# Date 2008-01-16 Time 00:45:18 PST -0800 (1200473118.48 s)
#phil __OFF__

Command line arguments: "../129.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17798
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 129

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 45.7567, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.95239
Completeness in resolution range: 0.945872
Completeness with d_max=infinity: 0.943003

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8310
                             d_min =   1.9524

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.831 1.95239
Completeness in resolution range: 0.945872
Completeness with d_max=infinity: 0.943003

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8314 -  4.1779 [2177/2201]  1956   221  10.2%
  bin  2:  4.1779 -  3.3284 [2092/2112]  1885   207   9.9%
  bin  3:  3.3284 -  2.9113 [2063/2082]  1860   203   9.8%
  bin  4:  2.9113 -  2.6468 [2032/2062]  1822   210  10.3%
  bin  5:  2.6468 -  2.4580 [2035/2054]  1834   201   9.9%
  bin  6:  2.4580 -  2.3136 [2032/2057]  1826   206  10.1%
  bin  7:  2.3136 -  2.1982 [2003/2031]  1805   198   9.9%
  bin  8:  2.1982 -  2.1027 [1999/2035]  1800   199  10.0%
  bin  9:  2.1027 -  2.0220 [1990/2038]  1796   194   9.7%
  bin 10:  2.0220 -  1.9524 [1166/2038]  1046   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.32 -     2.04: 26
        2.04 -     2.75: 407
        2.75 -     3.47: 4713
        3.47 -     4.18: 9562
        4.18 -     4.90: 14156
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.321 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.404 3.040 -x+1/2,-y+1,z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.461 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.508 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 169 " - " O   HOH Z  43 "  1.508 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28859 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_129/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 45.75675 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: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5188   r_free= 0.5195   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.98 A                  |
| x-ray target function (ml) for work reflections: 6.312437                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6599 0.99   1413  154 0.4428 0.4453      6.6654      6.6939|
|  2:  4.6599 -  3.7179 0.99   1358  154 0.4590 0.4773      6.8646      6.8861|
|  3:  3.7179 -  3.2536 0.99   1328  149 0.4942 0.4485      6.7394      6.7361|
|  4:  3.2536 -  2.9587 0.99   1336  147 0.5188 0.5134      6.5808       6.536|
|  5:  2.9587 -  2.7481 0.99   1304  146 0.5525 0.5212      6.3914        6.44|
|  6:  2.7481 -  2.5869 0.99   1316  148 0.5394 0.5420      6.3077       6.223|
|  7:  2.5869 -  2.4580 0.99   1302  144 0.5450 0.5390      6.2498      6.1698|
|  8:  2.4580 -  2.3514 0.98   1308  141 0.5695 0.5210      6.2007      6.2235|
|  9:  2.3514 -  2.2612 0.98   1288  143 0.5410 0.6013      6.1227      6.2095|
| 10:  2.2612 -  2.1835 1.00   1293  144 0.5541 0.6054      6.1157      6.1073|
| 11:  2.1835 -  2.1154 0.98   1280  149 0.5475 0.5539      6.0318      6.0512|
| 12:  2.1154 -  2.0551 0.98   1304  136 0.5461 0.5477      5.9743       5.997|
| 13:  2.0551 -  2.0011 0.93   1213  136 0.5555 0.5551      5.8929      5.8331|
| 14:  2.0011 -  1.9524 0.45    587   68 0.5512 0.5315      5.9112      5.8057|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6599  1413   154  0.61  42.16   0.77     0.67     103047.20|
|  2:  4.6599 -  3.7179  1358   154  0.59  44.18   0.84     0.68     152857.51|
|  3:  3.7179 -  3.2536  1328   149  0.46  55.00   0.82     0.59     159577.57|
|  4:  3.2536 -  2.9587  1336   147  0.34  63.91   0.77     0.45     141753.43|
|  5:  2.9587 -  2.7481  1304   146  0.25  71.24   0.71     0.33     104581.79|
|  6:  2.7481 -  2.5869  1316   148  0.22  73.90   0.70     0.26      89566.23|
|  7:  2.5869 -  2.4580  1302   144  0.16  78.11   0.73     0.19      78824.92|
|  8:  2.4580 -  2.3514  1308   141  0.16  78.18   0.71     0.20      72040.60|
|  9:  2.3514 -  2.2612  1288   143  0.14  79.59   0.73     0.17      66437.88|
| 10:  2.2612 -  2.1835  1293   144  0.17  77.65   0.73     0.20      57911.27|
| 11:  2.1835 -  2.1154  1280   149  0.14  79.89   0.75     0.18      56914.06|
| 12:  2.1154 -  2.0551  1304   136  0.17  77.23   0.75     0.23      49729.30|
| 13:  2.0551 -  2.0011  1213   136  0.21  74.42   0.71     0.28      42327.31|
| 14:  2.0011 -  1.9524   587    68  0.34  64.96   0.73     0.38      31092.49|
|alpha:            min =        0.17 max =            0.68 mean =         0.35|
|beta:             min =    31092.49 max =       159577.57 mean =     89241.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           90.00 mean =        68.43|
|phase err.(test): min =        0.00 max =           89.99 mean =        68.72|
|-----------------------------------------------------------------------------|

============================== 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 = 35.407494             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.980479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.909   (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:        9 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       47 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      185 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      742 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1538 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2694 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4012 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5182 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6639 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7881 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.917 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       3.133 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    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 = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5229   r_free= 0.5181   ksol= 0.00   Bsol= 0.00   scale= 0.743    |
|                                                                             |
| 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:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.312305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5111   r_free= 0.5088   ksol= 0.38   Bsol= 20.00   scale= 0.952   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.23,8.34,8.71,0.00,0.00,0.00); trace/3= 7.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.308728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.281953             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.513   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.417801              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.836   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5111      final r-factor (work) = 0.4554          |
| start r-factor (free) = 0.5088      final r-factor (free) = 0.4863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 132.6545 = 25.28 * 0.50 * 6.3078 + 1.00 * 52.9172                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.4435 = 25.28 * 0.50 * 6.2710 + 1.00 * 0.1714                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4554      final r-factor (work) = 0.4215          |
| start r-factor (free) = 0.4863      final r-factor (free) = 0.4866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.1765 = 2.42 * 1.00 * 6.2710 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.1039 = 2.42 * 1.00 * 6.2375 + 1.00 * 0.0229                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.86   16.70    None  None   None       |
|    all(noH): 2823   0      0.00    93.86   16.70    None  None   None       |
|    Sol.    : 438    0      0.00    93.86   22.46    None  None   None       |
|    Mac.    : 2385   0      0.00    75.80   15.64    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 -   9.386:  934   |   5:    46.929 -  56.315:   51        |
|      1:     9.386 -  18.772:  857   |   6:    56.315 -  65.701:   18        |
|      2:    18.772 -  28.158:  548   |   7:    65.701 -  75.087:   10        |
|      3:    28.158 -  37.543:  272   |   8:    75.087 -  84.473:    1        |
