# Date 2008-01-16 Time 01:39:01 PST -0800 (1200476341.28 s)
#phil __OFF__

Command line arguments: "../503.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1763
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 503

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.96289
Completeness in resolution range: 0.941824
Completeness with d_max=infinity: 0.939025

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9629

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.96289
Completeness in resolution range: 0.941824
Completeness with d_max=infinity: 0.939025

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2009 [2186/2211]  1966   220  10.1%
  bin  2:  4.2009 -  3.3465 [2094/2114]  1885   209  10.0%
  bin  3:  3.3465 -  2.9271 [2083/2102]  1878   205   9.8%
  bin  4:  2.9271 -  2.6611 [2035/2065]  1826   209  10.3%
  bin  5:  2.6611 -  2.4712 [2055/2074]  1853   202   9.8%
  bin  6:  2.4712 -  2.3261 [2023/2048]  1821   202  10.0%
  bin  7:  2.3261 -  2.2100 [2017/2045]  1813   204  10.1%
  bin  8:  2.2100 -  2.1141 [2015/2051]  1809   206  10.2%
  bin  9:  2.1141 -  2.0329 [2009/2051]  1816   193   9.6%
  bin 10:  2.0329 -  1.9629 [1072/2038]   963   109  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.57 -     2.24: 25
        2.24 -     2.90: 1417
        2.90 -     3.57: 4522
        3.57 -     4.23: 9251
        4.23 -     4.90: 13239
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.574 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.787 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.919 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28449 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_503/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.9914 87.68585 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: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4925   r_free= 0.4820   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.295741                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6858 0.99   1421  156 0.4152 0.3992      6.6268      6.6334|
|  2:  4.6858 -  3.7382 0.99   1368  155 0.4207 0.4116      6.8242      6.7966|
|  3:  3.7382 -  3.2712 0.99   1332  145 0.4487 0.3751      6.6925      6.6303|
|  4:  3.2712 -  2.9747 0.99   1335  151 0.4845 0.4805      6.5516      6.5127|
|  5:  2.9747 -  2.7629 0.99   1311  149 0.5278 0.5061      6.3708       6.405|
|  6:  2.7629 -  2.6009 0.99   1323  143 0.5279 0.5462      6.2912      6.2131|
|  7:  2.6009 -  2.4712 0.99   1318  146 0.5225 0.5178      6.2449      6.2026|
|  8:  2.4712 -  2.3641 0.98   1291  145 0.5463 0.5159      6.1887      6.1813|
|  9:  2.3641 -  2.2734 0.98   1308  140 0.5332 0.5446      6.1269      6.1914|
| 10:  2.2734 -  2.1952 1.00   1284  150 0.5350 0.5392      6.1034      6.0892|
| 11:  2.1952 -  2.1268 0.98   1302  144 0.5167 0.5278      6.0308      6.0563|
| 12:  2.1268 -  2.0661 0.98   1278  142 0.5299 0.5500      5.9619       5.977|
| 13:  2.0661 -  2.0119 0.96   1263  139 0.5390 0.5288       5.889      5.8034|
| 14:  2.0119 -  1.9629 0.38    496   54 0.5616 0.4929      5.8974      5.8264|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6858  1421   156  0.68  36.17   0.78     0.73      78688.73|
|  2:  4.6858 -  3.7382  1368   155  0.70  35.33   0.86     0.79     108284.82|
|  3:  3.7382 -  3.2712  1332   145  0.59  44.48   0.85     0.72     116349.89|
|  4:  3.2712 -  2.9747  1335   151  0.49  52.68   0.77     0.58     105716.25|
|  5:  2.9747 -  2.7629  1311   149  0.35  63.56   0.73     0.43      90081.72|
|  6:  2.7629 -  2.6009  1323   143  0.30  67.17   0.71     0.35      80524.69|
|  7:  2.6009 -  2.4712  1318   146  0.22  73.47   0.74     0.27      77518.84|
|  8:  2.4712 -  2.3641  1291   145  0.22  73.62   0.71     0.27      69542.84|
|  9:  2.3641 -  2.2734  1308   140  0.22  73.72   0.73     0.27      63111.79|
| 10:  2.2734 -  2.1952  1284   150  0.27  69.71   0.74     0.32      53056.73|
| 11:  2.1952 -  2.1268  1302   144  0.26  70.45   0.76     0.33      51482.75|
| 12:  2.1268 -  2.0661  1278   142  0.26  70.39   0.75     0.34      45927.81|
| 13:  2.0661 -  2.0119  1263   139  0.27  70.03   0.72     0.35      40553.11|
| 14:  2.0119 -  1.9629   496    54  0.33  65.43   0.72     0.39      31499.44|
|alpha:            min =        0.27 max =            0.79 mean =         0.45|
|beta:             min =    31499.44 max =       116349.89 mean =     74638.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.37|
|phase err.(test): min =        0.00 max =           89.88 mean =        61.63|
|-----------------------------------------------------------------------------|

============================== 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 = 18.430330             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.803   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.677714              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.141   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       37 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2665 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3939 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5118 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6588 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7743 |
|-----------------------------------------------------------------------------|
|-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 |       53.504 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.116 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    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 = 11.707)------------------------------------------|
|    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: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4986   r_free= 0.4836   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.296734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4843   r_free= 0.4692   ksol= 0.34   Bsol= 0.97   scale= 0.992    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,9.68,10.10,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.290647                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.672721             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.254   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.432820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.442   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4843      final r-factor (work) = 0.4128          |
| start r-factor (free) = 0.4692      final r-factor (free) = 0.4369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.5043 = 13.67 * 0.50 * 6.2899 + 1.00 * 53.5045                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6935 = 13.67 * 0.50 * 6.2238 + 1.00 * 0.1452                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4128      final r-factor (work) = 0.3729          |
| start r-factor (free) = 0.4369      final r-factor (free) = 0.4352          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9321 = 1.43 * 1.00 * 6.2238 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8422 = 1.43 * 1.00 * 6.1577 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.21   15.19    None  None   None       |
|    all(noH): 2823   0      0.00    81.21   15.19    None  None   None       |
|    Sol.    : 438    0      0.00    81.21   24.78    None  None   None       |
|    Mac.    : 2385   0      0.00    68.83   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.121:  944   |   5:    40.606 -  48.727:   69        |
|      1:     8.121 -  16.242:  811   |   6:    48.727 -  56.848:   40        |
|      2:    16.242 -  24.364:  533   |   7:    56.848 -  64.969:   15        |
|      3:    24.364 -  32.485:  277   |   8:    64.969 -  73.091:    5        |
|      4:    32.485 -  40.606:  126   |   9:    73.091 -  81.212:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3729 r_free = 0.4352             target_work(ml) = 6.150         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3726 r_free = 0.4356             target_work(ml) = 6.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3726   r_free= 0.4356   ksol= 0.34   Bsol= 0.97   scale= 1.133    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,9.68,10.10,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.149660                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3691   r_free= 0.4290   ksol= 0.35   Bsol= 31.24   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,5.44,5.91,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.150284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.928352             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.745  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.640271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.039  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3691      final r-factor (work) = 0.2943          |
