2 VAL A 296 " =    1.094
peak=   -3.819 closest distance to " CD1 TYR A 247 " =    2.362
peak=   -3.817 closest distance to " O   HOH Z 423 " =    2.381
peak=   -3.804 closest distance to " O   PRO A 198 " =    1.326
peak=   -3.802 closest distance to " O   HOH Z 135 " =    1.395
peak=   -3.800 closest distance to " CG  PRO A 243 " =    1.666
peak=   -3.792 closest distance to " O   VAL A 197 " =    1.167
peak=   -3.767 closest distance to " N   THR A 235 " =    1.167
peak=   -3.757 closest distance to " CG2 THR A  18 " =    2.694
peak=   -3.756 closest distance to " OXT GLY A 302 " =    2.823
peak=   -3.754 closest distance to " CD  ARG A 156 " =    2.014
peak=   -3.747 closest distance to " O   HOH Z 340 " =    0.851
peak=   -3.744 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.738 closest distance to " CD2 LEU A 237 " =    2.359
peak=   -3.737 closest distance to " CG  MET A  93 " =    2.509
peak=   -3.728 closest distance to " N   VAL A  72 " =    1.345
peak=   -3.727 closest distance to " O  BHOH Z 338 " =    1.442
peak=   -3.701 closest distance to " OD1 ASN A 301 " =    0.821
peak=   -3.678 closest distance to " O   HOH Z 120 " =    0.917
peak=   -3.676 closest distance to " O   HOH Z 151 " =    0.891
peak=   -3.667 closest distance to " O   HOH Z 119 " =    1.688
peak=   -3.645 closest distance to " O   HOH Z 407 " =    3.030
peak=   -3.642 closest distance to " N   ASP A 272 " =    1.230
peak=   -3.642 closest distance to " O   SER A 273 " =    1.086
peak=   -3.639 closest distance to " CG BARG A 275 " =    0.932
peak=   -3.635 closest distance to " CE2 TYR A  30 " =    2.683
peak=   -3.629 closest distance to " O   HOH Z  29 " =    1.369
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.085
peak=   -3.618 closest distance to " O   HOH Z 166 " =    0.994
peak=   -3.616 closest distance to " O   GLY A 241 " =    2.112
peak=   -3.611 closest distance to " CG  ASP A 286 " =    1.049
peak=   -3.605 closest distance to " O   ASN A 187 " =    1.541
peak=   -3.604 closest distance to " CB  LEU A 167 " =    2.017
peak=   -3.594 closest distance to " O   HOH Z 101 " =    1.432
peak=   -3.589 closest distance to " O   ARG A 219 " =    1.774
peak=   -3.589 closest distance to " CD  ARG A 195 " =    4.992
peak=   -3.584 closest distance to " O   GLY A  80 " =    2.596
peak=   -3.576 closest distance to " O   HOH Z 176 " =    1.705
peak=   -3.556 closest distance to " O   HOH Z  46 " =    1.180
peak=   -3.554 closest distance to " CD1 TYR A 169 " =    2.106
peak=   -3.543 closest distance to " N   ALA A 226 " =    1.853
peak=   -3.534 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.531 closest distance to " CA  ASP A 298 " =    1.087
peak=   -3.528 closest distance to " CG2 VAL A 189 " =    1.986
peak=   -3.521 closest distance to " O   HOH Z 384 " =    1.801
peak=   -3.521 closest distance to " O   HOH Z 196 " =    1.799
peak=   -3.508 closest distance to " OG BSER A 134 " =    1.542
peak=   -3.498 closest distance to " CG1 VAL A 112 " =    2.412
peak=   -3.498 closest distance to " CA  SER A 164 " =    1.975
peak=   -3.496 closest distance to " O   PHE A 218 " =    1.448
