# Date 2008-01-16 Time 03:25:44 PST -0800 (1200482744.39 s)
#phil __OFF__

Command line arguments: "../1232.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 = 3321
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1232

-------------------------------------------------------------------------------
  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: (72.0062, 46.2261, 84.2302, 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: 3.25, 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: (72.0062, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95113
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928477

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1542
                             d_min =   1.9511

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: (72.0062, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95113
Completeness in resolution range: 0.931169
Completeness with d_max=infinity: 0.928477

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1547 -  4.1770 [2209/2239]  1992   217   9.8%
  bin  2:  4.1770 -  3.3269 [2122/2138]  1907   215  10.1%
  bin  3:  3.3269 -  2.9098 [2093/2112]  1878   215  10.3%
  bin  4:  2.9098 -  2.6453 [2085/2115]  1885   200   9.6%
  bin  5:  2.6453 -  2.4565 [2061/2080]  1860   201   9.8%
  bin  6:  2.4565 -  2.3122 [2047/2072]  1827   220  10.7%
  bin  7:  2.3122 -  2.1968 [2048/2082]  1846   202   9.9%
  bin  8:  2.1968 -  2.1014 [2042/2072]  1842   200   9.8%
  bin  9:  2.1014 -  2.0207 [1945/2070]  1753   192   9.9%
  bin 10:  2.0207 -  1.9511 [ 937/2057]   840    97  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/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: 0.15 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:
        1.41 -     2.11: 17
        2.11 -     2.81: 834
        2.81 -     3.51: 4535
        3.51 -     4.20: 9443
        4.20 -     4.90: 13802
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.413 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.557 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.638 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.708 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28626 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_1232/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 72.00625 46.22605 84.23025 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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5190   r_free= 0.5114   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.311733                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6598 0.99   1431  162 0.4305 0.4737      6.6484      6.7085|
|  2:  4.6598 -  3.7166 0.99   1382  148 0.4685 0.4579        6.88      6.9033|
|  3:  3.7166 -  3.2521 0.99   1362  148 0.5116 0.4636      6.7338      6.7564|
|  4:  3.2521 -  2.9571 0.99   1346  160 0.5104 0.4874      6.5688      6.5409|
|  5:  2.9571 -  2.7465 0.99   1338  145 0.5385 0.5206      6.3881      6.3423|
|  6:  2.7465 -  2.5854 0.99   1327  151 0.5589 0.5506      6.3042      6.3054|
|  7:  2.5854 -  2.4565 0.99   1336  134 0.5525 0.4780      6.2651      6.1701|
|  8:  2.4565 -  2.3500 0.98   1307  162 0.5604 0.5334      6.1728      6.2066|
|  9:  2.3500 -  2.2598 0.98   1309  144 0.5483 0.5068      6.1436      6.0841|
| 10:  2.2598 -  2.1821 0.99   1311  146 0.5476 0.5644      6.0956        6.11|
| 11:  2.1821 -  2.1140 0.99   1338  136 0.5447 0.5932      6.0398      6.0658|
| 12:  2.1140 -  2.0538 0.97   1270  147 0.5386 0.5445      5.9482      5.9659|
| 13:  2.0538 -  1.9998 0.83   1099  135 0.5569 0.5454      5.8755      5.8443|
| 14:  1.9998 -  1.9511 0.35    474   41 0.5748 0.5143      5.8308      5.8018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1547 -  4.6598  1431   162  0.60  42.84   0.77     0.67     105076.60|
|  2:  4.6598 -  3.7166  1382   148  0.60  43.85   0.84     0.69     152808.18|
|  3:  3.7166 -  3.2521  1362   148  0.46  55.28   0.79     0.61     161330.33|
|  4:  3.2521 -  2.9571  1346   160  0.36  62.46   0.78     0.49     139709.43|
|  5:  2.9571 -  2.7465  1338   145  0.26  70.16   0.71     0.34     105235.11|
|  6:  2.7465 -  2.5854  1327   151  0.28  69.10   0.70     0.34      84292.85|
|  7:  2.5854 -  2.4565  1336   134  0.29  68.10   0.71     0.34      69223.98|
|  8:  2.4565 -  2.3500  1307   162  0.34  64.75   0.70     0.41      60208.10|
|  9:  2.3500 -  2.2598  1309   144  0.31  66.98   0.74     0.37      56041.35|
| 10:  2.2598 -  2.1821  1311   146  0.27  70.17   0.74     0.33      53674.16|
| 11:  2.1821 -  2.1140  1338   136  0.20  75.17   0.75     0.25      53450.07|
| 12:  2.1140 -  2.0538  1270   147  0.17  77.68   0.74     0.22      48719.50|
| 13:  2.0538 -  1.9998  1099   135  0.14  79.31   0.72     0.20      43632.72|
| 14:  1.9998 -  1.9511   474    41  0.14  79.68   0.71     0.19      37692.28|
|alpha:            min =        0.19 max =            0.69 mean =         0.40|
|beta:             min =    37692.28 max =       161330.33 mean =     87129.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.02|
|phase err.(test): min =        0.00 max =           89.88 mean =        64.97|
|-----------------------------------------------------------------------------|

============================== 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 = 27.067084             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.777   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.241976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.581   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      181 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      708 |
| 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:     2685 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3953 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5128 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6630 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7790 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.260 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.169 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    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 = 11.678)------------------------------------------|
|    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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5216   r_free= 0.5147   ksol= 0.00   Bsol= 0.00   scale= 0.740    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.312366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5120   r_free= 0.4979   ksol= 0.33   Bsol= 0.00   scale= 0.923    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.46,6.55,6.74,0.00,0.00,0.00); trace/3= 6.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.00 A                  |
| x-ray target function (ml) for work reflections: 6.153032                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.570183             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.961   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.714610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.741   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5120      final r-factor (work) = 0.4612          |
| start r-factor (free) = 0.4979      final r-factor (free) = 0.4854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 118.1265 = 20.57 * 0.50 * 6.3068 + 1.00 * 53.2602                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.0001 = 20.57 * 0.50 * 6.1100 + 1.00 * 0.1577                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4612      final r-factor (work) = 0.4252          |
| start r-factor (free) = 0.4854      final r-factor (free) = 0.4800          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4907 = 1.71 * 1.00 * 6.1100 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6983 = 1.71 * 1.00 * 6.2287 + 1.00 * 0.0185                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.64   17.54    None  None   None       |
|    all(noH): 2823   0      0.00    98.64   17.54    None  None   None       |
|    Sol.    : 438    0      0.00    94.53   24.46    None  None   None       |
|    Mac.    : 2385   0      0.00    98.64   16.27    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 -   9.864:  969   |   5:    49.318 -  59.182:   53        |
|      1:     9.864 -  19.727:  844   |   6:    59.182 -  69.045:   24        |
|      2:    19.727 -  29.591:  535   |   7:    69.045 -  78.909:    9        |
|      3:    29.591 -  39.455:  256   |   8:    78.909 -  88.773:    2        |