| start r-factor (free) = 0.4290      final r-factor (free) = 0.3616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8458 = 11.93 * 0.50 * 6.1535 + 1.00 * 0.1452                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2472 = 11.93 * 0.50 * 6.0608 + 1.00 * 0.0996                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2943      final r-factor (work) = 0.2698          |
| start r-factor (free) = 0.3616      final r-factor (free) = 0.3436          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9003 = 0.64 * 1.00 * 6.0608 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8168 = 0.64 * 1.00 * 5.9399 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.76   14.39    None  None   None       |
|    all(noH): 2823   0      0.00    85.76   14.39    None  None   None       |
|    Sol.    : 438    0      0.00    85.76   30.86    None  None   None       |
|    Mac.    : 2385   0      0.00    66.13   11.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.576: 1142   |   5:    42.879 -  51.455:   61        |
|      1:     8.576 -  17.152:  832   |   6:    51.455 -  60.031:   23        |
|      2:    17.152 -  25.728:  403   |   7:    60.031 -  68.607:   10        |
|      3:    25.728 -  34.304:  215   |   8:    68.607 -  77.183:    2        |
|      4:    34.304 -  42.879:  134   |   9:    77.183 -  85.759:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2698 r_free = 0.3436             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2695 r_free = 0.3436             target_work(ml) = 5.914         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2695   r_free= 0.3436   ksol= 0.35   Bsol= 31.24   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.21,5.44,5.91,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.914187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2676   r_free= 0.3408   ksol= 0.34   Bsol= 49.45   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.76,3.67,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.913722                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.582287              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.521  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.786076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.528  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2676      final r-factor (work) = 0.2170          |
| start r-factor (free) = 0.3408      final r-factor (free) = 0.2760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7429 = 3.58 * 0.50 * 5.9422 + 1.00 * 0.0996                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5050 = 3.58 * 0.50 * 5.8310 + 1.00 * 0.0608                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2170      final r-factor (work) = 0.1998          |
| start r-factor (free) = 0.2760      final r-factor (free) = 0.2620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5993 = 0.79 * 1.00 * 5.8310 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4923 = 0.79 * 1.00 * 5.6780 + 1.00 * 0.0290                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.50   15.16    None  None   None       |
|    all(noH): 2823   0      0.00    91.50   15.16    None  None   None       |
|    Sol.    : 438    0      0.80    91.50   38.26    None  None   None       |
|    Mac.    : 2385   0      0.00    81.99   10.92    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 -   9.150: 1320   |   5:    45.750 -  54.900:   97        |
|      1:     9.150 -  18.300:  774   |   6:    54.900 -  64.050:   52        |
|      2:    18.300 -  27.450:  266   |   7:    64.050 -  73.200:   19        |
|      3:    27.450 -  36.600:  158   |   8:    73.200 -  82.350:    7        |
|      4:    36.600 -  45.750:  127   |   9:    82.350 -  91.499:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1998 r_free = 0.2620             target_work(ml) = 5.653         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1996 r_free = 0.2618             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1996   r_free= 0.2618   ksol= 0.34   Bsol= 49.45   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.76,3.67,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.652471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1991   r_free= 0.2617   ksol= 0.33   Bsol= 49.45   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,1.36,2.82,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.651894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.696944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.303  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.930462              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.188   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1991      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2617      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5606 = 3.70 * 0.50 * 5.6803 + 1.00 * 0.0608                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3135 = 3.70 * 0.50 * 5.5434 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1539      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2085      final r-factor (free) = 0.1947          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1768 = 0.93 * 1.00 * 5.5434 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0287 = 0.93 * 1.00 * 5.3897 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.57   14.93    None  None   None       |
|    all(noH): 2823   0      0.00    93.57   14.93    None  None   None       |
|    Sol.    : 438    0      3.00    93.57   41.07    None  None   None       |
|    Mac.    : 2385   0      0.00    86.68   10.12    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 -   9.357: 1491   |   5:    46.783 -  56.139:  113        |
|      1:     9.357 -  18.713:  705   |   6:    56.139 -  65.496:   61        |
|      2:    18.713 -  28.070:  189   |   7:    65.496 -  74.853:   27        |
|      3:    28.070 -  37.426:  121   |   8:    74.853 -  84.209:    9        |
|      4:    37.426 -  46.783:  103   |   9:    84.209 -  93.566:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1419 r_free = 0.1947             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1417 r_free = 0.1945             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.1945   ksol= 0.33   Bsol= 49.45   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,1.36,2.82,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1944   ksol= 0.32   Bsol= 52.68   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,0.88,2.75,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.918080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.081076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.756  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1420      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1944      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9304 = 2.92 * 0.50 * 5.3897 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8081 = 2.92 * 0.50 * 5.3087 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3704 = 3.08 * 1.00 * 5.3087 + 1.00 * 0.0138                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.1570 = 3.08 * 1.00 * 5.2393 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.87   14.81    None  None   None       |
|    all(noH): 2823   0      0.00    98.87   14.81    None  None   None       |
|    Sol.    : 438    0      2.75    98.87   42.01    None  None   None       |
|    Mac.    : 2385   0      0.00    97.83   9.81     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 -   9.887: 1628   |   5:    49.436 -  59.323:   95        |
|      1:     9.887 -  19.774:  625   |   6:    59.323 -  69.210:   62        |
|      2:    19.774 -  29.662:  175   |   7:    69.210 -  79.098:   24        |
|      3:    29.662 -  39.549:  107   |   8:    79.098 -  88.985:   12        |