|      4:    37.543 -  46.929:  130   |   9:    84.473 -  93.858:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4215 r_free = 0.4866             target_work(ml) = 6.232         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4209 r_free = 0.4881             target_work(ml) = 6.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4209   r_free= 0.4881   ksol= 0.38   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.23,8.34,8.71,0.00,0.00,0.00); trace/3= 7.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.231051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4205   r_free= 0.4854   ksol= 0.36   Bsol= 30.64   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.88,5.37,5.85,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.232068                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.233994             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.461  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.099186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.896  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4205      final r-factor (work) = 0.3826          |
| start r-factor (free) = 0.4854      final r-factor (free) = 0.4615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3106 = 12.23 * 0.50 * 6.2350 + 1.00 * 0.1714                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.0293 = 12.23 * 0.50 * 6.1998 + 1.00 * 0.1050                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3826      final r-factor (work) = 0.3746          |
| start r-factor (free) = 0.4615      final r-factor (free) = 0.4535          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8381 = 1.10 * 1.00 * 6.1998 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7939 = 1.10 * 1.00 * 6.1668 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.49   16.55    None  None   None       |
|    all(noH): 2823   0      0.00    90.49   16.55    None  None   None       |
|    Sol.    : 438    0      0.00    90.49   23.05    None  None   None       |
|    Mac.    : 2385   0      0.00    64.53   15.36    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 -   9.049:  824   |   5:    45.244 -  54.293:   53        |
|      1:     9.049 -  18.098:  932   |   6:    54.293 -  63.342:   12        |
|      2:    18.098 -  27.147:  611   |   7:    63.342 -  72.391:    9        |
|      3:    27.147 -  36.195:  283   |   8:    72.391 -  81.440:    0        |
|      4:    36.195 -  45.244:   97   |   9:    81.440 -  90.488:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3746 r_free = 0.4535             target_work(ml) = 6.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3744 r_free = 0.4536             target_work(ml) = 6.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3744   r_free= 0.4536   ksol= 0.36   Bsol= 30.64   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.88,5.37,5.85,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.161632                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3750   r_free= 0.4541   ksol= 0.36   Bsol= 51.28   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,3.74,4.31,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.164487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.426243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.971   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.158122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.524  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3750      final r-factor (work) = 0.3344          |
| start r-factor (free) = 0.4541      final r-factor (free) = 0.4094          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1681 = 9.43 * 0.50 * 6.1664 + 1.00 * 0.1050                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9765 = 9.43 * 0.50 * 6.1293 + 1.00 * 0.0884                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3344      final r-factor (work) = 0.3100          |
| start r-factor (free) = 0.4094      final r-factor (free) = 0.4055          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.2430 = 2.16 * 1.00 * 6.1293 + 1.00 * 0.0153                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0922 = 2.16 * 1.00 * 6.0548 + 1.00 * 0.0251                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.44   17.96    None  None   None       |
|    all(noH): 2823   0      0.00    95.44   17.96    None  None   None       |
|    Sol.    : 438    0      0.00    95.44   30.97    None  None   None       |
|    Mac.    : 2385   0      0.00    93.71   15.58    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 -   9.544: 1013   |   5:    47.718 -  57.262:   79        |
|      1:     9.544 -  19.087:  746   |   6:    57.262 -  66.806:   43        |
|      2:    19.087 -  28.631:  489   |   7:    66.806 -  76.350:   17        |
|      3:    28.631 -  38.175:  277   |   8:    76.350 -  85.893:   13        |
|      4:    38.175 -  47.718:  143   |   9:    85.893 -  95.437:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3100 r_free = 0.4055             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3100 r_free = 0.4053             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3100   r_free= 0.4053   ksol= 0.36   Bsol= 51.28   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,3.74,4.31,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.044602                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3099   r_free= 0.4048   ksol= 0.36   Bsol= 62.85   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.63,3.49,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.044570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.062154             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.436  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.018  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3099      final r-factor (work) = 0.2642          |
| start r-factor (free) = 0.4048      final r-factor (free) = 0.3539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.6258 = 13.06 * 0.50 * 6.0537 + 1.00 * 0.0884                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.2232 = 13.06 * 0.50 * 5.9898 + 1.00 * 0.1034                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2642      final r-factor (work) = 0.2535          |
| start r-factor (free) = 0.3539      final r-factor (free) = 0.3290          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4186 = 0.40 * 1.00 * 5.9898 + 1.00 * 0.0254                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3861 = 0.40 * 1.00 * 5.8995 + 1.00 * 0.0289                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    150.16  17.42    None  None   None       |
|    all(noH): 2823   0      0.00    150.16  17.42    None  None   None       |
|    Sol.    : 438    0      0.00    88.94   32.71    None  None   None       |
|    Mac.    : 2385   0      0.00    150.16  14.61    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 -  15.016: 1547   |   5:    75.079 -  90.095:   14        |
|      1:    15.016 -  30.032:  845   |   6:    90.095 - 105.111:    1        |
|      2:    30.032 -  45.048:  278   |   7:   105.111 - 120.127:    0        |
|      3:    45.048 -  60.064:  109   |   8:   120.127 - 135.143:    0        |
|      4:    60.064 -  75.079:   28   |   9:   135.143 - 150.159:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2535 r_free = 0.3290             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2530 r_free = 0.3283             target_work(ml) = 5.859         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2530   r_free= 0.3283   ksol= 0.36   Bsol= 62.85   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.63,3.49,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.858679                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2520   r_free= 0.3255   ksol= 0.34   Bsol= 53.04   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.09,2.17,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.856802                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.935401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.671  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.045798              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.183   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2520      final r-factor (work) = 0.2140          |
| start r-factor (free) = 0.3255      final r-factor (free) = 0.2758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6570 = 4.94 * 0.50 * 5.8977 + 1.00 * 0.1034                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3654 = 4.94 * 0.50 * 5.7936 + 1.00 * 0.0684                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2140      final r-factor (work) = 0.1844          |
| start r-factor (free) = 0.2758      final r-factor (free) = 0.2514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8741 = 2.05 * 1.00 * 5.7936 + 1.00 * 0.0216                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5532 = 2.05 * 1.00 * 5.6388 + 1.00 * 0.0172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.48  17.40    None  None   None       |
|    all(noH): 2823   0      0.00    101.48  17.40    None  None   None       |
|    Sol.    : 438    0      1.82    100.08  43.69    None  None   None       |
|    Mac.    : 2385   0      0.00    101.48  12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.148: 1304   |   5:    50.741 -  60.889:   96        |