|      4:    39.455 -  49.318:  127   |   9:    88.773 -  98.636:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4252 r_free = 0.4800             target_work(ml) = 6.224         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4248 r_free = 0.4818             target_work(ml) = 6.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4248   r_free= 0.4818   ksol= 0.33   Bsol= 0.00   scale= 1.089    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.46,6.55,6.74,0.00,0.00,0.00); trace/3= 6.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.223498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4244   r_free= 0.4787   ksol= 0.33   Bsol= 21.16   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.40,3.77,4.85,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.223759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.884266             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.607  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.354  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4244      final r-factor (work) = 0.3634          |
| start r-factor (free) = 0.4787      final r-factor (free) = 0.4319          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.4946 = 14.88 * 0.50 * 6.2263 + 1.00 * 0.1577                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0322 = 14.88 * 0.50 * 6.1704 + 1.00 * 0.1113                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3634      final r-factor (work) = 0.3452          |
| start r-factor (free) = 0.4319      final r-factor (free) = 0.4222          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9299 = 0.80 * 1.00 * 6.1704 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8694 = 0.80 * 1.00 * 6.1029 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.46  17.19    None  None   None       |
|    all(noH): 2823   0      0.00    101.46  17.19    None  None   None       |
|    Sol.    : 438    0      0.00    90.03   28.42    None  None   None       |
|    Mac.    : 2385   0      0.00    101.46  15.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.146: 1024   |   5:    50.731 -  60.878:   39        |
|      1:    10.146 -  20.293:  880   |   6:    60.878 -  71.024:    6        |
|      2:    20.293 -  30.439:  502   |   7:    71.024 -  81.170:    4        |
|      3:    30.439 -  40.585:  244   |   8:    81.170 -  91.316:    3        |
|      4:    40.585 -  50.731:  118   |   9:    91.316 - 101.463:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3452 r_free = 0.4222             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3451 r_free = 0.4220             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3451   r_free= 0.4220   ksol= 0.33   Bsol= 21.16   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.40,3.77,4.85,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.089767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.4221   ksol= 0.35   Bsol= 49.52   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,1.47,2.50,0.00,0.00,0.00); trace/3= 2.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.089484                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.677579             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.808  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467014              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.253  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3436      final r-factor (work) = 0.2610          |
| start r-factor (free) = 0.4221      final r-factor (free) = 0.3341          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.7972 = 12.68 * 0.50 * 6.1031 + 1.00 * 0.1113                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1668 = 12.68 * 0.50 * 6.0040 + 1.00 * 0.1085                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2610      final r-factor (work) = 0.2357          |
| start r-factor (free) = 0.3341      final r-factor (free) = 0.3064          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8158 = 0.47 * 1.00 * 6.0040 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7355 = 0.47 * 1.00 * 5.8364 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.59   16.43    None  None   None       |
|    all(noH): 2823   0      0.00    96.59   16.43    None  None   None       |
|    Sol.    : 438    0      2.07    87.85   35.00    None  None   None       |
|    Mac.    : 2385   0      0.00    96.59   13.02    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 -   9.660: 1093   |   5:    48.297 -  57.957:   74        |
|      1:     9.660 -  19.319:  923   |   6:    57.957 -  67.616:    9        |
|      2:    19.319 -  28.978:  326   |   7:    67.616 -  77.276:    4        |
|      3:    28.978 -  38.638:  247   |   8:    77.276 -  86.935:    2        |
|      4:    38.638 -  48.297:  141   |   9:    86.935 -  96.595:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2357 r_free = 0.3064             target_work(ml) = 5.792         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2354 r_free = 0.3059             target_work(ml) = 5.791         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2354   r_free= 0.3059   ksol= 0.35   Bsol= 49.52   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,1.47,2.50,0.00,0.00,0.00); trace/3= 2.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.791097                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.3040   ksol= 0.35   Bsol= 49.52   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,-0.30,0.72,-0.00,0.00,0.00); trace/3= 0.36                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.789125                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.577703              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.637   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.271115              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.983  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2339      final r-factor (work) = 0.1801          |
| start r-factor (free) = 0.3040      final r-factor (free) = 0.2410          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3211 = 6.58 * 0.50 * 5.8417 + 1.00 * 0.1085                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8101 = 6.58 * 0.50 * 5.6948 + 1.00 * 0.0807                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1801      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2410      final r-factor (free) = 0.2188          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2485 = 1.27 * 1.00 * 5.6948 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0261 = 1.27 * 1.00 * 5.5173 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.19  17.12    None  None   None       |
|    all(noH): 2823   0      0.00    107.19  17.12    None  None   None       |
|    Sol.    : 438    0      4.25    99.15   44.11    None  None   None       |
|    Mac.    : 2385   0      0.00    107.19  12.16    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 -  10.719: 1405   |   5:    53.594 -  64.312:   96        |
|      1:    10.719 -  21.437:  802   |   6:    64.312 -  75.031:   55        |
|      2:    21.437 -  32.156:  197   |   7:    75.031 -  85.750:   12        |
|      3:    32.156 -  42.875:  128   |   8:    85.750 -  96.468:    7        |
|      4:    42.875 -  53.594:  118   |   9:    96.468 - 107.187:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1590 r_free = 0.2188             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1588 r_free = 0.2183             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1588   r_free= 0.2183   ksol= 0.35   Bsol= 49.52   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,-0.30,0.72,-0.00,0.00,0.00); trace/3= 0.36                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.467671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1594   r_free= 0.2183   ksol= 0.33   Bsol= 48.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.99,-0.17,-0.00,-0.00,-0.00); trace/3= -0.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.467158                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.705171              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.674  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.076  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2183      final r-factor (free) = 0.1967          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5492 = 2.71 * 0.50 * 5.5216 + 1.00 * 0.0807                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3995 = 2.71 * 0.50 * 5.4258 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.1967      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8789 = 0.34 * 1.00 * 5.4258 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8504 = 0.34 * 1.00 * 5.3500 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.98  16.58    None  None   None       |