|      4:    39.549 -  49.436:   87   |   9:    88.985 -  98.872:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1734             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1732             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1732   ksol= 0.32   Bsol= 52.68   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,0.88,2.75,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.227067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6858 0.99   1421  156 0.0994 0.1306      5.3995      5.6003|
|  2:  4.6858 -  3.7382 0.99   1368  155 0.0873 0.1218      5.4632       5.685|
|  3:  3.7382 -  3.2712 0.99   1332  145 0.1134 0.1510      5.5366      5.8303|
|  4:  3.2712 -  2.9747 0.99   1335  151 0.1331 0.1981      5.5235      5.7332|
|  5:  2.9747 -  2.7629 0.99   1311  149 0.1452 0.1854      5.4146      5.6425|
|  6:  2.7629 -  2.6009 0.99   1323  143 0.1341 0.2256       5.291      5.6016|
|  7:  2.6009 -  2.4712 0.99   1318  146 0.1398 0.1743      5.2623      5.3877|
|  8:  2.4712 -  2.3641 0.98   1291  145 0.1357 0.1831      5.1758      5.4119|
|  9:  2.3641 -  2.2734 0.98   1308  140 0.1342 0.1979      5.1325      5.4187|
| 10:  2.2734 -  2.1952 1.00   1284  150 0.1235 0.1883      5.0415      5.2857|
| 11:  2.1952 -  2.1268 0.98   1302  144 0.1255 0.2064      5.0332      5.3849|
| 12:  2.1268 -  2.0661 0.98   1278  142 0.1280 0.1965       4.982      5.2785|
| 13:  2.0661 -  2.0119 0.96   1263  139 0.1157 0.1747      4.8402      5.0353|
| 14:  2.0119 -  1.9629 0.38    496   54 0.1029 0.1500      4.6811      4.9224|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6858  1421   156  0.94   9.64   0.97     0.94       7574.21|
|  2:  4.6858 -  3.7382  1368   155  0.95   8.54   1.02     1.01       9853.74|
|  3:  3.7382 -  3.2712  1332   145  0.92  12.74   1.05     1.04      12015.22|
|  4:  3.2712 -  2.9747  1335   151  0.90  15.60   1.02     1.00      12185.31|
|  5:  2.9747 -  2.7629  1311   149  0.89  17.70   1.01     0.98      10146.79|
|  6:  2.7629 -  2.6009  1323   143  0.88  18.40   0.98     0.95       8570.70|
|  7:  2.6009 -  2.4712  1318   146  0.89  17.82   1.00     0.96       7667.83|
|  8:  2.4712 -  2.3641  1291   145  0.89  17.66   1.00     0.97       6635.24|
|  9:  2.3641 -  2.2734  1308   140  0.89  17.51   0.99     0.94       5980.32|
| 10:  2.2734 -  2.1952  1284   150  0.89  17.50   1.01     0.96       5288.17|
| 11:  2.1952 -  2.1268  1302   144  0.88  18.62   0.99     0.93       5351.04|
| 12:  2.1268 -  2.0661  1278   142  0.89  18.12   1.01     1.00       5014.60|
| 13:  2.0661 -  2.0119  1263   139  0.89  17.81   1.00     0.98       3873.75|
| 14:  2.0119 -  1.9629   496    54  0.92  13.79   0.99     0.96       2640.94|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2640.94 max =        12185.31 mean =      7601.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.83|
|phase err.(test): min =        0.00 max =           89.23 mean =        15.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1732   ksol= 0.32   Bsol= 54.22   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.63,1.30,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1732   ksol= 0.32   Bsol= 54.22   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.63,1.30,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226927                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6858 0.99   1421  156 0.0994 0.1306      5.3984      5.6007|
|  2:  4.6858 -  3.7382 0.99   1368  155 0.0874 0.1219      5.4639       5.686|
|  3:  3.7382 -  3.2712 0.99   1332  145 0.1135 0.1511      5.5373      5.8312|
|  4:  3.2712 -  2.9747 0.99   1335  151 0.1331 0.1981      5.5235      5.7331|
|  5:  2.9747 -  2.7629 0.99   1311  149 0.1452 0.1853      5.4143      5.6419|
|  6:  2.7629 -  2.6009 0.99   1323  143 0.1341 0.2255      5.2906      5.6015|
|  7:  2.6009 -  2.4712 0.99   1318  146 0.1398 0.1745      5.2623      5.3884|
|  8:  2.4712 -  2.3641 0.98   1291  145 0.1357 0.1830      5.1759      5.4114|
|  9:  2.3641 -  2.2734 0.98   1308  140 0.1342 0.1978      5.1326      5.4186|
| 10:  2.2734 -  2.1952 1.00   1284  150 0.1235 0.1883      5.0415      5.2863|
| 11:  2.1952 -  2.1268 0.98   1302  144 0.1256 0.2063      5.0331       5.385|
| 12:  2.1268 -  2.0661 0.98   1278  142 0.1279 0.1963      4.9818      5.2779|
| 13:  2.0661 -  2.0119 0.96   1263  139 0.1157 0.1744      4.8395      5.0338|
| 14:  2.0119 -  1.9629 0.38    496   54 0.1030 0.1497      4.6801       4.921|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6858  1421   156  0.94   9.63   0.97     0.94       7561.96|
|  2:  4.6858 -  3.7382  1368   155  0.95   8.55   1.03     1.01       9861.30|
|  3:  3.7382 -  3.2712  1332   145  0.92  12.76   1.05     1.04      12038.82|
|  4:  3.2712 -  2.9747  1335   151  0.90  15.60   1.03     1.00      12187.32|
|  5:  2.9747 -  2.7629  1311   149  0.89  17.69   1.01     0.99      10140.33|
|  6:  2.7629 -  2.6009  1323   143  0.88  18.40   0.99     0.95       8563.51|
|  7:  2.6009 -  2.4712  1318   146  0.89  17.82   1.00     0.96       7668.22|
|  8:  2.4712 -  2.3641  1291   145  0.89  17.67   1.00     0.98       6636.72|
|  9:  2.3641 -  2.2734  1308   140  0.89  17.52   1.00     0.95       5984.59|
| 10:  2.2734 -  2.1952  1284   150  0.89  17.50   1.01     0.96       5288.18|
| 11:  2.1952 -  2.1268  1302   144  0.88  18.62   0.99     0.94       5352.16|
| 12:  2.1268 -  2.0661  1278   142  0.89  18.11   1.01     1.01       5010.80|
| 13:  2.0661 -  2.0119  1263   139  0.89  17.79   1.00     0.98       3865.71|
| 14:  2.0119 -  1.9629   496    54  0.92  13.74   1.00     0.97       2631.07|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2631.07 max =        12187.32 mean =      7601.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.83|
|phase err.(test): min =        0.00 max =           89.43 mean =        15.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.707)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    100.40  16.34    None  None   None       |
|    all(noH): 2823   0      1.53    100.40  16.34    None  None   None       |
|    Sol.    : 438    0      4.28    100.40  43.54    None  None   None       |
|    Mac.    : 2385   0      1.53    99.36   11.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.531 -  11.418: 1628   |   5:    50.966 -  60.854:   95        |
|      1:    11.418 -  21.305:  625   |   6:    60.854 -  70.741:   62        |
|      2:    21.305 -  31.192:  175   |   7:    70.741 -  80.628:   24        |
|      3:    31.192 -  41.079:  107   |   8:    80.628 -  90.515:   12        |
|      4:    41.079 -  50.966:   87   |   9:    90.515 - 100.402:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.308 - 4.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 313
   mapped sites are within: 0.714 - 4.639

peak=   10.083 closest distance to " CB  VAL A 230 " =    1.432
peak=    9.400 closest distance to " CB  VAL A 296 " =    1.537
peak=    8.132 closest distance to " O   HOH Z 130 " =    1.786
peak=    6.840 closest distance to " CD2 LEU A   5 " =    1.337
peak=    6.618 closest distance to " CD1AILE A 234 " =    1.009
peak=    5.688 closest distance to " O   HOH Z  65 " =    1.553
peak=    5.538 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.536 closest distance to " CG  PRO A  54 " =    1.448
peak=    5.227 closest distance to " NH2 ARG A  56 " =    2.139
peak=    5.211 closest distance to " CG  LEU A 228 " =    1.136
peak=    5.169 closest distance to " O   HOH Z 222 " =    1.269
peak=    5.131 closest distance to " CG  ARG A 138 " =    1.034
peak=    5.097 closest distance to " O   HOH Z 142 " =    1.991
peak=    5.049 closest distance to " O   HOH Z 232 " =    2.238
peak=    5.025 closest distance to " CB  PRO A  54 " =    1.077
peak=    5.024 closest distance to " O   HOH Z 375 " =    1.079
peak=    4.979 closest distance to " CG  LEU A   5 " =    1.189
peak=    4.965 closest distance to " O   HOH Z 425 " =    1.657
peak=    4.884 closest distance to " O   HOH Z 427 " =    2.258
peak=    4.862 closest distance to " NH1 ARG A 138 " =    1.013
peak=    4.816 closest distance to " O   HOH Z   9 " =    2.292
peak=    4.805 closest distance to " O   HOH Z 427 " =    1.162
peak=    4.799 closest distance to " O   HOH Z 417 " =    1.927
peak=    4.786 closest distance to " O   HOH Z 287 " =    1.846
peak=    4.698 closest distance to " O   HOH Z 369 " =    2.205