|      1:    10.148 -  20.296:  806   |   6:    60.889 -  71.037:   63        |
|      2:    20.296 -  30.444:  223   |   7:    71.037 -  81.185:   35        |
|      3:    30.444 -  40.593:  143   |   8:    81.185 -  91.333:   10        |
|      4:    40.593 -  50.741:  140   |   9:    91.333 - 101.481:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1844 r_free = 0.2514             target_work(ml) = 5.588         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1842 r_free = 0.2512             target_work(ml) = 5.587         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1842   r_free= 0.2512   ksol= 0.34   Bsol= 53.04   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.09,2.17,0.00,0.00,0.00); trace/3= 1.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.587041                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6599 0.99   1413  154 0.1285 0.1600      5.6166      5.7771|
|  2:  4.6599 -  3.7179 0.99   1358  154 0.1308 0.2047      5.8285      6.1998|
|  3:  3.7179 -  3.2536 0.99   1328  149 0.1739 0.2406      5.9533      6.2432|
|  4:  3.2536 -  2.9587 0.99   1336  147 0.2021 0.2874      5.9061      6.0925|
|  5:  2.9587 -  2.7481 0.99   1304  146 0.2106 0.2446      5.7564      5.9272|
|  6:  2.7481 -  2.5869 0.99   1316  148 0.1989 0.2990      5.6266      5.8154|
|  7:  2.5869 -  2.4580 0.99   1302  144 0.2109 0.2643       5.599      5.7481|
|  8:  2.4580 -  2.3514 0.98   1308  141 0.2098 0.2912      5.5575      5.8046|
|  9:  2.3514 -  2.2612 0.98   1288  143 0.2050 0.2730      5.4737      5.6944|
| 10:  2.2612 -  2.1835 1.00   1293  144 0.1936 0.2706      5.4121      5.5589|
| 11:  2.1835 -  2.1154 0.98   1280  149 0.1915 0.2786      5.3777       5.688|
| 12:  2.1154 -  2.0551 0.98   1304  136 0.1979 0.2785      5.3296      5.6466|
| 13:  2.0551 -  2.0011 0.93   1213  136 0.2113 0.2711      5.2895      5.3985|
| 14:  2.0011 -  1.9524 0.45    587   68 0.2017 0.3163      5.2542      5.4838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6599  1413   154  0.91  13.39   0.98     0.97      12231.74|
|  2:  4.6599 -  3.7179  1358   154  0.91  14.46   1.06     1.04      20597.36|
|  3:  3.7179 -  3.2536  1328   149  0.84  22.55   1.09     1.07      31455.47|
|  4:  3.2536 -  2.9587  1336   147  0.81  25.24   1.06     0.99      28230.85|
|  5:  2.9587 -  2.7481  1304   146  0.79  27.23   1.04     0.99      22059.67|
|  6:  2.7481 -  2.5869  1316   148  0.80  26.84   1.01     0.93      17069.99|
|  7:  2.5869 -  2.4580  1302   144  0.79  27.69   1.04     1.00      16392.47|
|  8:  2.4580 -  2.3514  1308   141  0.78  28.22   1.05     0.98      15169.07|
|  9:  2.3514 -  2.2612  1288   143  0.81  25.93   1.03     0.94      12215.24|
| 10:  2.2612 -  2.1835  1293   144  0.80  26.27   1.05     0.96      10845.13|
| 11:  2.1835 -  2.1154  1280   149  0.79  27.96   1.09     0.99      11197.80|
| 12:  2.1154 -  2.0551  1304   136  0.79  28.03   1.08     1.01      10450.87|
| 13:  2.0551 -  2.0011  1213   136  0.76  29.90   1.06     0.96       9282.71|
| 14:  2.0011 -  1.9524   587    68  0.81  25.81   1.04     0.94       7796.07|
|alpha:            min =        0.93 max =            1.07 mean =         0.99|
|beta:             min =     7796.07 max =        31455.47 mean =     16489.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.94 mean =        24.79|
|phase err.(test): min =        0.00 max =           89.59 mean =        23.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1838   r_free= 0.2515   ksol= 0.33   Bsol= 53.47   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,-0.42,1.34,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.585119                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1838   r_free= 0.2515   ksol= 0.33   Bsol= 53.47   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,-0.42,1.34,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.585119                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8314 -  4.6599 0.99   1413  154 0.1252 0.1584      5.5987      5.7722|
|  2:  4.6599 -  3.7179 0.99   1358  154 0.1309 0.2043      5.8305      6.2045|
|  3:  3.7179 -  3.2536 0.99   1328  149 0.1749 0.2385      5.9561      6.2442|
|  4:  3.2536 -  2.9587 0.99   1336  147 0.2023 0.2887      5.9062      6.0927|
|  5:  2.9587 -  2.7481 0.99   1304  146 0.2108 0.2446      5.7558      5.9269|
|  6:  2.7481 -  2.5869 0.99   1316  148 0.1981 0.2997      5.6243      5.8149|
|  7:  2.5869 -  2.4580 0.99   1302  144 0.2108 0.2651      5.5989      5.7477|
|  8:  2.4580 -  2.3514 0.98   1308  141 0.2094 0.2912      5.5566      5.8045|
|  9:  2.3514 -  2.2612 0.98   1288  143 0.2051 0.2725      5.4739      5.6926|
| 10:  2.2612 -  2.1835 1.00   1293  144 0.1930 0.2708      5.4103      5.5601|
| 11:  2.1835 -  2.1154 0.98   1280  149 0.1907 0.2788       5.376       5.689|
| 12:  2.1154 -  2.0551 0.98   1304  136 0.1972 0.2782      5.3277      5.6467|
| 13:  2.0551 -  2.0011 0.93   1213  136 0.2111 0.2691      5.2876      5.3946|
| 14:  2.0011 -  1.9524 0.45    587   68 0.2023 0.3172      5.2522       5.486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8314 -  4.6599  1413   154  0.91  13.30   0.97     0.96      12042.27|
|  2:  4.6599 -  3.7179  1358   154  0.91  14.43   1.05     1.03      20546.43|
|  3:  3.7179 -  3.2536  1328   149  0.83  22.65   1.08     1.05      31649.89|
|  4:  3.2536 -  2.9587  1336   147  0.81  25.25   1.04     0.97      28240.54|
|  5:  2.9587 -  2.7481  1304   146  0.79  27.22   1.02     0.96      22046.20|
|  6:  2.7481 -  2.5869  1316   148  0.80  26.78   0.98     0.91      17031.85|
|  7:  2.5869 -  2.4580  1302   144  0.79  27.65   1.01     0.97      16371.46|
|  8:  2.4580 -  2.3514  1308   141  0.78  28.17   1.01     0.95      15141.30|
|  9:  2.3514 -  2.2612  1288   143  0.81  25.92   0.99     0.90      12226.83|
| 10:  2.2612 -  2.1835  1293   144  0.80  26.25   1.01     0.93      10834.93|
| 11:  2.1835 -  2.1154  1280   149  0.79  27.95   1.04     0.95      11194.44|
| 12:  2.1154 -  2.0551  1304   136  0.79  27.99   1.04     0.97      10427.01|
| 13:  2.0551 -  2.0011  1213   136  0.77  29.85   1.01     0.92       9263.25|
| 14:  2.0011 -  1.9524   587    68  0.81  25.67   0.99     0.89       7747.31|
|alpha:            min =        0.89 max =            1.05 mean =         0.96|
|beta:             min =     7747.31 max =        31649.89 mean =     16473.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.99 mean =        24.77|
|phase err.(test): min =        0.00 max =           89.66 mean =        23.41|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.405)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.42    101.90  17.83    None  None   None       |
|    all(noH): 2823   0      0.42    101.90  17.83    None  None   None       |
|    Sol.    : 438    0      2.24    100.50  44.11    None  None   None       |
|    Mac.    : 2385   0      0.42    101.90  13.00    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:     0.423 -  10.571: 1304   |   5:    51.164 -  61.312:   96        |
|      1:    10.571 -  20.720:  806   |   6:    61.312 -  71.460:   63        |
|      2:    20.720 -  30.868:  223   |   7:    71.460 -  81.608:   35        |
|      3:    30.868 -  41.016:  143   |   8:    81.608 -  91.756:   10        |
|      4:    41.016 -  51.164:  140   |   9:    91.756 - 101.905:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.279 - 5.838
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 344
   mapped sites are within: 0.717 - 5.838

peak=    7.257 closest distance to " CG  ASP A  27 " =    1.132
peak=    7.168 closest distance to " N   ARG A 275 " =    1.031
peak=    6.547 closest distance to " OD2 ASP A 253 " =    1.071
peak=    6.184 closest distance to " CB  VAL A 296 " =    1.545
peak=    5.884 closest distance to " CB  VAL A 230 " =    1.424
peak=    5.882 closest distance to " O  BHOH Z  74 " =    1.146
peak=    5.830 closest distance to " CE  LYS A 289 " =    1.516
peak=    5.829 closest distance to " O   HOH Z 103 " =    1.171
peak=    5.780 closest distance to " CB  ASP A  27 " =    1.247
peak=    5.628 closest distance to " O   HOH Z 130 " =    2.059
peak=    5.620 closest distance to " OD2 ASP A  27 " =    1.055
peak=    5.546 closest distance to " O   ARG A 275 " =    0.860
peak=    5.514 closest distance to " O   HOH Z 390 " =    1.247
peak=    5.493 closest distance to " O   HOH Z 422 " =    1.513
peak=    5.439 closest distance to " O   HOH Z 268 " =    1.418
peak=    5.389 closest distance to " O   HOH Z 227 " =    2.243
peak=    5.293 closest distance to " CG  ARG A 138 " =    1.108
peak=    5.287 closest distance to " CG  LEU A   5 " =    1.555
peak=    5.267 closest distance to " O   VAL A  72 " =    1.187
peak=    5.161 closest distance to " O   HOH Z 113 " =    2.382