peak=   -3.488 closest distance to " OG  SER A  97 " =    2.115
peak=   -3.481 closest distance to " N   GLY A  17 " =    1.616
peak=   -3.469 closest distance to " C   GLY A  91 " =    1.255
peak=   -3.462 closest distance to " O   HOH Z 165 " =    2.105
peak=   -3.454 closest distance to " O   HOH Z   6 " =    1.999
peak=   -3.454 closest distance to " C   ASN A 285 " =    2.034
peak=   -3.444 closest distance to " CD1 LEU A 228 " =    2.151
peak=   -3.437 closest distance to " NE2 GLN A  11 " =    1.701
peak=   -3.434 closest distance to " NH2 ARG A  79 " =    2.141
peak=   -3.431 closest distance to " O   HOH Z 351 " =    1.549
peak=   -3.429 closest distance to " O   HOH Z 234 " =    3.929
peak=   -3.429 closest distance to " O   ASN A 285 " =    1.096
peak=   -3.419 closest distance to " O   VAL A 174 " =    2.175
peak=   -3.417 closest distance to " OG BSER A  99 " =    1.064
peak=   -3.396 closest distance to " O   HOH Z 424 " =    3.088
peak=   -3.395 closest distance to " O   HOH Z 313 " =    2.163
peak=   -3.389 closest distance to " CG2 THR A 182 " =    2.238
peak=   -3.388 closest distance to " O   HOH Z 126 " =    1.842
peak=   -3.387 closest distance to " CA  SER A 276 " =    1.372
peak=   -3.382 closest distance to " OD2 ASP A  50 " =    1.373
peak=   -3.365 closest distance to " CD  GLN A 223 " =    0.795
peak=   -3.365 closest distance to " O   TRP A  92 " =    2.073
peak=   -3.361 closest distance to " C   GLN A 144 " =    0.861
peak=   -3.354 closest distance to " O   HOH Z 388 " =    2.092
peak=   -3.350 closest distance to " OG  SER A  32 " =    1.065
peak=   -3.350 closest distance to " O   HOH Z 124 " =    1.512
peak=   -3.347 closest distance to " CD2 LEU A 237 " =    2.634
peak=   -3.344 closest distance to " CB  ALA A 291 " =    2.122
peak=   -3.343 closest distance to " C   PRO A 213 " =    1.459
peak=   -3.343 closest distance to " O   HOH Z 145 " =    2.286
peak=   -3.339 closest distance to " C   ILE A 239 " =    2.195
peak=   -3.337 closest distance to " O   HOH Z 203 " =    1.646
peak=   -3.332 closest distance to " CG2 THR A 279 " =    1.396
peak=   -3.330 closest distance to " OD1 ASN A  39 " =    2.208
peak=   -3.326 closest distance to " O   HOH Z 166 " =    1.668
peak=   -3.324 closest distance to " CD  GLN A  73 " =    0.714
peak=   -3.323 closest distance to " O   HOH Z 425 " =    1.121
peak=   -3.320 closest distance to " OG  SER A 206 " =    1.408
peak=   -3.318 closest distance to " NE2 GLN A  88 " =    0.955
peak=   -3.316 closest distance to " O   LEU A 101 " =    1.537
peak=   -3.315 closest distance to " O   HOH Z 221 " =    1.310
peak=   -3.314 closest distance to " O   HOH Z 222 " =    1.204
peak=   -3.313 closest distance to " O   HOH Z 205 " =    0.961
peak=   -3.311 closest distance to " O   HOH Z 290 " =    0.848
peak=   -3.309 closest distance to " CE2 TYR A  30 " =    2.816
peak=   -3.307 closest distance to " O   HOH Z 150 " =    1.491
peak=   -3.306 closest distance to " CB  ASP A 286 " =    1.231
peak=   -3.305 closest distance to " N   GLN A  58 " =    1.945
peak=   -3.296 closest distance to " O   HOH Z 426 " =    1.716
peak=   -3.293 closest distance to " CE3 TRP A  70 " =    1.854