|    all(noH): 2823   0      0.00    102.98  16.58    None  None   None       |
|    Sol.    : 438    0      5.31    96.42   42.55    None  None   None       |
|    Mac.    : 2385   0      0.00    102.98  11.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.298: 1367   |   5:    51.489 -  61.787:   99        |
|      1:    10.298 -  20.596:  862   |   6:    61.787 -  72.085:   52        |
|      2:    20.596 -  30.894:  187   |   7:    72.085 -  82.383:   14        |
|      3:    30.894 -  41.191:  135   |   8:    82.383 -  92.681:    8        |
|      4:    41.191 -  51.489:   94   |   9:    92.681 - 102.979:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1374 r_free = 0.1886             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1372 r_free = 0.1886             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1886   ksol= 0.33   Bsol= 48.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.99,-0.17,-0.00,-0.00,-0.00); trace/3= -0.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323679                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6598 0.99   1431  162 0.1106 0.1491       5.492      5.6847|
|  2:  4.6598 -  3.7166 0.99   1382  148 0.1007 0.1457      5.6008      5.8958|
|  3:  3.7166 -  3.2521 0.99   1362  148 0.1339 0.1732      5.6675      5.9484|
|  4:  3.2521 -  2.9571 0.99   1346  160 0.1520 0.1905      5.6352      5.7726|
|  5:  2.9571 -  2.7465 0.99   1338  145 0.1609 0.2031      5.4888      5.6539|
|  6:  2.7465 -  2.5854 0.99   1327  151 0.1570 0.2214      5.3984      5.6366|
|  7:  2.5854 -  2.4565 0.99   1336  134 0.1524 0.2095      5.3228      5.5136|
|  8:  2.4565 -  2.3500 0.98   1307  162 0.1445 0.1885      5.2213      5.4079|
|  9:  2.3500 -  2.2598 0.98   1309  144 0.1451 0.2444      5.1941      5.5152|
| 10:  2.2598 -  2.1821 0.99   1311  146 0.1423 0.2056      5.1482      5.3819|
| 11:  2.1821 -  2.1140 0.99   1338  136 0.1433 0.2162      5.1195      5.4419|
| 12:  2.1140 -  2.0538 0.97   1270  147 0.1375 0.1978      5.0311      5.2394|
| 13:  2.0538 -  1.9998 0.83   1099  135 0.1458 0.1986      4.9512      5.1949|
| 14:  1.9998 -  1.9511 0.35    474   41 0.1315 0.1638      4.8112      4.9657|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1547 -  4.6598  1431   162  0.93  10.89   0.98     0.96       9385.00|
|  2:  4.6598 -  3.7166  1382   148  0.94  10.43   1.02     1.00      13009.80|
|  3:  3.7166 -  3.2521  1362   148  0.90  15.48   1.04     1.04      15535.85|
|  4:  3.2521 -  2.9571  1346   160  0.89  17.55   1.03     1.01      14954.27|
|  5:  2.9571 -  2.7465  1338   145  0.87  19.24   1.01     0.99      11638.25|
|  6:  2.7465 -  2.5854  1327   151  0.87  20.03   0.99     0.96      10223.22|
|  7:  2.5854 -  2.4565  1336   134  0.87  19.44   1.00     0.97       8671.44|
|  8:  2.4565 -  2.3500  1307   162  0.88  18.74   1.00     0.96       7186.25|
|  9:  2.3500 -  2.2598  1309   144  0.87  19.70   1.02     0.98       6922.30|
| 10:  2.2598 -  2.1821  1311   146  0.88  18.92   1.02     0.99       6421.38|
| 11:  2.1821 -  2.1140  1338   136  0.86  20.71   1.01     0.96       6434.82|
| 12:  2.1140 -  2.0538  1270   147  0.88  19.16   1.01     1.00       5515.33|
| 13:  2.0538 -  1.9998  1099   135  0.87  19.91   1.02     1.01       4608.79|
| 14:  1.9998 -  1.9511   474    41  0.88  18.50   1.01     0.98       3462.21|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     3462.21 max =        15535.85 mean =      9223.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.63|
|phase err.(test): min =        0.00 max =           89.42 mean =        16.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1885   ksol= 0.32   Bsol= 48.01   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-1.25,-0.48,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1885   ksol= 0.32   Bsol= 48.01   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-1.25,-0.48,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323398                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6598 0.99   1431  162 0.1103 0.1488      5.4886      5.6836|
|  2:  4.6598 -  3.7166 0.99   1382  148 0.1008 0.1459      5.6007      5.8976|
|  3:  3.7166 -  3.2521 0.99   1362  148 0.1339 0.1732      5.6681      5.9486|
|  4:  3.2521 -  2.9571 0.99   1346  160 0.1520 0.1905      5.6353      5.7727|
|  5:  2.9571 -  2.7465 0.99   1338  145 0.1609 0.2031      5.4889       5.654|
|  6:  2.7465 -  2.5854 0.99   1327  151 0.1570 0.2215      5.3983      5.6369|
|  7:  2.5854 -  2.4565 0.99   1336  134 0.1524 0.2094      5.3228      5.5135|
|  8:  2.4565 -  2.3500 0.98   1307  162 0.1445 0.1883      5.2211      5.4074|
|  9:  2.3500 -  2.2598 0.98   1309  144 0.1450 0.2443      5.1939      5.5156|
| 10:  2.2598 -  2.1821 0.99   1311  146 0.1423 0.2056      5.1482      5.3819|
| 11:  2.1821 -  2.1140 0.99   1338  136 0.1433 0.2161      5.1192      5.4412|
| 12:  2.1140 -  2.0538 0.97   1270  147 0.1374 0.1977      5.0311      5.2391|
| 13:  2.0538 -  1.9998 0.83   1099  135 0.1457 0.1986      4.9513      5.1952|
| 14:  1.9998 -  1.9511 0.35    474   41 0.1315 0.1640      4.8112       4.966|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1547 -  4.6598  1431   162  0.93  10.86   0.97     0.96       9342.09|
|  2:  4.6598 -  3.7166  1382   148  0.94  10.43   1.02     1.00      12996.76|
|  3:  3.7166 -  3.2521  1362   148  0.90  15.49   1.04     1.03      15562.22|
|  4:  3.2521 -  2.9571  1346   160  0.89  17.55   1.02     1.00      14956.00|
|  5:  2.9571 -  2.7465  1338   145  0.87  19.23   1.00     0.98      11638.43|
|  6:  2.7465 -  2.5854  1327   151  0.87  20.02   0.98     0.96      10221.70|
|  7:  2.5854 -  2.4565  1336   134  0.87  19.43   0.99     0.96       8670.80|
|  8:  2.4565 -  2.3500  1307   162  0.88  18.74   0.99     0.95       7187.03|
|  9:  2.3500 -  2.2598  1309   144  0.87  19.69   1.01     0.97       6921.90|
| 10:  2.2598 -  2.1821  1311   146  0.88  18.91   1.01     0.98       6420.06|
| 11:  2.1821 -  2.1140  1338   136  0.86  20.70   0.99     0.95       6431.96|
| 12:  2.1140 -  2.0538  1270   147  0.88  19.15   1.00     0.98       5512.24|
| 13:  2.0538 -  1.9998  1099   135  0.87  19.90   1.00     0.99       4607.90|
| 14:  1.9998 -  1.9511   474    41  0.88  18.49   0.99     0.97       3462.05|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3462.05 max =        15562.22 mean =      9220.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.62|
|phase err.(test): min =        0.00 max =           89.41 mean =        16.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.678)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.98  16.58    None  None   None       |
|    all(noH): 2823   0      0.00    102.98  16.58    None  None   None       |
|    Sol.    : 438    0      5.32    96.42   42.56    None  None   None       |
|    Mac.    : 2385   0      0.00    102.98  11.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.301: 1367   |   5:    51.492 -  61.790:   99        |
|      1:    10.301 -  20.599:  862   |   6:    61.790 -  72.088:   52        |
|      2:    20.599 -  30.897:  187   |   7:    72.088 -  82.386:   14        |
|      3:    30.897 -  41.194:  135   |   8:    82.386 -  92.684:    8        |
|      4:    41.194 -  51.492:   94   |   9:    92.684 - 102.982:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.731 - 5.222
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 317
   mapped sites are within: 0.731 - 5.222

peak=    9.603 closest distance to " CB  VAL A 230 " =    1.404
peak=    8.067 closest distance to " O   HOH Z 178 " =    1.579
peak=    7.817 closest distance to " CG2 VAL A 296 " =    1.390
peak=    6.306 closest distance to " O   HOH Z 130 " =    1.060
peak=    6.297 closest distance to " CG  ARG A 138 " =    1.251
peak=    6.144 closest distance to " O   HOH Z  37 " =    1.861
peak=    6.083 closest distance to " O   HOH Z  65 " =    1.568
peak=    6.077 closest distance to " NH2AARG A 102 " =    1.100
peak=    5.949 closest distance to " O   HOH Z 278 " =    2.124
