# Date 2008-01-16 Time 02:33:08 PST -0800 (1200479588.44 s)
#phil __OFF__

Command line arguments: "../878.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2954
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 878

-------------------------------------------------------------------------------
  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, 46.2261, 88.1178, 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: 3.32, per 1000 atoms: 1.18


================================== 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, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.97345
Completeness in resolution range: 0.934055
Completeness with d_max=infinity: 0.931346

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1841
                             d_min =   1.9734

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, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1841 1.97345
Completeness in resolution range: 0.934055
Completeness with d_max=infinity: 0.931346

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1846 -  4.2240 [2202/2228]  1981   221  10.0%
  bin  2:  4.2240 -  3.3647 [2124/2144]  1912   212  10.0%
  bin  3:  3.3647 -  2.9429 [2085/2104]  1879   206   9.9%
  bin  4:  2.9429 -  2.6754 [2065/2095]  1852   213  10.3%
  bin  5:  2.6754 -  2.4846 [2062/2081]  1864   198   9.6%
  bin  6:  2.4846 -  2.3386 [2055/2080]  1845   210  10.2%
  bin  7:  2.3386 -  2.2219 [2010/2038]  1804   206  10.2%
  bin  8:  2.2219 -  2.1254 [2060/2096]  1852   208  10.1%
  bin  9:  2.1254 -  2.0438 [2025/2067]  1833   192   9.5%
  bin 10:  2.0438 -  1.9734 [ 901/2039]   808    93  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/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:
        1.81 -     2.42: 32
        2.42 -     3.04: 2172
        3.04 -     3.66: 4677
        3.66 -     4.28: 8962
        4.28 -     4.90: 12281
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.988 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.074 3.040 -x+1,y+1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.092 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28119 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_878/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 46.22605 88.1178 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: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4934   r_free= 0.4796   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.294688                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7119 0.99   1426  157 0.4144 0.3862      6.6305      6.5859|
|  2:  4.7119 -  3.7586 0.99   1381  156 0.4167 0.4135      6.8222      6.8164|
|  3:  3.7586 -  3.2890 0.99   1356  147 0.4502 0.4236      6.6746      6.6354|
|  4:  3.2890 -  2.9908 0.99   1337  151 0.4916 0.4467       6.553      6.4835|
|  5:  2.9908 -  2.7778 0.99   1333  151 0.5292 0.5092      6.3761      6.3892|
|  6:  2.7778 -  2.6149 0.99   1325  145 0.5235 0.5341      6.2713      6.2109|
|  7:  2.6149 -  2.4846 0.99   1330  143 0.5373 0.4943      6.2505      6.2083|
|  8:  2.4846 -  2.3768 0.98   1297  151 0.5449 0.5251      6.1818       6.179|
|  9:  2.3768 -  2.2857 0.98   1313  145 0.5277 0.5442      6.1243      6.2106|
| 10:  2.2857 -  2.2070 1.00   1325  149 0.5330 0.5367      6.0955      6.0807|
| 11:  2.2070 -  2.1382 0.98   1301  140 0.5171 0.5285      6.0397      6.0158|
| 12:  2.1382 -  2.0772 0.98   1303  143 0.5429 0.5335      5.9433      5.9731|
| 13:  2.0772 -  2.0227 0.95   1249  139 0.5396 0.5280      5.8851      5.8014|
| 14:  2.0227 -  1.9734 0.27    354   42 0.5339 0.4329      5.8664      5.8436|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7119  1426   157  0.69  34.71   0.78     0.74      73538.97|
|  2:  4.7119 -  3.7586  1381   156  0.71  34.44   0.86     0.79     106245.27|
|  3:  3.7586 -  3.2890  1356   147  0.60  44.25   0.83     0.73     112559.97|
|  4:  3.2890 -  2.9908  1337   151  0.51  51.07   0.76     0.61     101666.32|
|  5:  2.9908 -  2.7778  1333   151  0.41  58.69   0.72     0.50      82993.20|
|  6:  2.7778 -  2.6149  1325   145  0.36  62.59   0.70     0.43      74531.86|
|  7:  2.6149 -  2.4846  1330   143  0.31  66.76   0.72     0.36      70136.29|
|  8:  2.4846 -  2.3768  1297   151  0.28  69.30   0.71     0.33      64321.54|
|  9:  2.3768 -  2.2857  1313   145  0.26  70.37   0.72     0.32      61134.88|
| 10:  2.2857 -  2.2070  1325   149  0.27  70.09   0.73     0.32      53918.51|
| 11:  2.2070 -  2.1382  1301   140  0.25  71.41   0.76     0.31      52784.05|
| 12:  2.1382 -  2.0772  1303   143  0.26  71.00   0.71     0.33      46041.53|
| 13:  2.0772 -  2.0227  1249   139  0.27  70.29   0.71     0.35      40116.68|
