# Date 2008-01-16 Time 02:34:46 PST -0800 (1200479686.61 s)
#phil __OFF__

Command line arguments: "../891.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26498
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 891

-------------------------------------------------------------------------------
  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: (70.9525, 46.6953, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95125
Completeness in resolution range: 0.935259
Completeness with d_max=infinity: 0.932499

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9512

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: (70.9525, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95125
Completeness in resolution range: 0.935259
Completeness with d_max=infinity: 0.932499

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1764 [2197/2227]  1980   217   9.9%
  bin  2:  4.1764 -  3.3268 [2112/2131]  1899   213  10.1%
  bin  3:  3.3268 -  2.9098 [2079/2099]  1870   209  10.1%
  bin  4:  2.9098 -  2.6453 [2079/2104]  1880   199   9.6%
  bin  5:  2.6453 -  2.4566 [2051/2070]  1837   214  10.4%
  bin  6:  2.4566 -  2.3123 [2037/2084]  1835   202   9.9%
  bin  7:  2.3123 -  2.1969 [2028/2060]  1825   203  10.0%
  bin  8:  2.1969 -  2.1015 [2021/2058]  1820   201   9.9%
  bin  9:  2.1015 -  2.0208 [2024/2053]  1821   203  10.0%
  bin 10:  2.0208 -  1.9512 [ 961/2059]   863    98  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.58 -     2.25: 24
        2.25 -     2.91: 1482
        2.91 -     3.57: 4522
        3.57 -     4.24: 9278
        4.24 -     4.90: 13294
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.584 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.661 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.846 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28595 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_891/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/model_refine_001.geo

CPU time processing inputs: 9.79


============================ 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 = 70.9525 46.69535 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 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4736   r_free= 0.4657   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.275958                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6587 0.99   1424  159 0.3941 0.3978      6.5865      6.6041|
|  2:  4.6587 -  3.7163 0.99   1377  148 0.3928 0.3899      6.7745      6.8052|
|  3:  3.7163 -  3.2520 0.99   1343  155 0.4427 0.3932      6.6653      6.7037|
|  4:  3.2520 -  2.9571 0.99   1348  148 0.4514 0.4437      6.5074      6.4896|
|  5:  2.9571 -  2.7466 0.99   1320  148 0.5013 0.4781      6.3626      6.3596|
|  6:  2.7466 -  2.5855 0.98   1329  151 0.5010 0.5412      6.2669      6.2432|
|  7:  2.5855 -  2.4566 0.99   1325  143 0.5115 0.4666      6.2503      6.1507|
|  8:  2.4566 -  2.3501 0.98   1303  144 0.5269 0.5283      6.1551      6.1944|
|  9:  2.3501 -  2.2599 0.98   1317  147 0.5136 0.4895      6.1197      6.0696|
| 10:  2.2599 -  2.1822 0.98   1290  147 0.5224 0.5335      6.0875      6.1014|
| 11:  2.1822 -  2.1142 0.99   1327  142 0.5173 0.5087      6.0283      6.0344|
| 12:  2.1142 -  2.0539 0.98   1291  141 0.5193 0.5471      5.9453      5.9913|
| 13:  2.0539 -  1.9999 0.92   1206  146 0.5312 0.5122      5.8849      5.8279|
| 14:  1.9999 -  1.9512 0.32    430   40 0.5373 0.5965      5.8148      5.7864|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6587  1424   159  0.68  35.64   0.80     0.72      75214.35|
|  2:  4.6587 -  3.7163  1377   148  0.70  35.44   0.88     0.78     107302.49|
|  3:  3.7163 -  3.2520  1343   155  0.59  44.59   0.84     0.73     115974.71|
|  4:  3.2520 -  2.9571  1348   148  0.51  51.21   0.82     0.63     104534.67|
|  5:  2.9571 -  2.7466  1320   148  0.41  59.17   0.74     0.50      85644.21|
|  6:  2.7466 -  2.5855  1329   151  0.39  60.37   0.73     0.48      72899.71|
|  7:  2.5855 -  2.4566  1325   143  0.40  60.10   0.75     0.44      62033.54|
|  8:  2.4566 -  2.3501  1303   144  0.39  60.68   0.72     0.47      56512.69|
|  9:  2.3501 -  2.2599  1317   147  0.38  61.20   0.76     0.45      50564.48|
| 10:  2.2599 -  2.1822  1290   147  0.36  63.37   0.76     0.44      49820.92|
| 11:  2.1822 -  2.1142  1327   142  0.31  66.67   0.78     0.39      47232.42|
| 12:  2.1142 -  2.0539  1291   141  0.26  70.69   0.75     0.34      46035.88|
| 13:  2.0539 -  1.9999  1206   146  0.24  72.31   0.75     0.31      40315.75|
| 14:  1.9999 -  1.9512   430    40  0.24  72.39   0.70     0.29      33663.45|
|alpha:            min =        0.29 max =            0.78 mean =         0.51|
|beta:             min =    33663.45 max =       115974.71 mean =     69958.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.06|
|phase err.(test): min =        0.00 max =           89.99 mean =        57.30|
|-----------------------------------------------------------------------------|