peak=    5.924 closest distance to " O   HOH Z  61 " =    1.435
peak=    5.908 closest distance to " CD1AILE A 234 " =    1.121
peak=    5.902 closest distance to " O   HOH Z 117 " =    1.565
peak=    5.840 closest distance to " O   HOH Z 102 " =    1.208
peak=    5.678 closest distance to " O   HOH Z 222 " =    1.395
peak=    5.434 closest distance to " O   HOH Z 321 " =    0.964
peak=    5.425 closest distance to " O   HOH Z 255 " =    1.161
peak=    5.350 closest distance to " NH1 ARG A  56 " =    1.215
peak=    5.328 closest distance to " O   HOH Z 344 " =    1.687
peak=    5.324 closest distance to " O   HOH Z 124 " =    1.662
peak=    5.296 closest distance to " O   HOH Z 147 " =    1.486
peak=    5.256 closest distance to " O   HOH Z 120 " =    1.145
peak=    5.250 closest distance to " O   HOH Z   7 " =    2.223
peak=    5.244 closest distance to " O   HOH Z 126 " =    1.819
peak=    5.234 closest distance to " O   HOH Z 138 " =    1.062
peak=    5.198 closest distance to " O   HOH Z 205 " =    1.146
peak=    5.112 closest distance to " CD2 LEU A   5 " =    1.215
peak=    5.104 closest distance to " O   HOH Z  97 " =    1.621
peak=    5.053 closest distance to " O   HOH Z 111 " =    2.118
peak=    5.019 closest distance to " O   HOH Z 214 " =    1.725
peak=    4.956 closest distance to " O   HOH Z 186 " =    2.448
peak=    4.935 closest distance to " O   HOH Z 410 " =    1.527
peak=    4.915 closest distance to " O   HOH Z 374 " =    1.259
peak=    4.862 closest distance to " O   HOH Z 183 " =    1.747
peak=    4.860 closest distance to " O   HOH Z 132 " =    1.818
peak=    4.836 closest distance to " CG  PRO A 213 " =    1.351
peak=    4.810 closest distance to " O   HOH Z 113 " =    1.192
peak=    4.757 closest distance to " CG  LEU A   5 " =    1.244
peak=    4.743 closest distance to " CB  GLN A 223 " =    1.429
peak=    4.699 closest distance to " NH1 ARG A 138 " =    1.078
peak=    4.655 closest distance to " O   HOH Z 282 " =    1.787
peak=    4.647 closest distance to " O   HOH Z 116 " =    1.346
peak=    4.639 closest distance to " NH1AARG A 145 " =    1.065
peak=    4.589 closest distance to " O   HOH Z 144 " =    1.721
peak=    4.589 closest distance to " O   HOH Z  41 " =    1.110
peak=    4.589 closest distance to " O   HOH Z 112 " =    1.452
peak=    4.588 closest distance to " O   HOH Z 134 " =    1.506
peak=    4.539 closest distance to " O   HOH Z 143 " =    1.624
peak=    4.493 closest distance to " O   HOH Z 182 " =    1.435
peak=    4.485 closest distance to " CB  ASN A 148 " =    1.308
peak=    4.466 closest distance to " NE2 GLN A  11 " =    1.175
peak=    4.444 closest distance to " O   HOH Z 403 " =    1.489
peak=    4.436 closest distance to " O   HOH Z 284 " =    2.793
peak=    4.391 closest distance to " O   HOH Z 179 " =    0.979
peak=    4.388 closest distance to " O   HOH Z  11 " =    1.303
peak=    4.385 closest distance to " CD  ARG A 138 " =    0.941
peak=    4.378 closest distance to " O   HOH Z 427 " =    3.029
peak=    4.364 closest distance to " O   HOH Z 236 " =    1.995
peak=    4.360 closest distance to " O   HOH Z 193 " =    1.994
peak=    4.348 closest distance to " O   HOH Z 326 " =    1.604
peak=    4.337 closest distance to " CB  SER A 216 " =    0.990
peak=    4.309 closest distance to " O   HOH Z 411 " =    3.691
peak=    4.306 closest distance to " O   HOH Z 108 " =    1.744
peak=    4.306 closest distance to " O   HOH Z 127 " =    1.282
peak=    4.292 closest distance to " CG  PRO A 198 " =    1.388
peak=    4.263 closest distance to " O   HOH Z 133 " =    1.716
peak=    4.251 closest distance to " O   PRO A 198 " =    1.319
peak=    4.246 closest distance to " CB  VAL A 230 " =    1.171
peak=    4.233 closest distance to " O   HOH Z 239 " =    1.672
peak=    4.226 closest distance to " O   HOH Z 316 " =    2.823
peak=    4.154 closest distance to " CA  GLN A  55 " =    0.786
peak=    4.152 closest distance to " CG  LEU A 228 " =    1.190
peak=    4.145 closest distance to " CZ BARG A 190 " =    1.634
peak=    4.139 closest distance to " O   HOH Z 227 " =    1.912
peak=    4.124 closest distance to " CB  SER A   3 " =    1.469
peak=    4.122 closest distance to " O   HOH Z  97 " =    1.942
peak=    4.112 closest distance to " O   HOH Z 373 " =    2.059
peak=    4.105 closest distance to " CG  PRO A 280 " =    1.053
peak=    4.104 closest distance to " NE2 GLN A  55 " =    1.119
peak=    4.099 closest distance to " O   HOH Z 260 " =    1.616
peak=    4.095 closest distance to " CE3 TRP A 274 " =    2.368
peak=    4.093 closest distance to " CG  LEU A 167 " =    1.233
peak=    4.091 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.061 closest distance to " OD2 ASP A 286 " =    2.794
peak=    4.056 closest distance to " CB  ASN A  60 " =    0.969
peak=    4.053 closest distance to " O   HOH Z 272 " =    2.046
peak=    4.024 closest distance to " O   HOH Z 357 " =    1.740
peak=    4.022 closest distance to " O   HOH Z 232 " =    2.156
peak=    4.006 closest distance to " CB  ARG A 275 " =    0.942
peak=    3.999 closest distance to " CD2 TRP A 179 " =    2.157
peak=    3.981 closest distance to " O   HOH Z 151 " =    1.810
peak=    3.968 closest distance to " CB  ALA A   1 " =    4.451
peak=    3.967 closest distance to " O   HOH Z  63 " =    1.321
peak=    3.958 closest distance to " O   HOH Z  47 " =    2.006
peak=    3.955 closest distance to " O   HOH Z 184 " =    1.589
peak=    3.934 closest distance to " OE1 GLN A  58 " =    1.413
peak=    3.933 closest distance to " O   HOH Z 220 " =    1.625
peak=    3.931 closest distance to " C   ASP A  50 " =    1.117
peak=    3.930 closest distance to " CD2 LEU A 228 " =    1.301
peak=    3.926 closest distance to " CA  LEU A 282 " =    1.198
peak=    3.919 closest distance to " O   HOH Z 269 " =    1.537
peak=    3.910 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.908 closest distance to " CG1 VAL A 153 " =    0.946
peak=    3.904 closest distance to " O   HOH Z 202 " =    1.679
peak=    3.887 closest distance to " O   HOH Z 133 " =    2.104
peak=    3.883 closest distance to " O   HOH Z  67 " =    1.792
peak=    3.879 closest distance to " O   HOH Z 246 " =    1.409
peak=    3.861 closest distance to " O   HOH Z  80 " =    1.655
peak=    3.858 closest distance to " O   HOH Z 369 " =    2.169
peak=    3.848 closest distance to " CA  ALA A 295 " =    0.984
peak=    3.841 closest distance to " NE2 GLN A  58 " =    5.222
peak=    3.820 closest distance to " O   HOH Z 204 " =    1.718
peak=    3.803 closest distance to " CG2 THR A 221 " =    1.299
peak=    3.802 closest distance to " O   HOH Z  92 " =    1.371
peak=    3.796 closest distance to " O   HOH Z 371 " =    2.860
peak=    3.795 closest distance to " O   HOH Z 128 " =    1.485
peak=    3.792 closest distance to " O   HOH Z  51 " =    1.787
peak=    3.787 closest distance to " OG ASER A 134 " =    1.292
peak=    3.782 closest distance to " CD1 LEU A 300 " =    1.140
peak=    3.781 closest distance to " CD  ARG A  56 " =    1.102
peak=    3.781 closest distance to " O   HOH Z  53 " =    2.462
peak=    3.767 closest distance to " O   HOH Z 217 " =    2.646
peak=    3.756 closest distance to " OE1 GLU A   2 " =    2.036
peak=    3.742 closest distance to " O   HOH Z 347 " =    1.127
peak=    3.741 closest distance to " O   HOH Z 390 " =    1.209
peak=    3.733 closest distance to " CA  ALA A  21 " =    1.177
peak=    3.726 closest distance to " ND2 ASN A  60 " =    2.966
peak=    3.724 closest distance to " NE AARG A 275 " =    1.455
peak=    3.719 closest distance to " O   HOH Z  59 " =    2.087
peak=    3.718 closest distance to " CB  SER A  63 " =    1.428
peak=    3.717 closest distance to " CA  ARG A 102 " =    1.130
peak=    3.695 closest distance to " CB  ASP A 124 " =    0.931
peak=    3.693 closest distance to " O   HOH Z 389 " =    1.913
peak=    3.693 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.687 closest distance to " O   HOH Z 302 " =    1.764
peak=    3.687 closest distance to " CA  VAL A  41 " =    0.906
peak=    3.676 closest distance to " NE2 GLN A  55 " =    1.449
peak=    3.675 closest distance to " CB  ARG A  56 " =    1.033
peak=    3.675 closest distance to " CG2 VAL A 112 " =    0.880
peak=    3.657 closest distance to " CZ  PHE A 192 " =    1.200
peak=    3.650 closest distance to " CA  SER A  87 " =    0.827
peak=    3.646 closest distance to " CB  ASN A 148 " =    1.921
peak=    3.642 closest distance to " CG  LYS A 166 " =    1.282