peak=    5.156 closest distance to " NH1 ARG A 138 " =    1.148
peak=    5.092 closest distance to " O   HOH Z   8 " =    0.942
peak=    5.082 closest distance to " N   GLU A 277 " =    0.770
peak=    5.060 closest distance to " OD2 ASP A  27 " =    0.966
peak=    5.059 closest distance to " O   HOH Z 428 " =    1.596
peak=    5.048 closest distance to " O   HOH Z 350 " =    1.921
peak=    4.976 closest distance to " NH2 ARG A 269 " =    0.931
peak=    4.972 closest distance to " O   HOH Z 381 " =    1.247
peak=    4.967 closest distance to " O   HOH Z 139 " =    1.509
peak=    4.962 closest distance to " O   HOH Z 366 " =    2.382
peak=    4.960 closest distance to " O   HOH Z 399 " =    1.105
peak=    4.945 closest distance to " N   LEU A  25 " =    0.878
peak=    4.921 closest distance to " C   SER A 276 " =    0.893
peak=    4.899 closest distance to " C   HIS A 115 " =    0.943
peak=    4.884 closest distance to " O   HOH Z 331 " =    1.915
peak=    4.872 closest distance to " OD1 ASP A  50 " =    1.050
peak=    4.815 closest distance to " O   HOH Z 425 " =    1.933
peak=    4.761 closest distance to " O   HOH Z 188 " =    1.677
peak=    4.709 closest distance to " NE2 GLN A 205 " =    1.202
peak=    4.695 closest distance to " O   HOH Z 402 " =    2.097
peak=    4.670 closest distance to " O   HOH Z 120 " =    1.442
peak=    4.619 closest distance to " O   HOH Z  63 " =    1.907
peak=    4.616 closest distance to " O   HOH Z 244 " =    1.799
peak=    4.572 closest distance to " O   HOH Z 404 " =    1.398
peak=    4.570 closest distance to " O   THR A  82 " =    0.921
peak=    4.560 closest distance to " N   SER A  63 " =    0.945
peak=    4.528 closest distance to " OD1 ASP A 286 " =    1.176
peak=    4.519 closest distance to " O   SER A 273 " =    0.879
peak=    4.501 closest distance to " CB  VAL A 230 " =    1.302
peak=    4.465 closest distance to " NE2 GLN A 103 " =    1.027
peak=    4.456 closest distance to " CB  LYS A 290 " =    0.926
peak=    4.437 closest distance to " OD1 ASN A  45 " =    1.283
peak=    4.431 closest distance to " C   GLN A  11 " =    1.093
peak=    4.418 closest distance to " CD1 LEU A 281 " =    1.121
peak=    4.413 closest distance to " O   HOH Z 402 " =    1.495
peak=    4.403 closest distance to " O   HOH Z 245 " =    1.314
peak=    4.376 closest distance to " O   HOH Z 124 " =    2.081
peak=    4.300 closest distance to " CG2 ILE A 120 " =    1.413
peak=    4.278 closest distance to " O   PRO A 198 " =    1.518
peak=    4.267 closest distance to " O   HOH Z  59 " =    1.794
peak=    4.254 closest distance to " O   HOH Z  83 " =    1.298
peak=    4.250 closest distance to " CE2 PHE A  16 " =    1.019
peak=    4.228 closest distance to " CG2 ILE A 234 " =    0.896
peak=    4.204 closest distance to " O   HOH Z  46 " =    1.686
peak=    4.176 closest distance to " CB  ARG A 275 " =    1.438
peak=    4.173 closest distance to " O   HOH Z   7 " =    2.065
peak=    4.168 closest distance to " O   HOH Z 359 " =    1.401
peak=    4.155 closest distance to " C   GLN A  73 " =    1.145
peak=    4.153 closest distance to " CD1AILE A 234 " =    0.915
peak=    4.146 closest distance to " O   HOH Z  66 " =    1.554
peak=    4.134 closest distance to " CD1 LEU A   5 " =    1.183
peak=    4.131 closest distance to " O   HOH Z 330 " =    1.380
peak=    4.126 closest distance to " CB  LEU A  83 " =    0.774
peak=    4.116 closest distance to " CZ  PHE A 218 " =    1.186
peak=    4.088 closest distance to " N   GLY A 302 " =    1.002
peak=    4.078 closest distance to " C   ARG A  66 " =    0.965
peak=    4.068 closest distance to " CZ3 TRP A 274 " =    1.329
peak=    4.053 closest distance to " O   HOH Z 383 " =    1.134
peak=    4.048 closest distance to " O   HOH Z 416 " =    1.419
peak=    4.041 closest distance to " CB  ALA A 114 " =    0.993
peak=    4.040 closest distance to " O   HOH Z 287 " =    1.652
peak=    4.035 closest distance to " N   ASP A  27 " =    0.995
peak=    4.029 closest distance to " O   HOH Z  54 " =    1.575
peak=    4.027 closest distance to " NZ  LYS A 117 " =    3.393
peak=    4.009 closest distance to " O   HOH Z 219 " =    2.213
peak=    4.008 closest distance to " CD1 PHE A 283 " =    1.213
peak=    4.003 closest distance to " O   HOH Z 406 " =    1.907
peak=    3.999 closest distance to " O   HOH Z  21 " =    1.487
peak=    3.998 closest distance to " CZ BARG A 145 " =    1.839
peak=    3.995 closest distance to " CB  ALA A   8 " =    0.915
peak=    3.995 closest distance to " O   HOH Z 255 " =    1.220
peak=    3.984 closest distance to " O   HOH Z 293 " =    1.538
peak=    3.974 closest distance to " O   HOH Z  40 " =    1.202
peak=    3.963 closest distance to " CG  LYS A  76 " =    1.840
peak=    3.963 closest distance to " CG  PRO A 243 " =    1.445
peak=    3.962 closest distance to " N   ARG A 156 " =    1.326
peak=    3.954 closest distance to " OH  TYR A 293 " =    1.194
peak=    3.947 closest distance to " O   HOH Z  77 " =    1.311
peak=    3.941 closest distance to " O   HOH Z 385 " =    1.829
peak=    3.935 closest distance to " N   SER A  26 " =    1.075
peak=    3.922 closest distance to " NE1 TRP A 266 " =    1.874
peak=    3.912 closest distance to " OG ASER A 258 " =    2.727
peak=    3.912 closest distance to " O   HOH Z 360 " =    1.453
peak=    3.910 closest distance to " O   HOH Z  91 " =    2.516
peak=    3.890 closest distance to " O   HOH Z 358 " =    1.417
peak=    3.885 closest distance to " O   HOH Z 177 " =    1.312
peak=    3.858 closest distance to " CG2AVAL A  72 " =    0.978
peak=    3.855 closest distance to " CZ  PHE A  16 " =    1.203
peak=    3.837 closest distance to " CG1 VAL A 265 " =    1.006
peak=    3.821 closest distance to " CB  SER A  62 " =    1.520
peak=    3.821 closest distance to " CG  GLN A  73 " =    1.288
peak=    3.809 closest distance to " ND2BASN A 224 " =    0.948
peak=    3.802 closest distance to " CA  ARG A  36 " =    1.278
peak=    3.800 closest distance to " O   HOH Z 159 " =    1.155
peak=    3.799 closest distance to " OD1 ASP A 272 " =    0.915
peak=    3.799 closest distance to " CG1 VAL A 125 " =    1.033
peak=    3.791 closest distance to " O   HOH Z  69 " =    1.484
peak=    3.787 closest distance to " O   HOH Z 426 " =    1.206
peak=    3.780 closest distance to " CD2 LEU A 297 " =    1.124
peak=    3.779 closest distance to " CA  GLY A 118 " =    0.884
peak=    3.777 closest distance to " O   THR A 251 " =    0.935
peak=    3.768 closest distance to " CE1 PHE A  38 " =    0.792
peak=    3.765 closest distance to " O   HOH Z  92 " =    1.677
peak=    3.763 closest distance to " C   ALA A  10 " =    1.150
peak=    3.763 closest distance to " CB  ALA A 256 " =    1.028
peak=    3.752 closest distance to " O   HOH Z 371 " =    2.211
peak=    3.749 closest distance to " CE2 TRP A 274 " =    1.125
peak=    3.747 closest distance to " O   HOH Z 223 " =    1.195
peak=    3.742 closest distance to " O   HOH Z 303 " =    1.093
peak=    3.740 closest distance to " CE AMET A  47 " =    1.499
peak=    3.734 closest distance to " OG  SER A 276 " =    0.977
peak=    3.730 closest distance to " O   HOH Z 218 " =    2.290
peak=    3.727 closest distance to " O   HOH Z 388 " =    1.458
peak=    3.727 closest distance to " O   GLN A  55 " =    0.790
peak=    3.725 closest distance to " O   HOH Z 279 " =    2.483
peak=    3.707 closest distance to " N   TYR A  15 " =    1.095
peak=    3.704 closest distance to " O   HOH Z 101 " =    0.827
peak=    3.702 closest distance to " N   TYR A 186 " =    1.209
peak=    3.694 closest distance to " O   HOH Z  24 " =    1.561
peak=    3.690 closest distance to " SD  MET A 105 " =    0.823
peak=    3.689 closest distance to " CD  GLN A 240 " =    1.563
peak=    3.674 closest distance to " O   HOH Z 130 " =    2.039
peak=    3.669 closest distance to " O   HOH Z  53 " =    2.302
peak=    3.650 closest distance to " O   HOH Z 291 " =    1.473
peak=    3.648 closest distance to " O   SER A 271 " =    1.260
peak=    3.648 closest distance to " O   GLU A   2 " =    1.136
peak=    3.644 closest distance to " CB  GLN A 122 " =    1.348
peak=    3.629 closest distance to " O   HOH Z  65 " =    2.416
peak=    3.627 closest distance to " CZ3 TRP A 266 " =    1.219
peak=    3.627 closest distance to " CB  ASN A 301 " =    1.562
peak=    3.623 closest distance to " NH1BARG A 102 " =    1.118
peak=    3.611 closest distance to " O   THR A  29 " =    0.921
peak=    3.598 closest distance to " O   HOH Z 278 " =    1.120
peak=    3.594 closest distance to " ND2 ASN A 249 " =    0.732
peak=    3.592 closest distance to " NE2 GLN A  58 " =    5.571
peak=    3.592 closest distance to " O   HOH Z 352 " =    1.580
peak=    3.592 closest distance to " OG1 THR A  42 " =    0.939
peak=    3.591 closest distance to " O   HOH Z   3 " =    1.952
peak=    3.589 closest distance to " N   GLY A 287 " =    1.065