peak=    4.665 closest distance to " O   HOH Z 127 " =    1.149
peak=    4.609 closest distance to " CB  VAL A 230 " =    1.246
peak=    4.543 closest distance to " O   HOH Z 418 " =    1.038
peak=    4.538 closest distance to " O   HOH Z 124 " =    1.379
peak=    4.536 closest distance to " O   HOH Z 126 " =    2.148
peak=    4.499 closest distance to " O   HOH Z 385 " =    1.125
peak=    4.473 closest distance to " O   HOH Z   7 " =    1.386
peak=    4.408 closest distance to " O   HOH Z 423 " =    1.802
peak=    4.377 closest distance to " CB  ARG A 275 " =    1.050
peak=    4.372 closest distance to " CB  GLN A 223 " =    1.563
peak=    4.353 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.348 closest distance to " O   HOH Z 424 " =    1.049
peak=    4.309 closest distance to " CB  ASN A 148 " =    1.377
peak=    4.250 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.237 closest distance to " O   HOH Z  59 " =    1.674
peak=    4.231 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.215 closest distance to " NH2AARG A 145 " =    1.080
peak=    4.213 closest distance to " O   HOH Z 298 " =    1.658
peak=    4.194 closest distance to " O   HOH Z  63 " =    1.488
peak=    4.194 closest distance to " O   HOH Z 389 " =    1.482
peak=    4.176 closest distance to " CD  LYS A  76 " =    1.754
peak=    4.173 closest distance to " O   HOH Z 112 " =    1.216
peak=    4.157 closest distance to " CH2 TRP A 266 " =    1.071
peak=    4.150 closest distance to " CB  SER A  63 " =    1.281
peak=    4.137 closest distance to " O   HOH Z 415 " =    1.080
peak=    4.133 closest distance to " O   HOH Z  30 " =    1.975
peak=    4.108 closest distance to " O   HOH Z  69 " =    1.077
peak=    4.098 closest distance to " O   HOH Z 225 " =    1.538
peak=    4.073 closest distance to " CB  GLU A 277 " =    3.530
peak=    4.066 closest distance to " O   HOH Z 419 " =    2.183
peak=    4.057 closest distance to " O   HOH Z 258 " =    2.104
peak=    4.053 closest distance to " CG  LEU A 167 " =    1.255
peak=    4.051 closest distance to " O   HOH Z 272 " =    1.811
peak=    4.028 closest distance to " O   HOH Z  39 " =    1.510
peak=    4.026 closest distance to " O   HOH Z   2 " =    1.971
peak=    4.020 closest distance to " O   HOH Z 380 " =    2.109
peak=    4.018 closest distance to " CB  ASN A 142 " =    0.949
peak=    4.012 closest distance to " O   HOH Z 214 " =    2.608
peak=    4.010 closest distance to " O   HOH Z 425 " =    2.111
peak=    3.996 closest distance to " CB  SER A 276 " =    1.112
peak=    3.991 closest distance to " CB  SER A 216 " =    0.951
peak=    3.989 closest distance to " O   HOH Z  66 " =    1.220
peak=    3.983 closest distance to " CB  LYS A 117 " =    1.213
peak=    3.971 closest distance to " O   HOH Z 346 " =    1.593
peak=    3.957 closest distance to " O   HOH Z  91 " =    2.437
peak=    3.952 closest distance to " O   HOH Z 193 " =    1.665
peak=    3.946 closest distance to " O   HOH Z 362 " =    1.786
peak=    3.934 closest distance to " CB  ASN A  39 " =    1.038
peak=    3.934 closest distance to " O   HOH Z 130 " =    2.429
peak=    3.924 closest distance to " O   HOH Z 123 " =    1.082
peak=    3.923 closest distance to " O   HOH Z 316 " =    3.057
peak=    3.920 closest distance to " O   PRO A 198 " =    1.264
peak=    3.915 closest distance to " CB  SER A   3 " =    1.397
peak=    3.915 closest distance to " CE3 TRP A 150 " =    1.104
peak=    3.913 closest distance to " CA  ASN A 127 " =    1.139
peak=    3.903 closest distance to " O   HOH Z 392 " =    1.177
peak=    3.902 closest distance to " O   HOH Z 359 " =    1.397
peak=    3.898 closest distance to " O   HOH Z 139 " =    1.142
peak=    3.883 closest distance to " CG  TRP A 179 " =    2.187
peak=    3.876 closest distance to " O   HOH Z  76 " =    1.068
peak=    3.864 closest distance to " N   SER A 271 " =    1.015
peak=    3.861 closest distance to " CG2 ILE A  20 " =    1.669
peak=    3.850 closest distance to " O   HOH Z 368 " =    3.469
peak=    3.839 closest distance to " O   HOH Z 422 " =    2.562
peak=    3.835 closest distance to " O   HOH Z  49 " =    0.976
peak=    3.824 closest distance to " CG  GLN A  58 " =    0.933
peak=    3.815 closest distance to " O   HOH Z 352 " =    1.735
peak=    3.805 closest distance to " O   HOH Z 327 " =    1.647
peak=    3.802 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.793 closest distance to " O   HOH Z 145 " =    2.100
peak=    3.787 closest distance to " NH1AARG A 145 " =    1.141
peak=    3.778 closest distance to " O   HOH Z 146 " =    1.597
peak=    3.774 closest distance to " CB  VAL A 202 " =    1.670
peak=    3.774 closest distance to " CD2 LEU A 228 " =    1.256
peak=    3.770 closest distance to " CA  PHE A 283 " =    1.284
peak=    3.759 closest distance to " CG2 ILE A 234 " =    0.987
peak=    3.742 closest distance to " CB  ARG A 190 " =    1.706
peak=    3.732 closest distance to " O   HOH Z 411 " =    3.443
peak=    3.731 closest distance to " O   HOH Z 365 " =    3.029
peak=    3.728 closest distance to " O   HOH Z 371 " =    2.847
peak=    3.719 closest distance to " CB  VAL A 265 " =    1.312
peak=    3.713 closest distance to " O   HOH Z 143 " =    1.419
peak=    3.697 closest distance to " CB  LEU A 237 " =    0.882
peak=    3.694 closest distance to " O   HOH Z 290 " =    0.994
peak=    3.691 closest distance to " CG BARG A 102 " =    1.906
peak=    3.686 closest distance to " CB AVAL A  41 " =    1.161
peak=    3.682 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.682 closest distance to " CD  ARG A 269 " =    1.062
peak=    3.681 closest distance to " ND2BASN A 224 " =    0.804
peak=    3.677 closest distance to " CB  GLN A  88 " =    1.382
peak=    3.677 closest distance to " CD  ARG A 159 " =    0.714
peak=    3.670 closest distance to " O   HOH Z 361 " =    1.243
peak=    3.668 closest distance to " CB  TRP A 266 " =    1.157
peak=    3.667 closest distance to " CG AARG A 275 " =    1.134
peak=    3.664 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.662 closest distance to " CB  PHE A 204 " =    1.047
peak=    3.661 closest distance to " CB  ASN A 215 " =    1.252
peak=    3.659 closest distance to " O   HOH Z  51 " =    1.718
peak=    3.657 closest distance to " O   HOH Z   1 " =    1.860
peak=    3.653 closest distance to " N   ALA A 256 " =    1.022
peak=    3.651 closest distance to " NZ  LYS A 117 " =    2.806
peak=    3.647 closest distance to " O   HOH Z 258 " =    1.103
peak=    3.646 closest distance to " CB  TRP A 179 " =    1.454
peak=    3.644 closest distance to " CG  PRO A 213 " =    1.198
peak=    3.636 closest distance to " O   HOH Z 184 " =    1.382
peak=    3.614 closest distance to " O   HOH Z  11 " =    1.414
peak=    3.613 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.610 closest distance to " CG2 VAL A 197 " =    1.161
peak=    3.606 closest distance to " O   HOH Z  69 " =    1.990
peak=    3.602 closest distance to " OG  SER A  62 " =    2.955
peak=    3.596 closest distance to " O   HOH Z 218 " =    1.441
peak=    3.594 closest distance to " N   ASN A 127 " =    1.328
peak=    3.593 closest distance to " O   HOH Z 193 " =    1.508
peak=    3.588 closest distance to " O   HOH Z 234 " =    3.672
peak=    3.583 closest distance to " CB  MET A  47 " =    1.154
peak=    3.578 closest distance to " O   HOH Z 117 " =    1.985
peak=    3.572 closest distance to " NE2 GLN A  58 " =    4.223
peak=    3.571 closest distance to " O   HOH Z  88 " =    3.400
peak=    3.568 closest distance to " NZ  LYS A 119 " =    2.727
peak=    3.566 closest distance to " O   HOH Z 438 " =    2.103
peak=    3.561 closest distance to " O   HOH Z 403 " =    1.565
peak=    3.557 closest distance to " CG2 THR A 221 " =    1.196
peak=    3.543 closest distance to " NH2AARG A 190 " =    1.728
peak=    3.538 closest distance to " O   HOH Z 193 " =    1.698
peak=    3.535 closest distance to " CB  SER A  26 " =    1.654
peak=    3.533 closest distance to " OG BSER A 164 " =    2.148
peak=    3.532 closest distance to " N   PHE A 130 " =    1.231
peak=    3.518 closest distance to " O   HOH Z 236 " =    1.536
peak=    3.516 closest distance to " OG1 THR A 221 " =    1.161
peak=    3.516 closest distance to " CD  ARG A  24 " =    1.045
peak=    3.514 closest distance to " O   HOH Z 158 " =    3.120
peak=    3.505 closest distance to " CA  ARG A 195 " =    1.277