peak=    3.635 closest distance to " CB  LEU A 228 " =    1.168
peak=    3.629 closest distance to " CG  GLN A  88 " =    0.983
peak=    3.625 closest distance to " CB  GLN A 183 " =    1.204
peak=    3.623 closest distance to " CA  SER A  62 " =    1.095
peak=    3.621 closest distance to " CB  PHE A  16 " =    1.170
peak=    3.620 closest distance to " CA  TYR A  30 " =    1.111
peak=    3.616 closest distance to " CB  PRO A 198 " =    1.014
peak=    3.603 closest distance to " NZ  LYS A 117 " =    1.340
peak=    3.603 closest distance to " CD  ARG A 159 " =    0.768
peak=    3.603 closest distance to " OG  SER A 276 " =    1.137
peak=    3.599 closest distance to " N   TRP A 177 " =    1.593
peak=    3.573 closest distance to " CD1 LEU A   5 " =    1.356
peak=    3.569 closest distance to " O   HOH Z 257 " =    1.131
peak=    3.565 closest distance to " CB  VAL A 265 " =    1.269
peak=    3.565 closest distance to " O   PRO A 198 " =    1.774
peak=    3.558 closest distance to " NE BARG A 102 " =    1.302
peak=    3.542 closest distance to " CG BARG A 102 " =    2.005
peak=    3.541 closest distance to " O   HOH Z 355 " =    1.788
peak=    3.534 closest distance to " O   HOH Z 171 " =    2.891
peak=    3.529 closest distance to " O   HOH Z 227 " =    2.110
peak=    3.528 closest distance to " CG2 VAL A 257 " =    0.956
peak=    3.528 closest distance to " CA  TYR A 116 " =    1.488
peak=    3.518 closest distance to " CB  GLU A 128 " =    1.116
peak=    3.517 closest distance to " N   ARG A  56 " =    0.888
peak=    3.515 closest distance to " N   GLN A 278 " =    0.924
peak=    3.513 closest distance to " OD1 ASN A  69 " =    2.530
peak=    3.508 closest distance to " CG2 THR A  82 " =    1.039
peak=    3.504 closest distance to " O   HOH Z 345 " =    3.304
peak=    3.504 closest distance to " OE1 GLN A 240 " =    1.575
peak=    3.494 closest distance to " NH1 ARG A  14 " =    1.001
peak=    3.487 closest distance to " O   HOH Z 226 " =    1.095
peak=    3.482 closest distance to " NH1BARG A 145 " =    2.174
peak=    3.479 closest distance to " CA  GLU A 152 " =    0.910
peak=    3.476 closest distance to " O   HOH Z  33 " =    1.933
peak=    3.475 closest distance to " CA  GLY A  98 " =    0.971
peak=    3.474 closest distance to " O   ALA A 165 " =    1.206
peak=    3.473 closest distance to " CB  VAL A 202 " =    1.648
peak=    3.466 closest distance to " CG  LYS A  76 " =    1.544
peak=    3.465 closest distance to " O   HOH Z 207 " =    2.251
peak=    3.457 closest distance to " O   HOH Z 261 " =    2.017
peak=    3.444 closest distance to " O   HOH Z 407 " =    2.697
peak=    3.443 closest distance to " O   HOH Z 155 " =    1.669
peak=    3.440 closest distance to " O   ASN A 217 " =    1.221
peak=    3.439 closest distance to " CA  ASP A 124 " =    0.731
peak=    3.437 closest distance to " CE  LYS A 166 " =    1.953
peak=    3.430 closest distance to " CA  VAL A 126 " =    1.244
peak=    3.428 closest distance to " CB  ARG A 139 " =    0.963
peak=    3.427 closest distance to " O   HOH Z 253 " =    1.730
peak=    3.427 closest distance to " O   HOH Z 222 " =    2.325
peak=    3.422 closest distance to " CA  TRP A  92 " =    0.892
peak=    3.418 closest distance to " O   HOH Z 331 " =    1.246
peak=    3.415 closest distance to " O   HOH Z 180 " =    2.062
peak=    3.414 closest distance to " CA  ASN A 127 " =    1.009
peak=    3.414 closest distance to " CD BLYS A 290 " =    1.031
peak=    3.411 closest distance to " CA  LEU A 101 " =    1.537
peak=    3.410 closest distance to " O   HOH Z 298 " =    2.509
peak=    3.407 closest distance to " CB  ALA A 104 " =    0.988
peak=    3.405 closest distance to " O   HOH Z 276 " =    1.449
peak=    3.401 closest distance to " O   HOH Z 298 " =    2.085
peak=    3.394 closest distance to " O   HOH Z 249 " =    1.463
peak=    3.390 closest distance to " O   HOH Z   9 " =    2.183
peak=    3.388 closest distance to " O   PRO A 198 " =    1.521
peak=    3.377 closest distance to " O   HOH Z 368 " =    2.110
peak=    3.375 closest distance to " O   HOH Z  69 " =    2.301
peak=    3.373 closest distance to " CA  PHE A 283 " =    1.079
peak=    3.364 closest distance to " CB  TYR A 116 " =    1.097
peak=    3.364 closest distance to " O   HOH Z 148 " =    3.567
peak=    3.364 closest distance to " O   HOH Z  47 " =    2.003
peak=    3.363 closest distance to " N   GLY A  57 " =    1.107
peak=    3.361 closest distance to " NE2 GLN A  58 " =    2.965
peak=    3.355 closest distance to " CA  THR A 221 " =    0.893
peak=    3.354 closest distance to " CB  MET A  47 " =    1.147
peak=    3.351 closest distance to " O   HOH Z 281 " =    2.140
peak=    3.349 closest distance to " O   HOH Z  78 " =    1.986
peak=    3.349 closest distance to " CB  PHE A  16 " =    0.982
peak=    3.346 closest distance to " CA  GLY A 147 " =    0.874
peak=    3.345 closest distance to " CG1 ILE A  49 " =    1.163
peak=    3.341 closest distance to " CG1 VAL A 296 " =    1.196
peak=    3.336 closest distance to " O   HOH Z 153 " =    3.868
peak=    3.332 closest distance to " O   ASP A 132 " =    3.765
peak=    3.331 closest distance to " CA  GLY A 267 " =    1.470
peak=    3.329 closest distance to " CA  ASP A 149 " =    1.572
peak=    3.328 closest distance to " CB  ALA A 161 " =    1.005
peak=    3.325 closest distance to " CB  PHE A 225 " =    1.326
peak=    3.324 closest distance to " CB  ASP A 132 " =    3.943
peak=    3.323 closest distance to " O   HOH Z 181 " =    1.760
peak=    3.317 closest distance to " CA  ILE A 263 " =    1.192
peak=    3.313 closest distance to " O   HOH Z 426 " =    3.166
peak=    3.311 closest distance to " NZ BLYS A 290 " =    1.337
peak=    3.306 closest distance to " CB  MET A  40 " =    0.776
peak=    3.306 closest distance to " O   HOH Z 295 " =    1.319
peak=    3.300 closest distance to " N   PHE A 130 " =    1.341
peak=    3.295 closest distance to " CA  LYS A  48 " =    1.408
peak=    3.293 closest distance to " CB  VAL A 250 " =    0.991
peak=    3.287 closest distance to " O   HOH Z 191 " =    1.682
peak=    3.285 closest distance to " CG  GLU A  37 " =    0.877
peak=    3.283 closest distance to " CB  LEU A 300 " =    1.000
peak=    3.279 closest distance to " CG2 VAL A 202 " =    1.452
peak=    3.276 closest distance to " O   HOH Z 192 " =    1.314
peak=    3.273 closest distance to " O   HOH Z   7 " =    3.079
peak=    3.272 closest distance to " NE1 TRP A 274 " =    1.118
peak=    3.270 closest distance to " O   HOH Z  22 " =    2.072
peak=    3.268 closest distance to " O   HOH Z 139 " =    2.821
peak=    3.264 closest distance to " O   HOH Z  89 " =    2.022
peak=    3.263 closest distance to " O   HOH Z 325 " =    1.993
peak=    3.262 closest distance to " CD1 ILE A  33 " =    1.700
peak=    3.262 closest distance to " C   ASP A 298 " =    1.337
peak=    3.259 closest distance to " O   HOH Z 104 " =    3.496
peak=    3.258 closest distance to " CA  ARG A  36 " =    1.195
peak=    3.255 closest distance to " CZ2 TRP A 266 " =    1.134
peak=    3.250 closest distance to " C   ALA A 299 " =    0.882
peak=    3.249 closest distance to " O   HOH Z  55 " =    2.209
peak=    3.247 closest distance to " CB  ALA A 244 " =    1.137
peak=    3.242 closest distance to " O   HOH Z 346 " =    1.418
peak=    3.240 closest distance to " CD2 LEU A 143 " =    1.822
peak=    3.239 closest distance to " CA  MET A  47 " =    1.062
peak=    3.238 closest distance to " O   HOH Z 271 " =    1.964
peak=    3.238 closest distance to " NH2 ARG A 269 " =    0.842
peak=    3.235 closest distance to " CB  SER A  99 " =    0.973
peak=    3.234 closest distance to " CB  ASN A 187 " =    0.994
peak=    3.224 closest distance to " N   ASN A 110 " =    1.182
peak=    3.220 closest distance to " C   GLN A  88 " =    1.439
peak=    3.218 closest distance to " CG1 ILE A  33 " =    1.398
peak=    3.213 closest distance to " O   SER A  62 " =    0.878
peak=    3.211 closest distance to " CE2 TYR A 186 " =    0.910
peak=    3.208 closest distance to " O   HOH Z   4 " =    1.197
peak=    3.205 closest distance to " O   GLN A  58 " =    1.766
peak=    3.201 closest distance to " O   HOH Z 196 " =    1.262
peak=    3.200 closest distance to " O   HOH Z 189 " =    2.428
peak=    3.200 closest distance to " O   MET A 105 " =    1.651
peak=    3.199 closest distance to " CB  ALA A  34 " =    1.096
peak=    3.196 closest distance to " O   HOH Z 371 " =    2.656