peak=    3.588 closest distance to " CA  TYR A  30 " =    1.125
peak=    3.586 closest distance to " O   HOH Z 197 " =    2.496
peak=    3.583 closest distance to " OD1 ASP A  27 " =    2.349
peak=    3.582 closest distance to " NH2 ARG A  36 " =    1.337
peak=    3.581 closest distance to " O   HOH Z 353 " =    1.795
peak=    3.577 closest distance to " O   HOH Z 188 " =    3.003
peak=    3.576 closest distance to " CB  ASN A  39 " =    0.885
peak=    3.573 closest distance to " OG1 THR A 279 " =    1.179
peak=    3.567 closest distance to " O   ASP A 124 " =    1.145
peak=    3.558 closest distance to " O   HOH Z 193 " =    1.649
peak=    3.552 closest distance to " N   VAL A  72 " =    0.839
peak=    3.550 closest distance to " O   HOH Z 223 " =    1.219
peak=    3.548 closest distance to " OE1 GLU A  44 " =    0.993
peak=    3.544 closest distance to " OE2 GLU A  53 " =    0.959
peak=    3.529 closest distance to " CB  ARG A  79 " =    1.223
peak=    3.527 closest distance to " O   HOH Z 148 " =    1.642
peak=    3.523 closest distance to " CG1 VAL A 232 " =    1.265
peak=    3.520 closest distance to " O   HOH Z 147 " =    1.602
peak=    3.512 closest distance to " CB  GLU A 277 " =    1.074
peak=    3.512 closest distance to " CA  ALA A  51 " =    1.138
peak=    3.510 closest distance to " O   VAL A 250 " =    0.960
peak=    3.509 closest distance to " CA  GLY A  80 " =    0.806
peak=    3.506 closest distance to " CB  ALA A 242 " =    1.764
peak=    3.504 closest distance to " CB  ALA A  10 " =    1.004
peak=    3.499 closest distance to " O   PHE A  59 " =    0.876
peak=    3.496 closest distance to " OG  SER A  62 " =    2.772
peak=    3.494 closest distance to " NE BARG A 275 " =    1.678
peak=    3.490 closest distance to " O   HOH Z 417 " =    2.532
peak=    3.485 closest distance to " O   HOH Z  69 " =    1.645
peak=    3.484 closest distance to " O   HOH Z  57 " =    2.114
peak=    3.479 closest distance to " O   HOH Z 232 " =    2.168
peak=    3.473 closest distance to " N   PHE A  61 " =    1.054
peak=    3.464 closest distance to " O   GLU A  46 " =    0.888
peak=    3.464 closest distance to " O   HOH Z 258 " =    2.188
peak=    3.462 closest distance to " CB  GLN A 223 " =    1.636
peak=    3.459 closest distance to " O   HOH Z 262 " =    1.080
peak=    3.455 closest distance to " CG  LEU A  25 " =    1.028
peak=    3.455 closest distance to " O   HOH Z 142 " =    1.723
peak=    3.454 closest distance to " O   HOH Z 368 " =    3.479
peak=    3.454 closest distance to " CG  PRO A  90 " =    1.351
peak=    3.452 closest distance to " O   HOH Z 258 " =    1.725
peak=    3.451 closest distance to " O   HOH Z  47 " =    1.853
peak=    3.443 closest distance to " O   HOH Z 146 " =    1.508
peak=    3.442 closest distance to " O   HOH Z   7 " =    3.129
peak=    3.440 closest distance to " O   ALA A  10 " =    0.929
peak=    3.439 closest distance to " N   ASP A 162 " =    1.042
peak=    3.438 closest distance to " O   HOH Z 112 " =    1.250
peak=    3.438 closest distance to " O   HOH Z 344 " =    1.675
peak=    3.435 closest distance to " NE2 GLN A  11 " =    1.149
peak=    3.432 closest distance to " O   HOH Z 342 " =    1.175
peak=    3.431 closest distance to " CA  LYS A 289 " =    0.850
peak=    3.428 closest distance to " O   HOH Z 236 " =    1.682
peak=    3.423 closest distance to " O   HOH Z  66 " =    2.101
peak=    3.421 closest distance to " O   HOH Z 181 " =    2.311
peak=    3.417 closest distance to " O   HOH Z 400 " =    1.017
peak=    3.413 closest distance to " CB  THR A  31 " =    1.755
peak=    3.412 closest distance to " O   PHE A 155 " =    1.639
peak=    3.408 closest distance to " OG  SER A  32 " =    1.186
peak=    3.406 closest distance to " O   HOH Z 105 " =    1.050
peak=    3.405 closest distance to " O   HOH Z 392 " =    1.568
peak=    3.404 closest distance to " O   ASN A 110 " =    0.879
peak=    3.402 closest distance to " O   HOH Z 410 " =    1.338
peak=    3.402 closest distance to " O   HOH Z 412 " =    2.031
peak=    3.401 closest distance to " O   HOH Z 119 " =    4.724
peak=    3.398 closest distance to " CA  ASN A 284 " =    1.086
peak=    3.392 closest distance to " OE1 GLU A  46 " =    1.045
peak=    3.392 closest distance to " OD2 ASP A  50 " =    0.842
peak=    3.388 closest distance to " O   HOH Z  39 " =    2.151
peak=    3.387 closest distance to " O   HOH Z 225 " =    2.083
peak=    3.385 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.377 closest distance to " CG2 THR A  29 " =    1.095
peak=    3.364 closest distance to " CG1 ILE A 120 " =    1.430
peak=    3.363 closest distance to " O   HOH Z 343 " =    1.678
peak=    3.361 closest distance to " CA  ILE A 234 " =    1.571
peak=    3.356 closest distance to " CG2 VAL A 202 " =    0.968
peak=    3.354 closest distance to " O   ALA A 129 " =    1.426
peak=    3.354 closest distance to " O   PHE A  61 " =    1.039
peak=    3.351 closest distance to " O   HOH Z 158 " =    2.670
peak=    3.348 closest distance to " O   HOH Z 326 " =    2.111
peak=    3.347 closest distance to " O   HOH Z  85 " =    2.160
peak=    3.347 closest distance to " N   GLU A   2 " =    1.413
peak=    3.343 closest distance to " O   HOH Z 415 " =    1.332
peak=    3.335 closest distance to " O   HOH Z   9 " =    1.914
peak=    3.332 closest distance to " O   HOH Z 110 " =    1.707
peak=    3.331 closest distance to " N   ASP A  65 " =    0.810
peak=    3.331 closest distance to " CA  ALA A 154 " =    1.175
peak=    3.331 closest distance to " CB  ASN A 110 " =    1.084
peak=    3.330 closest distance to " O   HOH Z  61 " =    2.032
peak=    3.330 closest distance to " O   HOH Z 321 " =    1.104
peak=    3.318 closest distance to " CG2 ILE A 239 " =    1.083
peak=    3.317 closest distance to " O   HOH Z 240 " =    1.958
peak=    3.314 closest distance to " CE  MET A  93 " =    1.418
peak=    3.312 closest distance to " CZ2 TRP A  85 " =    1.346
peak=    3.311 closest distance to " O   HOH Z 427 " =    1.870
peak=    3.309 closest distance to " C   LEU A  25 " =    0.870
peak=    3.308 closest distance to " O   GLU A 277 " =    2.053
peak=    3.307 closest distance to " O   HOH Z 424 " =    2.254
peak=    3.303 closest distance to " O   HOH Z 181 " =    1.540
peak=    3.303 closest distance to " NZ BLYS A 290 " =    1.192
peak=    3.301 closest distance to " CA  ALA A  19 " =    0.832
peak=    3.301 closest distance to " O   HOH Z 194 " =    2.594
peak=    3.298 closest distance to " OH  TYR A  30 " =    1.056
peak=    3.297 closest distance to " CB  GLU A 152 " =    1.151
peak=    3.294 closest distance to " O   HOH Z 403 " =    1.508
peak=    3.287 closest distance to " CZ3 TRP A  70 " =    1.595
peak=    3.286 closest distance to " CE1 PHE A 208 " =    0.717
peak=    3.284 closest distance to " CB  ARG A 159 " =    1.148
peak=    3.283 closest distance to " CB  ALA A 291 " =    0.965
peak=    3.283 closest distance to " O   ASP A 272 " =    0.943
peak=    3.281 closest distance to " CD BLYS A 290 " =    1.485
peak=    3.281 closest distance to " O   HOH Z 368 " =    1.930
peak=    3.276 closest distance to " CZ  ARG A  14 " =    1.116
peak=    3.275 closest distance to " O   HOH Z  40 " =    2.562
peak=    3.270 closest distance to " CB  PRO A  90 " =    1.358
peak=    3.267 closest distance to " CB  TRP A 266 " =    1.095
peak=    3.266 closest distance to " CB  VAL A 202 " =    1.499
peak=    3.264 closest distance to " CA  GLY A  57 " =    1.404
peak=    3.261 closest distance to " ND2 ASN A 252 " =    1.211
peak=    3.261 closest distance to " O   HOH Z  89 " =    1.864
peak=    3.260 closest distance to " O   HOH Z  28 " =    1.677
peak=    3.259 closest distance to " N   PHE A  59 " =    0.720
peak=    3.259 closest distance to " OD1 ASP A  65 " =    0.977
peak=    3.258 closest distance to " O   HOH Z 123 " =    1.830
peak=    3.258 closest distance to " O   HOH Z 249 " =    1.628
peak=    3.257 closest distance to " O   THR A 220 " =    1.038
peak=    3.253 closest distance to " O   HOH Z 199 " =    1.458
peak=    3.251 closest distance to " O   SER A 288 " =    0.898
peak=    3.250 closest distance to " O   HOH Z 153 " =    3.363
peak=    3.243 closest distance to " CG BARG A 190 " =    1.192
peak=    3.240 closest distance to " CG2 VAL A 202 " =    1.153
peak=    3.239 closest distance to " CB  PHE A 204 " =    0.885
peak=    3.225 closest distance to " O   HOH Z 316 " =    1.264
peak=    3.221 closest distance to " N   PHE A 130 " =    1.293
peak=    3.220 closest distance to " OD1 ASP A 298 " =    2.566
peak=    3.212 closest distance to " O   HOH Z 272 " =    1.920
peak=    3.207 closest distance to " O   HOH Z 172 " =    5.838
peak=    3.206 closest distance to " O   HOH Z 266 " =    2.047
peak=    3.205 closest distance to " ND2 ASN A 284 " =    1.007
peak=    3.201 closest distance to " OG  SER A 273 " =    0.943