peak=    3.503 closest distance to " O   HOH Z 222 " =    1.854
peak=    3.496 closest distance to " O   HOH Z 153 " =    3.688
peak=    3.495 closest distance to " CB  ASP A 124 " =    0.811
peak=    3.488 closest distance to " NZ  LYS A 117 " =    1.167
peak=    3.488 closest distance to " NH1 ARG A  14 " =    1.072
peak=    3.484 closest distance to " OG  SER A  62 " =    2.700
peak=    3.483 closest distance to " CA  LYS A 117 " =    1.188
peak=    3.482 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.482 closest distance to " CA  SER A 210 " =    1.353
peak=    3.482 closest distance to " CD1 LEU A 281 " =    1.038
peak=    3.472 closest distance to " O   HOH Z 419 " =    1.518
peak=    3.462 closest distance to " O   HOH Z 405 " =    1.514
peak=    3.461 closest distance to " O   HOH Z  40 " =    1.936
peak=    3.451 closest distance to " N   GLN A 278 " =    1.508
peak=    3.451 closest distance to " O   HOH Z 421 " =    2.036
peak=    3.445 closest distance to " O   HOH Z 128 " =    2.152
peak=    3.445 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.438 closest distance to " CB  ARG A  79 " =    1.404
peak=    3.432 closest distance to " CA  ILE A 234 " =    1.079
peak=    3.431 closest distance to " O   HOH Z 378 " =    0.951
peak=    3.431 closest distance to " CG1 ILE A 151 " =    1.177
peak=    3.425 closest distance to " CB  GLN A  89 " =    1.262
peak=    3.424 closest distance to " O   HOH Z 357 " =    2.125
peak=    3.418 closest distance to " O   HOH Z 329 " =    4.042
peak=    3.417 closest distance to " NH2BARG A 190 " =    1.371
peak=    3.413 closest distance to " CB  SER A 212 " =    1.303
peak=    3.411 closest distance to " CB  LEU A 228 " =    1.307
peak=    3.411 closest distance to " O   HOH Z  68 " =    2.045
peak=    3.408 closest distance to " O   HOH Z 424 " =    2.332
peak=    3.402 closest distance to " O   HOH Z   2 " =    1.129
peak=    3.399 closest distance to " OE2 GLU A  44 " =    1.165
peak=    3.397 closest distance to " CE1 HIS A 115 " =    3.764
peak=    3.394 closest distance to " NE2 GLN A  73 " =    1.433
peak=    3.393 closest distance to " CB  ALA A 114 " =    0.898
peak=    3.392 closest distance to " O   HOH Z  26 " =    1.373
peak=    3.385 closest distance to " O   HOH Z  44 " =    1.801
peak=    3.384 closest distance to " O   ASP A 124 " =    0.966
peak=    3.384 closest distance to " CD2 TRP A 179 " =    1.366
peak=    3.380 closest distance to " O   HOH Z 133 " =    1.277
peak=    3.379 closest distance to " O   HOH Z 209 " =    2.543
peak=    3.378 closest distance to " CA  ALA A 129 " =    1.256
peak=    3.378 closest distance to " O   HOH Z  10 " =    1.711
peak=    3.378 closest distance to " O   HOH Z  56 " =    1.908
peak=    3.377 closest distance to " O   HOH Z 218 " =    2.031
peak=    3.375 closest distance to " O   HOH Z 425 " =    2.126
peak=    3.375 closest distance to " CD  GLN A  77 " =    1.183
peak=    3.375 closest distance to " CA  ALA A 158 " =    1.174
peak=    3.375 closest distance to " O   HOH Z 373 " =    1.447
peak=    3.373 closest distance to " CB  GLU A 128 " =    1.105
peak=    3.372 closest distance to " CA  ALA A  51 " =    1.102
peak=    3.371 closest distance to " OG BSER A 212 " =    2.870
peak=    3.364 closest distance to " CG  PRO A 243 " =    1.100
peak=    3.342 closest distance to " O   HOH Z   3 " =    2.203
peak=    3.340 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.334 closest distance to " O   HOH Z 265 " =    1.779
peak=    3.331 closest distance to " O   HOH Z 167 " =    1.738
peak=    3.330 closest distance to " CG2 ILE A 120 " =    1.148
peak=    3.329 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.327 closest distance to " O   HOH Z 195 " =    1.419
peak=    3.323 closest distance to " O   HOH Z  78 " =    2.160
peak=    3.323 closest distance to " CA  MET A 105 " =    0.877
peak=    3.323 closest distance to " CG2 VAL A 257 " =    0.761
peak=    3.318 closest distance to " O   HOH Z 175 " =    2.138
peak=    3.314 closest distance to " CE3 TRP A 274 " =    1.244
peak=    3.310 closest distance to " O   HOH Z 423 " =    1.688
peak=    3.304 closest distance to " O   HOH Z 222 " =    2.106
peak=    3.304 closest distance to " CB  ASN A 110 " =    1.042
peak=    3.302 closest distance to " NH2AARG A 145 " =    2.334
peak=    3.301 closest distance to " CA  GLY A 267 " =    1.236
peak=    3.301 closest distance to " O  BHOH Z 338 " =    2.475
peak=    3.297 closest distance to " O   HOH Z 233 " =    1.650
peak=    3.297 closest distance to " OE2 GLU A   2 " =    1.974
peak=    3.296 closest distance to " CA  SER A  87 " =    1.038
peak=    3.295 closest distance to " CD  PRO A 243 " =    1.641
peak=    3.295 closest distance to " CB  SER A 210 " =    0.908
peak=    3.294 closest distance to " CA  LYS A 290 " =    1.286
peak=    3.293 closest distance to " CA  LEU A 282 " =    1.209
peak=    3.287 closest distance to " CE1 TYR A 116 " =    1.392
peak=    3.284 closest distance to " O   THR A 220 " =    1.324
peak=    3.279 closest distance to " O  BHOH Z  74 " =    1.341
peak=    3.275 closest distance to " ND1 HIS A  81 " =    1.701
peak=    3.274 closest distance to " CA  THR A 221 " =    0.989
peak=    3.274 closest distance to " O   HOH Z 305 " =    3.539
peak=    3.274 closest distance to " O   HOH Z 188 " =    3.068
peak=    3.273 closest distance to " C   ALA A 299 " =    0.963
peak=    3.263 closest distance to " O   HOH Z  88 " =    2.967
peak=    3.261 closest distance to " CB  PRO A  90 " =    1.113
peak=    3.256 closest distance to " O   HOH Z  32 " =    2.187
peak=    3.253 closest distance to " OE1 GLU A   2 " =    1.502
peak=    3.252 closest distance to " OG BSER A  99 " =    2.202
peak=    3.252 closest distance to " O   HOH Z 258 " =    1.271
peak=    3.250 closest distance to " CA  LEU A 101 " =    1.382
peak=    3.250 closest distance to " O   HOH Z 392 " =    1.678
peak=    3.245 closest distance to " O   HOH Z 261 " =    2.218
peak=    3.245 closest distance to " O   HOH Z 343 " =    2.876
peak=    3.238 closest distance to " O   HOH Z 323 " =    1.687
peak=    3.230 closest distance to " O   HOH Z 350 " =    1.450
peak=    3.228 closest distance to " O   ILE A  20 " =    1.943
peak=    3.223 closest distance to " O   PHE A 192 " =    1.401
peak=    3.222 closest distance to " CB  ARG A 219 " =    0.956
peak=    3.218 closest distance to " CB  ALA A   1 " =    4.639
peak=    3.213 closest distance to " O   HOH Z 116 " =    1.076
peak=    3.206 closest distance to " O   HOH Z   1 " =    1.698
peak=    3.204 closest distance to " CB  SER A  99 " =    0.844
peak=    3.197 closest distance to " O   HOH Z 148 " =    2.287
peak=    3.196 closest distance to " O   HOH Z 368 " =    4.257
peak=    3.193 closest distance to " CD  GLN A 240 " =    1.496
peak=    3.193 closest distance to " O   HOH Z 368 " =    1.946
peak=    3.189 closest distance to " CB  ALA A 248 " =    1.011
peak=    3.188 closest distance to " CD1 ILE A  33 " =    1.812
peak=    3.182 closest distance to " O   HOH Z 272 " =    2.304
peak=    3.178 closest distance to " CB  MET A  40 " =    0.829
peak=    3.171 closest distance to " CB  LEU A 300 " =    0.870
peak=    3.168 closest distance to " O   HOH Z 379 " =    1.330
peak=    3.168 closest distance to " O   HOH Z  22 " =    2.047
peak=    3.165 closest distance to " O   HOH Z 109 " =    2.386
peak=    3.165 closest distance to " O   HOH Z 207 " =    2.458
peak=    3.165 closest distance to " CB  ARG A  79 " =    0.891
peak=    3.160 closest distance to " CB  THR A  31 " =    1.595
peak=    3.155 closest distance to " CB  ARG A 156 " =    1.117
peak=    3.155 closest distance to " CB  ILE A 234 " =    1.221
peak=    3.155 closest distance to " O   HOH Z 368 " =    2.814
peak=    3.152 closest distance to " O   HOH Z 302 " =    1.466
peak=    3.145 closest distance to " OD1 ASN A  69 " =    2.560
peak=    3.144 closest distance to " CA  ASN A 217 " =    1.235
peak=    3.141 closest distance to " OG  SER A 135 " =    1.207
peak=    3.135 closest distance to " N   TYR A  15 " =    1.086
peak=    3.132 closest distance to " O   ASN A 209 " =    1.617
peak=    3.130 closest distance to " O   MET A 105 " =    1.709
peak=    3.130 closest distance to " CG  LYS A 119 " =    1.051
peak=    3.128 closest distance to " ND2 ASN A 187 " =    1.604
peak=    3.128 closest distance to " CA  ASP A 149 " =    1.234