peak=    3.191 closest distance to " CG1BVAL A 121 " =    1.253
peak=    3.191 closest distance to " CB  TRP A 150 " =    1.405
peak=    3.190 closest distance to " ND2 ASN A  60 " =    1.122
peak=    3.187 closest distance to " CD  ARG A  14 " =    1.353
peak=    3.187 closest distance to " OE2 GLU A  53 " =    1.831
peak=    3.187 closest distance to " O   HOH Z  13 " =    2.019
peak=    3.185 closest distance to " O   HOH Z 195 " =    1.684
peak=    3.181 closest distance to " CE  MET A  93 " =    1.457
peak=    3.179 closest distance to " CB  LEU A 255 " =    0.991
peak=    3.179 closest distance to " O   HOH Z  99 " =    2.252
peak=    3.178 closest distance to " O   HOH Z 115 " =    1.580
peak=    3.172 closest distance to " CA  ALA A 160 " =    0.828
peak=    3.169 closest distance to " CA  ILE A 234 " =    1.013
peak=    3.162 closest distance to " CB  ALA A  10 " =    1.099
peak=    3.155 closest distance to " CD  ARG A 219 " =    1.064
peak=    3.154 closest distance to " O   HOH Z 122 " =    1.723
peak=    3.152 closest distance to " CA  ARG A  66 " =    0.798
peak=    3.151 closest distance to " O   HOH Z 412 " =    4.962
peak=    3.150 closest distance to " NH2BARG A 145 " =    1.002
peak=    3.142 closest distance to " OE1 GLN A  88 " =    3.278
peak=    3.139 closest distance to " CA  TYR A 186 " =    1.523
peak=    3.131 closest distance to " O   HOH Z 124 " =    2.383
peak=    3.128 closest distance to " O   HOH Z 207 " =    1.831
peak=    3.126 closest distance to " CA  ARG A 195 " =    1.378
peak=    3.124 closest distance to " O   HOH Z 345 " =    1.879
peak=    3.122 closest distance to " O   HOH Z 193 " =    2.009
peak=    3.120 closest distance to " NE2 GLN A 223 " =    1.714
peak=    3.118 closest distance to " O   HOH Z  64 " =    2.110
peak=    3.118 closest distance to " O   HOH Z 145 " =    2.996
peak=    3.118 closest distance to " CH2 TRP A 150 " =    1.013
peak=    3.112 closest distance to " O   HOH Z 394 " =    1.879
peak=    3.109 closest distance to " CA  GLN A 223 " =    0.913
peak=    3.103 closest distance to " O   HOH Z 181 " =    2.539
peak=    3.088 closest distance to " CB  ALA A 180 " =    1.377
peak=    3.080 closest distance to " O   HOH Z 433 " =    2.280
peak=    3.079 closest distance to " CE3 TRP A 274 " =    1.189
peak=    3.072 closest distance to " CB  GLU A 277 " =    3.766
peak=    3.070 closest distance to " CG  GLN A 278 " =    3.888
peak=    3.056 closest distance to " N   ASN A  39 " =    1.119
peak=    3.055 closest distance to " CG  GLU A   2 " =    1.244
peak=    3.047 closest distance to " OG ASER A  99 " =    1.080
peak=    3.041 closest distance to " O   HOH Z 132 " =    2.325
peak=    3.035 closest distance to " O   HOH Z 149 " =    1.321

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.235 - 5.661
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 191
   mapped sites are within: 0.707 - 5.661

peak=   -5.798 closest distance to " CD  ARG A 138 " =    1.095
peak=   -5.401 closest distance to " O   ASP A  50 " =    0.941
peak=   -5.317 closest distance to " CG2 VAL A 230 " =    0.879
peak=   -5.009 closest distance to " OG ASER A 134 " =    1.093
peak=   -4.818 closest distance to " O   HOH Z 102 " =    0.731
peak=   -4.776 closest distance to " O   HOH Z 138 " =    0.843
peak=   -4.698 closest distance to " CB  GLN A  55 " =    1.042
peak=   -4.523 closest distance to " O   ALA A  51 " =    1.359
peak=   -4.522 closest distance to " OE1 GLN A  88 " =    0.919
peak=   -4.491 closest distance to " CA  ARG A  56 " =    1.176
peak=   -4.344 closest distance to " CB  ASN A 285 " =    2.412
peak=   -4.285 closest distance to " O   PRO A 198 " =    1.218
peak=   -4.270 closest distance to " ND1 HIS A 115 " =    1.036
peak=   -4.268 closest distance to " O   HOH Z 388 " =    1.432
peak=   -4.264 closest distance to " O   HOH Z 231 " =    1.281
peak=   -4.237 closest distance to " CG  MET A 105 " =    1.005
peak=   -4.217 closest distance to " O   HOH Z 407 " =    3.199
peak=   -4.188 closest distance to " CB  ASP A  27 " =    2.662
peak=   -4.174 closest distance to " NH2AARG A 275 " =    5.488
peak=   -4.148 closest distance to " CD  GLN A  88 " =    0.955
peak=   -4.144 closest distance to " O   HOH Z 198 " =    2.459
peak=   -4.078 closest distance to " O   HOH Z 255 " =    0.817
peak=   -4.060 closest distance to " O   HOH Z 178 " =    1.219
peak=   -4.023 closest distance to " O   GLY A  98 " =    2.044
peak=   -3.971 closest distance to " O   HOH Z 103 " =    1.138
peak=   -3.971 closest distance to " O   HOH Z  61 " =    0.841
peak=   -3.966 closest distance to " OG BSER A 134 " =    1.772
peak=   -3.939 closest distance to " O   HOH Z  19 " =    2.166
peak=   -3.921 closest distance to " O   ALA A   1 " =    1.203
peak=   -3.915 closest distance to " O   HOH Z 166 " =    1.376
peak=   -3.874 closest distance to " CB  PRO A  54 " =    2.382
peak=   -3.865 closest distance to " CB  ALA A  51 " =    1.826
peak=   -3.854 closest distance to " O   HOH Z 377 " =    1.624
peak=   -3.805 closest distance to " O   HOH Z 292 " =    4.502
peak=   -3.802 closest distance to " NH1 ARG A  56 " =    2.487
peak=   -3.801 closest distance to " NH2 ARG A  79 " =    1.704
peak=   -3.777 closest distance to " CD  ARG A 156 " =    1.969
peak=   -3.734 closest distance to " O   HOH Z 166 " =    1.521
peak=   -3.732 closest distance to " CA  GLY A 133 " =    1.969
peak=   -3.730 closest distance to " CB  TRP A  85 " =    2.376
peak=   -3.691 closest distance to " O   HOH Z 100 " =    1.297
peak=   -3.689 closest distance to " CA  GLY A 241 " =    2.161
peak=   -3.678 closest distance to " O   HOH Z 266 " =    4.438
peak=   -3.669 closest distance to " CE2 TYR A  30 " =    3.012
peak=   -3.669 closest distance to " OG  SER A  97 " =    2.076
peak=   -3.620 closest distance to " O   HOH Z  95 " =    1.627
peak=   -3.619 closest distance to " N   GLN A  58 " =    1.188
peak=   -3.614 closest distance to " O   HOH Z 179 " =    1.068
peak=   -3.613 closest distance to " CB  TYR A  15 " =    2.181
peak=   -3.602 closest distance to " NE2 GLN A  58 " =    4.887
peak=   -3.597 closest distance to " O   HOH Z 350 " =    2.110
peak=   -3.596 closest distance to " O   HOH Z 317 " =    2.929
peak=   -3.581 closest distance to " O   HOH Z 290 " =    1.020
peak=   -3.576 closest distance to " CG1 VAL A 230 " =    1.108
peak=   -3.569 closest distance to " C   GLY A  23 " =    1.952
peak=   -3.563 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.560 closest distance to " CG  LEU A 101 " =    2.509
peak=   -3.551 closest distance to " O   HOH Z 350 " =    0.998
peak=   -3.547 closest distance to " CB  ALA A 227 " =    2.432
peak=   -3.540 closest distance to " O   HOH Z 275 " =    1.459
peak=   -3.529 closest distance to " O   HOH Z 220 " =    0.950
peak=   -3.529 closest distance to " O   HOH Z  61 " =    1.202
peak=   -3.512 closest distance to " O   ASP A  65 " =    0.927
peak=   -3.511 closest distance to " CD  ARG A  14 " =    3.102
peak=   -3.510 closest distance to " O   HOH Z 431 " =    1.276
peak=   -3.503 closest distance to " O   HOH Z 364 " =    2.665
peak=   -3.501 closest distance to " O   HOH Z  92 " =    2.421
peak=   -3.496 closest distance to " CD2 LEU A 237 " =    2.738
peak=   -3.494 closest distance to " CG1 VAL A 296 " =    2.235
peak=   -3.490 closest distance to " O   HOH Z 331 " =    1.287
peak=   -3.490 closest distance to " O   HOH Z 124 " =    1.145
peak=   -3.475 closest distance to " CB  PRO A 163 " =    2.689
peak=   -3.470 closest distance to " O   HOH Z 139 " =    3.630
peak=   -3.467 closest distance to " CD2 LEU A 237 " =    2.443
peak=   -3.452 closest distance to " O   HOH Z  51 " =    0.950
peak=   -3.439 closest distance to " CG2BVAL A 121 " =    1.102
peak=   -3.438 closest distance to " O   HOH Z 430 " =    1.718
peak=   -3.432 closest distance to " OG  SER A 245 " =    1.187
peak=   -3.429 closest distance to " O   HOH Z  43 " =    1.684
peak=   -3.428 closest distance to " C   ALA A 158 " =    1.173
peak=   -3.426 closest distance to " O   HOH Z  98 " =    1.676
peak=   -3.425 closest distance to " O   GLN A 194 " =    1.321
peak=   -3.423 closest distance to " CG  ARG A 138 " =    0.877
peak=   -3.421 closest distance to " O   SER A 135 " =    1.591
peak=   -3.418 closest distance to " O   HOH Z 257 " =    1.414
peak=   -3.416 closest distance to " O   HOH Z 359 " =    2.002
peak=   -3.411 closest distance to " NH1BARG A 145 " =    1.813