peak=    3.199 closest distance to " CG  HIS A 115 " =    1.040
peak=    3.196 closest distance to " CG1 ILE A 263 " =    1.291
peak=    3.190 closest distance to " CB  THR A 182 " =    1.095
peak=    3.190 closest distance to " O   HOH Z 204 " =    1.430
peak=    3.189 closest distance to " O   HOH Z 422 " =    2.041
peak=    3.188 closest distance to " OE1 GLN A  94 " =    1.884
peak=    3.185 closest distance to " C   SER A 273 " =    1.257
peak=    3.185 closest distance to " O   HOH Z 143 " =    1.616
peak=    3.183 closest distance to " O   HOH Z 266 " =    2.000
peak=    3.177 closest distance to " CD2 TYR A 186 " =    0.992
peak=    3.177 closest distance to " CG  LEU A 101 " =    0.898
peak=    3.176 closest distance to " CA  VAL A 202 " =    1.181
peak=    3.175 closest distance to " O   HOH Z 423 " =    1.547
peak=    3.174 closest distance to " ND1 HIS A  81 " =    0.732
peak=    3.166 closest distance to " C   GLY A 229 " =    1.074
peak=    3.157 closest distance to " NE2 GLN A  73 " =    1.801
peak=    3.155 closest distance to " CB  LEU A 300 " =    0.965
peak=    3.152 closest distance to " O   HOH Z  39 " =    2.841
peak=    3.146 closest distance to " CA  ASN A 215 " =    1.125
peak=    3.137 closest distance to " O   ARG A  14 " =    1.067
peak=    3.128 closest distance to " CA  ARG A  36 " =    0.881
peak=    3.124 closest distance to " N   ASN A 142 " =    1.437
peak=    3.120 closest distance to " O   HOH Z 109 " =    2.570
peak=    3.118 closest distance to " OD1 ASN A 249 " =    1.109
peak=    3.116 closest distance to " CD2 LEU A 143 " =    1.611
peak=    3.115 closest distance to " CG2 THR A 221 " =    1.175
peak=    3.114 closest distance to " O   HOH Z  63 " =    1.857
peak=    3.109 closest distance to " CB  ALA A 137 " =    0.898
peak=    3.107 closest distance to " O   HOH Z 118 " =    2.682
peak=    3.103 closest distance to " CG  LYS A 193 " =    1.371
peak=    3.090 closest distance to " O   HOH Z  49 " =    2.785
peak=    3.088 closest distance to " OD2 ASP A  50 " =    2.630
peak=    3.071 closest distance to " CB  ALA A 227 " =    1.220
peak=    3.071 closest distance to " CG2 THR A 264 " =    1.160
peak=    3.067 closest distance to " O   HOH Z 369 " =    1.517
peak=    3.063 closest distance to " OE1 GLN A 223 " =    3.808
peak=    3.063 closest distance to " O   GLY A  17 " =    1.329
peak=    3.060 closest distance to " CB  ALA A  43 " =    1.570
peak=    3.054 closest distance to " CA  GLU A 152 " =    0.953
peak=    3.052 closest distance to " CG  ARG A 156 " =    1.096
peak=    3.003 closest distance to " O   HOH Z 258 " =    1.558

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.660 - 5.708
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.745 - 5.708

peak=   -5.602 closest distance to " C   SER A 276 " =    1.264
peak=   -4.436 closest distance to " CG  ASP A  27 " =    1.085
peak=   -4.397 closest distance to " O   ALA A  10 " =    1.298
peak=   -4.276 closest distance to " OG  SER A  97 " =    2.187
peak=   -4.045 closest distance to " CE2 TYR A  30 " =    2.818
peak=   -4.025 closest distance to " O   SER A 245 " =    1.282
peak=   -4.022 closest distance to " CD  ARG A 138 " =    1.289
peak=   -3.996 closest distance to " CG  GLN A  88 " =    1.064
peak=   -3.976 closest distance to " O   PRO A 198 " =    1.209
peak=   -3.961 closest distance to " O   ALA A  51 " =    1.231
peak=   -3.938 closest distance to " C   TRP A 274 " =    0.966
peak=   -3.935 closest distance to " OD2 ASP A 253 " =    0.765
peak=   -3.920 closest distance to " OG BSER A 134 " =    2.034
peak=   -3.909 closest distance to " CD1 ILE A  33 " =    2.233
peak=   -3.907 closest distance to " NE1 TRP A 177 " =    1.582
peak=   -3.893 closest distance to " N   SER A  62 " =    2.581
peak=   -3.889 closest distance to " O   HOH Z 244 " =    1.247
peak=   -3.879 closest distance to " N   LYS A 290 " =    1.081
peak=   -3.840 closest distance to " O   HOH Z 336 " =    5.376
peak=   -3.836 closest distance to " O   PHE A  61 " =    0.904
peak=   -3.833 closest distance to " OD2 ASP A 270 " =    0.942
peak=   -3.821 closest distance to " CA  GLY A  35 " =    1.898
peak=   -3.816 closest distance to " O   HOH Z 385 " =    1.841
peak=   -3.799 closest distance to " O   SER A  26 " =    1.162
peak=   -3.793 closest distance to " O   SER A 271 " =    1.783
peak=   -3.783 closest distance to " CD1 LEU A 255 " =    2.597
peak=   -3.756 closest distance to " C   LEU A  25 " =    1.009
peak=   -3.751 closest distance to " CD1 TRP A 266 " =    1.238
peak=   -3.739 closest distance to " OG  SER A 276 " =    0.745
peak=   -3.731 closest distance to " OD2 ASP A 272 " =    1.102
peak=   -3.712 closest distance to " O   HOH Z 242 " =    1.649
peak=   -3.708 closest distance to " CD2 TYR A 293 " =    1.724
peak=   -3.700 closest distance to " C   ARG A 275 " =    1.235
peak=   -3.685 closest distance to " O   HOH Z 207 " =    1.686
peak=   -3.677 closest distance to " CG2 ILE A 120 " =    1.260
peak=   -3.676 closest distance to " CE3 TRP A 274 " =    1.584
peak=   -3.676 closest distance to " C   PHE A  59 " =    0.848
peak=   -3.662 closest distance to " N   LYS A 289 " =    1.113
peak=   -3.635 closest distance to " CG  TYR A 169 " =    2.351
peak=   -3.611 closest distance to " OH  TYR A 293 " =    1.085
peak=   -3.598 closest distance to " N   SER A  63 " =    1.082
peak=   -3.597 closest distance to " CG  ASP A  50 " =    1.035
peak=   -3.596 closest distance to " O   LYS A 193 " =    0.982
peak=   -3.591 closest distance to " O   HOH Z 276 " =    1.080
peak=   -3.584 closest distance to " CG  GLU A 277 " =    1.367
peak=   -3.579 closest distance to " CD1 PHE A  59 " =    0.986
peak=   -3.575 closest distance to " CD1 PHE A  38 " =    1.093
peak=   -3.571 closest distance to " O   THR A   4 " =    1.329
peak=   -3.566 closest distance to " O   LEU A 222 " =    1.580
peak=   -3.561 closest distance to " CB  SER A 273 " =    1.124
peak=   -3.554 closest distance to " CG  PRO A 213 " =    2.051
peak=   -3.552 closest distance to " CB  ALA A  84 " =    2.180
peak=   -3.543 closest distance to " O   THR A 178 " =    1.083
peak=   -3.539 closest distance to " OG  SER A  28 " =    1.024
peak=   -3.539 closest distance to " CE  LYS A 289 " =    0.939
peak=   -3.534 closest distance to " O   HOH Z 235 " =    1.253
peak=   -3.526 closest distance to " O   HOH Z 316 " =    2.021
peak=   -3.525 closest distance to " CB  ALA A  10 " =    1.855
peak=   -3.522 closest distance to " CB  ASN A 285 " =    1.696
peak=   -3.516 closest distance to " N   THR A 279 " =    0.922
peak=   -3.512 closest distance to " O   LYS A  76 " =    0.918
peak=   -3.510 closest distance to " CA  GLY A  57 " =    2.274
peak=   -3.506 closest distance to " CD2 LEU A 300 " =    2.849
peak=   -3.505 closest distance to " O   SER A  22 " =    1.061
peak=   -3.504 closest distance to " O   HOH Z 131 " =    4.394
peak=   -3.503 closest distance to " O   ARG A  56 " =    1.067
peak=   -3.494 closest distance to " NE1 TRP A 274 " =    1.676
peak=   -3.491 closest distance to " O   HOH Z 205 " =    1.220
peak=   -3.490 closest distance to " O   HOH Z 186 " =    1.236
peak=   -3.489 closest distance to " N   THR A 220 " =    1.537
peak=   -3.486 closest distance to " O   HOH Z 224 " =    1.093
peak=   -3.486 closest distance to " O   HOH Z 345 " =    1.576
peak=   -3.481 closest distance to " CG2 VAL A 230 " =    0.757
peak=   -3.471 closest distance to " CB  PHE A  59 " =    1.395
peak=   -3.470 closest distance to " CE2 PHE A  59 " =    1.529
peak=   -3.466 closest distance to " O   HOH Z  20 " =    1.264
peak=   -3.466 closest distance to " OG1 THR A  42 " =    1.007
peak=   -3.461 closest distance to " CB  ALA A 248 " =    1.991
peak=   -3.452 closest distance to " CA  THR A  29 " =    0.907
peak=   -3.452 closest distance to " O   HOH Z  62 " =    2.815
peak=   -3.449 closest distance to " OG  SER A 245 " =    1.751
peak=   -3.447 closest distance to " O   HOH Z  66 " =    1.395
peak=   -3.437 closest distance to " C   HIS A 115 " =    1.077
peak=   -3.432 closest distance to " CB  ILE A 234 " =    1.183
peak=   -3.431 closest distance to " ND2 ASN A  39 " =    1.762
peak=   -3.428 closest distance to " OD2 ASP A  50 " =    1.554
peak=   -3.427 closest distance to " NE2 GLN A 223 " =    1.406
peak=   -3.421 closest distance to " N   GLN A  11 " =    0.885
peak=   -3.420 closest distance to " O   HOH Z 117 " =    1.683
peak=   -3.410 closest distance to " O   HOH Z 138 " =    1.141
peak=   -3.402 closest distance to " O   ARG A  66 " =    0.994
peak=   -3.400 closest distance to " N   ALA A  43 " =    2.460
peak=   -3.400 closest distance to " NE2 GLN A 194 " =    2.184
peak=   -3.399 closest distance to " OG  SER A  28 " =    1.006
peak=   -3.399 closest distance to " O   ALA A 226 " =    1.143
peak=   -3.396 closest distance to " CA  ASP A  27 " =    1.343