peak=   -3.288 closest distance to " O   HOH Z 198 " =    1.227
peak=   -3.284 closest distance to " C   THR A 235 " =    1.766
peak=   -3.284 closest distance to " O   SER A  95 " =    1.531
peak=   -3.282 closest distance to " SG  CYS A 260 " =    2.466
peak=   -3.281 closest distance to " O   HOH Z 405 " =    0.914
peak=   -3.279 closest distance to " O   SER A   3 " =    0.924
peak=   -3.278 closest distance to " OD1 ASN A 249 " =    2.459
peak=   -3.277 closest distance to " CE BMET A  47 " =    1.091
peak=   -3.277 closest distance to " N   ASP A 191 " =    1.644
peak=   -3.275 closest distance to " O   HOH Z 105 " =    1.911
peak=   -3.270 closest distance to " O   ASN A  45 " =    1.797
peak=   -3.270 closest distance to " CD  ARG A 139 " =    1.569
peak=   -3.268 closest distance to " O   HOH Z 191 " =    5.655
peak=   -3.265 closest distance to " NH2 ARG A  66 " =    1.418
peak=   -3.263 closest distance to " CD2 LEU A 237 " =    2.129
peak=   -3.261 closest distance to " CA  ALA A 114 " =    1.026
peak=   -3.255 closest distance to " N   ALA A  43 " =    2.663
peak=   -3.254 closest distance to " CB  ASP A 200 " =    2.553
peak=   -3.253 closest distance to " O   HOH Z  71 " =    1.397
peak=   -3.252 closest distance to " O   HOH Z  37 " =    1.516
peak=   -3.247 closest distance to " O   HOH Z 428 " =    2.474
peak=   -3.247 closest distance to " CB  PHE A 208 " =    2.339
peak=   -3.246 closest distance to " O   HOH Z 112 " =    1.014
peak=   -3.243 closest distance to " CE1 PHE A 204 " =    2.410
peak=   -3.237 closest distance to " N   SER A 210 " =    1.253
peak=   -3.237 closest distance to " OG BSER A 212 " =    1.487
peak=   -3.237 closest distance to " OG  SER A  26 " =    1.462
peak=   -3.237 closest distance to " O   HOH Z 298 " =    3.582
peak=   -3.232 closest distance to " O   ILE A 234 " =    1.336
peak=   -3.231 closest distance to " O   HOH Z 249 " =    1.490
peak=   -3.226 closest distance to " O   HOH Z 353 " =    1.182
peak=   -3.223 closest distance to " OXT GLY A 302 " =    3.386
peak=   -3.221 closest distance to " O   HOH Z 397 " =    1.179
peak=   -3.219 closest distance to " OG  SER A   3 " =    1.412
peak=   -3.213 closest distance to " O   HOH Z 433 " =    0.912
peak=   -3.208 closest distance to " O   LEU A 300 " =    2.375
peak=   -3.208 closest distance to " O   HOH Z 345 " =    2.809
peak=   -3.207 closest distance to " N   ARG A  66 " =    1.873
peak=   -3.206 closest distance to " O   ALA A 227 " =    1.170
peak=   -3.205 closest distance to " OE2 GLU A   2 " =    1.680
peak=   -3.204 closest distance to " N   ALA A 248 " =    1.877
peak=   -3.204 closest distance to " CD  PRO A 198 " =    1.057
peak=   -3.189 closest distance to " ND2 ASN A  69 " =    1.513
peak=   -3.186 closest distance to " O   HOH Z 105 " =    3.155
peak=   -3.185 closest distance to " C   LYS A  76 " =    1.613
peak=   -3.184 closest distance to " O   HOH Z 109 " =    3.364
peak=   -3.183 closest distance to " O   HOH Z 231 " =    1.081
peak=   -3.183 closest distance to " O   HOH Z 109 " =    2.983
peak=   -3.181 closest distance to " O   HOH Z   7 " =    1.148