peak=    3.127 closest distance to " OG BSER A 164 " =    2.555
peak=    3.122 closest distance to " CA  LEU A 261 " =    1.398
peak=    3.122 closest distance to " CA  ASN A 176 " =    1.331
peak=    3.121 closest distance to " O   HOH Z 216 " =    3.588
peak=    3.121 closest distance to " NE2 HIS A 207 " =    1.181
peak=    3.115 closest distance to " O   HOH Z 154 " =    1.811
peak=    3.111 closest distance to " O   HOH Z  47 " =    1.417
peak=    3.100 closest distance to " CA  ILE A 106 " =    0.716
peak=    3.098 closest distance to " N   GLU A   2 " =    1.500
peak=    3.098 closest distance to " NE  ARG A  56 " =    3.537
peak=    3.097 closest distance to " OD2 ASP A 286 " =    2.509
peak=    3.096 closest distance to " O   HOH Z 303 " =    2.648
peak=    3.089 closest distance to " O   HOH Z 150 " =    1.130
peak=    3.087 closest distance to " O   HOH Z 371 " =    1.979
peak=    3.081 closest distance to " O   HOH Z 172 " =    2.457
peak=    3.080 closest distance to " CA  ARG A 156 " =    1.112
peak=    3.070 closest distance to " CG  ARG A 159 " =    0.879
peak=    3.068 closest distance to " CB  ALA A 114 " =    0.969
peak=    3.066 closest distance to " CA  GLY A 136 " =    1.102
peak=    3.064 closest distance to " O   HOH Z 344 " =    3.017
peak=    3.028 closest distance to " O   HOH Z  57 " =    1.823

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.687 - 5.597
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.767 - 5.597

peak=   -4.638 closest distance to " O   HOH Z 131 " =    4.019
peak=   -4.399 closest distance to " CG2 VAL A 230 " =    0.767
peak=   -4.284 closest distance to " CA  ASP A  27 " =    2.367
peak=   -4.271 closest distance to " OG BSER A 134 " =    1.414
peak=   -4.250 closest distance to " CB  ALA A  43 " =    2.495
peak=   -4.163 closest distance to " CG  ARG A 219 " =    2.481
peak=   -4.159 closest distance to " O   HOH Z 415 " =    1.102
peak=   -4.111 closest distance to " CB  VAL A 230 " =    1.108
peak=   -4.100 closest distance to " O   HOH Z 103 " =    1.419
peak=   -4.074 closest distance to " O   VAL A  67 " =    2.425
peak=   -4.068 closest distance to " O   HOH Z 185 " =    1.968
peak=   -4.056 closest distance to " O   PRO A 198 " =    1.201
peak=   -4.025 closest distance to " O   HOH Z  69 " =    1.807
peak=   -4.023 closest distance to " CG  ARG A 138 " =    1.001
peak=   -4.016 closest distance to " O   HOH Z 266 " =    5.051
peak=   -3.976 closest distance to " C   HIS A 108 " =    1.270
peak=   -3.973 closest distance to " O   HOH Z 100 " =    1.000
peak=   -3.942 closest distance to " CD  ARG A 156 " =    1.991
peak=   -3.911 closest distance to " CE2 PHE A 218 " =    2.490
peak=   -3.894 closest distance to " O   SER A 135 " =    1.449
peak=   -3.876 closest distance to " CD1 LEU A 255 " =    2.874
peak=   -3.872 closest distance to " O   HOH Z 231 " =    2.066
peak=   -3.846 closest distance to " CD  ARG A  14 " =    3.046
peak=   -3.813 closest distance to " N   THR A 157 " =    1.439
peak=   -3.813 closest distance to " O   HOH Z 211 " =    1.116
peak=   -3.810 closest distance to " O   HOH Z 231 " =    0.807
peak=   -3.777 closest distance to " CE BMET A  47 " =    1.058
peak=   -3.767 closest distance to " O   SER A  22 " =    2.452
peak=   -3.758 closest distance to " O   PRO A 243 " =    2.540
peak=   -3.752 closest distance to " ND2 ASN A 187 " =    1.481
peak=   -3.742 closest distance to " OG  SER A  87 " =    1.397
peak=   -3.727 closest distance to " CE2 TYR A  30 " =    2.600
peak=   -3.711 closest distance to " N   PRO A 163 " =    1.549
peak=   -3.710 closest distance to " O   HOH Z 389 " =    1.414
peak=   -3.698 closest distance to " O   HOH Z  11 " =    1.754
peak=   -3.695 closest distance to " O   HOH Z 238 " =    0.948
peak=   -3.693 closest distance to " N   ALA A  43 " =    2.637
peak=   -3.669 closest distance to " O   HOH Z  24 " =    1.193
peak=   -3.660 closest distance to " OG  SER A  62 " =    4.213
peak=   -3.659 closest distance to " O   HOH Z 359 " =    1.686
peak=   -3.652 closest distance to " O   PRO A 163 " =    1.934
peak=   -3.652 closest distance to " ND2 ASN A 249 " =    2.064
peak=   -3.649 closest distance to " O   HOH Z 385 " =    1.320
peak=   -3.645 closest distance to " CB  ALA A 248 " =    2.127
peak=   -3.636 closest distance to " CG2 THR A  52 " =    3.036
peak=   -3.627 closest distance to " CA  GLY A  35 " =    2.096
peak=   -3.622 closest distance to " O   HOH Z  39 " =    1.048
peak=   -3.621 closest distance to " CA  GLY A  98 " =    1.890
peak=   -3.617 closest distance to " CD2 LEU A 237 " =    2.647
peak=   -3.606 closest distance to " OE1 GLU A 277 " =    2.158
peak=   -3.600 closest distance to " CA  ASN A 127 " =    1.210
peak=   -3.598 closest distance to " CD1 LEU A 101 " =    2.287
peak=   -3.596 closest distance to " OH  TYR A 172 " =    1.731
peak=   -3.594 closest distance to " CD2 TYR A 293 " =    1.813
peak=   -3.589 closest distance to " O   HOH Z 359 " =    3.346
peak=   -3.586 closest distance to " OG  SER A 245 " =    1.372
peak=   -3.585 closest distance to " CG2 VAL A 202 " =    2.692
peak=   -3.567 closest distance to " CD  LYS A 289 " =    2.365
peak=   -3.567 closest distance to " O   MET A  40 " =    2.800
peak=   -3.558 closest distance to " O   HOH Z 368 " =    2.409
peak=   -3.551 closest distance to " O   HOH Z 292 " =    1.645
peak=   -3.549 closest distance to " O   HOH Z 275 " =    1.692
peak=   -3.547 closest distance to " NH2 ARG A  79 " =    2.150
peak=   -3.528 closest distance to " C   MET A 188 " =    1.557
peak=   -3.527 closest distance to " O   HOH Z 298 " =    2.934
peak=   -3.527 closest distance to " O   HOH Z  43 " =    1.921
peak=   -3.525 closest distance to " O   HOH Z 352 " =    1.413
peak=   -3.523 closest distance to " O   HOH Z  60 " =    1.802
peak=   -3.523 closest distance to " CG  PHE A 283 " =    2.588
peak=   -3.520 closest distance to " O   ALA A  84 " =    1.679
peak=   -3.518 closest distance to " CZ2 TRP A 274 " =    0.904
peak=   -3.515 closest distance to " CG2 VAL A 296 " =    2.167
peak=   -3.511 closest distance to " O   HOH Z 427 " =    1.828
peak=   -3.504 closest distance to " O   HOH Z 111 " =    1.722
peak=   -3.504 closest distance to " ND2 ASN A  45 " =    2.304
peak=   -3.496 closest distance to " NE2 GLN A  55 " =    1.149
peak=   -3.495 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.494 closest distance to " O   HOH Z 348 " =    1.758
peak=   -3.492 closest distance to " OD2 ASP A  27 " =    1.597
peak=   -3.481 closest distance to " CB  PRO A 213 " =    2.188
peak=   -3.481 closest distance to " CB  GLN A  55 " =    1.141
peak=   -3.478 closest distance to " CE BMET A  47 " =    1.282
peak=   -3.477 closest distance to " CG  GLN A  58 " =    0.978
peak=   -3.473 closest distance to " O   HOH Z 166 " =    1.791
peak=   -3.459 closest distance to " CB  ASN A  39 " =    2.258
peak=   -3.458 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.452 closest distance to " CB  PHE A 130 " =    1.215
peak=   -3.448 closest distance to " C   ALA A 158 " =    1.318
peak=   -3.446 closest distance to " CB  PRO A 243 " =    2.706
peak=   -3.443 closest distance to " CD2 LEU A   5 " =    0.993
peak=   -3.443 closest distance to " CG  TRP A 266 " =    1.911
peak=   -3.443 closest distance to " O   HOH Z 183 " =    1.584
peak=   -3.442 closest distance to " CB  ASP A 132 " =    2.408
peak=   -3.429 closest distance to " CE  MET A 105 " =    2.339
peak=   -3.427 closest distance to " CG  LEU A 281 " =    1.844
peak=   -3.425 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.420 closest distance to " CB  PRO A 280 " =    2.137
peak=   -3.419 closest distance to " ND2 ASN A 285 " =    1.955
peak=   -3.414 closest distance to " O   HOH Z 189 " =    1.192
peak=   -3.410 closest distance to " O   HOH Z 351 " =    1.643
peak=   -3.406 closest distance to " O   HOH Z 350 " =    1.904
peak=   -3.406 closest distance to " O   HOH Z 404 " =    1.461
peak=   -3.399 closest distance to " NH2 ARG A 219 " =    1.684
peak=   -3.395 closest distance to " O   HOH Z 196 " =    2.293
peak=   -3.393 closest distance to " CB  ALA A   7 " =    2.056
peak=   -3.388 closest distance to " O   HOH Z  64 " =    1.305
peak=   -3.384 closest distance to " O   HOH Z 119 " =    2.069
peak=   -3.381 closest distance to " O   HOH Z 313 " =    1.488