| 14:  2.0227 -  1.9734   354    42  0.35  63.96   0.72     0.39      31124.33|
|alpha:            min =        0.31 max =            0.79 mean =         0.47|
|beta:             min =    31124.33 max =       112559.97 mean =     71908.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.35|
|phase err.(test): min =        0.00 max =           89.96 mean =        59.57|
|-----------------------------------------------------------------------------|

============================== 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 = 16.893488             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.186   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.475466              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.997   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1494 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3904 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5050 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6518 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7633 |
|-----------------------------------------------------------------------------|
|-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 |       54.070 |
| 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 |       1.830 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    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 = 12.023)------------------------------------------|
|    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: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4993   r_free= 0.4820   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.296008                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4861   r_free= 0.4677   ksol= 0.33   Bsol= 12.08   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.59,10.81,0.00,0.00,0.00); trace/3= 8.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.289887                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.822630             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.307   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.309677              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.784   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4861      final r-factor (work) = 0.4078          |
| start r-factor (free) = 0.4677      final r-factor (free) = 0.4303          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.5272 = 13.82 * 0.50 * 6.2879 + 1.00 * 54.0698                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0971 = 13.82 * 0.50 * 6.2140 + 1.00 * 0.1505                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4078      final r-factor (work) = 0.3650          |
| start r-factor (free) = 0.4303      final r-factor (free) = 0.4215          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1527 = 1.31 * 1.00 * 6.2140 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0599 = 1.31 * 1.00 * 6.1399 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.27   14.92    None  None   None       |
|    all(noH): 2823   0      0.00    77.27   14.92    None  None   None       |
|    Sol.    : 438    0      0.00    77.27   26.32    None  None   None       |
|    Mac.    : 2385   0      0.00    65.54   12.83    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 -   7.727:  949   |   5:    38.634 -  46.360:   75        |
|      1:     7.727 -  15.453:  797   |   6:    46.360 -  54.087:   42        |
|      2:    15.453 -  23.180:  515   |   7:    54.087 -  61.814:   33        |
|      3:    23.180 -  30.907:  260   |   8:    61.814 -  69.540:    4        |
|      4:    30.907 -  38.634:  144   |   9:    69.540 -  77.267:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3650 r_free = 0.4215             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3646 r_free = 0.4223             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3646   r_free= 0.4223   ksol= 0.33   Bsol= 12.08   scale= 1.124   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.59,10.81,0.00,0.00,0.00); trace/3= 8.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.126660                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3611   r_free= 0.4179   ksol= 0.34   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.82,4.52,6.80,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.128032                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.369783              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.576148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.470  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3611      final r-factor (work) = 0.2788          |