============================== 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 = 13.517032             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.489   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.235086              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.045   (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:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2674 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3940 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5149 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6614 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7803 |
|-----------------------------------------------------------------------------|
|-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 |       53.286 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.956 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    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 = 11.672)------------------------------------------|
|    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 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4795   r_free= 0.4736   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.278803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4648   r_free= 0.4569   ksol= 0.34   Bsol= 0.00   scale= 1.003    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.74,7.80,9.98,0.00,0.00,0.00); trace/3= 8.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.273007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.790914             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.286   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.121867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.803   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4648      final r-factor (work) = 0.3905          |
| start r-factor (free) = 0.4569      final r-factor (free) = 0.4133          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.1389 = 10.79 * 0.50 * 6.2744 + 1.00 * 53.2856                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5405 = 10.79 * 0.50 * 6.1919 + 1.00 * 0.1325                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3905      final r-factor (work) = 0.3462          |
| start r-factor (free) = 0.4133      final r-factor (free) = 0.4034          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9608 = 1.12 * 1.00 * 6.1919 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8667 = 1.12 * 1.00 * 6.1066 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.57   13.20    None  None   None       |
|    all(noH): 2823   0      0.00    93.57   13.20    None  None   None       |
|    Sol.    : 438    0      0.00    71.48   26.34    None  None   None       |
|    Mac.    : 2385   0      0.00    93.57   10.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.357: 1351   |   5:    46.786 -  56.143:   37        |
|      1:     9.357 -  18.714:  797   |   6:    56.143 -  65.500:   11        |
|      2:    18.714 -  28.072:  349   |   7:    65.500 -  74.858:    7        |
|      3:    28.072 -  37.429:  178   |   8:    74.858 -  84.215:    2        |
|      4:    37.429 -  46.786:   90   |   9:    84.215 -  93.572:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3462 r_free = 0.4034             target_work(ml) = 6.093         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3457 r_free = 0.4036             target_work(ml) = 6.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3457   r_free= 0.4036   ksol= 0.34   Bsol= 0.00   scale= 1.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.74,7.80,9.98,0.00,0.00,0.00); trace/3= 8.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.092245                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3412   r_free= 0.3980   ksol= 0.32   Bsol= 28.60   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.80,3.63,6.37,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.090616                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.465627              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.162   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482741              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.855  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3412      final r-factor (work) = 0.2598          |
| start r-factor (free) = 0.3980      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9141 = 7.47 * 0.50 * 6.1031 + 1.00 * 0.1325                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4079 = 7.47 * 0.50 * 5.9814 + 1.00 * 0.0804                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2598      final r-factor (work) = 0.2390          |
| start r-factor (free) = 0.3207      final r-factor (free) = 0.3019          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9033 = 0.48 * 1.00 * 5.9814 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8301 = 0.48 * 1.00 * 5.8402 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.97   13.19    None  None   None       |
|    all(noH): 2823   0      0.00    87.97   13.19    None  None   None       |
|    Sol.    : 438    0      0.00    72.82   31.54    None  None   None       |
|    Mac.    : 2385   0      0.00    87.97   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:     0.000 -   8.797: 1427   |   5:    43.985 -  52.782:   60        |
|      1:     8.797 -  17.594:  703   |   6:    52.782 -  61.579:   20        |
|      2:    17.594 -  26.391:  281   |   7:    61.579 -  70.376:    4        |
|      3:    26.391 -  35.188:  179   |   8:    70.376 -  79.173:    2        |
|      4:    35.188 -  43.985:  144   |   9:    79.173 -  87.970:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2390 r_free = 0.3019             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2389 r_free = 0.3016             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2389   r_free= 0.3016   ksol= 0.32   Bsol= 28.60   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.80,3.63,6.37,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.811738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.2990   ksol= 0.33   Bsol= 39.27   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.10,3.89,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.809929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.208094              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.517  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.319666              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.747  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2378      final r-factor (work) = 0.1691          |
| start r-factor (free) = 0.2990      final r-factor (free) = 0.2232          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1424 = 7.21 * 0.50 * 5.8440 + 1.00 * 0.0804                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.5554 = 7.21 * 0.50 * 5.6818 + 1.00 * 0.0780                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1691      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2232      final r-factor (free) = 0.2020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5087 = 1.32 * 1.00 * 5.6818 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2032 = 1.32 * 1.00 * 5.4484 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.51   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    96.51   13.93    None  None   None       |
|    Sol.    : 438    0      2.47    81.05   38.78    None  None   None       |
|    Mac.    : 2385   0      0.00    96.51   9.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.652: 1654   |   5:    48.257 -  57.909:   81        |
|      1:     9.652 -  19.303:  591   |   6:    57.909 -  67.560:   51        |
|      2:    19.303 -  28.954:  171   |   7:    67.560 -  77.212:   19        |
|      3:    28.954 -  38.606:  141   |   8:    77.212 -  86.863:    5        |
|      4:    38.606 -  48.257:  108   |   9:    86.863 -  96.515:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.2020             target_work(ml) = 5.392         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1473 r_free = 0.2015             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.2015   ksol= 0.33   Bsol= 39.27   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.10,3.89,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.390527                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1998   ksol= 0.33   Bsol= 39.27   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,1.61,2.47,0.00,0.00,0.00); trace/3= 1.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.385705                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.021851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.974  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.540646              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.507  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1998      final r-factor (free) = 0.1736          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0407 = 4.02 * 0.50 * 5.4516 + 1.00 * 0.0780                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7834 = 4.02 * 0.50 * 5.3266 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8928 = 0.54 * 1.00 * 5.3266 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8382 = 0.54 * 1.00 * 5.2285 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.15  13.59    None  None   None       |