peak=   -3.408 closest distance to " O   THR A  18 " =    1.660
peak=   -3.402 closest distance to " O   HOH Z  20 " =    2.415
peak=   -3.396 closest distance to " O   HOH Z 221 " =    1.235
peak=   -3.396 closest distance to " N   GLN A  58 " =    1.899
peak=   -3.394 closest distance to " CA  GLY A  91 " =    2.406
peak=   -3.389 closest distance to " O   HOH Z 124 " =    3.065
peak=   -3.387 closest distance to " CD  GLN A  58 " =    0.987
peak=   -3.382 closest distance to " O   HOH Z 438 " =    0.725
peak=   -3.377 closest distance to " OD1 ASN A  60 " =    0.966
peak=   -3.375 closest distance to " OG  SER A  87 " =    1.127
peak=   -3.375 closest distance to " O   TYR A  30 " =    2.658
peak=   -3.368 closest distance to " NE  ARG A  24 " =    2.190
peak=   -3.366 closest distance to " CA  LEU A 143 " =    0.801
peak=   -3.364 closest distance to " CG2 ILE A 151 " =    2.342
peak=   -3.359 closest distance to " O   HOH Z  61 " =    1.334
peak=   -3.356 closest distance to " CD  LYS A 289 " =    2.460
peak=   -3.345 closest distance to " CE  LYS A  76 " =    2.733
peak=   -3.345 closest distance to " CD2 LEU A   5 " =    0.975
peak=   -3.343 closest distance to " CD1 LEU A 282 " =    2.505
peak=   -3.341 closest distance to " O   HOH Z 306 " =    3.145
peak=   -3.339 closest distance to " O   HOH Z 298 " =    1.310
peak=   -3.331 closest distance to " CD  LYS A 166 " =    2.527
peak=   -3.328 closest distance to " O   GLY A 196 " =    1.130
peak=   -3.326 closest distance to " C   GLN A 240 " =    2.252
peak=   -3.319 closest distance to " OG1 THR A 178 " =    1.166
peak=   -3.319 closest distance to " CB  ALA A   9 " =    2.636
peak=   -3.316 closest distance to " OG  SER A 206 " =    1.705
peak=   -3.311 closest distance to " CE  MET A  93 " =    1.227
peak=   -3.311 closest distance to " OH  TYR A 169 " =    1.004
peak=   -3.305 closest distance to " O   HOH Z 433 " =    1.313
peak=   -3.302 closest distance to " O   VAL A 174 " =    2.180
peak=   -3.300 closest distance to " O   PRO A 163 " =    1.941
peak=   -3.295 closest distance to " CB  ALA A  43 " =    2.296
peak=   -3.294 closest distance to " OE1 GLU A 277 " =    2.298
peak=   -3.293 closest distance to " CA  GLY A 203 " =    2.172
peak=   -3.291 closest distance to " O   HOH Z 134 " =    2.180
peak=   -3.289 closest distance to " O   HOH Z  28 " =    1.647
peak=   -3.279 closest distance to " N   HIS A 115 " =    2.050
peak=   -3.279 closest distance to " CD1 LEU A 255 " =    3.009
peak=   -3.278 closest distance to " CG2 VAL A 112 " =    2.659
peak=   -3.275 closest distance to " O   PHE A  59 " =    2.195
peak=   -3.273 closest distance to " O   HOH Z 117 " =    1.654
peak=   -3.271 closest distance to " CG  PRO A 163 " =    2.504
peak=   -3.270 closest distance to " O   HOH Z 111 " =    1.002
peak=   -3.269 closest distance to " O   HOH Z 427 " =    1.585
peak=   -3.262 closest distance to " CD1 LEU A   5 " =    2.444
peak=   -3.261 closest distance to " O   HOH Z 266 " =    5.209
peak=   -3.258 closest distance to " O   PRO A 243 " =    2.402
peak=   -3.256 closest distance to " O   HOH Z 393 " =    4.775
peak=   -3.249 closest distance to " O   HOH Z 211 " =    1.246
peak=   -3.248 closest distance to " NH2 ARG A  66 " =    2.883
peak=   -3.248 closest distance to " O   HOH Z 426 " =    1.647
peak=   -3.246 closest distance to " CB  PHE A  61 " =    1.409
peak=   -3.243 closest distance to " ND2 ASN A  45 " =    0.894
peak=   -3.231 closest distance to " CB  ALA A 100 " =    2.361
peak=   -3.231 closest distance to " OG1 THR A  82 " =    1.866
peak=   -3.230 closest distance to " CG1 ILE A  20 " =    2.275
peak=   -3.228 closest distance to " O   HOH Z  71 " =    1.287
peak=   -3.223 closest distance to " OE1 GLN A 278 " =    1.286
peak=   -3.222 closest distance to " CZ2 TRP A  92 " =    2.604
peak=   -3.222 closest distance to " O   HOH Z 435 " =    2.010
peak=   -3.221 closest distance to " O   ILE A 239 " =    1.232
peak=   -3.221 closest distance to " CD1 ILE A  33 " =    1.787
peak=   -3.219 closest distance to " O   GLY A 118 " =    2.085
peak=   -3.218 closest distance to " CG2BVAL A  41 " =    2.571
peak=   -3.216 closest distance to " O   HOH Z 423 " =    0.998
peak=   -3.211 closest distance to " O   HOH Z 117 " =    0.853
peak=   -3.211 closest distance to " CG  ASP A 231 " =    0.800
peak=   -3.210 closest distance to " O   ALA A   1 " =    1.786
peak=   -3.197 closest distance to " O   HOH Z 407 " =    5.661
peak=   -3.197 closest distance to " OD1 ASP A 200 " =    1.150
peak=   -3.195 closest distance to " CB  GLN A  58 " =    1.198
peak=   -3.191 closest distance to " O   HOH Z 155 " =    2.156
peak=   -3.188 closest distance to " O   HOH Z 236 " =    4.788
peak=   -3.185 closest distance to " N   ALA A  43 " =    2.305
peak=   -3.183 closest distance to " O   HOH Z 236 " =    1.243
peak=   -3.180 closest distance to " N   PHE A 283 " =    1.828
peak=   -3.180 closest distance to " CD2 TYR A 293 " =    2.062
peak=   -3.179 closest distance to " O   HOH Z  85 " =    2.162
peak=   -3.178 closest distance to " O   HOH Z  97 " =    1.278
peak=   -3.175 closest distance to " N   ALA A  84 " =    1.602
peak=   -3.172 closest distance to " O   HOH Z  56 " =    0.746
peak=   -3.171 closest distance to " CB  SER A 271 " =    1.737
peak=   -3.163 closest distance to " O   HOH Z  40 " =    3.984
peak=   -3.155 closest distance to " O   HOH Z 336 " =    1.224
peak=   -3.142 closest distance to " OD1 ASN A 249 " =    1.341
peak=   -3.137 closest distance to " O   HOH Z 198 " =    0.784
peak=   -3.133 closest distance to " CA  GLY A  35 " =    1.999
peak=   -3.126 closest distance to " O   ALA A 226 " =    1.351
peak=   -3.122 closest distance to " O   HOH Z  50 " =    5.179
peak=   -3.121 closest distance to " O   SER A  97 " =    1.476
peak=   -3.118 closest distance to " O   LEU A 101 " =    1.117
peak=   -3.108 closest distance to " N   GLY A  23 " =    2.178
peak=   -3.102 closest distance to " O   HOH Z 198 " =    2.088
peak=   -3.101 closest distance to " O   HOH Z  63 " =    0.863
peak=   -3.097 closest distance to " O   GLN A  11 " =    1.571
peak=   -3.096 closest distance to " OG  SER A  87 " =    1.647
peak=   -3.088 closest distance to " OG  SER A   3 " =    1.115
peak=   -3.081 closest distance to " N   GLN A  77 " =    1.418
peak=   -3.068 closest distance to " C   PHE A 155 " =    0.707
peak=   -3.065 closest distance to " CB  THR A 157 " =    1.251
peak=   -3.060 closest distance to " O   HOH Z  57 " =    2.105

================= 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    :  0.5190 0.5114   6.311733e+00   6.307251e+00
   1_bss:  0.5120 0.4979   6.153032e+00   6.180917e+00
   1_xyz:  0.4612 0.4854   6.257909e+00   6.280495e+00
   1_adp:  0.4252 0.4800   6.223540e+00   6.278227e+00
   1_occ:  0.4248 0.4818   6.223498e+00   6.278992e+00
   2_bss:  0.4244 0.4787   6.223759e+00   6.277951e+00
   2_xyz:  0.3634 0.4319   6.116755e+00   6.219875e+00
   2_adp:  0.3452 0.4222   6.090368e+00   6.204759e+00
   2_occ:  0.3451 0.4220   6.089767e+00   6.204057e+00
   3_bss:  0.3436 0.4221   6.089484e+00   6.203314e+00
   3_xyz:  0.2610 0.3341   5.880341e+00   6.048768e+00
   3_adp:  0.2357 0.3064   5.791999e+00   5.981176e+00
   3_occ:  0.2354 0.3059   5.791097e+00   5.980336e+00
   4_bss:  0.2339 0.3040   5.789125e+00   5.975702e+00
   4_xyz:  0.1801 0.2410   5.566909e+00   5.779632e+00
   4_adp:  0.1590 0.2188   5.469580e+00   5.699758e+00
   4_occ:  0.1588 0.2183   5.467671e+00   5.697539e+00
   5_bss:  0.1594 0.2183   5.467158e+00   5.696198e+00
   5_xyz:  0.1419 0.1967   5.361577e+00   5.596737e+00
   5_adp:  0.1374 0.1886   5.324928e+00   5.554315e+00
   5_occ:  0.1372 0.1886   5.323679e+00   5.553061e+00
   5_bss:  0.1371 0.1885   5.323398e+00   5.553098e+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:  0.326   0.000   7.463   6.553   6.739   0.000   0.000   0.000
   1_xyz:  0.326   0.000   7.463   6.553   6.739   0.000   0.000   0.000
   1_adp:  0.326   0.000   7.463   6.553   6.739   0.000   0.000   0.000
   1_occ:  0.326   0.000   7.463   6.553   6.739   0.000   0.000   0.000
   2_bss:  0.328  21.162   4.404   3.770   4.853   0.000   0.000   0.000
   2_xyz:  0.328  21.162   4.404   3.770   4.853   0.000   0.000   0.000
   2_adp:  0.328  21.162   4.404   3.770   4.853   0.000   0.000   0.000
   2_occ:  0.328  21.162   4.404   3.770   4.853   0.000   0.000   0.000
   3_bss:  0.349  49.518   2.387   1.472   2.498   0.000   0.000   0.000