| start r-factor (free) = 0.4179      final r-factor (free) = 0.3410          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8286 = 8.37 * 0.50 * 6.1359 + 1.00 * 0.1505                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3029 = 8.37 * 0.50 * 6.0243 + 1.00 * 0.0917                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2788      final r-factor (work) = 0.2518          |
| start r-factor (free) = 0.3410      final r-factor (free) = 0.3183          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4895 = 0.58 * 1.00 * 6.0243 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4027 = 0.58 * 1.00 * 5.8816 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.25   14.16    None  None   None       |
|    all(noH): 2823   0      0.00    88.25   14.16    None  None   None       |
|    Sol.    : 438    0      0.00    88.25   33.42    None  None   None       |
|    Mac.    : 2385   0      0.00    66.13   10.62    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 -   8.825: 1237   |   5:    44.125 -  52.950:   74        |
|      1:     8.825 -  17.650:  845   |   6:    52.950 -  61.775:   30        |
|      2:    17.650 -  26.475:  331   |   7:    61.775 -  70.600:   15        |
|      3:    26.475 -  35.300:  177   |   8:    70.600 -  79.425:    2        |
|      4:    35.300 -  44.125:  109   |   9:    79.425 -  88.250:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2518 r_free = 0.3183             target_work(ml) = 5.851         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2516 r_free = 0.3179             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2516   r_free= 0.3179   ksol= 0.34   Bsol= 50.00   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.82,4.52,6.80,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.850140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2499   r_free= 0.3170   ksol= 0.34   Bsol= 61.03   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.22,4.32,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.850833                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.238451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.467  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.404  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2499      final r-factor (work) = 0.1845          |
| start r-factor (free) = 0.3170      final r-factor (free) = 0.2398          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5621 = 4.24 * 0.50 * 5.8844 + 1.00 * 0.0917                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2251 = 4.24 * 0.50 * 5.7352 + 1.00 * 0.0709                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1845      final r-factor (work) = 0.1672          |
| start r-factor (free) = 0.2398      final r-factor (free) = 0.2237          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0222 = 0.70 * 1.00 * 5.7352 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8791 = 0.70 * 1.00 * 5.5311 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.85   14.22    None  None   None       |
|    all(noH): 2823   0      0.00    90.85   14.22    None  None   None       |
|    Sol.    : 438    0      1.52    90.85   37.53    None  None   None       |
|    Mac.    : 2385   0      0.00    70.09   9.94     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 -   9.085: 1444   |   5:    45.424 -  54.508:  103        |
|      1:     9.085 -  18.170:  723   |   6:    54.508 -  63.593:   43        |
|      2:    18.170 -  27.254:  221   |   7:    63.593 -  72.678:   16        |
|      3:    27.254 -  36.339:  130   |   8:    72.678 -  81.763:    1        |
|      4:    36.339 -  45.424:  139   |   9:    81.763 -  90.847:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1672 r_free = 0.2237             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1671 r_free = 0.2235             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2235   ksol= 0.34   Bsol= 61.03   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.22,4.32,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.496899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2222   ksol= 0.33   Bsol= 61.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.17,3.30,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.495801                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.168698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.231  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.132345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.686  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1667      final r-factor (work) = 0.1432          |