|    all(noH): 2823   0      0.00    100.15  13.59    None  None   None       |
|    Sol.    : 438    0      2.84    88.59   37.92    None  None   None       |
|    Mac.    : 2385   0      0.00    100.15  9.13     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 -  10.015: 1723   |   5:    50.076 -  60.091:   68        |
|      1:    10.015 -  20.030:  575   |   6:    60.091 -  70.106:   36        |
|      2:    20.030 -  30.045:  150   |   7:    70.106 -  80.121:   15        |
|      3:    30.045 -  40.060:  141   |   8:    80.121 -  90.136:    4        |
|      4:    40.060 -  50.076:  109   |   9:    90.136 - 100.151:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1675             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1200 r_free = 0.1670             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1670   ksol= 0.33   Bsol= 39.27   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,1.61,2.47,0.00,0.00,0.00); trace/3= 1.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.205359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1676   ksol= 0.32   Bsol= 40.78   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,1.52,2.08,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.207450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.330855              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.608  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1658 = 2.33 * 0.50 * 5.2291 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1136 = 2.33 * 0.50 * 5.1931 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1623      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4385 = 0.27 * 1.00 * 5.1931 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4325 = 0.27 * 1.00 * 5.1772 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.39   13.16    None  None   None       |
|    all(noH): 2823   0      0.00    98.39   13.16    None  None   None       |
|    Sol.    : 438    0      2.71    89.97   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    98.39   8.96     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 -   9.839: 1741   |   5:    49.195 -  59.034:   65        |
|      1:     9.839 -  19.678:  572   |   6:    59.034 -  68.873:   25        |
|      2:    19.678 -  29.517:  157   |   7:    68.873 -  78.712:   14        |
|      3:    29.517 -  39.356:  136   |   8:    78.712 -  88.551:    2        |
|      4:    39.356 -  49.195:  108   |   9:    88.551 -  98.390:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1605             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1602             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1602   ksol= 0.32   Bsol= 40.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,1.52,2.08,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170418                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6587 0.99   1424  159 0.0990 0.1310      5.3924      5.5502|
|  2:  4.6587 -  3.7163 0.99   1377  148 0.0889 0.1139      5.4551      5.6553|
|  3:  3.7163 -  3.2520 0.99   1343  155 0.1084 0.1628      5.4809      5.8721|
|  4:  3.2520 -  2.9571 0.99   1348  148 0.1276 0.1564      5.4763      5.6014|
|  5:  2.9571 -  2.7466 0.99   1320  148 0.1319 0.1661      5.3302      5.4982|
|  6:  2.7466 -  2.5855 0.98   1329  151 0.1292 0.1885      5.2392      5.4873|
|  7:  2.5855 -  2.4566 0.99   1325  143 0.1305 0.1748      5.2091      5.4351|
|  8:  2.4566 -  2.3501 0.98   1303  144 0.1164 0.1690      5.0556      5.3039|
|  9:  2.3501 -  2.2599 0.98   1317  147 0.1165 0.1948      5.0251      5.3317|
| 10:  2.2599 -  2.1822 0.98   1290  147 0.1167 0.1706      4.9764      5.2088|
| 11:  2.1822 -  2.1142 0.99   1327  142 0.1174 0.1824      4.9618      5.2919|
| 12:  2.1142 -  2.0539 0.98   1291  141 0.1172 0.1653      4.8904      5.0906|
| 13:  2.0539 -  1.9999 0.92   1206  146 0.1197 0.1837      4.8006      5.0572|
| 14:  1.9999 -  1.9512 0.32    430   40 0.1095 0.1639      4.6698      4.8857|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6587  1424   159  0.94   8.92   0.98     0.96       7289.26|
|  2:  4.6587 -  3.7163  1377   148  0.95   8.15   1.02     1.00       9032.44|
|  3:  3.7163 -  3.2520  1343   155  0.93  11.62   1.03     1.03      10505.95|
|  4:  3.2520 -  2.9571  1348   148  0.92  14.22   1.01     0.98      10556.44|
|  5:  2.9571 -  2.7466  1320   148  0.90  16.22   0.99     0.96       8360.44|
|  6:  2.7466 -  2.5855  1329   151  0.89  16.97   0.99     0.96       7501.83|
|  7:  2.5855 -  2.4566  1325   143  0.90  15.87   1.00     0.97       6721.45|
|  8:  2.4566 -  2.3501  1303   144  0.90  15.88   0.98     0.95       5261.15|
|  9:  2.3501 -  2.2599  1317   147  0.90  15.99   1.02     0.99       5054.29|
| 10:  2.2599 -  2.1822  1290   147  0.91  15.48   1.00     0.97       4514.26|
| 11:  2.1822 -  2.1142  1327   142  0.90  16.79   1.00     0.97       4595.57|
| 12:  2.1142 -  2.0539  1291   141  0.90  16.44   1.01     1.01       4108.37|
| 13:  2.0539 -  1.9999  1206   146  0.90  15.99   1.00     0.99       3351.27|
| 14:  1.9999 -  1.9512   430    40  0.90  16.26   1.00     0.98       2637.03|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2637.03 max =        10556.44 mean =      6635.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.47|
|phase err.(test): min =        0.00 max =           89.86 mean =        13.89|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1602   ksol= 0.32   Bsol= 41.82   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.18,0.27,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170452                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1602   ksol= 0.32   Bsol= 41.82   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.18,0.27,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170452                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6587 0.99   1424  159 0.0990 0.1309      5.3926      5.5497|
|  2:  4.6587 -  3.7163 0.99   1377  148 0.0888 0.1138      5.4541      5.6542|
|  3:  3.7163 -  3.2520 0.99   1343  155 0.1084 0.1628      5.4803      5.8717|
|  4:  3.2520 -  2.9571 0.99   1348  148 0.1277 0.1564      5.4762      5.6016|
|  5:  2.9571 -  2.7466 0.99   1320  148 0.1319 0.1662      5.3303      5.4983|
|  6:  2.7466 -  2.5855 0.98   1329  151 0.1292 0.1887      5.2396      5.4883|
|  7:  2.5855 -  2.4566 0.99   1325  143 0.1305 0.1749      5.2097      5.4356|
|  8:  2.4566 -  2.3501 0.98   1303  144 0.1164 0.1689       5.056      5.3042|
|  9:  2.3501 -  2.2599 0.98   1317  147 0.1166 0.1949      5.0254      5.3319|
| 10:  2.2599 -  2.1822 0.98   1290  147 0.1167 0.1706      4.9765      5.2082|
| 11:  2.1822 -  2.1142 0.99   1327  142 0.1173 0.1825      4.9618      5.2919|
| 12:  2.1142 -  2.0539 0.98   1291  141 0.1172 0.1653        4.89      5.0901|
| 13:  2.0539 -  1.9999 0.92   1206  146 0.1197 0.1836      4.8007      5.0567|
| 14:  1.9999 -  1.9512 0.32    430   40 0.1096 0.1644      4.6706      4.8891|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9965 -  4.6587  1424   159  0.94   8.91   0.98     0.96       7285.33|
|  2:  4.6587 -  3.7163  1377   148  0.95   8.14   1.02     1.00       9019.64|
|  3:  3.7163 -  3.2520  1343   155  0.93  11.61   1.03     1.03      10491.80|
|  4:  3.2520 -  2.9571  1348   148  0.92  14.21   1.01     0.98      10553.50|
|  5:  2.9571 -  2.7466  1320   148  0.90  16.23   0.99     0.96       8367.44|
|  6:  2.7466 -  2.5855  1329   151  0.89  16.98   0.99     0.96       7508.59|
|  7:  2.5855 -  2.4566  1325   143  0.90  15.88   1.00     0.97       6731.34|
|  8:  2.4566 -  2.3501  1303   144  0.90  15.89   0.98     0.95       5267.34|
|  9:  2.3501 -  2.2599  1317   147  0.90  16.00   1.02     0.99       5056.34|
| 10:  2.2599 -  2.1822  1290   147  0.91  15.48   1.00     0.97       4514.92|
| 11:  2.1822 -  2.1142  1327   142  0.90  16.78   1.00     0.97       4594.37|
| 12:  2.1142 -  2.0539  1291   141  0.90  16.43   1.01     1.01       4104.47|
| 13:  2.0539 -  1.9999  1206   146  0.90  15.99   1.00     0.99       3352.79|
| 14:  1.9999 -  1.9512   430    40  0.90  16.27   1.00     0.98       2641.82|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2641.82 max =        10553.50 mean =      6635.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.47|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    100.14  14.91    None  None   None       |
|    all(noH): 2823   0      1.75    100.14  14.91    None  None   None       |
|    Sol.    : 438    0      4.46    91.72   37.75    None  None   None       |
|    Mac.    : 2385   0      1.75    100.14  10.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.750 -  11.589: 1741   |   5:    50.945 -  60.784:   65        |
|      1:    11.589 -  21.428:  572   |   6:    60.784 -  70.623:   25        |
|      2:    21.428 -  31.267:  157   |   7:    70.623 -  80.462:   14        |
|      3:    31.267 -  41.106:  136   |   8:    80.462 -  90.301:    2        |
|      4:    41.106 -  50.945:  108   |   9:    90.301 - 100.140:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.408 - 5.676
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 326
   mapped sites are within: 0.708 - 5.676