peak=   -3.179 closest distance to " O   HOH Z 384 " =    1.192
peak=   -3.178 closest distance to " O   HOH Z 407 " =    1.470
peak=   -3.177 closest distance to " O   ALA A 161 " =    1.333
peak=   -3.177 closest distance to " O   HOH Z 251 " =    1.236
peak=   -3.177 closest distance to " O   HOH Z 120 " =    1.256
peak=   -3.171 closest distance to " O   PRO A  54 " =    1.715
peak=   -3.159 closest distance to " N   VAL A 230 " =    1.151
peak=   -3.155 closest distance to " CD1 LEU A   5 " =    1.974
peak=   -3.150 closest distance to " NE1 TRP A 177 " =    1.956
peak=   -3.142 closest distance to " CG  GLU A  46 " =    3.083
peak=   -3.140 closest distance to " NH1 ARG A 195 " =    2.583
peak=   -3.140 closest distance to " O   HOH Z 219 " =    2.674
peak=   -3.130 closest distance to " CE1 TYR A 169 " =    2.180
peak=   -3.130 closest distance to " CD2 LEU A 143 " =    2.424
peak=   -3.129 closest distance to " OE1 GLN A 223 " =    4.912
peak=   -3.129 closest distance to " OD2 ASP A 171 " =    2.455
peak=   -3.128 closest distance to " CE1 HIS A  81 " =    1.582
peak=   -3.126 closest distance to " O   HOH Z 265 " =    1.345
peak=   -3.124 closest distance to " CG AARG A 102 " =    2.081
peak=   -3.114 closest distance to " O   ALA A  34 " =    2.374
peak=   -3.114 closest distance to " O  BHOH Z 338 " =    2.520
peak=   -3.113 closest distance to " CD1 LEU A  96 " =    2.125
peak=   -3.098 closest distance to " O   HOH Z 250 " =    1.546
peak=   -3.098 closest distance to " O   HOH Z 389 " =    1.347
peak=   -3.096 closest distance to " O   HOH Z 171 " =    2.387
peak=   -3.083 closest distance to " O   HOH Z 396 " =    1.493
peak=   -3.079 closest distance to " CG  ASN A  45 " =    1.523
peak=   -3.076 closest distance to " N   ASP A 286 " =    1.218
peak=   -3.075 closest distance to " O   HOH Z 412 " =    4.795
peak=   -3.071 closest distance to " O   ASP A 107 " =    1.528
peak=   -3.068 closest distance to " O   THR A  52 " =    1.822
peak=   -3.065 closest distance to " CG  ARG A 269 " =    2.113
peak=   -3.062 closest distance to " O   THR A  18 " =    1.412
peak=   -3.061 closest distance to " O   HOH Z 377 " =    1.112

================= 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    :  0.5120 0.4971   6.306948e+00   6.299410e+00
   1_bss:  0.5044 0.4919   6.301731e+00   6.295432e+00
   1_xyz:  0.4516 0.4679   6.107052e+00   6.128873e+00
   1_adp:  0.4113 0.4647   6.206821e+00   6.262698e+00
   1_occ:  0.4107 0.4637   6.205872e+00   6.262312e+00
   2_bss:  0.4090 0.4550   6.205995e+00   6.261242e+00
   2_xyz:  0.3466 0.4025   6.086559e+00   6.189150e+00
   2_adp:  0.3296 0.3926   6.056694e+00   6.172507e+00
   2_occ:  0.3295 0.3921   6.055988e+00   6.171924e+00
   3_bss:  0.3271 0.3897   6.055499e+00   6.171472e+00
   3_xyz:  0.2565 0.3146   5.851896e+00   6.007230e+00
   3_adp:  0.2353 0.2918   5.786861e+00   5.946724e+00
   3_occ:  0.2349 0.2915   5.785935e+00   5.946452e+00
   4_bss:  0.2336 0.2904   5.784481e+00   5.943807e+00
   4_xyz:  0.1747 0.2184   5.515511e+00   5.705573e+00
   4_adp:  0.1584 0.2020   5.429268e+00   5.625031e+00
   4_occ:  0.1581 0.2020   5.428679e+00   5.625302e+00