| start r-factor (free) = 0.2222      final r-factor (free) = 0.1962          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0727 = 2.17 * 0.50 * 5.5349 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9525 = 2.17 * 0.50 * 5.4360 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.1962      final r-factor (free) = 0.1898          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1685 = 1.13 * 1.00 * 5.4360 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0718 = 1.13 * 1.00 * 5.3496 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.28   14.46    None  None   None       |
|    all(noH): 2823   0      0.00    91.28   14.46    None  None   None       |
|    Sol.    : 438    0      2.70    91.28   40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    77.35   9.66     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 -   9.128: 1521   |   5:    45.641 -  54.769:   99        |
|      1:     9.128 -  18.256:  682   |   6:    54.769 -  63.897:   65        |
|      2:    18.256 -  27.385:  189   |   7:    63.897 -  73.025:   37        |
|      3:    27.385 -  36.513:  113   |   8:    73.025 -  82.153:    9        |
|      4:    36.513 -  45.641:  104   |   9:    82.153 -  91.282:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1373 r_free = 0.1898             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1372 r_free = 0.1897             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1897   ksol= 0.33   Bsol= 61.03   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.17,3.30,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.332352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1901   ksol= 0.33   Bsol= 64.31   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.01,3.14,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.333384                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.736387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.868  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.617134              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.738  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1901      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7027 = 1.74 * 0.50 * 5.3499 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6638 = 1.74 * 0.50 * 5.3063 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1288      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.5141 = 4.62 * 1.00 * 5.3063 + 1.00 * 0.0141                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.3403 = 4.62 * 1.00 * 5.2682 + 1.00 * 0.0161                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.45  14.73    None  None   None       |
|    all(noH): 2823   0      0.00    109.45  14.73    None  None   None       |
|    Sol.    : 438    0      2.81    109.45  42.42    None  None   None       |
|    Mac.    : 2385   0      0.00    91.29   9.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.945: 1754   |   5:    54.725 -  65.670:   80        |
|      1:    10.945 -  21.890:  550   |   6:    65.670 -  76.614:   39        |
|      2:    21.890 -  32.835:  161   |   7:    76.614 -  87.559:   23        |
|      3:    32.835 -  43.780:  104   |   8:    87.559 -  98.504:    9        |
|      4:    43.780 -  54.725:  101   |   9:    98.504 - 109.449:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1265 r_free = 0.1783             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1264 r_free = 0.1783             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1783   ksol= 0.33   Bsol= 64.31   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.01,3.14,0.00,0.00,0.00); trace/3= 1.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.263125                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7119 0.99   1426  157 0.0989 0.1320      5.3933      5.5715|
|  2:  4.7119 -  3.7586 0.99   1381  156 0.0877 0.1190      5.4636      5.6665|
|  3:  3.7586 -  3.2890 0.99   1356  147 0.1160 0.1667      5.5479      5.8946|
|  4:  3.2890 -  2.9908 0.99   1337  151 0.1398 0.1902      5.5519      5.7277|
|  5:  2.9908 -  2.7778 0.99   1333  151 0.1538 0.1920      5.4551       5.649|
|  6:  2.7778 -  2.6149 0.99   1325  145 0.1447 0.2331      5.3414      5.6461|
|  7:  2.6149 -  2.4846 0.99   1330  143 0.1462 0.1810      5.3081      5.4339|
|  8:  2.4846 -  2.3768 0.98   1297  151 0.1404 0.1952      5.2217      5.4591|
|  9:  2.3768 -  2.2857 0.98   1313  145 0.1404 0.2169      5.1799      5.4628|
| 10:  2.2857 -  2.2070 1.00   1325  149 0.1349 0.1855      5.0824      5.2739|
| 11:  2.2070 -  2.1382 0.98   1301  140 0.1286 0.2204      5.0598      5.4624|
| 12:  2.1382 -  2.0772 0.98   1303  143 0.1325 0.1976      4.9857      5.2478|
| 13:  2.0772 -  2.0227 0.95   1249  139 0.1250 0.1799      4.8962      5.0957|