peak=   -3.395 closest distance to " CG1 VAL A 112 " =    2.605
peak=   -3.393 closest distance to " OD1 ASP A 272 " =    1.974
peak=   -3.387 closest distance to " O   GLY A  17 " =    0.980
peak=   -3.385 closest distance to " CD1 TYR A 214 " =    1.564
peak=   -3.376 closest distance to " O   HOH Z 359 " =    3.308
peak=   -3.362 closest distance to " CG2 ILE A 120 " =    0.795
peak=   -3.361 closest distance to " O   HOH Z 126 " =    1.817
peak=   -3.359 closest distance to " C   GLU A   2 " =    1.893
peak=   -3.349 closest distance to " O   SER A 273 " =    0.772
peak=   -3.348 closest distance to " O   HOH Z  88 " =    1.962
peak=   -3.348 closest distance to " O   ASN A 252 " =    0.912
peak=   -3.342 closest distance to " O   ASP A  65 " =    0.962
peak=   -3.337 closest distance to " CA  GLN A  55 " =    1.116
peak=   -3.333 closest distance to " O   HOH Z 313 " =    0.787
peak=   -3.332 closest distance to " CG2 THR A 178 " =    2.257
peak=   -3.325 closest distance to " CD2 HIS A 207 " =    1.673
peak=   -3.323 closest distance to " CG2 ILE A 263 " =    2.221
peak=   -3.315 closest distance to " O   HIS A 115 " =    1.439
peak=   -3.309 closest distance to " ND2 ASN A 249 " =    1.306
peak=   -3.308 closest distance to " O   LYS A 289 " =    2.102
peak=   -3.307 closest distance to " N   GLU A  37 " =    0.946
peak=   -3.307 closest distance to " CG  GLN A  73 " =    1.162
peak=   -3.307 closest distance to " ND2 ASN A 284 " =    1.312
peak=   -3.306 closest distance to " O   HOH Z 128 " =    2.542
peak=   -3.306 closest distance to " CG1 VAL A 125 " =    0.929
peak=   -3.299 closest distance to " OG BSER A 212 " =    2.202
peak=   -3.293 closest distance to " CB  VAL A  78 " =    2.118
peak=   -3.291 closest distance to " OD2 ASP A  27 " =    1.189
peak=   -3.284 closest distance to " CG  ASP A 140 " =    1.318
peak=   -3.282 closest distance to " O   ARG A  24 " =    1.479
peak=   -3.281 closest distance to " CB  VAL A 125 " =    1.309
peak=   -3.272 closest distance to " CZ BARG A 145 " =    1.076
peak=   -3.265 closest distance to " N   ALA A   1 " =    1.387
peak=   -3.264 closest distance to " O   HOH Z 350 " =    1.722
peak=   -3.262 closest distance to " ND2 ASN A 127 " =    1.942
peak=   -3.259 closest distance to " O   GLU A 175 " =    1.301
peak=   -3.259 closest distance to " N   ASN A 127 " =    1.203
peak=   -3.253 closest distance to " CE1 HIS A 115 " =    1.126
peak=   -3.250 closest distance to " CG1 VAL A 153 " =    2.103
peak=   -3.246 closest distance to " CZ  ARG A  66 " =    1.775
peak=   -3.242 closest distance to " N   GLN A  58 " =    0.980
peak=   -3.242 closest distance to " OE1 GLN A  88 " =    1.102
peak=   -3.241 closest distance to " O   HOH Z 268 " =    1.658
peak=   -3.241 closest distance to " NH1 ARG A 195 " =    0.873
peak=   -3.240 closest distance to " CE BLYS A 290 " =    1.913
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.708
peak=   -3.237 closest distance to " O   PHE A 208 " =    1.843
peak=   -3.235 closest distance to " N   ASP A 200 " =    1.701
peak=   -3.234 closest distance to " O   THR A 235 " =    1.219
peak=   -3.232 closest distance to " N   LEU A  25 " =    0.899
peak=   -3.227 closest distance to " N   VAL A  67 " =    1.073
peak=   -3.226 closest distance to " O   HOH Z 257 " =    1.458
peak=   -3.225 closest distance to " O   HOH Z 422 " =    3.292
peak=   -3.225 closest distance to " OE2 GLU A  44 " =    1.270
peak=   -3.216 closest distance to " CA  GLY A 147 " =    1.614
peak=   -3.215 closest distance to " CG2 THR A  29 " =    2.542
peak=   -3.215 closest distance to " OE1 GLN A 183 " =    1.810
peak=   -3.215 closest distance to " O   HOH Z  68 " =    1.606
peak=   -3.211 closest distance to " O   HOH Z  69 " =    1.750
peak=   -3.209 closest distance to " OD2 ASP A 191 " =    1.422
peak=   -3.207 closest distance to " OD2 ASP A  27 " =    0.831
peak=   -3.206 closest distance to " O   HOH Z 438 " =    2.876
peak=   -3.204 closest distance to " CG  TRP A 266 " =    1.663
peak=   -3.204 closest distance to " O   HOH Z  82 " =    1.509
peak=   -3.203 closest distance to " O   TRP A  92 " =    1.600
peak=   -3.201 closest distance to " CG  LYS A 289 " =    1.207
peak=   -3.191 closest distance to " O   HOH Z 370 " =    1.486
peak=   -3.187 closest distance to " CA  ILE A 263 " =    1.075
peak=   -3.186 closest distance to " CD2 PHE A  61 " =    1.010
peak=   -3.184 closest distance to " O   ILE A 234 " =    1.146
peak=   -3.178 closest distance to " O   HOH Z   4 " =    0.822
peak=   -3.178 closest distance to " O   HOH Z  75 " =    1.254
peak=   -3.176 closest distance to " O   HOH Z 223 " =    1.725
peak=   -3.166 closest distance to " CB  SER A 276 " =    2.054
peak=   -3.162 closest distance to " CG  PRO A 243 " =    1.735
peak=   -3.162 closest distance to " O   HOH Z 150 " =    0.864
peak=   -3.160 closest distance to " N   HIS A 115 " =    1.660
peak=   -3.154 closest distance to " O   HOH Z 430 " =    4.822
peak=   -3.152 closest distance to " C   LEU A 297 " =    1.068
peak=   -3.149 closest distance to " O   HOH Z   9 " =    1.541
peak=   -3.148 closest distance to " O   HOH Z 137 " =    1.234
peak=   -3.145 closest distance to " CE2 PHE A 130 " =    1.257
peak=   -3.144 closest distance to " O   HOH Z 372 " =    1.063
peak=   -3.143 closest distance to " O   ALA A 100 " =    1.323
peak=   -3.141 closest distance to " O   HOH Z 165 " =    2.032
peak=   -3.139 closest distance to " O   HOH Z 407 " =    1.738
peak=   -3.135 closest distance to " NH1 ARG A  36 " =    0.786
peak=   -3.134 closest distance to " O  BHOH Z 338 " =    1.487
peak=   -3.124 closest distance to " O   HOH Z 314 " =    1.075
peak=   -3.124 closest distance to " O   HOH Z 390 " =    2.623
peak=   -3.123 closest distance to " CH2 TRP A 177 " =    2.399
peak=   -3.116 closest distance to " O   HOH Z 151 " =    2.798
peak=   -3.116 closest distance to " O   THR A 279 " =    0.775
peak=   -3.116 closest distance to " CG  ASP A 149 " =    1.098
peak=   -3.112 closest distance to " OD1 ASN A 284 " =    1.524
peak=   -3.110 closest distance to " O   GLN A  73 " =    1.096
peak=   -3.109 closest distance to " CD1 LEU A 281 " =    0.984
peak=   -3.106 closest distance to " O   HOH Z 412 " =    3.119
peak=   -3.103 closest distance to " CG2BVAL A  41 " =    1.303
peak=   -3.102 closest distance to " O   TRP A 150 " =    1.664
peak=   -3.099 closest distance to " O   HOH Z  24 " =    1.582
peak=   -3.096 closest distance to " OG  SER A  87 " =    1.944
peak=   -3.075 closest distance to " O   HOH Z 332 " =    1.766
peak=   -3.069 closest distance to " O   HOH Z 214 " =    0.996
peak=   -3.057 closest distance to " CB  ALA A 248 " =    2.129
peak=   -3.053 closest distance to " CD2 LEU A  83 " =    1.458
peak=   -3.050 closest distance to " O   HOH Z 235 " =    1.149
peak=   -3.050 closest distance to " O   ARG A 159 " =    1.108
peak=   -3.043 closest distance to " O   ARG A 275 " =    0.829
peak=   -3.040 closest distance to " O   LEU A 222 " =    1.203
peak=   -3.039 closest distance to " O   SER A  26 " =    0.834
peak=   -3.023 closest distance to " O   HOH Z 366 " =    2.909
peak=   -3.022 closest distance to " CG  ASP A  27 " =    1.143

================= 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    :  0.5188 0.5195   6.312437e+00   6.307158e+00
   1_bss:  0.5111 0.5088   6.308728e+00   6.301033e+00
   1_xyz:  0.4554 0.4863   6.261067e+00   6.284677e+00
   1_adp:  0.4215 0.4866   6.231598e+00   6.281084e+00
   1_occ:  0.4209 0.4881   6.231051e+00   6.281784e+00
   2_bss:  0.4205 0.4854   6.232068e+00   6.281317e+00
   2_xyz:  0.3826 0.4615   6.169268e+00   6.251082e+00
   2_adp:  0.3746 0.4535   6.161271e+00   6.248250e+00
   2_occ:  0.3744 0.4536   6.161632e+00   6.248515e+00
   3_bss:  0.3750 0.4541   6.164487e+00   6.249487e+00
   3_xyz:  0.3344 0.4094   6.077895e+00   6.195870e+00
   3_adp:  0.3100 0.4055   6.044894e+00   6.186766e+00
   3_occ:  0.3100 0.4053   6.044602e+00   6.186447e+00
   4_bss:  0.3099 0.4048   6.044570e+00   6.186974e+00
   4_xyz:  0.2642 0.3539   5.911102e+00   6.093387e+00
   4_adp:  0.2535 0.3290   5.860622e+00   6.035076e+00
   4_occ:  0.2530 0.3283   5.858679e+00   6.033128e+00
   5_bss:  0.2520 0.3255   5.856802e+00   6.030394e+00
   5_xyz:  0.2140 0.2758   5.706820e+00   5.896980e+00
   5_adp:  0.1844 0.2514   5.588047e+00   5.809781e+00
   5_occ:  0.1842 0.2512   5.587041e+00   5.808999e+00
   5_bss:  0.1838 0.2515   5.585119e+00   5.808832e+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:  0.384  20.000   6.227   8.345   8.708   0.000   0.000   0.000
   1_xyz:  0.384  20.000   6.227   8.345   8.708   0.000   0.000   0.000
   1_adp:  0.384  20.000   6.227   8.345   8.708   0.000   0.000   0.000
   1_occ:  0.384  20.000   6.227   8.345   8.708   0.000   0.000   0.000
   2_bss:  0.356  30.641   3.879   5.372   5.849   0.000   0.000   0.000