   5_bss:  0.1576 0.2020   5.431194e+00   5.627559e+00
   5_xyz:  0.1365 0.1827   5.310338e+00   5.523776e+00
   5_adp:  0.1315 0.1779   5.282334e+00   5.500850e+00
   5_occ:  0.1314 0.1779   5.282083e+00   5.500908e+00
   5_bss:  0.1314 0.1779   5.282013e+00   5.501059e+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:  0.335   0.075   7.670  11.137   7.465   0.000   0.000   0.000
   1_xyz:  0.335   0.075   7.670  11.137   7.465   0.000   0.000   0.000
   1_adp:  0.335   0.075   7.670  11.137   7.465   0.000   0.000   0.000
   1_occ:  0.335   0.075   7.670  11.137   7.465   0.000   0.000   0.000
   2_bss:  0.297  20.000   3.756   6.358   4.216   0.000   0.000   0.000
   2_xyz:  0.297  20.000   3.756   6.358   4.216   0.000   0.000   0.000
   2_adp:  0.297  20.000   3.756   6.358   4.216   0.000   0.000   0.000
   2_occ:  0.297  20.000   3.756   6.358   4.216   0.000   0.000   0.000
   3_bss:  0.319  44.453   1.026   3.317   2.088   0.000   0.000   0.000
   3_xyz:  0.319  44.453   1.026   3.317   2.088   0.000   0.000   0.000
   3_adp:  0.319  44.453   1.026   3.317   2.088   0.000   0.000   0.000
   3_occ:  0.319  44.453   1.026   3.317   2.088   0.000   0.000   0.000
   4_bss:  0.307  40.680  -0.711   1.652   0.701   0.000   0.000   0.000
   4_xyz:  0.307  40.680  -0.711   1.652   0.701   0.000   0.000   0.000
   4_adp:  0.307  40.680  -0.711   1.652   0.701   0.000   0.000   0.000
   4_occ:  0.307  40.680  -0.711   1.652   0.701   0.000   0.000   0.000
   5_bss:  0.319  45.183  -1.720   0.336   0.028   0.000   0.000   0.000
   5_xyz:  0.319  45.183  -1.720   0.336   0.028   0.000   0.000   0.000
   5_adp:  0.319  45.183  -1.720   0.336   0.028   0.000   0.000   0.000
   5_occ:  0.319  45.183  -1.720   0.336   0.028   0.000   0.000   0.000
   5_bss:  0.322  47.081  -1.785   0.055  -0.029   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.498 0.3357  0.4011    82350.503
   1_bss:  65.685 0.3185  0.4845    81606.380
   1_xyz:  60.274 0.3876  0.5802    70214.419
   1_adp:  56.024 0.4433  0.7584    66775.566
   1_occ:  55.917 0.4446  0.7592    66545.524
   2_bss:  55.295 0.4526  0.6803    65527.095
   2_xyz:  46.473 0.5628  0.8399    48261.751
   2_adp:  44.358 0.5892  0.8893    45053.570
   2_occ:  44.311 0.5897  0.8895    44935.123
   3_bss:  43.996 0.5935  0.8178    44498.741
   3_xyz:  33.459 0.7176  0.9552    26929.540
   3_adp:  30.334 0.7539  0.9834    23236.385
   3_occ:  30.307 0.7543  0.9841    23211.398
   4_bss:  30.168 0.7557  0.9297    22985.667
   4_xyz:  21.732 0.8440  0.9988    12575.128
   4_adp:  19.470 0.8668  1.0098    10642.014
   4_occ:  19.469 0.8668  1.0099    10646.744
   5_bss:  19.508 0.8666  0.9740    10738.759
   5_xyz:  17.130 0.8883  0.9825     8608.854
   5_adp:  16.558 0.8938  0.9801     8284.434
   5_occ:  16.554 0.8938  0.9801     8289.562
   5_bss:  16.552 0.8939  0.9759     8293.543
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3327e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3327e+01
   1_xyz:   1.689  0.013  0.105 18.616  0.006  4.117   1.4949e-01
   1_adp:   1.689  0.013  0.105 18.616  0.006  4.117   1.4949e-01
   1_occ:   1.689  0.013  0.105 18.616  0.006  4.117   1.4949e-01