| 14:  2.0227 -  1.9734 0.27    354   42 0.1152 0.1753      4.7895      4.9909|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7119  1426   157  0.94   9.43   0.97     0.94       7500.84|
|  2:  4.7119 -  3.7586  1381   156  0.95   8.42   1.01     1.00       9611.40|
|  3:  3.7586 -  3.2890  1356   147  0.92  12.70   1.03     1.04      12013.26|
|  4:  3.2890 -  2.9908  1337   151  0.90  15.95   1.01     0.99      12542.55|
|  5:  2.9908 -  2.7778  1333   151  0.88  18.47   1.00     0.98      10935.77|
|  6:  2.7778 -  2.6149  1325   145  0.87  19.15   0.98     0.95       9353.13|
|  7:  2.6149 -  2.4846  1330   143  0.88  18.87   0.99     0.94       8495.01|
|  8:  2.4846 -  2.3768  1297   151  0.88  18.92   0.99     0.96       7404.13|
|  9:  2.3768 -  2.2857  1313   145  0.88  18.92   0.99     0.93       6826.24|
| 10:  2.2857 -  2.2070  1325   149  0.88  18.26   0.99     0.94       5580.12|
| 11:  2.2070 -  2.1382  1301   140  0.88  18.56   0.98     0.92       5511.97|
| 12:  2.1382 -  2.0772  1303   143  0.89  18.16   0.99     0.98       4978.72|
| 13:  2.0772 -  2.0227  1249   139  0.87  19.71   0.98     0.95       4429.41|
| 14:  2.0227 -  1.9734   354    42  0.90  16.30   0.97     0.93       3409.65|
|alpha:            min =        0.92 max =            1.04 mean =         0.96|
|beta:             min =     3409.65 max =        12542.55 mean =      8034.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.47|
|phase err.(test): min =        0.00 max =           89.41 mean =        15.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1782   ksol= 0.33   Bsol= 66.27   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.79,1.27,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.263246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1782   ksol= 0.33   Bsol= 66.27   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.79,1.27,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.263246                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1846 -  4.7119 0.99   1426  157 0.0990 0.1321       5.394      5.5727|
|  2:  4.7119 -  3.7586 0.99   1381  156 0.0877 0.1191      5.4641       5.667|
|  3:  3.7586 -  3.2890 0.99   1356  147 0.1160 0.1668      5.5481      5.8953|
|  4:  3.2890 -  2.9908 0.99   1337  151 0.1398 0.1902      5.5521      5.7277|
|  5:  2.9908 -  2.7778 0.99   1333  151 0.1537 0.1918      5.4549      5.6486|
|  6:  2.7778 -  2.6149 0.99   1325  145 0.1447 0.2333      5.3415      5.6469|
|  7:  2.6149 -  2.4846 0.99   1330  143 0.1462 0.1811      5.3083      5.4343|
|  8:  2.4846 -  2.3768 0.98   1297  151 0.1404 0.1952       5.222      5.4591|
|  9:  2.3768 -  2.2857 0.98   1313  145 0.1403 0.2171        5.18      5.4638|
| 10:  2.2857 -  2.2070 1.00   1325  149 0.1349 0.1851      5.0824      5.2726|
| 11:  2.2070 -  2.1382 0.98   1301  140 0.1286 0.2202      5.0596      5.4615|
| 12:  2.1382 -  2.0772 0.98   1303  143 0.1325 0.1977      4.9851      5.2479|
| 13:  2.0772 -  2.0227 0.95   1249  139 0.1251 0.1799      4.8964      5.0955|
| 14:  2.0227 -  1.9734 0.27    354   42 0.1152 0.1749      4.7898      4.9902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1846 -  4.7119  1426   157  0.94   9.43   0.97     0.94       7514.94|
|  2:  4.7119 -  3.7586  1381   156  0.95   8.43   1.01     1.00       9625.54|
|  3:  3.7586 -  3.2890  1356   147  0.92  12.71   1.04     1.04      12025.58|
|  4:  3.2890 -  2.9908  1337   151  0.90  15.95   1.02     1.00      12545.99|
|  5:  2.9908 -  2.7778  1333   151  0.88  18.47   1.00     0.99      10939.80|
|  6:  2.7778 -  2.6149  1325   145  0.87  19.15   0.99     0.95       9353.97|
|  7:  2.6149 -  2.4846  1330   143  0.88  18.88   0.99     0.95       8500.31|
|  8:  2.4846 -  2.3768  1297   151  0.88  18.94   1.00     0.96       7410.92|
|  9:  2.3768 -  2.2857  1313   145  0.88  18.93   0.99     0.94       6834.63|
| 10:  2.2857 -  2.2070  1325   149  0.88  18.25   1.00     0.95       5575.12|
| 11:  2.2070 -  2.1382  1301   140  0.88  18.54   0.99     0.93       5502.95|
| 12:  2.1382 -  2.0772  1303   143  0.89  18.14   1.00     0.99       4970.16|
| 13:  2.0772 -  2.0227  1249   139  0.87  19.71   0.99     0.96       4427.94|
| 14:  2.0227 -  1.9734   354    42  0.90  16.31   0.98     0.94       3411.00|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3411.00 max =        12545.99 mean =      8038.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.48|
|phase err.(test): min =        0.00 max =           89.41 mean =        15.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.023)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.97    111.42  16.69    None  None   None       |
|    all(noH): 2823   0      1.97    111.42  16.69    None  None   None       |
|    Sol.    : 438    0      4.78    111.42  44.39    None  None   None       |