peak=   10.549 closest distance to " CB  VAL A 230 " =    1.429
peak=    8.030 closest distance to " CG2 VAL A 296 " =    1.226
peak=    6.274 closest distance to " O   HOH Z 278 " =    1.452
peak=    6.131 closest distance to " CG  LEU A   5 " =    1.213
peak=    6.119 closest distance to " CD1AILE A 234 " =    1.081
peak=    6.098 closest distance to " NH2 ARG A  56 " =    2.163
peak=    6.058 closest distance to " O   HOH Z  37 " =    1.469
peak=    5.645 closest distance to " NE2 GLN A  11 " =    1.203
peak=    5.638 closest distance to " O   HOH Z 132 " =    1.635
peak=    5.558 closest distance to " CD2 LEU A   5 " =    1.230
peak=    5.263 closest distance to " O   HOH Z 202 " =    1.544
peak=    5.155 closest distance to " CG  PRO A  54 " =    1.248
peak=    5.135 closest distance to " CB  GLN A 223 " =    1.420
peak=    5.101 closest distance to " CB  SER A  63 " =    1.332
peak=    5.000 closest distance to " CG  LEU A 228 " =    1.228
peak=    4.852 closest distance to " CG  PRO A 198 " =    1.367
peak=    4.850 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.767 closest distance to " O   HOH Z 126 " =    1.830
peak=    4.707 closest distance to " CB  PRO A  54 " =    0.878
peak=    4.634 closest distance to " NH2BARG A 102 " =    0.954
peak=    4.629 closest distance to " O   HOH Z 193 " =    1.818
peak=    4.621 closest distance to " CB  SER A   3 " =    1.414
peak=    4.602 closest distance to " O   HOH Z 427 " =    2.938
peak=    4.554 closest distance to " O   HOH Z 247 " =    1.291
peak=    4.541 closest distance to " O   HOH Z 124 " =    1.415
peak=    4.539 closest distance to " CD2 LEU A 228 " =    1.240
peak=    4.526 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.521 closest distance to " O   HOH Z 144 " =    1.725
peak=    4.515 closest distance to " O   HOH Z 232 " =    2.195
peak=    4.490 closest distance to " O   HOH Z 371 " =    3.168
peak=    4.460 closest distance to " CB  ASN A 148 " =    1.377
peak=    4.440 closest distance to " CB  TYR A 169 " =    0.905
peak=    4.431 closest distance to " CA  GLY A 241 " =    3.797
peak=    4.425 closest distance to " O   HOH Z   3 " =    1.896
peak=    4.413 closest distance to " O   HOH Z  48 " =    1.631
peak=    4.412 closest distance to " CB  VAL A 296 " =    1.108
peak=    4.385 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.383 closest distance to " O   HOH Z 260 " =    1.289
peak=    4.380 closest distance to " O   PRO A 198 " =    1.556
peak=    4.371 closest distance to " O   HOH Z 263 " =    1.507
peak=    4.357 closest distance to " O   HOH Z 133 " =    1.595
peak=    4.348 closest distance to " CB  VAL A 230 " =    1.205
peak=    4.317 closest distance to " O   HOH Z 108 " =    1.653
peak=    4.311 closest distance to " CB  GLU A 152 " =    1.177
peak=    4.300 closest distance to " O   HOH Z 303 " =    2.103
peak=    4.280 closest distance to " CA  VAL A  41 " =    0.903
peak=    4.250 closest distance to " OD1 ASN A  69 " =    2.659
peak=    4.238 closest distance to " CB  GLU A 128 " =    1.152
peak=    4.215 closest distance to " O   HOH Z 346 " =    1.552
peak=    4.214 closest distance to " O   SER A  87 " =    2.322
peak=    4.182 closest distance to " O   HOH Z  97 " =    2.102
peak=    4.174 closest distance to " O   HOH Z  78 " =    2.140
peak=    4.147 closest distance to " O   HOH Z 368 " =    1.963
peak=    4.134 closest distance to " O   HOH Z 316 " =    2.837
peak=    4.119 closest distance to " O   HOH Z 280 " =    3.010
peak=    4.116 closest distance to " O   HOH Z 134 " =    1.434
peak=    4.115 closest distance to " O   HOH Z 203 " =    1.645
peak=    4.102 closest distance to " O   HOH Z 236 " =    1.909
peak=    4.096 closest distance to " O   HOH Z 193 " =    1.614
peak=    4.071 closest distance to " O   HOH Z  15 " =    2.270
peak=    4.065 closest distance to " O   HOH Z 128 " =    1.901
peak=    4.051 closest distance to " CB  LEU A 228 " =    1.345
peak=    4.035 closest distance to " CA  ALA A  21 " =    1.157
peak=    4.009 closest distance to " CB  VAL A 265 " =    1.197
peak=    3.984 closest distance to " O   HOH Z 357 " =    1.822
peak=    3.971 closest distance to " CA  TYR A  30 " =    0.998
peak=    3.971 closest distance to " OD2 ASP A 286 " =    2.731
peak=    3.971 closest distance to " CG1BVAL A  72 " =    1.500
peak=    3.970 closest distance to " O   HOH Z 234 " =    3.700
peak=    3.964 closest distance to " O   HOH Z 126 " =    1.724
peak=    3.958 closest distance to " O   HOH Z 193 " =    1.896
peak=    3.954 closest distance to " CA  THR A 221 " =    0.929
peak=    3.945 closest distance to " CG  PRO A 243 " =    1.165
peak=    3.944 closest distance to " CA  LEU A 282 " =    1.081
peak=    3.944 closest distance to " O   HOH Z  88 " =    3.236
peak=    3.937 closest distance to " O   HOH Z 126 " =    1.598
peak=    3.934 closest distance to " O   HOH Z 298 " =    1.804
peak=    3.933 closest distance to " O   HOH Z 389 " =    1.805
peak=    3.919 closest distance to " NZ  LYS A 117 " =    3.235
peak=    3.913 closest distance to " O   HOH Z  59 " =    1.908
peak=    3.893 closest distance to " O   HOH Z 272 " =    1.850
peak=    3.891 closest distance to " O   HOH Z 112 " =    1.319
peak=    3.875 closest distance to " CB  SER A 216 " =    0.830
peak=    3.859 closest distance to " O   HOH Z 344 " =    2.781
peak=    3.853 closest distance to " CG  GLN A  88 " =    1.066
peak=    3.850 closest distance to " CB  GLU A 277 " =    3.549
peak=    3.848 closest distance to " O   HOH Z  68 " =    1.688
peak=    3.842 closest distance to " CA  ASN A 215 " =    1.210
peak=    3.828 closest distance to " O   HOH Z  93 " =    2.598
peak=    3.828 closest distance to " CB  ARG A 139 " =    0.950
peak=    3.826 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.818 closest distance to " CG2 THR A 221 " =    1.025
peak=    3.798 closest distance to " O   HOH Z 217 " =    1.387
peak=    3.792 closest distance to " O   HOH Z 227 " =    1.702
peak=    3.784 closest distance to " O   HOH Z 326 " =    1.488
peak=    3.783 closest distance to " CB  ARG A  79 " =    1.387
peak=    3.782 closest distance to " C   ALA A 299 " =    0.970
peak=    3.780 closest distance to " O   HOH Z 425 " =    1.351
peak=    3.779 closest distance to " O   HOH Z 116 " =    1.740
peak=    3.762 closest distance to " CA  ALA A  51 " =    1.016
peak=    3.755 closest distance to " O   HOH Z 344 " =    1.218
peak=    3.754 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.752 closest distance to " CG  LEU A 167 " =    1.164
peak=    3.749 closest distance to " O   HOH Z 345 " =    3.218
peak=    3.738 closest distance to " O   HOH Z  58 " =    1.572
peak=    3.736 closest distance to " O   HOH Z 214 " =    1.181
peak=    3.732 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.713 closest distance to " O   HOH Z  20 " =    1.668
peak=    3.713 closest distance to " O   HOH Z  54 " =    1.582
peak=    3.699 closest distance to " O   HOH Z 276 " =    1.307
peak=    3.693 closest distance to " O   HOH Z  97 " =    1.513
peak=    3.692 closest distance to " NH1 ARG A  14 " =    0.998
peak=    3.685 closest distance to " CG2 VAL A 257 " =    0.875
peak=    3.678 closest distance to " O   HOH Z 271 " =    1.981
peak=    3.676 closest distance to " O   HOH Z 189 " =    2.561
peak=    3.666 closest distance to " CG2 VAL A 174 " =    1.337
peak=    3.664 closest distance to " O   HOH Z 295 " =    1.546
peak=    3.659 closest distance to " O   HOH Z 273 " =    2.723
peak=    3.658 closest distance to " O   HOH Z 209 " =    2.452
peak=    3.653 closest distance to " CA  THR A 264 " =    0.769
peak=    3.639 closest distance to " CB  TRP A 179 " =    1.345
peak=    3.632 closest distance to " O   HOH Z  80 " =    1.653
peak=    3.629 closest distance to " CD2 LEU A 255 " =    1.361
peak=    3.622 closest distance to " CA  ASN A  74 " =    1.187
peak=    3.618 closest distance to " NE2 GLN A  58 " =    5.466
peak=    3.610 closest distance to " CG BARG A 102 " =    1.891
peak=    3.606 closest distance to " O   HOH Z  61 " =    1.642
peak=    3.603 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.599 closest distance to " CA  ALA A 154 " =    1.118
peak=    3.591 closest distance to " O   HOH Z  49 " =    2.366
peak=    3.591 closest distance to " O   HOH Z 426 " =    1.467
peak=    3.591 closest distance to " O   HOH Z  21 " =    1.736
peak=    3.587 closest distance to " O   MET A 105 " =    1.674
peak=    3.579 closest distance to " O   HOH Z 369 " =    1.905
peak=    3.570 closest distance to " O   HOH Z 135 " =    1.860
peak=    3.569 closest distance to " O   HOH Z 132 " =    2.945
peak=    3.567 closest distance to " CA  VAL A 126 " =    0.967
peak=    3.564 closest distance to " O   HOH Z 255 " =    1.726
peak=    3.556 closest distance to " NH2 ARG A 156 " =    1.134
peak=    3.551 closest distance to " CB  LEU A 143 " =    1.159
peak=    3.550 closest distance to " O   TRP A 274 " =    1.853
peak=    3.549 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.541 closest distance to " O   HOH Z 291 " =    1.575
peak=    3.533 closest distance to " CD  ARG A 269 " =    0.949
peak=    3.529 closest distance to " NH1AARG A 145 " =    0.994
peak=    3.514 closest distance to " CG  ARG A  66 " =    2.574
peak=    3.514 closest distance to " CB  LEU A 255 " =    0.849
peak=    3.511 closest distance to " O   HOH Z 374 " =    2.457
peak=    3.510 closest distance to " O   HOH Z  92 " =    0.835
peak=    3.508 closest distance to " CB  PRO A 198 " =    0.921
peak=    3.508 closest distance to " O   HOH Z 281 " =    4.427
peak=    3.505 closest distance to " O   HOH Z  44 " =    1.883
peak=    3.504 closest distance to " O   HOH Z 261 " =    1.764
peak=    3.503 closest distance to " OE1 GLU A   2 " =    2.063
peak=    3.495 closest distance to " CD BLYS A 290 " =    1.147
peak=    3.494 closest distance to " CG1 ILE A  33 " =    1.344
peak=    3.493 closest distance to " CB  ASN A 187 " =    1.094
peak=    3.489 closest distance to " CB  ALA A 248 " =    0.965
peak=    3.484 closest distance to " O   HOH Z 171 " =    2.284
peak=    3.477 closest distance to " OG  SER A  22 " =    2.880
peak=    3.471 closest distance to " NZ  LYS A  76 " =    1.179