   2_bss:   1.689  0.013  0.105 18.616  0.006  4.117   1.4949e-01
   2_xyz:   1.291  0.009  0.082 16.924  0.005  4.103   9.8837e-02
   2_adp:   1.291  0.009  0.082 16.924  0.005  4.103   9.8837e-02
   2_occ:   1.291  0.009  0.082 16.924  0.005  4.103   9.8837e-02
   3_bss:   1.291  0.009  0.082 16.924  0.005  4.103   9.8837e-02
   3_xyz:   1.272  0.009  0.089 16.547  0.006  4.105   9.1894e-02
   3_adp:   1.272  0.009  0.089 16.547  0.006  4.105   9.1894e-02
   3_occ:   1.272  0.009  0.089 16.547  0.006  4.105   9.1894e-02
   4_bss:   1.272  0.009  0.089 16.547  0.006  4.105   9.1894e-02
   4_xyz:   1.115  0.008  0.077 16.244  0.005  4.108   7.5124e-02
   4_adp:   1.115  0.008  0.077 16.244  0.005  4.108   7.5124e-02
   4_occ:   1.115  0.008  0.077 16.244  0.005  4.108   7.5124e-02
   5_bss:   1.115  0.008  0.077 16.244  0.005  4.108   7.5124e-02
   5_xyz:   1.013  0.006  0.077 15.541  0.004  4.113   6.0907e-02
   5_adp:   1.013  0.006  0.077 15.541  0.004  4.113   6.0907e-02
   5_occ:   1.013  0.006  0.077 15.541  0.004  4.113   6.0907e-02
   5_bss:   1.013  0.006  0.077 15.541  0.004  4.113   6.0907e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.653   6.9014e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.653   6.9014e+00
   1_xyz:  14.906  0.165  0.463 86.321  0.045  2.076   9.6055e-02
   1_adp:  14.906  0.165  0.463 86.321  0.045  2.076   9.6055e-02
   1_occ:  14.906  0.165  0.463 86.321  0.045  2.076   9.6055e-02
   2_bss:  14.906  0.165  0.463 86.321  0.045  2.076   9.6055e-02
   2_xyz:   8.418  0.120  0.258 79.263  0.044  2.028   7.6668e-02
   2_adp:   8.418  0.120  0.258 79.263  0.044  2.028   7.6668e-02
   2_occ:   8.418  0.120  0.258 79.263  0.044  2.028   7.6668e-02
   3_bss:   8.418  0.120  0.258 79.263  0.044  2.028   7.6668e-02
   3_xyz:   8.837  0.068  0.335 87.807  0.055  2.325   1.2293e-01
   3_adp:   8.837  0.068  0.335 87.807  0.055  2.325   1.2293e-01
   3_occ:   8.837  0.068  0.335 87.807  0.055  2.325   1.2293e-01
   4_bss:   8.837  0.068  0.335 87.807  0.055  2.325   1.2293e-01
   4_xyz:   7.611  0.056  0.376 80.439  0.037  2.037   5.3545e-02
   4_adp:   7.611  0.056  0.376 80.439  0.037  2.037   5.3545e-02
   4_occ:   7.611  0.056  0.376 80.439  0.037  2.037   5.3545e-02
   5_bss:   7.611  0.056  0.376 80.439  0.037  2.037   5.3545e-02
   5_xyz:   7.093  0.047  0.467 81.912  0.033  2.245   3.4193e-02
   5_adp:   7.093  0.047  0.467 81.912  0.033  2.245   3.4193e-02
   5_occ:   7.093  0.047  0.467 81.912  0.033  2.245   3.4193e-02
   5_bss:   7.093  0.047  0.467 81.912  0.033  2.245   3.4193e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp: 105.56   0.00  17.20  80.59   0.00  15.50 105.56   0.00  26.44
   1_occ: 105.56   0.00  17.20  80.59   0.00  15.50 105.56   0.00  26.44
   2_bss: 105.56   0.00  17.20  80.59   0.00  15.50 105.56   0.00  26.44
   2_xyz: 105.56   0.00  17.20  80.59   0.00  15.50 105.56   0.00  26.44
   2_adp: 108.80   0.00  16.81  87.16   0.00  14.32 108.80   0.00  30.38
   2_occ: 108.80   0.00  16.81  87.16   0.00  14.32 108.80   0.00  30.38
   3_bss: 108.80   0.00  16.81  87.16   0.00  14.32 108.80   0.00  30.38
   3_xyz: 108.80   0.00  16.81  87.16   0.00  14.32 108.80   0.00  30.38