|    Mac.    : 2385   0      1.97    93.26   11.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.968 -  12.913: 1754   |   5:    56.692 -  67.637:   80        |
|      1:    12.913 -  23.858:  550   |   6:    67.637 -  78.582:   39        |
|      2:    23.858 -  34.803:  161   |   7:    78.582 -  89.527:   23        |
|      3:    34.803 -  45.747:  104   |   8:    89.527 - 100.472:    9        |
|      4:    45.747 -  56.692:  101   |   9:   100.472 - 111.417:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.337 - 5.237
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 320
   mapped sites are within: 0.727 - 5.237

peak=    9.910 closest distance to " CB  VAL A 230 " =    1.444
peak=    8.135 closest distance to " CG2 VAL A 296 " =    1.408
peak=    7.051 closest distance to " CG  ARG A 138 " =    1.192
peak=    6.978 closest distance to " CD2 LEU A   5 " =    1.306
peak=    6.106 closest distance to " NH1 ARG A 138 " =    1.018
peak=    5.873 closest distance to " O   HOH Z 130 " =    1.149
peak=    5.767 closest distance to " CD1AILE A 234 " =    1.072
peak=    5.504 closest distance to " CG  PRO A  54 " =    1.445
peak=    5.386 closest distance to " O   HOH Z 222 " =    1.381
peak=    5.207 closest distance to " NE2 GLN A  11 " =    1.110
peak=    5.102 closest distance to " O   HOH Z 232 " =    2.196
peak=    5.090 closest distance to " CG  LEU A 228 " =    1.210
peak=    5.067 closest distance to " CB  ASN A 148 " =    1.401
peak=    5.010 closest distance to " CB  GLN A 223 " =    1.464
peak=    4.858 closest distance to " CG  PRO A 198 " =    1.279
peak=    4.837 closest distance to " OE1 GLN A  73 " =    2.206
peak=    4.806 closest distance to " O   HOH Z 427 " =    2.453
peak=    4.763 closest distance to " CG  LEU A   5 " =    1.199
peak=    4.761 closest distance to " O   HOH Z 287 " =    2.002
peak=    4.659 closest distance to " CB  PRO A  54 " =    1.119
peak=    4.659 closest distance to " O   HOH Z 298 " =    1.896
peak=    4.628 closest distance to " O   HOH Z   7 " =    1.501
peak=    4.601 closest distance to " O   HOH Z   9 " =    2.359
peak=    4.559 closest distance to " CG  LEU A 167 " =    1.243
peak=    4.547 closest distance to " O   HOH Z  65 " =    1.225
peak=    4.546 closest distance to " O   HOH Z 369 " =    2.145
peak=    4.517 closest distance to " NH2 ARG A  56 " =    2.031
peak=    4.496 closest distance to " CB  VAL A 230 " =    1.234
peak=    4.462 closest distance to " CD  ARG A 138 " =    0.960
peak=    4.434 closest distance to " CB  ASP A 124 " =    0.876
peak=    4.412 closest distance to " O   HOH Z 425 " =    1.637
peak=    4.339 closest distance to " O   HOH Z 423 " =    1.665
peak=    4.336 closest distance to " CG  PRO A 243 " =    1.114
peak=    4.336 closest distance to " CZ  PHE A 218 " =    1.182
peak=    4.327 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.319 closest distance to " O   HOH Z  78 " =    1.751
peak=    4.294 closest distance to " CB  SER A 216 " =    1.008
peak=    4.241 closest distance to " O   PRO A 198 " =    1.344
peak=    4.240 closest distance to " CA  ALA A 160 " =    1.034
peak=    4.202 closest distance to " O   HOH Z 126 " =    2.145
peak=    4.194 closest distance to " CB  ASN A 142 " =    0.977
peak=    4.175 closest distance to " O   HOH Z 427 " =    1.171
peak=    4.160 closest distance to " O   SER A  87 " =    2.437
peak=    4.160 closest distance to " CB  SER A 210 " =    0.874
peak=    4.158 closest distance to " O   HOH Z 127 " =    1.156
peak=    4.130 closest distance to " CD2 LEU A 228 " =    1.192
peak=    4.126 closest distance to " O   HOH Z 437 " =    1.897
peak=    4.097 closest distance to " CB  SER A  63 " =    1.260
peak=    4.065 closest distance to " NH2AARG A 190 " =    1.828
peak=    4.059 closest distance to " CA  ALA A  51 " =    1.055
peak=    4.035 closest distance to " CE3 TRP A 274 " =    1.315
peak=    4.028 closest distance to " CG  PRO A 213 " =    1.271
peak=    4.022 closest distance to " CZ3 TRP A 266 " =    1.171
peak=    4.012 closest distance to " O   HOH Z 362 " =    2.290
peak=    3.971 closest distance to " NH1AARG A 145 " =    1.198
peak=    3.943 closest distance to " O   HOH Z 316 " =    3.071
peak=    3.925 closest distance to " CB  VAL A 202 " =    1.627
peak=    3.922 closest distance to " CB  ASN A  39 " =    1.021
peak=    3.918 closest distance to " CG2 THR A 221 " =    1.214
peak=    3.911 closest distance to " N   ALA A 256 " =    1.056
peak=    3.892 closest distance to " O   HOH Z  59 " =    1.796
peak=    3.891 closest distance to " O   HOH Z 303 " =    2.141
peak=    3.891 closest distance to " O   HOH Z 290 " =    1.102
peak=    3.889 closest distance to " CB  TYR A 169 " =    0.836