   2_xyz:  0.356  30.641   3.879   5.372   5.849   0.000   0.000   0.000
   2_adp:  0.356  30.641   3.879   5.372   5.849   0.000   0.000   0.000
   2_occ:  0.356  30.641   3.879   5.372   5.849   0.000   0.000   0.000
   3_bss:  0.357  51.279   2.511   3.744   4.315   0.000   0.000   0.000
   3_xyz:  0.357  51.279   2.511   3.744   4.315   0.000   0.000   0.000
   3_adp:  0.357  51.279   2.511   3.744   4.315   0.000   0.000   0.000
   3_occ:  0.357  51.279   2.511   3.744   4.315   0.000   0.000   0.000
   4_bss:  0.358  62.851   1.782   2.626   3.494   0.000   0.000   0.000
   4_xyz:  0.358  62.851   1.782   2.626   3.494   0.000   0.000   0.000
   4_adp:  0.358  62.851   1.782   2.626   3.494   0.000   0.000   0.000
   4_occ:  0.358  62.851   1.782   2.626   3.494   0.000   0.000   0.000
   5_bss:  0.342  53.042   0.327   1.089   2.167   0.000   0.000   0.000
   5_xyz:  0.342  53.042   0.327   1.089   2.167   0.000   0.000   0.000
   5_adp:  0.342  53.042   0.327   1.089   2.167   0.000   0.000   0.000
   5_occ:  0.342  53.042   0.327   1.089   2.167   0.000   0.000   0.000
   5_bss:  0.328  53.465  -0.914  -0.425   1.339  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  68.458 0.2836  0.3464    89251.352
   1_bss:  67.397 0.2969  0.4517    87376.200
   1_xyz:  63.343 0.3488  0.5185    79927.819
   1_adp:  62.216 0.3634  0.5992    78969.017
   1_occ:  62.305 0.3622  0.5952    79109.371
   2_bss:  62.101 0.3648  0.5485    78522.614
   2_xyz:  56.134 0.4413  0.6656    66955.502
   2_adp:  54.886 0.4574  0.7087    65600.789
   2_occ:  54.959 0.4565  0.7073    65701.869
   3_bss:  54.936 0.4570  0.6733    66002.574
   3_xyz:  47.260 0.5535  0.8152    51471.403
   3_adp:  45.714 0.5727  0.8352    49139.071
   3_occ:  45.694 0.5729  0.8355    49086.866
   4_bss:  45.604 0.5740  0.8112    49019.319
   4_xyz:  38.374 0.6611  0.9229    35694.795
   4_adp:  34.232 0.7105  0.9858    30187.760
   4_occ:  34.129 0.7116  0.9863    29946.236
   5_bss:  34.000 0.7129  0.9371    29638.030
   5_xyz:  27.752 0.7820  0.9846    20371.769
   5_adp:  24.691 0.8148  0.9854    16552.154
   5_occ:  24.659 0.8151  0.9851    16490.942
   5_bss:  24.633 0.8153  0.9577    16474.924
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2917e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2917e+01
   1_xyz:   1.856  0.015  0.112 18.501  0.007  4.101   1.7141e-01
   1_adp:   1.856  0.015  0.112 18.501  0.007  4.101   1.7141e-01
   1_occ:   1.856  0.015  0.112 18.501  0.007  4.101   1.7141e-01
   2_bss:   1.856  0.015  0.112 18.501  0.007  4.101   1.7141e-01
   2_xyz:   1.205  0.009  0.076 16.666  0.005  4.117   1.0500e-01
   2_adp:   1.205  0.009  0.076 16.666  0.005  4.117   1.0500e-01
   2_occ:   1.205  0.009  0.076 16.666  0.005  4.117   1.0500e-01
   3_bss:   1.205  0.009  0.076 16.666  0.005  4.117   1.0500e-01
   3_xyz:   1.189  0.009  0.078 16.280  0.005  4.108   8.8435e-02
   3_adp:   1.189  0.009  0.078 16.280  0.005  4.108   8.8435e-02
   3_occ:   1.189  0.009  0.078 16.280  0.005  4.108   8.8435e-02
   4_bss:   1.189  0.009  0.078 16.280  0.005  4.108   8.8435e-02
   4_xyz:   1.273  0.010  0.090 16.579  0.005  4.108   1.0338e-01
   4_adp:   1.273  0.010  0.090 16.579  0.005  4.108   1.0338e-01
   4_occ:   1.273  0.010  0.090 16.579  0.005  4.108   1.0338e-01
   5_bss:   1.273  0.010  0.090 16.579  0.005  4.108   1.0338e-01
   5_xyz:   1.028  0.007  0.073 15.866  0.004  4.122   6.8439e-02
   5_adp:   1.028  0.007  0.073 15.866  0.004  4.122   6.8439e-02
   5_occ:   1.028  0.007  0.073 15.866  0.004  4.122   6.8439e-02
   5_bss:   1.028  0.007  0.073 15.866  0.004  4.122   6.8439e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8501e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8501e+00
   1_xyz:  15.515  0.196  0.484 88.673  0.035  2.150   1.0866e-01
   1_adp:  15.515  0.196  0.484 88.673  0.035  2.150   1.0866e-01
   1_occ:  15.515  0.196  0.484 88.673  0.035  2.150   1.0866e-01
   2_bss:  15.515  0.196  0.484 88.673  0.035  2.150   1.0866e-01
   2_xyz:   7.001  0.084  0.288 82.702  0.044  2.133   2.1527e-01
   2_adp:   7.001  0.084  0.288 82.702  0.044  2.133   2.1527e-01
   2_occ:   7.001  0.084  0.288 82.702  0.044  2.133   2.1527e-01
   3_bss:   7.001  0.084  0.288 82.702  0.044  2.133   2.1527e-01
   3_xyz:   7.790  0.060  0.232 83.868  0.033  2.105   5.6765e-02
   3_adp:   7.790  0.060  0.232 83.868  0.033  2.105   5.6765e-02
   3_occ:   7.790  0.060  0.232 83.868  0.033  2.105   5.6765e-02
   4_bss:   7.790  0.060  0.232 83.868  0.033  2.105   5.6765e-02
   4_xyz:   8.423  0.052  0.274 87.026  0.050  1.975   9.9142e-02
   4_adp:   8.423  0.052  0.274 87.026  0.050  1.975   9.9142e-02
   4_occ:   8.423  0.052  0.274 87.026  0.050  1.975   9.9142e-02
   5_bss:   8.423  0.052  0.274 87.026  0.050  1.975   9.9142e-02
   5_xyz:   7.396  0.050  0.249 77.835  0.035  2.273   6.3032e-02
   5_adp:   7.396  0.050  0.249 77.835  0.035  2.273   6.3032e-02
   5_occ:   7.396  0.050  0.249 77.835  0.035  2.273   6.3032e-02
   5_bss:   7.396  0.050  0.249 77.835  0.035  2.273   6.3032e-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:  93.86   0.00  16.70  75.80   0.00  15.64  93.86   0.00  22.46
   1_occ:  93.86   0.00  16.70  75.80   0.00  15.64  93.86   0.00  22.46
   2_bss:  93.86   0.00  16.70  75.80   0.00  15.64  93.86   0.00  22.46
   2_xyz:  93.86   0.00  16.70  75.80   0.00  15.64  93.86   0.00  22.46
   2_adp:  90.49   0.00  16.55  64.53   0.00  15.36  90.49   0.00  23.05
   2_occ:  90.49   0.00  16.55  64.53   0.00  15.36  90.49   0.00  23.05
   3_bss:  90.49   0.00  16.55  64.53   0.00  15.36  90.49   0.00  23.05
   3_xyz:  90.49   0.00  16.55  64.53   0.00  15.36  90.49   0.00  23.05
   3_adp:  95.44   0.00  17.96  93.71   0.00  15.58  95.44   0.00  30.97
   3_occ:  95.44   0.00  17.96  93.71   0.00  15.58  95.44   0.00  30.97
   4_bss:  95.44   0.00  17.96  93.71   0.00  15.58  95.44   0.00  30.97
   4_xyz:  95.44   0.00  17.96  93.71   0.00  15.58  95.44   0.00  30.97
   4_adp: 150.16   0.00  17.42 150.16   0.00  14.61  88.94   0.00  32.71
   4_occ: 150.16   0.00  17.42 150.16   0.00  14.61  88.94   0.00  32.71
   5_bss: 150.16   0.00  17.42 150.16   0.00  14.61  88.94   0.00  32.71
   5_xyz: 150.16   0.00  17.42 150.16   0.00  14.61  88.94   0.00  32.71
   5_adp: 101.48   0.00  17.40 101.48   0.00  12.58 100.08   1.82  43.69
   5_occ: 101.48   0.00  17.40 101.48   0.00  12.58 100.08   1.82  43.69
   5_bss: 101.90   0.42  17.83 101.90   0.42  13.00 100.50   2.24  44.11
------------------------------------------------------------------------
 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:    1.338    0.026    0.423
   1_adp:    1.338    0.026    0.423
   1_occ:    1.338    0.026    0.423
   2_bss:    1.338    0.026    0.423
   2_xyz:    1.716    0.040    0.544
   2_adp:    1.716    0.040    0.544
   2_occ:    1.716    0.040    0.544
   3_bss:    1.716    0.040    0.544
   3_xyz:    1.573    0.031    0.655
   3_adp:    1.573    0.031    0.655
   3_occ:    1.573    0.031    0.655
   4_bss:    1.573    0.031    0.655
   4_xyz:    1.914    0.037    0.818
   4_adp:    1.914    0.037    0.818
   4_occ:    1.914    0.037    0.818
   5_bss:    1.914    0.037    0.818
   5_xyz:    2.036    0.030    0.903
   5_adp:    2.036    0.030    0.903
   5_occ:    2.036    0.030    0.903
   5_bss:    2.036    0.030    0.903
------------------------------------------------------------------------

CPU time actual refinement: 331.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/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_129/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_129/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.72 
  Macro-tasks:
    bulk solvent and scale       = 42.79  
    individual site refinement   = 141.48 
    weights calculation          = 31.79  
    collect and process          = 6.15   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 222.34 
  Micro-tasks:
    mask                            = 2.97   
    f_calc                          = 102.08 
    alpha_beta                      = 8.32   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 111.93 
    fmodel                         = 6.86   
    r_factors                      = 0.27   
    phase_errors                   = 9.22   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 242.96 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.738 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    596 calls, 101.76 s
gradients_fft:          541 calls,  99.55 s

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

# Date 2008-01-16 Time 00:51:03 PST -0800 (1200473463.13 s)
Start R-work = 0.5188, R-free = 0.5195 (no bulk solvent and anisotropic scale)
Final R-work = 0.1976, R-free = 0.2653 (no bulk solvent and anisotropic scale)

Start R-work = 0.5111, R-free = 0.5088
Final R-work = 0.1838, R-free = 0.2515