   3_adp: 101.14   0.00  16.03  88.76   0.00  12.67 101.14   3.26  34.33
   3_occ: 101.14   0.00  16.03  88.76   0.00  12.67 101.14   3.26  34.33
   4_bss: 101.14   0.00  16.03  88.76   0.00  12.67 101.14   3.26  34.33
   4_xyz: 101.14   0.00  16.03  88.76   0.00  12.67 101.14   3.26  34.33
   4_adp:  93.87   0.00  16.11  90.97   0.00  11.91  93.87   3.33  38.98
   4_occ:  93.87   0.00  16.11  90.97   0.00  11.91  93.87   3.33  38.98
   5_bss:  93.87   0.00  16.11  90.97   0.00  11.91  93.87   3.33  38.98
   5_xyz:  93.87   0.00  16.11  90.97   0.00  11.91  93.87   3.33  38.98
   5_adp:  94.48   0.00  16.32  94.48   0.00  11.75  85.46   4.93  41.21
   5_occ:  94.48   0.00  16.32  94.48   0.00  11.75  85.46   4.93  41.21
   5_bss:  94.48   0.00  16.32  94.48   0.00  11.75  85.46   4.93  41.21
------------------------------------------------------------------------
 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:    1.160    0.005    0.406
   1_adp:    1.160    0.005    0.406
   1_occ:    1.160    0.005    0.406
   2_bss:    1.160    0.005    0.406
   2_xyz:    1.698    0.030    0.577
   2_adp:    1.698    0.030    0.577
   2_occ:    1.698    0.030    0.577
   3_bss:    1.698    0.030    0.577
   3_xyz:    1.844    0.061    0.722
   3_adp:    1.844    0.061    0.722
   3_occ:    1.844    0.061    0.722
   4_bss:    1.844    0.061    0.722
   4_xyz:    2.044    0.060    0.840
   4_adp:    2.044    0.060    0.840
   4_occ:    2.044    0.060    0.840
   5_bss:    2.044    0.060    0.840
   5_xyz:    2.029    0.037    0.876
   5_adp:    2.029    0.037    0.876
   5_occ:    2.029    0.037    0.876
   5_bss:    2.029    0.037    0.876
------------------------------------------------------------------------

CPU time actual refinement: 351.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/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_102/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_102/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.09 
  Macro-tasks:
    bulk solvent and scale       = 46.46  
    individual site refinement   = 146.91 
    weights calculation          = 32.07  
    collect and process          = 6.28   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 231.84 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 109.70 
    alpha_beta                      = 8.36   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.53 
    fmodel                         = 7.80   
    r_factors                      = 0.33   
    phase_errors                   = 9.97   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 259.50 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.908 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    648 calls, 109.31 s
gradients_fft:          592 calls, 106.19 s

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

# Date 2008-01-16 Time 00:45:38 PST -0800 (1200473138.63 s)
Start R-work = 0.5120, R-free = 0.4971 (no bulk solvent and anisotropic scale)
Final R-work = 0.1500, R-free = 0.1937 (no bulk solvent and anisotropic scale)

Start R-work = 0.5044, R-free = 0.4919
Final R-work = 0.1314, R-free = 0.1779