peak=    3.885 closest distance to " CA  ASN A 127 " =    1.169
peak=    3.882 closest distance to " CB  SER A   3 " =    1.536
peak=    3.870 closest distance to " CD  ARG A 159 " =    0.727
peak=    3.870 closest distance to " CB  MET A  40 " =    0.836
peak=    3.850 closest distance to " O   HOH Z 211 " =    1.168
peak=    3.844 closest distance to " O   HOH Z   3 " =    2.172
peak=    3.840 closest distance to " O   HOH Z 411 " =    3.171
peak=    3.826 closest distance to " CD  ARG A 269 " =    1.014
peak=    3.818 closest distance to " O   TYR A 116 " =    1.196
peak=    3.802 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.786 closest distance to " OE1 GLN A 240 " =    1.618
peak=    3.786 closest distance to " O   HOH Z  69 " =    0.960
peak=    3.785 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.784 closest distance to " O   ASP A 200 " =    1.529
peak=    3.777 closest distance to " O   HOH Z 103 " =    0.942
peak=    3.777 closest distance to " O   HOH Z 145 " =    1.913
peak=    3.767 closest distance to " O   HOH Z 167 " =    1.756
peak=    3.767 closest distance to " O   HOH Z 422 " =    2.642
peak=    3.766 closest distance to " O   HOH Z 417 " =    1.151
peak=    3.757 closest distance to " CE  LYS A  76 " =    0.925
peak=    3.751 closest distance to " O   HOH Z 126 " =    1.607
peak=    3.741 closest distance to " CG1 ILE A 151 " =    1.130
peak=    3.735 closest distance to " CE3 TRP A 150 " =    1.152
peak=    3.725 closest distance to " CB  GLU A 277 " =    3.679
peak=    3.719 closest distance to " CA  ILE A 234 " =    1.056
peak=    3.718 closest distance to " CB  GLN A  89 " =    1.257
peak=    3.717 closest distance to " CB  VAL A 265 " =    1.265
peak=    3.705 closest distance to " CD  LYS A  76 " =    1.836
peak=    3.703 closest distance to " CB  THR A  52 " =    1.001
peak=    3.691 closest distance to " O   HOH Z 361 " =    1.310
peak=    3.688 closest distance to " O   HOH Z 392 " =    1.193
peak=    3.688 closest distance to " CB  GLU A 128 " =    1.058
peak=    3.682 closest distance to " O   HOH Z 258 " =    1.202
peak=    3.669 closest distance to " CB  LEU A 237 " =    0.894
peak=    3.656 closest distance to " CD1 LEU A 300 " =    1.113
peak=    3.652 closest distance to " O   HOH Z 255 " =    0.995
peak=    3.648 closest distance to " CD1 ILE A  33 " =    1.896
peak=    3.644 closest distance to " CA  MET A 105 " =    0.945
peak=    3.640 closest distance to " O   HOH Z 143 " =    1.448
peak=    3.640 closest distance to " CB  PRO A  90 " =    1.156
peak=    3.639 closest distance to " CA  VAL A 125 " =    1.177
peak=    3.638 closest distance to " CG2 ILE A 234 " =    0.884
peak=    3.635 closest distance to " O   HOH Z 272 " =    1.826
peak=    3.633 closest distance to " O   HOH Z 389 " =    1.413
peak=    3.631 closest distance to " ND2BASN A 224 " =    0.910
peak=    3.629 closest distance to " O   HOH Z 148 " =    2.408
peak=    3.628 closest distance to " CA  TYR A  30 " =    0.986
peak=    3.625 closest distance to " O   HOH Z 329 " =    4.076
peak=    3.620 closest distance to " O   HOH Z 365 " =    3.124
peak=    3.620 closest distance to " O   HOH Z   1 " =    1.798
peak=    3.618 closest distance to " CB  ARG A 138 " =    1.352
peak=    3.617 closest distance to " O   HOH Z 368 " =    3.498
peak=    3.612 closest distance to " O   HOH Z  63 " =    1.253
peak=    3.610 closest distance to " O   HOH Z 153 " =    3.663
peak=    3.607 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.599 closest distance to " O   HOH Z 133 " =    2.872
peak=    3.589 closest distance to " O   HOH Z 359 " =    1.467
peak=    3.588 closest distance to " CA  ARG A 195 " =    1.260
peak=    3.584 closest distance to " N   SER A 271 " =    0.995
peak=    3.583 closest distance to " O   HOH Z 265 " =    1.804
peak=    3.583 closest distance to " O   HOH Z 214 " =    2.472
peak=    3.580 closest distance to " O   HOH Z 373 " =    1.572
peak=    3.580 closest distance to " CG BARG A 275 " =    1.298
peak=    3.579 closest distance to " CG2 VAL A 257 " =    0.898
peak=    3.577 closest distance to " CA  ARG A 156 " =    1.069
peak=    3.576 closest distance to " O   HOH Z  57 " =    1.930
peak=    3.574 closest distance to " O   HOH Z 122 " =    2.007
peak=    3.572 closest distance to " CE  MET A  93 " =    1.527
peak=    3.568 closest distance to " CB  TRP A 179 " =    1.467
peak=    3.566 closest distance to " ND2 ASN A 187 " =    1.725
peak=    3.563 closest distance to " CE3 TRP A  85 " =    1.081
peak=    3.562 closest distance to " CB AVAL A  41 " =    1.238
peak=    3.556 closest distance to " CA  GLY A 267 " =    1.222
peak=    3.552 closest distance to " O   HOH Z 218 " =    1.526