peak=    3.471 closest distance to " OG BSER A 164 " =    2.283
peak=    3.465 closest distance to " CB  SER A 273 " =    0.884
peak=    3.462 closest distance to " CB  ASN A 148 " =    1.854
peak=    3.457 closest distance to " O   HOH Z 403 " =    1.667
peak=    3.457 closest distance to " CG  GLU A 277 " =    2.271
peak=    3.455 closest distance to " O   HOH Z 118 " =    1.683
peak=    3.454 closest distance to " O   HOH Z 284 " =    1.462
peak=    3.449 closest distance to " O   ALA A 158 " =    1.287
peak=    3.447 closest distance to " O   HOH Z 329 " =    3.442
peak=    3.446 closest distance to " O   ALA A   1 " =    1.503
peak=    3.438 closest distance to " CA  TYR A 186 " =    1.458
peak=    3.434 closest distance to " CB  ILE A 234 " =    0.839
peak=    3.434 closest distance to " CG  ARG A 138 " =    1.055
peak=    3.431 closest distance to " CD1 ILE A  33 " =    1.510
peak=    3.427 closest distance to " O   HOH Z 392 " =    2.933
peak=    3.424 closest distance to " O   HOH Z  10 " =    1.829
peak=    3.423 closest distance to " CB  TYR A  30 " =    1.532
peak=    3.421 closest distance to " O   HOH Z 136 " =    1.112
peak=    3.417 closest distance to " O   HOH Z 334 " =    1.405
peak=    3.416 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.410 closest distance to " CD  LYS A 119 " =    1.637
peak=    3.403 closest distance to " O   HOH Z 180 " =    2.166
peak=    3.403 closest distance to " O   HOH Z 303 " =    1.711
peak=    3.386 closest distance to " CZ  PHE A 192 " =    1.017
peak=    3.386 closest distance to " OD1 ASN A 217 " =    1.621
peak=    3.386 closest distance to " O   HOH Z  68 " =    2.040
peak=    3.385 closest distance to " O   HOH Z  59 " =    2.103
peak=    3.382 closest distance to " CA  SER A  87 " =    0.894
peak=    3.379 closest distance to " CG  MET A 188 " =    1.336
peak=    3.371 closest distance to " CA  ALA A 233 " =    1.828
peak=    3.371 closest distance to " O   HOH Z 192 " =    1.162
peak=    3.370 closest distance to " O   HOH Z 158 " =    2.793
peak=    3.363 closest distance to " O   HOH Z 423 " =    1.803
peak=    3.362 closest distance to " O   HOH Z 285 " =    3.121
peak=    3.362 closest distance to " C   LYS A 290 " =    1.269
peak=    3.361 closest distance to " O   HOH Z 172 " =    3.705
peak=    3.359 closest distance to " O   HOH Z 214 " =    1.914
peak=    3.358 closest distance to " CB  ALA A 161 " =    0.902
peak=    3.357 closest distance to " O   HOH Z 419 " =    1.763
peak=    3.356 closest distance to " O   HOH Z 151 " =    1.733
peak=    3.355 closest distance to " CB  ARG A 102 " =    0.708
peak=    3.352 closest distance to " OG  SER A 206 " =    1.212
peak=    3.350 closest distance to " O   HOH Z 332 " =    1.515
peak=    3.349 closest distance to " O   HOH Z  89 " =    2.027
peak=    3.348 closest distance to " CA  MET A  40 " =    1.062
peak=    3.346 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.345 closest distance to " O   HOH Z 380 " =    1.957
peak=    3.344 closest distance to " O   HOH Z 108 " =    1.711
peak=    3.340 closest distance to " CB  ASN A 142 " =    0.949
peak=    3.340 closest distance to " CB  THR A 157 " =    1.003
peak=    3.338 closest distance to " O   HOH Z 322 " =    2.069
peak=    3.333 closest distance to " CA  GLN A 194 " =    1.189
peak=    3.331 closest distance to " NH2BARG A 190 " =    1.722
peak=    3.331 closest distance to " N   ARG A 156 " =    1.295
peak=    3.327 closest distance to " CA  ALA A 248 " =    1.283
peak=    3.326 closest distance to " O   HOH Z  30 " =    1.247
peak=    3.322 closest distance to " O   HOH Z 184 " =    1.248
peak=    3.322 closest distance to " O   HOH Z 148 " =    3.710
peak=    3.321 closest distance to " O   HOH Z 407 " =    2.273
peak=    3.320 closest distance to " NH1 ARG A  56 " =    0.912
peak=    3.320 closest distance to " O   HOH Z 133 " =    2.218
peak=    3.319 closest distance to " O   HOH Z 355 " =    1.806
peak=    3.316 closest distance to " CB  TRP A 150 " =    1.484
peak=    3.313 closest distance to " ND1 HIS A  86 " =    1.731
peak=    3.311 closest distance to " CB  ALA A 291 " =    1.468
peak=    3.307 closest distance to " O   HOH Z 248 " =    1.845
peak=    3.303 closest distance to " N   ASN A  39 " =    1.230
peak=    3.298 closest distance to " O   HOH Z 189 " =    3.112
peak=    3.296 closest distance to " CA  ASP A 191 " =    0.764
peak=    3.295 closest distance to " O   HOH Z 236 " =    1.654
peak=    3.293 closest distance to " CH2 TRP A 274 " =    2.133
peak=    3.291 closest distance to " O   HOH Z 425 " =    2.124
peak=    3.288 closest distance to " OE2 GLU A  53 " =    2.047
peak=    3.285 closest distance to " O   HOH Z 422 " =    2.615
peak=    3.282 closest distance to " O   GLN A  58 " =    1.571
peak=    3.279 closest distance to " CB  ALA A 180 " =    1.217
peak=    3.278 closest distance to " CB  MET A  40 " =    0.855
peak=    3.276 closest distance to " O   HOH Z 145 " =    1.789
peak=    3.273 closest distance to " CD2 HIS A  81 " =    1.122
peak=    3.271 closest distance to " O   HOH Z  30 " =    2.081
peak=    3.270 closest distance to " O   HOH Z 394 " =    1.758
peak=    3.270 closest distance to " O   ASN A 217 " =    1.254
peak=    3.269 closest distance to " CB  ALA A 295 " =    1.416
peak=    3.269 closest distance to " O   HOH Z 209 " =    2.418
peak=    3.268 closest distance to " ND2 ASN A 187 " =    1.639
peak=    3.264 closest distance to " NE AARG A 275 " =    1.359
peak=    3.261 closest distance to " NZ ALYS A 290 " =    1.073
peak=    3.260 closest distance to " O   HOH Z 367 " =    3.613
peak=    3.260 closest distance to " O   HOH Z 409 " =    3.303
peak=    3.259 closest distance to " O   HOH Z 359 " =    3.740
peak=    3.258 closest distance to " OD1 ASP A 231 " =    1.796
peak=    3.256 closest distance to " CG2 ILE A 120 " =    1.323
peak=    3.256 closest distance to " CB  LYS A 117 " =    1.219
peak=    3.255 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.251 closest distance to " CA  PHE A 283 " =    1.322
peak=    3.250 closest distance to " O   HOH Z 109 " =    2.768
peak=    3.249 closest distance to " O   HOH Z 266 " =    1.453
peak=    3.246 closest distance to " CB  SER A  62 " =    1.226
peak=    3.245 closest distance to " O   HOH Z 410 " =    1.700
peak=    3.245 closest distance to " O   HOH Z 266 " =    2.470
peak=    3.239 closest distance to " OE1 GLN A  11 " =    1.686
peak=    3.237 closest distance to " CD2 TYR A 186 " =    0.871
peak=    3.234 closest distance to " O   HOH Z 183 " =    1.356
peak=    3.226 closest distance to " O   HOH Z 313 " =    1.783
peak=    3.226 closest distance to " O   HOH Z 114 " =    1.421
peak=    3.226 closest distance to " O   HOH Z 213 " =    1.957
peak=    3.224 closest distance to " N   PHE A 130 " =    1.318
peak=    3.224 closest distance to " O  BHOH Z 338 " =    2.561
peak=    3.217 closest distance to " NE2 GLN A  58 " =    4.006
peak=    3.214 closest distance to " O   HOH Z 328 " =    1.842
peak=    3.212 closest distance to " NH2AARG A 190 " =    1.393
peak=    3.209 closest distance to " O   HOH Z 215 " =    1.650
peak=    3.207 closest distance to " O   HOH Z 265 " =    2.130
peak=    3.202 closest distance to " O   SER A  26 " =    1.553
peak=    3.197 closest distance to " CA  ASP A 140 " =    1.188
peak=    3.194 closest distance to " CD  LYS A 166 " =    1.413
peak=    3.192 closest distance to " CG2AVAL A 121 " =    2.308
peak=    3.192 closest distance to " O   HOH Z 423 " =    2.900
peak=    3.188 closest distance to " O   HOH Z 216 " =    2.185
peak=    3.186 closest distance to " O   HOH Z  63 " =    0.993
peak=    3.182 closest distance to " CB  ASN A  39 " =    0.793
peak=    3.179 closest distance to " CB  SER A 212 " =    1.097
peak=    3.178 closest distance to " O   HOH Z 417 " =    1.982
peak=    3.176 closest distance to " NH2 ARG A 219 " =    1.803
peak=    3.176 closest distance to " O   HOH Z  43 " =    2.259
peak=    3.174 closest distance to " O   HOH Z 207 " =    2.114
peak=    3.170 closest distance to " O   HOH Z 175 " =    3.509
peak=    3.169 closest distance to " O   HOH Z 164 " =    1.911
peak=    3.168 closest distance to " O   HOH Z 272 " =    2.394
peak=    3.168 closest distance to " O   HOH Z 438 " =    2.114
peak=    3.157 closest distance to " CG2 THR A 294 " =    3.851
peak=    3.154 closest distance to " O   SER A 164 " =    1.355
peak=    3.145 closest distance to " CZ  PHE A 218 " =    1.050
peak=    3.143 closest distance to " OD1 ASP A 238 " =    0.944
peak=    3.139 closest distance to " CA  LYS A  48 " =    1.428
peak=    3.136 closest distance to " CA  LEU A 101 " =    1.466
peak=    3.135 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.134 closest distance to " O   HOH Z 145 " =    3.447
peak=    3.133 closest distance to " CG  PRO A 280 " =    0.708
peak=    3.133 closest distance to " O   HOH Z 280 " =    2.548
peak=    3.132 closest distance to " CB  LYS A 193 " =    1.073
peak=    3.131 closest distance to " CD  PRO A 243 " =    1.640
peak=    3.131 closest distance to " O   HOH Z 383 " =    2.190
peak=    3.130 closest distance to " CB  LEU A 237 " =    0.979
peak=    3.129 closest distance to " CG  MET A 185 " =    1.111
peak=    3.126 closest distance to " O   HOH Z  11 " =    1.367
peak=    3.118 closest distance to " CG  LYS A  76 " =    1.814
peak=    3.110 closest distance to " CG2 ILE A  20 " =    1.581
peak=    3.107 closest distance to " CB  GLU A 152 " =    1.319
peak=    3.104 closest distance to " O   HOH Z 128 " =    1.715
peak=    3.100 closest distance to " O   HOH Z 411 " =    1.791
peak=    3.099 closest distance to " C   GLU A 277 " =    1.375
peak=    3.083 closest distance to " O   HOH Z 365 " =    5.676
peak=    3.082 closest distance to " C   SER A  32 " =    1.129
peak=    3.079 closest distance to " CA  ASN A 176 " =    1.081
peak=    3.073 closest distance to " O   HOH Z  66 " =    2.182
peak=    3.072 closest distance to " CE  MET A  93 " =    1.471
peak=    3.067 closest distance to " O   HOH Z 388 " =    1.955
peak=    3.058 closest distance to " CA  ARG A  36 " =    1.077
peak=    3.043 closest distance to " O   HOH Z 175 " =    2.099
peak=    3.008 closest distance to " O   HOH Z  68 " =    2.582