   3_xyz:  0.349  49.518   2.387   1.472   2.498   0.000   0.000   0.000
   3_adp:  0.349  49.518   2.387   1.472   2.498   0.000   0.000   0.000
   3_occ:  0.349  49.518   2.387   1.472   2.498   0.000   0.000   0.000
   4_bss:  0.349  49.518   0.652  -0.301   0.720  -0.000   0.000   0.000
   4_xyz:  0.349  49.518   0.652  -0.301   0.720  -0.000   0.000   0.000
   4_adp:  0.349  49.518   0.652  -0.301   0.720  -0.000   0.000   0.000
   4_occ:  0.349  49.518   0.652  -0.301   0.720  -0.000   0.000   0.000
   5_bss:  0.327  48.002  -0.091  -0.987  -0.167  -0.000  -0.000  -0.000
   5_xyz:  0.327  48.002  -0.091  -0.987  -0.167  -0.000  -0.000  -0.000
   5_adp:  0.327  48.002  -0.091  -0.987  -0.167  -0.000  -0.000  -0.000
   5_occ:  0.327  48.002  -0.091  -0.987  -0.167  -0.000  -0.000  -0.000
   5_bss:  0.323  48.005  -0.372  -1.247  -0.484  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.013 0.3293  0.4043    87128.222
   1_bss:  66.043 0.3142  0.4625    85003.556
   1_xyz:  61.240 0.3755  0.5411    74046.789
   1_adp:  60.314 0.3875  0.6351    73320.369
   1_occ:  60.536 0.3847  0.6295    73654.127
   2_bss:  60.177 0.3892  0.5917    73210.114
   2_xyz:  50.902 0.5067  0.7684    55606.184
   2_adp:  48.596 0.5359  0.8183    52143.201
   2_occ:  48.565 0.5362  0.8182    51997.657
   3_bss:  48.227 0.5402  0.7650    51516.436
   3_xyz:  35.616 0.6935  0.9547    31022.409
   3_adp:  31.741 0.7381  0.9884    25571.712
   3_occ:  31.711 0.7384  0.9883    25497.313
   4_bss:  31.502 0.7405  0.9301    25160.011
   4_xyz:  24.203 0.8195  0.9884    15587.460
   4_adp:  21.718 0.8450  0.9936    12998.619
   4_occ:  21.656 0.8456  0.9938    12910.787
   5_bss:  21.588 0.8462  0.9666    12828.708
   5_xyz:  18.746 0.8736  0.9835    10080.932
   5_adp:  17.584 0.8848  0.9868     9260.385
   5_occ:  17.557 0.8850  0.9867     9224.214
   5_bss:  17.549 0.8851  0.9768     9221.154
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3260e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3260e+01
   1_xyz:   1.761  0.014  0.110 18.757  0.007  4.107   1.5774e-01
   1_adp:   1.761  0.014  0.110 18.757  0.007  4.107   1.5774e-01
   1_occ:   1.761  0.014  0.110 18.757  0.007  4.107   1.5774e-01
   2_bss:   1.761  0.014  0.110 18.757  0.007  4.107   1.5774e-01
   2_xyz:   1.250  0.009  0.087 17.248  0.005  4.100   1.1127e-01
   2_adp:   1.250  0.009  0.087 17.248  0.005  4.100   1.1127e-01
   2_occ:   1.250  0.009  0.087 17.248  0.005  4.100   1.1127e-01
   3_bss:   1.250  0.009  0.087 17.248  0.005  4.100   1.1127e-01
   3_xyz:   1.328  0.011  0.099 16.866  0.005  4.107   1.0855e-01
   3_adp:   1.328  0.011  0.099 16.866  0.005  4.107   1.0855e-01
   3_occ:   1.328  0.011  0.099 16.866  0.005  4.107   1.0855e-01
   4_bss:   1.328  0.011  0.099 16.866  0.005  4.107   1.0855e-01
   4_xyz:   1.140  0.008  0.080 16.107  0.004  4.107   8.0683e-02
   4_adp:   1.140  0.008  0.080 16.107  0.004  4.107   8.0683e-02
   4_occ:   1.140  0.008  0.080 16.107  0.004  4.107   8.0683e-02
   5_bss:   1.140  0.008  0.080 16.107  0.004  4.107   8.0683e-02
   5_xyz:   0.977  0.006  0.072 15.578  0.003  4.112   6.0602e-02
   5_adp:   0.977  0.006  0.072 15.578  0.003  4.112   6.0602e-02
   5_occ:   0.977  0.006  0.072 15.578  0.003  4.112   6.0602e-02
   5_bss:   0.977  0.006  0.072 15.578  0.003  4.112   6.0602e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9021e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9021e+00
   1_xyz:  13.935  0.169  0.472 84.140  0.063  2.081   1.0290e-01
   1_adp:  13.935  0.169  0.472 84.140  0.063  2.081   1.0290e-01
   1_occ:  13.935  0.169  0.472 84.140  0.063  2.081   1.0290e-01
   2_bss:  13.935  0.169  0.472 84.140  0.063  2.081   1.0290e-01
   2_xyz:   8.798  0.069  0.298 83.861  0.053  1.913   6.2019e-02
   2_adp:   8.798  0.069  0.298 83.861  0.053  1.913   6.2019e-02
   2_occ:   8.798  0.069  0.298 83.861  0.053  1.913   6.2019e-02
   3_bss:   8.798  0.069  0.298 83.861  0.053  1.913   6.2019e-02
   3_xyz:   9.883  0.073  0.390 83.666  0.029  2.171   1.3979e-01
   3_adp:   9.883  0.073  0.390 83.666  0.029  2.171   1.3979e-01
   3_occ:   9.883  0.073  0.390 83.666  0.029  2.171   1.3979e-01
   4_bss:   9.883  0.073  0.390 83.666  0.029  2.171   1.3979e-01
   4_xyz:   9.234  0.068  0.369 81.365  0.023  2.298   1.0314e-01
   4_adp:   9.234  0.068  0.369 81.365  0.023  2.298   1.0314e-01
   4_occ:   9.234  0.068  0.369 81.365  0.023  2.298   1.0314e-01
   5_bss:   9.234  0.068  0.369 81.365  0.023  2.298   1.0314e-01
   5_xyz:   8.078  0.057  0.333 83.529  0.033  2.233   3.7766e-02
   5_adp:   8.078  0.057  0.333 83.529  0.033  2.233   3.7766e-02
   5_occ:   8.078  0.057  0.333 83.529  0.033  2.233   3.7766e-02
   5_bss:   8.078  0.057  0.333 83.529  0.033  2.233   3.7766e-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:  98.64   0.00  17.54  98.64   0.00  16.27  94.53   0.00  24.46
   1_occ:  98.64   0.00  17.54  98.64   0.00  16.27  94.53   0.00  24.46
   2_bss:  98.64   0.00  17.54  98.64   0.00  16.27  94.53   0.00  24.46
   2_xyz:  98.64   0.00  17.54  98.64   0.00  16.27  94.53   0.00  24.46
   2_adp: 101.46   0.00  17.19 101.46   0.00  15.12  90.03   0.00  28.42
   2_occ: 101.46   0.00  17.19 101.46   0.00  15.12  90.03   0.00  28.42
   3_bss: 101.46   0.00  17.19 101.46   0.00  15.12  90.03   0.00  28.42
   3_xyz: 101.46   0.00  17.19 101.46   0.00  15.12  90.03   0.00  28.42
   3_adp:  96.59   0.00  16.43  96.59   0.00  13.02  87.85   2.07  35.00
   3_occ:  96.59   0.00  16.43  96.59   0.00  13.02  87.85   2.07  35.00
   4_bss:  96.59   0.00  16.43  96.59   0.00  13.02  87.85   2.07  35.00
   4_xyz:  96.59   0.00  16.43  96.59   0.00  13.02  87.85   2.07  35.00
   4_adp: 107.19   0.00  17.12 107.19   0.00  12.16  99.15   4.25  44.11
   4_occ: 107.19   0.00  17.12 107.19   0.00  12.16  99.15   4.25  44.11
   5_bss: 107.19   0.00  17.12 107.19   0.00  12.16  99.15   4.25  44.11
   5_xyz: 107.19   0.00  17.12 107.19   0.00  12.16  99.15   4.25  44.11
   5_adp: 102.98   0.00  16.58 102.98   0.00  11.81  96.42   5.31  42.55
   5_occ: 102.98   0.00  16.58 102.98   0.00  11.81  96.42   5.31  42.55
   5_bss: 102.98   0.00  16.58 102.98   0.00  11.81  96.42   5.32  42.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.275    0.021    0.412
   1_adp:    1.275    0.021    0.412
   1_occ:    1.275    0.021    0.412
   2_bss:    1.275    0.021    0.412
   2_xyz:    1.760    0.019    0.593
   2_adp:    1.760    0.019    0.593
   2_occ:    1.760    0.019    0.593
   3_bss:    1.760    0.019    0.593
   3_xyz:    2.136    0.022    0.782
   3_adp:    2.136    0.022    0.782
   3_occ:    2.136    0.022    0.782
   4_bss:    2.136    0.022    0.782
   4_xyz:    2.294    0.051    0.884
   4_adp:    2.294    0.051    0.884
   4_occ:    2.294    0.051    0.884
   5_bss:    2.294    0.051    0.884
   5_xyz:    2.327    0.051    0.915
   5_adp:    2.327    0.051    0.915
   5_occ:    2.327    0.051    0.915
   5_bss:    2.327    0.051    0.915
------------------------------------------------------------------------

CPU time actual refinement: 365.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/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_1232/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1232/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 365.49 
  Macro-tasks:
    bulk solvent and scale       = 49.27  
    individual site refinement   = 156.02 
    weights calculation          = 33.22  
    collect and process          = 6.39   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 245.06 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 114.24 
    alpha_beta                      = 8.10   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 123.80 
    fmodel                         = 8.38   
    r_factors                      = 0.31   
    phase_errors                   = 9.86   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 268.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.123 micro seconds
Total CPU time: 6.32 minutes
from_scatterers_fft:    624 calls, 113.95 s
gradients_fft:          568 calls, 110.63 s

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

# Date 2008-01-16 Time 03:32:02 PST -0800 (1200483122.78 s)
Start R-work = 0.5190, R-free = 0.5114 (no bulk solvent and anisotropic scale)
Final R-work = 0.1547, R-free = 0.2079 (no bulk solvent and anisotropic scale)

Start R-work = 0.5120, R-free = 0.4979
Final R-work = 0.1371, R-free = 0.1885