peak=   -3.376 closest distance to " OG  SER A  63 " =    1.339
peak=   -3.372 closest distance to " O   ALA A  10 " =    1.798
peak=   -3.369 closest distance to " O   HOH Z 191 " =    5.597
peak=   -3.366 closest distance to " CB  ALA A   9 " =    2.305
peak=   -3.357 closest distance to " O   HOH Z 134 " =    4.247
peak=   -3.357 closest distance to " O   HOH Z 377 " =    1.083
peak=   -3.356 closest distance to " CB  ASP A 132 " =    2.500
peak=   -3.355 closest distance to " N   GLN A  58 " =    1.335
peak=   -3.355 closest distance to " ND2 ASN A 252 " =    2.049
peak=   -3.355 closest distance to " N   ALA A 226 " =    2.095
peak=   -3.347 closest distance to " O   HOH Z 111 " =    4.642
peak=   -3.343 closest distance to " N   ALA A 248 " =    1.531
peak=   -3.329 closest distance to " CB  TYR A  68 " =    1.305
peak=   -3.324 closest distance to " CD  LYS A 166 " =    2.467
peak=   -3.322 closest distance to " CZ  PHE A  38 " =    2.422
peak=   -3.316 closest distance to " N   ALA A   1 " =    1.606
peak=   -3.316 closest distance to " CB  ALA A 114 " =    2.457
peak=   -3.315 closest distance to " ND2 ASN A  45 " =    1.194
peak=   -3.314 closest distance to " O   ASP A 191 " =    1.903
peak=   -3.314 closest distance to " CB  TRP A  85 " =    2.442
peak=   -3.311 closest distance to " C   ARG A 269 " =    1.332
peak=   -3.310 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.310 closest distance to " N   VAL A 232 " =    2.093
peak=   -3.309 closest distance to " O   HOH Z 374 " =    1.830
peak=   -3.306 closest distance to " CZ  TYR A 169 " =    1.814
peak=   -3.305 closest distance to " O   HOH Z 407 " =    2.828
peak=   -3.301 closest distance to " O   GLY A  80 " =    2.497
peak=   -3.296 closest distance to " CA  GLY A 133 " =    1.955
peak=   -3.295 closest distance to " N   ASP A 171 " =    2.548
peak=   -3.285 closest distance to " O   ILE A  49 " =    1.648
peak=   -3.285 closest distance to " N   VAL A  72 " =    1.872
peak=   -3.281 closest distance to " NH2AARG A 275 " =    5.154
peak=   -3.279 closest distance to " O   HOH Z 276 " =    1.619
peak=   -3.278 closest distance to " O   HOH Z  52 " =    1.530
peak=   -3.268 closest distance to " CG1BVAL A  72 " =    2.215
peak=   -3.258 closest distance to " O   HOH Z 193 " =    1.336
peak=   -3.258 closest distance to " O   ALA A  51 " =    1.214
peak=   -3.256 closest distance to " CE1 TYR A 247 " =    2.622
peak=   -3.251 closest distance to " O   HOH Z 128 " =    2.402
peak=   -3.250 closest distance to " O   GLU A 152 " =    1.524
peak=   -3.246 closest distance to " N   ARG A 138 " =    1.461
peak=   -3.237 closest distance to " O   HOH Z 133 " =    1.497
peak=   -3.235 closest distance to " CG  GLN A 240 " =    2.307
peak=   -3.233 closest distance to " O   HOH Z 331 " =    1.185
peak=   -3.220 closest distance to " O   HOH Z  73 " =    2.386
peak=   -3.216 closest distance to " O   HOH Z 295 " =    1.822
peak=   -3.214 closest distance to " O   HOH Z 232 " =    2.162
peak=   -3.214 closest distance to " O   HOH Z 198 " =    1.920
peak=   -3.206 closest distance to " OE2 GLU A 152 " =    1.217
peak=   -3.203 closest distance to " N   SER A 141 " =    1.909
peak=   -3.200 closest distance to " CG2 ILE A  20 " =    2.745
peak=   -3.195 closest distance to " O   ARG A  24 " =    1.987
peak=   -3.190 closest distance to " CB  ALA A 131 " =    1.924
peak=   -3.189 closest distance to " CG1 VAL A 230 " =    1.889
peak=   -3.188 closest distance to " OG  SER A  28 " =    2.009
peak=   -3.181 closest distance to " CD2 HIS A 207 " =    2.173
peak=   -3.176 closest distance to " CZ2 TRP A  92 " =    2.820
peak=   -3.172 closest distance to " CB  PRO A  54 " =    2.438
peak=   -3.171 closest distance to " O   HOH Z 155 " =    1.278
peak=   -3.171 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.171 closest distance to " O   HOH Z 411 " =    1.545
peak=   -3.170 closest distance to " O   HOH Z 117 " =    1.885
peak=   -3.167 closest distance to " O   SER A 164 " =    1.657
peak=   -3.164 closest distance to " CB  PRO A 163 " =    2.341
peak=   -3.163 closest distance to " O   ALA A 180 " =    1.190
peak=   -3.162 closest distance to " O   ALA A   1 " =    1.454
peak=   -3.160 closest distance to " CD  PRO A 243 " =    1.961
peak=   -3.159 closest distance to " O   HOH Z  65 " =    1.315
peak=   -3.159 closest distance to " CB  SER A 210 " =    1.027
peak=   -3.151 closest distance to " O   HOH Z 285 " =    2.023
peak=   -3.145 closest distance to " CG2 VAL A 189 " =    1.982
peak=   -3.141 closest distance to " O   HOH Z 165 " =    1.677
peak=   -3.141 closest distance to " CG1 VAL A 197 " =    2.362
peak=   -3.139 closest distance to " CE2 TRP A  70 " =    2.377
peak=   -3.133 closest distance to " OH  TYR A 247 " =    1.583
peak=   -3.131 closest distance to " O   HOH Z 353 " =    1.619
peak=   -3.130 closest distance to " O   ARG A 145 " =    1.432
peak=   -3.128 closest distance to " N   ALA A 244 " =    1.422
peak=   -3.127 closest distance to " O   HOH Z 414 " =    1.629
peak=   -3.127 closest distance to " O   HOH Z 364 " =    2.320
peak=   -3.124 closest distance to " CB  ASN A  45 " =    2.144
peak=   -3.116 closest distance to " O   GLN A 144 " =    1.395
peak=   -3.113 closest distance to " CD2 PHE A 225 " =    1.002
peak=   -3.111 closest distance to " O   HOH Z 286 " =    1.701
peak=   -3.111 closest distance to " CG  PRO A 163 " =    2.606
peak=   -3.110 closest distance to " O   HOH Z 368 " =    1.542
peak=   -3.106 closest distance to " O   HOH Z 151 " =    1.491
peak=   -3.094 closest distance to " CG  ASN A 301 " =    1.880
peak=   -3.094 closest distance to " N   HIS A 115 " =    2.157
peak=   -3.088 closest distance to " ND2 ASN A 209 " =    2.068
peak=   -3.075 closest distance to " O   HOH Z 318 " =    2.020
peak=   -3.057 closest distance to " O   GLY A  57 " =    1.476
peak=   -3.056 closest distance to " OG  SER A 206 " =    1.777
peak=   -3.052 closest distance to " N   VAL A 125 " =    0.957
peak=   -3.052 closest distance to " O   HOH Z 385 " =    0.974
peak=   -3.046 closest distance to " CE  LYS A  76 " =    2.735
peak=   -3.042 closest distance to " O   TRP A  70 " =    1.424
peak=   -3.031 closest distance to " CD2 LEU A 297 " =    2.129
peak=   -3.030 closest distance to " OD2 ASP A 171 " =    1.903

================= 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    :  0.4925 0.4820   6.295741e+00   6.278757e+00
   1_bss:  0.4843 0.4692   6.290647e+00   6.270617e+00
   1_xyz:  0.4128 0.4369   6.204038e+00   6.229779e+00
   1_adp:  0.3729 0.4352   6.149912e+00   6.227612e+00
   1_occ:  0.3726 0.4356   6.149660e+00   6.228054e+00
   2_bss:  0.3691 0.4290   6.150284e+00   6.226866e+00
   2_xyz:  0.2943 0.3616   5.971185e+00   6.109482e+00
   2_adp:  0.2698 0.3436   5.914266e+00   6.065550e+00
   2_occ:  0.2695 0.3436   5.914187e+00   6.065864e+00
   3_bss:  0.2676 0.3408   5.913722e+00   6.064633e+00
   3_xyz:  0.2170 0.2760   5.721690e+00   5.897751e+00
   3_adp:  0.1998 0.2620   5.653190e+00   5.852470e+00
   3_occ:  0.1996 0.2618   5.652471e+00   5.852374e+00
   4_bss:  0.1991 0.2617   5.651894e+00   5.851855e+00
   4_xyz:  0.1539 0.2085   5.425325e+00   5.651781e+00
   4_adp:  0.1419 0.1947   5.355366e+00   5.587354e+00
   4_occ:  0.1417 0.1945   5.354794e+00   5.586711e+00
   5_bss:  0.1420 0.1944   5.353740e+00   5.585899e+00
   5_xyz:  0.1262 0.1770   5.253936e+00   5.496489e+00
   5_adp:  0.1218 0.1734   5.227610e+00   5.473566e+00
   5_occ:  0.1217 0.1732   5.227067e+00   5.472776e+00
   5_bss:  0.1217 0.1732   5.226927e+00   5.472759e+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:  0.344   0.968   6.730   9.682  10.099   0.000   0.000   0.000
   1_xyz:  0.344   0.968   6.730   9.682  10.099   0.000   0.000   0.000
   1_adp:  0.344   0.968   6.730   9.682  10.099   0.000   0.000   0.000
   1_occ:  0.344   0.968   6.730   9.682  10.099   0.000   0.000   0.000
   2_bss:  0.346  31.243   3.207   5.436   5.912   0.000   0.000   0.000
   2_xyz:  0.346  31.243   3.207   5.436   5.912   0.000   0.000   0.000
   2_adp:  0.346  31.243   3.207   5.436   5.912   0.000   0.000   0.000
   2_occ:  0.346  31.243   3.207   5.436   5.912   0.000   0.000   0.000
   3_bss:  0.339  49.446   1.667   2.759   3.670   0.000   0.000   0.000
   3_xyz:  0.339  49.446   1.667   2.759   3.670   0.000   0.000   0.000