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.614 - 5.388
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.773 - 5.388

peak=   -5.573 closest distance to " CG2 VAL A 230 " =    0.783
peak=   -4.485 closest distance to " CG  LEU A 101 " =    2.612
peak=   -4.392 closest distance to " O   HOH Z  92 " =    1.262
peak=   -4.286 closest distance to " O   HOH Z 231 " =    1.428
peak=   -4.243 closest distance to " CD  ARG A 156 " =    2.018
peak=   -4.238 closest distance to " SG  CYS A 254 " =    3.212
peak=   -4.155 closest distance to " O   ILE A 109 " =    2.644
peak=   -4.056 closest distance to " O   HOH Z 377 " =    1.799
peak=   -4.048 closest distance to " O   HOH Z 290 " =    0.982
peak=   -3.995 closest distance to " O   HOH Z  98 " =    1.727
peak=   -3.963 closest distance to " CG2 THR A   4 " =    1.962
peak=   -3.951 closest distance to " N   SER A 276 " =    1.318
peak=   -3.945 closest distance to " CG  GLN A 223 " =    2.025
peak=   -3.890 closest distance to " O   HOH Z 274 " =    2.751
peak=   -3.885 closest distance to " O   HOH Z 266 " =    4.367
peak=   -3.874 closest distance to " CE2 TYR A  30 " =    2.868
peak=   -3.874 closest distance to " N   GLN A  58 " =    1.789
peak=   -3.860 closest distance to " CD  LYS A 289 " =    2.532
peak=   -3.858 closest distance to " O   PRO A 163 " =    1.999
peak=   -3.848 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.845 closest distance to " OG ASER A 134 " =    1.391
peak=   -3.793 closest distance to " CB  PRO A 243 " =    2.642
peak=   -3.781 closest distance to " OG BSER A 134 " =    1.679
peak=   -3.755 closest distance to " O   HOH Z 166 " =    1.918
peak=   -3.749 closest distance to " CB  ASN A  39 " =    1.952
peak=   -3.747 closest distance to " CB  PRO A 163 " =    2.621
peak=   -3.747 closest distance to " O   HOH Z  13 " =    1.280
peak=   -3.734 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.696 closest distance to " OG BSER A 134 " =    1.192
peak=   -3.681 closest distance to " NH2 ARG A  79 " =    1.831
peak=   -3.679 closest distance to " O   HOH Z  63 " =    0.837
peak=   -3.677 closest distance to " O   HOH Z  60 " =    2.372
peak=   -3.673 closest distance to " O   VAL A  67 " =    2.660
peak=   -3.667 closest distance to " O   HOH Z  97 " =    1.587
peak=   -3.661 closest distance to " ND2 ASN A  60 " =    1.455
peak=   -3.655 closest distance to " CD1 LEU A 228 " =    2.242
peak=   -3.654 closest distance to " CG  TRP A 266 " =    1.515
peak=   -3.653 closest distance to " CG  MET A 105 " =    0.948
peak=   -3.651 closest distance to " O   HOH Z 103 " =    1.806
peak=   -3.646 closest distance to " O   HOH Z 166 " =    1.428
peak=   -3.646 closest distance to " O   HOH Z 388 " =    1.837
peak=   -3.645 closest distance to " O   HOH Z  43 " =    1.878
peak=   -3.638 closest distance to " CB  ALA A  43 " =    2.307
peak=   -3.638 closest distance to " C   ASN A 187 " =    1.731
peak=   -3.630 closest distance to " O   ALA A 161 " =    1.616
peak=   -3.625 closest distance to " CG2 VAL A 296 " =    1.423
peak=   -3.596 closest distance to " CG1 VAL A 250 " =    2.716
peak=   -3.595 closest distance to " CZ  PHE A  59 " =    1.562
peak=   -3.588 closest distance to " O   HOH Z 407 " =    3.136
peak=   -3.581 closest distance to " CD  GLN A  88 " =    0.849
peak=   -3.568 closest distance to " O   ASP A 231 " =    2.490
peak=   -3.565 closest distance to " O   HOH Z 148 " =    1.683
peak=   -3.557 closest distance to " CE2 PHE A 218 " =    2.573
peak=   -3.555 closest distance to " N   THR A 157 " =    1.570
peak=   -3.551 closest distance to " N   HIS A 115 " =    2.109
peak=   -3.550 closest distance to " O   HOH Z 436 " =    1.521
peak=   -3.549 closest distance to " O   GLY A 196 " =    1.116
peak=   -3.548 closest distance to " ND2 ASN A  45 " =    0.981
peak=   -3.547 closest distance to " O   SER A 135 " =    1.541
peak=   -3.543 closest distance to " O   HOH Z  97 " =    0.834
peak=   -3.542 closest distance to " CA  GLY A 133 " =    1.900
peak=   -3.542 closest distance to " NH2 ARG A  66 " =    2.072
peak=   -3.530 closest distance to " CB  CYS A 254 " =    2.335
peak=   -3.528 closest distance to " CG  PHE A 283 " =    2.716
peak=   -3.523 closest distance to " CZ  TYR A 169 " =    1.718
peak=   -3.522 closest distance to " O   HOH Z  19 " =    2.322
peak=   -3.518 closest distance to " CD  GLN A  88 " =    2.277
peak=   -3.511 closest distance to " C   ALA A 158 " =    1.260
peak=   -3.510 closest distance to " CD  ARG A 139 " =    1.674
peak=   -3.508 closest distance to " CG  LEU A 228 " =    0.987
peak=   -3.503 closest distance to " CH2 TRP A 179 " =    1.354
peak=   -3.492 closest distance to " CD1 LEU A 101 " =    2.390
peak=   -3.488 closest distance to " CB  ALA A  51 " =    1.767
peak=   -3.484 closest distance to " CB  ALA A 248 " =    1.943
peak=   -3.482 closest distance to " O   ASP A 231 " =    2.427
peak=   -3.479 closest distance to " CG  PRO A 163 " =    2.519
peak=   -3.474 closest distance to " CD2 LEU A 300 " =    2.840
peak=   -3.473 closest distance to " CG1 VAL A 296 " =    1.338
peak=   -3.467 closest distance to " OD1 ASN A 249 " =    1.144
peak=   -3.465 closest distance to " CG2 ILE A 151 " =    2.512
peak=   -3.464 closest distance to " O   HOH Z 205 " =    0.977
peak=   -3.454 closest distance to " OG  SER A 206 " =    1.782
peak=   -3.454 closest distance to " NH2AARG A 275 " =    5.291
peak=   -3.452 closest distance to " CA  TYR A  68 " =    2.688
peak=   -3.452 closest distance to " O   HOH Z 266 " =    4.471
peak=   -3.451 closest distance to " N   ALA A 248 " =    1.642
peak=   -3.444 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.438 closest distance to " CG2 VAL A 112 " =    2.565
peak=   -3.436 closest distance to " N   ALA A 226 " =    2.084
peak=   -3.432 closest distance to " O   HOH Z 292 " =    4.403
peak=   -3.429 closest distance to " OE1 GLN A  73 " =    2.339
peak=   -3.425 closest distance to " O   HOH Z  71 " =    1.159
peak=   -3.424 closest distance to " CD2 PHE A  61 " =    1.844
peak=   -3.421 closest distance to " CB  TYR A  15 " =    2.164
peak=   -3.420 closest distance to " C   ASN A 285 " =    2.413
peak=   -3.416 closest distance to " CG  LYS A 193 " =    2.293
peak=   -3.415 closest distance to " O   GLY A 211 " =    1.369
peak=   -3.413 closest distance to " O   HOH Z  15 " =    1.666
peak=   -3.407 closest distance to " CB  ASP A 132 " =    2.258
peak=   -3.382 closest distance to " O   HOH Z 411 " =    3.688
peak=   -3.373 closest distance to " CD2 TYR A 293 " =    2.107
peak=   -3.366 closest distance to " O   HOH Z 426 " =    2.305
peak=   -3.361 closest distance to " CZ  TYR A 172 " =    1.676
peak=   -3.360 closest distance to " OD1 ASP A 191 " =    1.556
peak=   -3.356 closest distance to " O   HOH Z  93 " =    1.728
peak=   -3.356 closest distance to " O   HOH Z 351 " =    1.343
peak=   -3.355 closest distance to " CE  MET A  93 " =    1.067
peak=   -3.351 closest distance to " CA  GLY A 241 " =    2.240
peak=   -3.345 closest distance to " OH  TYR A 169 " =    1.022
peak=   -3.343 closest distance to " O   VAL A 153 " =    2.343
peak=   -3.342 closest distance to " CG  GLU A 277 " =    1.178
peak=   -3.338 closest distance to " O   VAL A 197 " =    1.351
peak=   -3.333 closest distance to " CA  GLY A  35 " =    1.963
peak=   -3.331 closest distance to " O   HOH Z 350 " =    2.497
peak=   -3.325 closest distance to " O   HOH Z 165 " =    2.064
peak=   -3.324 closest distance to " N   ALA A   9 " =    1.485
peak=   -3.322 closest distance to " CE  MET A 105 " =    1.954
peak=   -3.314 closest distance to " N   GLN A  55 " =    1.531
peak=   -3.311 closest distance to " O   HOH Z 389 " =    1.727
peak=   -3.307 closest distance to " CE BMET A  47 " =    1.448
peak=   -3.306 closest distance to " O   HOH Z  37 " =    1.378
peak=   -3.306 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.303 closest distance to " O   HOH Z  52 " =    1.559
peak=   -3.302 closest distance to " O   HOH Z 191 " =    5.388
peak=   -3.302 closest distance to " OG1 THR A  82 " =    1.479
peak=   -3.301 closest distance to " O   HOH Z 385 " =    2.014
peak=   -3.299 closest distance to " CD1 PHE A  59 " =    1.874
peak=   -3.297 closest distance to " O   HOH Z  11 " =    1.804
peak=   -3.294 closest distance to " OG  SER A  87 " =    1.328
peak=   -3.290 closest distance to " C   LEU A 143 " =    1.299
peak=   -3.290 closest distance to " CG  GLU A   2 " =    2.083
peak=   -3.288 closest distance to " CG  GLU A 152 " =    2.601
peak=   -3.287 closest distance to " O   HOH Z 134 " =    2.501
peak=   -3.275 closest distance to " CG  ASP A  50 " =    2.097
peak=   -3.262 closest distance to " O   HOH Z 292 " =    2.877
peak=   -3.258 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.252 closest distance to " CD2 LEU A 300 " =    2.632
peak=   -3.252 closest distance to " O   HOH Z 228 " =    1.419
peak=   -3.252 closest distance to " O   HOH Z 435 " =    2.790
peak=   -3.250 closest distance to " C   GLN A 240 " =    2.176
peak=   -3.248 closest distance to " NH1 ARG A  56 " =    2.479
peak=   -3.235 closest distance to " O   HOH Z 234 " =    4.176
peak=   -3.234 closest distance to " OD1 ASN A 187 " =    1.550
peak=   -3.234 closest distance to " OH  TYR A 214 " =    1.304
peak=   -3.229 closest distance to " O   HOH Z 423 " =    1.077
peak=   -3.225 closest distance to " CD1 ILE A 263 " =    2.450
peak=   -3.217 closest distance to " O   HOH Z 365 " =    1.471
peak=   -3.213 closest distance to " CB  ASP A 132 " =    2.226
peak=   -3.213 closest distance to " O   HOH Z 353 " =    2.240
peak=   -3.213 closest distance to " OXT GLY A 302 " =    3.438
peak=   -3.210 closest distance to " CA  ASN A 127 " =    1.118
peak=   -3.208 closest distance to " O   HOH Z 298 " =    1.297
peak=   -3.207 closest distance to " O   HOH Z 389 " =    4.486
peak=   -3.206 closest distance to " CD2 LEU A 167 " =    1.768
peak=   -3.203 closest distance to " N   GLN A  77 " =    1.665
peak=   -3.202 closest distance to " O   HOH Z 423 " =    2.219
peak=   -3.202 closest distance to " C   MET A 188 " =    1.580
peak=   -3.201 closest distance to " O   HOH Z 185 " =    2.303
peak=   -3.187 closest distance to " O   HOH Z 396 " =    1.595
peak=   -3.186 closest distance to " OG  SER A 245 " =    1.026
peak=   -3.183 closest distance to " OG  SER A  87 " =    1.539
peak=   -3.181 closest distance to " O   HOH Z  44 " =    2.077
peak=   -3.180 closest distance to " O   HOH Z  98 " =    1.378
peak=   -3.179 closest distance to " NE2 GLN A 278 " =    1.869
peak=   -3.174 closest distance to " O   HOH Z 252 " =    4.077
peak=   -3.173 closest distance to " O   THR A  18 " =    1.709
peak=   -3.170 closest distance to " N   PHE A  59 " =    2.126
peak=   -3.167 closest distance to " CE3 TRP A 150 " =    2.020
peak=   -3.164 closest distance to " O   HOH Z 189 " =    2.054
peak=   -3.164 closest distance to " CB  ALA A 227 " =    2.380
peak=   -3.162 closest distance to " CE  LYS A  76 " =    2.845
peak=   -3.162 closest distance to " CZ  ARG A 259 " =    0.895
peak=   -3.160 closest distance to " OE1 GLN A  88 " =    1.009
peak=   -3.159 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.159 closest distance to " O   HOH Z 137 " =    1.604
peak=   -3.157 closest distance to " O   HOH Z 410 " =    1.977
peak=   -3.156 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.155 closest distance to " CD1 TYR A 247 " =    2.915
peak=   -3.151 closest distance to " O   HOH Z 148 " =    3.014
peak=   -3.148 closest distance to " O   HOH Z 168 " =    1.761
peak=   -3.146 closest distance to " CD1 ILE A 239 " =    1.999
peak=   -3.142 closest distance to " OD1 ASN A 148 " =    1.693
peak=   -3.137 closest distance to " O   SER A 271 " =    2.178
peak=   -3.122 closest distance to " CA  ARG A 139 " =    0.985
peak=   -3.122 closest distance to " O   HOH Z 313 " =    1.730
peak=   -3.120 closest distance to " NH2 ARG A  66 " =    2.834
peak=   -3.110 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.104 closest distance to " O   HOH Z 139 " =    3.000
peak=   -3.097 closest distance to " OG ASER A 216 " =    0.961
peak=   -3.096 closest distance to " CD1 ILE A 199 " =    2.420
peak=   -3.093 closest distance to " N   GLY A  23 " =    2.043
peak=   -3.086 closest distance to " CG  GLU A 152 " =    0.793
peak=   -3.084 closest distance to " O   HOH Z 241 " =    1.391
peak=   -3.084 closest distance to " O   HOH Z 210 " =    1.100
peak=   -3.083 closest distance to " O   GLU A  44 " =    1.655
peak=   -3.083 closest distance to " CG1 VAL A 197 " =    2.252
peak=   -3.081 closest distance to " ND2 ASN A 249 " =    1.983
peak=   -3.077 closest distance to " O   ASP A 171 " =    2.021
peak=   -3.076 closest distance to " OD2 ASP A 270 " =    1.439
peak=   -3.070 closest distance to " O   HOH Z 310 " =    1.754
peak=   -3.066 closest distance to " O   VAL A 174 " =    2.055
peak=   -3.060 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.043 closest distance to " CD1 LEU A 101 " =    2.450