   3_adp:  0.339  49.446   1.667   2.759   3.670   0.000   0.000   0.000
   3_occ:  0.339  49.446   1.667   2.759   3.670   0.000   0.000   0.000
   4_bss:  0.327  49.446   0.684   1.356   2.822   0.000   0.000   0.000
   4_xyz:  0.327  49.446   0.684   1.356   2.822   0.000   0.000   0.000
   4_adp:  0.327  49.446   0.684   1.356   2.822   0.000   0.000   0.000
   4_occ:  0.327  49.446   0.684   1.356   2.822   0.000   0.000   0.000
   5_bss:  0.323  52.685   0.726   0.878   2.746   0.000   0.000   0.000
   5_xyz:  0.323  52.685   0.726   0.878   2.746   0.000   0.000   0.000
   5_adp:  0.323  52.685   0.726   0.878   2.746   0.000   0.000   0.000
   5_occ:  0.323  52.685   0.726   0.878   2.746   0.000   0.000   0.000
   5_bss:  0.319  54.215  -0.663  -0.634   1.297  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.392 0.3749  0.4453    74643.093
   1_bss:  60.849 0.3806  0.5788    72073.683
   1_xyz:  52.139 0.4918  0.7347    57577.617
   1_adp:  51.456 0.5000  0.8135    56779.377
   1_occ:  51.607 0.4980  0.8090    56982.060
   2_bss:  51.089 0.5044  0.7202    56088.462
   2_xyz:  39.796 0.6436  0.9106    36856.313
   2_adp:  36.381 0.6849  0.9498    32353.240
   2_occ:  36.403 0.6846  0.9492    32367.539
   3_bss:  36.151 0.6875  0.8826    32096.361
   3_xyz:  27.692 0.7822  0.9748    19984.706
   3_adp:  25.657 0.8045  0.9843    17670.639
   3_occ:  25.648 0.8046  0.9836    17630.145
   4_bss:  25.619 0.8049  0.9464    17623.847
   4_xyz:  20.270 0.8583  0.9804    11089.274
   4_adp:  18.620 0.8744  0.9780     9758.430
   4_occ:  18.602 0.8746  0.9778     9737.095
   5_bss:  18.560 0.8749  0.9719     9701.406
   5_xyz:  16.388 0.8946  0.9815     7915.147
   5_adp:  15.781 0.9003  0.9740     7615.106
   5_occ:  15.768 0.9004  0.9741     7602.383
   5_bss:  15.767 0.9004  0.9769     7602.305
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3504e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3504e+01
   1_xyz:   1.716  0.013  0.106 18.369  0.006  4.106   1.4516e-01
   1_adp:   1.716  0.013  0.106 18.369  0.006  4.106   1.4516e-01
   1_occ:   1.716  0.013  0.106 18.369  0.006  4.106   1.4516e-01
   2_bss:   1.716  0.013  0.106 18.369  0.006  4.106   1.4516e-01
   2_xyz:   1.263  0.009  0.089 16.496  0.005  4.124   9.9638e-02
   2_adp:   1.263  0.009  0.089 16.496  0.005  4.124   9.9638e-02
   2_occ:   1.263  0.009  0.089 16.496  0.005  4.124   9.9638e-02
   3_bss:   1.263  0.009  0.089 16.496  0.005  4.124   9.9638e-02
   3_xyz:   0.984  0.006  0.073 15.570  0.003  4.115   6.0798e-02
   3_adp:   0.984  0.006  0.073 15.570  0.003  4.115   6.0798e-02
   3_occ:   0.984  0.006  0.073 15.570  0.003  4.115   6.0798e-02
   4_bss:   0.984  0.006  0.073 15.570  0.003  4.115   6.0798e-02
   4_xyz:   1.040  0.007  0.078 15.823  0.004  4.122   6.6608e-02
   4_adp:   1.040  0.007  0.078 15.823  0.004  4.122   6.6608e-02
   4_occ:   1.040  0.007  0.078 15.823  0.004  4.122   6.6608e-02
   5_bss:   1.040  0.007  0.078 15.823  0.004  4.122   6.6608e-02
   5_xyz:   1.006  0.007  0.075 15.567  0.004  4.112   6.2453e-02
   5_adp:   1.006  0.007  0.075 15.567  0.004  4.112   6.2453e-02
   5_occ:   1.006  0.007  0.075 15.567  0.004  4.112   6.2453e-02
   5_bss:   1.006  0.007  0.075 15.567  0.004  4.112   6.2453e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9340e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9340e+00
   1_xyz:  13.455  0.185  0.408 84.840  0.035  2.111   9.8772e-02
   1_adp:  13.455  0.185  0.408 84.840  0.035  2.111   9.8772e-02
   1_occ:  13.455  0.185  0.408 84.840  0.035  2.111   9.8772e-02
   2_bss:  13.455  0.185  0.408 84.840  0.035  2.111   9.8772e-02
   2_xyz:   8.113  0.115  0.307 87.379  0.035  1.999   8.0260e-02
   2_adp:   8.113  0.115  0.307 87.379  0.035  1.999   8.0260e-02
   2_occ:   8.113  0.115  0.307 87.379  0.035  1.999   8.0260e-02
   3_bss:   8.113  0.115  0.307 87.379  0.035  1.999   8.0260e-02
   3_xyz:   7.243  0.042  0.271 82.991  0.027  2.359   4.8801e-02
   3_adp:   7.243  0.042  0.271 82.991  0.027  2.359   4.8801e-02
   3_occ:   7.243  0.042  0.271 82.991  0.027  2.359   4.8801e-02
   4_bss:   7.243  0.042  0.271 82.991  0.027  2.359   4.8801e-02
   4_xyz:   7.660  0.056  0.272 85.154  0.040  2.350   5.8276e-02
   4_adp:   7.660  0.056  0.272 85.154  0.040  2.350   5.8276e-02
   4_occ:   7.660  0.056  0.272 85.154  0.040  2.350   5.8276e-02
   5_bss:   7.660  0.056  0.272 85.154  0.040  2.350   5.8276e-02
   5_xyz:   6.397  0.053  0.246 81.941  0.037  2.314   4.3623e-02
   5_adp:   6.397  0.053  0.246 81.941  0.037  2.314   4.3623e-02
   5_occ:   6.397  0.053  0.246 81.941  0.037  2.314   4.3623e-02
   5_bss:   6.397  0.053  0.246 81.941  0.037  2.314   4.3623e-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:  81.21   0.00  15.19  68.83   0.00  13.42  81.21   0.00  24.78
   1_occ:  81.21   0.00  15.19  68.83   0.00  13.42  81.21   0.00  24.78
   2_bss:  81.21   0.00  15.19  68.83   0.00  13.42  81.21   0.00  24.78
   2_xyz:  81.21   0.00  15.19  68.83   0.00  13.42  81.21   0.00  24.78
   2_adp:  85.76   0.00  14.39  66.13   0.00  11.37  85.76   0.00  30.86
   2_occ:  85.76   0.00  14.39  66.13   0.00  11.37  85.76   0.00  30.86
   3_bss:  85.76   0.00  14.39  66.13   0.00  11.37  85.76   0.00  30.86
   3_xyz:  85.76   0.00  14.39  66.13   0.00  11.37  85.76   0.00  30.86
   3_adp:  91.50   0.00  15.16  81.99   0.00  10.92  91.50   0.80  38.26
   3_occ:  91.50   0.00  15.16  81.99   0.00  10.92  91.50   0.80  38.26
   4_bss:  91.50   0.00  15.16  81.99   0.00  10.92  91.50   0.80  38.26
   4_xyz:  91.50   0.00  15.16  81.99   0.00  10.92  91.50   0.80  38.26
   4_adp:  93.57   0.00  14.93  86.68   0.00  10.12  93.57   3.00  41.07
   4_occ:  93.57   0.00  14.93  86.68   0.00  10.12  93.57   3.00  41.07
   5_bss:  93.57   0.00  14.93  86.68   0.00  10.12  93.57   3.00  41.07
   5_xyz:  93.57   0.00  14.93  86.68   0.00  10.12  93.57   3.00  41.07
   5_adp:  98.87   0.00  14.81  97.83   0.00   9.81  98.87   2.75  42.01
   5_occ:  98.87   0.00  14.81  97.83   0.00   9.81  98.87   2.75  42.01
   5_bss: 100.40   1.53  16.34  99.36   1.53  11.34 100.40   4.28  43.54
------------------------------------------------------------------------
 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:    1.301    0.033    0.410
   1_adp:    1.301    0.033    0.410
   1_occ:    1.301    0.033    0.410
   2_bss:    1.301    0.033    0.410
   2_xyz:    1.676    0.024    0.592
   2_adp:    1.676    0.024    0.592
   2_occ:    1.676    0.024    0.592
   3_bss:    1.676    0.024    0.592
   3_xyz:    1.529    0.042    0.676
   3_adp:    1.529    0.042    0.676
   3_occ:    1.529    0.042    0.676
   4_bss:    1.529    0.042    0.676
   4_xyz:    1.709    0.060    0.773
   4_adp:    1.709    0.060    0.773
   4_occ:    1.709    0.060    0.773
   5_bss:    1.709    0.060    0.773
   5_xyz:    1.810    0.034    0.803
   5_adp:    1.810    0.034    0.803
   5_occ:    1.810    0.034    0.803
   5_bss:    1.810    0.034    0.803
------------------------------------------------------------------------

CPU time actual refinement: 342.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/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_503/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_503/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.74 
  Macro-tasks:
    bulk solvent and scale       = 41.67  
    individual site refinement   = 146.60 
    weights calculation          = 32.05  
    collect and process          = 6.56   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 227.01 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 105.59 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 117.22 
    fmodel                         = 7.37   
    r_factors                      = 0.21   
    phase_errors                   = 10.24  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 252.58 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.739 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    665 calls, 105.23 s
gradients_fft:          610 calls, 103.14 s

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

# Date 2008-01-16 Time 01:44:56 PST -0800 (1200476696.71 s)
Start R-work = 0.4925, R-free = 0.4820 (no bulk solvent and anisotropic scale)
Final R-work = 0.1380, R-free = 0.1871 (no bulk solvent and anisotropic scale)

Start R-work = 0.4843, R-free = 0.4692
Final R-work = 0.1217, R-free = 0.1732