================= 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    :  0.4736 0.4657   6.275958e+00   6.271246e+00
   1_bss:  0.4648 0.4569   6.273007e+00   6.264157e+00
   1_xyz:  0.3905 0.4133   6.167428e+00   6.205784e+00
   1_adp:  0.3462 0.4034   6.092814e+00   6.185749e+00
   1_occ:  0.3457 0.4036   6.092245e+00   6.185692e+00
   2_bss:  0.3412 0.3980   6.090616e+00   6.182072e+00
   2_xyz:  0.2598 0.3207   5.874866e+00   6.031391e+00
   2_adp:  0.2390 0.3019   5.812484e+00   5.983671e+00
   2_occ:  0.2389 0.3016   5.811738e+00   5.983626e+00
   3_bss:  0.2378 0.2990   5.809929e+00   5.980669e+00
   3_xyz:  0.1691 0.2232   5.507906e+00   5.718307e+00
   3_adp:  0.1475 0.2020   5.391939e+00   5.624613e+00
   3_occ:  0.1473 0.2015   5.390527e+00   5.622991e+00
   4_bss:  0.1468 0.1998   5.385705e+00   5.616374e+00
   4_xyz:  0.1251 0.1736   5.243720e+00   5.483666e+00
   4_adp:  0.1201 0.1675   5.206754e+00   5.446548e+00
   4_occ:  0.1200 0.1670   5.205359e+00   5.444808e+00
   5_bss:  0.1204 0.1676   5.207450e+00   5.446978e+00
   5_xyz:  0.1154 0.1623   5.177108e+00   5.418250e+00
   5_adp:  0.1152 0.1605   5.171434e+00   5.409297e+00
   5_occ:  0.1150 0.1602   5.170418e+00   5.408075e+00
   5_bss:  0.1150 0.1602   5.170452e+00   5.408022e+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:  0.339   0.000   7.745   7.799   9.983   0.000   0.000   0.000
   1_xyz:  0.339   0.000   7.745   7.799   9.983   0.000   0.000   0.000
   1_adp:  0.339   0.000   7.745   7.799   9.983   0.000   0.000   0.000
   1_occ:  0.339   0.000   7.745   7.799   9.983   0.000   0.000   0.000
   2_bss:  0.324  28.600   3.803   3.630   6.368   0.000   0.000   0.000
   2_xyz:  0.324  28.600   3.803   3.630   6.368   0.000   0.000   0.000
   2_adp:  0.324  28.600   3.803   3.630   6.368   0.000   0.000   0.000
   2_occ:  0.324  28.600   3.803   3.630   6.368   0.000   0.000   0.000
   3_bss:  0.331  39.266   2.139   2.100   3.894   0.000   0.000   0.000
   3_xyz:  0.331  39.266   2.139   2.100   3.894   0.000   0.000   0.000
   3_adp:  0.331  39.266   2.139   2.100   3.894   0.000   0.000   0.000
   3_occ:  0.331  39.266   2.139   2.100   3.894   0.000   0.000   0.000
   4_bss:  0.331  39.266   1.801   1.608   2.467   0.000   0.000   0.000
   4_xyz:  0.331  39.266   1.801   1.608   2.467   0.000   0.000   0.000
   4_adp:  0.331  39.266   1.801   1.608   2.467   0.000   0.000   0.000
   4_occ:  0.331  39.266   1.801   1.608   2.467   0.000   0.000   0.000
   5_bss:  0.320  40.785   1.643   1.521   2.078   0.000   0.000   0.000
   5_xyz:  0.320  40.785   1.643   1.521   2.078   0.000   0.000   0.000
   5_adp:  0.320  40.785   1.643   1.521   2.078   0.000   0.000   0.000
   5_occ:  0.320  40.785   1.643   1.521   2.078   0.000   0.000   0.000
   5_bss:  0.321  41.816  -0.086  -0.183   0.270   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.083 0.4312  0.5135    69964.089
   1_bss:  57.760 0.4198  0.6263    66652.143
   1_xyz:  48.092 0.5424  0.8022    50809.946
   1_adp:  45.404 0.5762  0.9006    47191.434
   1_occ:  45.469 0.5754  0.8988    47312.248
   2_bss:  45.028 0.5806  0.7967    46689.859
   2_xyz:  34.569 0.7050  0.9409    28586.021
   2_adp:  31.693 0.7385  0.9764    25103.640
   2_occ:  31.660 0.7388  0.9765    25052.140
   3_bss:  31.395 0.7415  0.9155    24728.840
   3_xyz:  22.182 0.8399  0.9911    13165.209
   3_adp:  19.604 0.8654  1.0023    10765.780
   3_occ:  19.553 0.8659  1.0023    10705.210
   4_bss:  19.363 0.8675  0.9757    10507.534
   4_xyz:  16.227 0.8957  0.9890     7771.679
   4_adp:  15.329 0.9038  0.9883     7221.459
   4_occ:  15.290 0.9042  0.9884     7195.485
   5_bss:  15.326 0.9040  0.9803     7260.529
   5_xyz:  14.685 0.9094  0.9819     6780.680
   5_adp:  14.440 0.9116  0.9802     6652.129
   5_occ:  14.416 0.9118  0.9803     6635.889
   5_bss:  14.416 0.9118  0.9803     6635.546
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3286e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3286e+01
   1_xyz:   1.613  0.012  0.103 18.282  0.006  4.108   1.3252e-01
   1_adp:   1.613  0.012  0.103 18.282  0.006  4.108   1.3252e-01
   1_occ:   1.613  0.012  0.103 18.282  0.006  4.108   1.3252e-01
   2_bss:   1.613  0.012  0.103 18.282  0.006  4.108   1.3252e-01
   2_xyz:   1.119  0.008  0.081 16.358  0.005  4.110   8.0402e-02
   2_adp:   1.119  0.008  0.081 16.358  0.005  4.110   8.0402e-02
   2_occ:   1.119  0.008  0.081 16.358  0.005  4.110   8.0402e-02
   3_bss:   1.119  0.008  0.081 16.358  0.005  4.110   8.0402e-02
   3_xyz:   1.167  0.008  0.087 16.142  0.004  4.108   7.7980e-02
   3_adp:   1.167  0.008  0.087 16.142  0.004  4.108   7.7980e-02
   3_occ:   1.167  0.008  0.087 16.142  0.004  4.108   7.7980e-02
   4_bss:   1.167  0.008  0.087 16.142  0.004  4.108   7.7980e-02
   4_xyz:   1.108  0.008  0.083 15.780  0.004  4.111   7.2077e-02
   4_adp:   1.108  0.008  0.083 15.780  0.004  4.111   7.2077e-02
   4_occ:   1.108  0.008  0.083 15.780  0.004  4.111   7.2077e-02
   5_bss:   1.108  0.008  0.083 15.780  0.004  4.111   7.2077e-02
   5_xyz:   1.014  0.007  0.078 15.457  0.004  4.114   6.1411e-02
   5_adp:   1.014  0.007  0.078 15.457  0.004  4.114   6.1411e-02
   5_occ:   1.014  0.007  0.078 15.457  0.004  4.114   6.1411e-02
   5_bss:   1.014  0.007  0.078 15.457  0.004  4.114   6.1411e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9069e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9069e+00
   1_xyz:  13.607  0.157  0.431 84.916  0.049  2.240   9.1258e-02
   1_adp:  13.607  0.157  0.431 84.916  0.049  2.240   9.1258e-02
   1_occ:  13.607  0.157  0.431 84.916  0.049  2.240   9.1258e-02
   2_bss:  13.607  0.157  0.431 84.916  0.049  2.240   9.1258e-02
   2_xyz:   7.404  0.069  0.268 83.111  0.037  2.162   6.0412e-02
   2_adp:   7.404  0.069  0.268 83.111  0.037  2.162   6.0412e-02
   2_occ:   7.404  0.069  0.268 83.111  0.037  2.162   6.0412e-02
   3_bss:   7.404  0.069  0.268 83.111  0.037  2.162   6.0412e-02
   3_xyz:   7.482  0.051  0.486 85.566  0.038  2.297   6.4637e-02
   3_adp:   7.482  0.051  0.486 85.566  0.038  2.297   6.4637e-02
   3_occ:   7.482  0.051  0.486 85.566  0.038  2.297   6.4637e-02
   4_bss:   7.482  0.051  0.486 85.566  0.038  2.297   6.4637e-02
   4_xyz:   7.849  0.047  0.537 81.657  0.038  2.292   7.5418e-02
   4_adp:   7.849  0.047  0.537 81.657  0.038  2.292   7.5418e-02
   4_occ:   7.849  0.047  0.537 81.657  0.038  2.292   7.5418e-02
   5_bss:   7.849  0.047  0.537 81.657  0.038  2.292   7.5418e-02
   5_xyz:   7.252  0.036  0.512 83.992  0.027  2.326   4.3862e-02
   5_adp:   7.252  0.036  0.512 83.992  0.027  2.326   4.3862e-02
   5_occ:   7.252  0.036  0.512 83.992  0.027  2.326   4.3862e-02
   5_bss:   7.252  0.036  0.512 83.992  0.027  2.326   4.3862e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  93.57   0.00  13.20  93.57   0.00  10.79  71.48   0.00  26.34
   1_occ:  93.57   0.00  13.20  93.57   0.00  10.79  71.48   0.00  26.34
   2_bss:  93.57   0.00  13.20  93.57   0.00  10.79  71.48   0.00  26.34
   2_xyz:  93.57   0.00  13.20  93.57   0.00  10.79  71.48   0.00  26.34
   2_adp:  87.97   0.00  13.19  87.97   0.00   9.82  72.82   0.00  31.54
   2_occ:  87.97   0.00  13.19  87.97   0.00   9.82  72.82   0.00  31.54
   3_bss:  87.97   0.00  13.19  87.97   0.00   9.82  72.82   0.00  31.54
   3_xyz:  87.97   0.00  13.19  87.97   0.00   9.82  72.82   0.00  31.54
   3_adp:  96.51   0.00  13.93  96.51   0.00   9.36  81.05   2.47  38.78
   3_occ:  96.51   0.00  13.93  96.51   0.00   9.36  81.05   2.47  38.78
   4_bss:  96.51   0.00  13.93  96.51   0.00   9.36  81.05   2.47  38.78
   4_xyz:  96.51   0.00  13.93  96.51   0.00   9.36  81.05   2.47  38.78
   4_adp: 100.15   0.00  13.59 100.15   0.00   9.13  88.59   2.84  37.92
   4_occ: 100.15   0.00  13.59 100.15   0.00   9.13  88.59   2.84  37.92
   5_bss: 100.15   0.00  13.59 100.15   0.00   9.13  88.59   2.84  37.92
   5_xyz: 100.15   0.00  13.59 100.15   0.00   9.13  88.59   2.84  37.92
   5_adp:  98.39   0.00  13.16  98.39   0.00   8.96  89.97   2.71  36.00
   5_occ:  98.39   0.00  13.16  98.39   0.00   8.96  89.97   2.71  36.00
   5_bss: 100.14   1.75  14.91 100.14   1.75  10.71  91.72   4.46  37.75
------------------------------------------------------------------------
 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:    1.226    0.027    0.404
   1_adp:    1.226    0.027    0.404
   1_occ:    1.226    0.027    0.404
   2_bss:    1.226    0.027    0.404
   2_xyz:    1.544    0.016    0.569
   2_adp:    1.544    0.016    0.569
   2_occ:    1.544    0.016    0.569
   3_bss:    1.544    0.016    0.569
   3_xyz:    1.676    0.053    0.676
   3_adp:    1.676    0.053    0.676
   3_occ:    1.676    0.053    0.676
   4_bss:    1.676    0.053    0.676
   4_xyz:    1.767    0.057    0.708
   4_adp:    1.767    0.057    0.708
   4_occ:    1.767    0.057    0.708
   5_bss:    1.767    0.057    0.708
   5_xyz:    1.850    0.053    0.719
   5_adp:    1.850    0.053    0.719
   5_occ:    1.850    0.053    0.719
   5_bss:    1.850    0.053    0.719
------------------------------------------------------------------------

CPU time actual refinement: 359.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/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_891/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_891/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.30 
  Macro-tasks:
    bulk solvent and scale       = 41.63  
    individual site refinement   = 158.34 
    weights calculation          = 32.18  
    collect and process          = 6.33   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 238.61 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 114.32 
    alpha_beta                      = 8.03   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 126.33 
    fmodel                         = 7.10   
    r_factors                      = 0.14   
    phase_errors                   = 10.20  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 270.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.927 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    670 calls, 113.93 s
gradients_fft:          615 calls, 111.91 s

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

# Date 2008-01-16 Time 02:40:58 PST -0800 (1200480058.43 s)
Start R-work = 0.4736, R-free = 0.4657 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1778 (no bulk solvent and anisotropic scale)

Start R-work = 0.4648, R-free = 0.4569
Final R-work = 0.1150, R-free = 0.1602