peak=    3.550 closest distance to " CD  ARG A  66 " =    2.392
peak=    3.549 closest distance to " O   HOH Z 225 " =    1.610
peak=    3.545 closest distance to " CA  ARG A  36 " =    1.107
peak=    3.543 closest distance to " O   HOH Z 380 " =    1.801
peak=    3.540 closest distance to " CA  ARG A 102 " =    1.117
peak=    3.538 closest distance to " CB  LYS A 117 " =    1.220
peak=    3.535 closest distance to " NH2AARG A 145 " =    1.101
peak=    3.535 closest distance to " CZ3 TRP A  92 " =    1.163
peak=    3.534 closest distance to " O   HOH Z  20 " =    1.621
peak=    3.533 closest distance to " CB  SER A 212 " =    1.384
peak=    3.518 closest distance to " CB  ARG A 275 " =    1.066
peak=    3.508 closest distance to " OE2 GLU A   2 " =    2.035
peak=    3.506 closest distance to " CB  ALA A 114 " =    0.805
peak=    3.505 closest distance to " O   HOH Z  68 " =    2.179
peak=    3.502 closest distance to " CG  GLN A  58 " =    1.245
peak=    3.500 closest distance to " N   GLY A 133 " =    3.915
peak=    3.496 closest distance to " O   HOH Z  78 " =    1.984
peak=    3.491 closest distance to " CB  ALA A 160 " =    1.559
peak=    3.491 closest distance to " CG2 ILE A  20 " =    1.578
peak=    3.482 closest distance to " O   HOH Z 158 " =    2.935
peak=    3.478 closest distance to " CZ  PHE A  38 " =    1.294
peak=    3.475 closest distance to " O   HOH Z   2 " =    1.568
peak=    3.472 closest distance to " O   HOH Z 109 " =    2.676
peak=    3.471 closest distance to " CB  ARG A  79 " =    1.403
peak=    3.466 closest distance to " CB  ARG A 190 " =    1.446
peak=    3.465 closest distance to " O   HOH Z 421 " =    2.183
peak=    3.464 closest distance to " NZ  LYS A 117 " =    3.036
peak=    3.451 closest distance to " O   HOH Z 193 " =    1.720
peak=    3.447 closest distance to " N   PHE A 130 " =    1.318
peak=    3.446 closest distance to " O   HOH Z  80 " =    1.578
peak=    3.446 closest distance to " CB  HIS A 108 " =    0.860
peak=    3.443 closest distance to " O   HOH Z 368 " =    1.983
peak=    3.442 closest distance to " CB  LEU A 228 " =    1.280
peak=    3.435 closest distance to " CB  LEU A 143 " =    1.203
peak=    3.431 closest distance to " O   HOH Z 406 " =    1.409
peak=    3.428 closest distance to " N   CYS A 260 " =    0.849
peak=    3.426 closest distance to " CA  VAL A 296 " =    1.077
peak=    3.422 closest distance to " NE2 HIS A 207 " =    1.105
peak=    3.422 closest distance to " OG  SER A  62 " =    2.731
peak=    3.421 closest distance to " O   HOH Z 325 " =    2.198
peak=    3.421 closest distance to " O   HOH Z 207 " =    0.919
peak=    3.420 closest distance to " OG1 THR A 157 " =    1.109
peak=    3.420 closest distance to " CA  ILE A 263 " =    1.005
peak=    3.410 closest distance to " ND2 ASN A 249 " =    0.842
peak=    3.408 closest distance to " O  BHOH Z  74 " =    1.224
peak=    3.407 closest distance to " O   HOH Z  88 " =    3.579
peak=    3.405 closest distance to " CE  LYS A  48 " =    1.097
peak=    3.394 closest distance to " O   HOH Z  69 " =    2.032
peak=    3.393 closest distance to " CB  SER A 273 " =    0.932
peak=    3.393 closest distance to " CB  VAL A 250 " =    1.092
peak=    3.391 closest distance to " CB  TYR A  30 " =    1.383
peak=    3.386 closest distance to " O   HOH Z  30 " =    1.804
peak=    3.383 closest distance to " O   HOH Z 236 " =    1.596
peak=    3.381 closest distance to " O   HOH Z 343 " =    3.279
peak=    3.380 closest distance to " O   THR A 294 " =    1.070
peak=    3.379 closest distance to " CB  ASP A 107 " =    1.154
peak=    3.373 closest distance to " O   HOH Z 303 " =    2.582
peak=    3.366 closest distance to " CD1 LEU A   5 " =    1.354
peak=    3.362 closest distance to " O   HOH Z 195 " =    1.390
peak=    3.361 closest distance to " O   HOH Z 410 " =    1.602
peak=    3.356 closest distance to " O   HOH Z 368 " =    4.225
peak=    3.354 closest distance to " OE2 GLU A  53 " =    1.855
peak=    3.354 closest distance to " O   HOH Z 403 " =    1.422
peak=    3.350 closest distance to " CB  TRP A 150 " =    1.082
peak=    3.347 closest distance to " CD BLYS A 290 " =    1.036
peak=    3.346 closest distance to " CG BARG A 102 " =    1.970
peak=    3.346 closest distance to " CE1 HIS A  81 " =    1.949
peak=    3.345 closest distance to " O   HOH Z 281 " =    2.342
peak=    3.343 closest distance to " CE1 TYR A 186 " =    1.304
peak=    3.338 closest distance to " CG  GLN A  89 " =    1.571
peak=    3.336 closest distance to " O   HOH Z  39 " =    0.967
peak=    3.330 closest distance to " CB  THR A 235 " =    1.130
peak=    3.329 closest distance to " NH1BARG A 145 " =    1.274
peak=    3.327 closest distance to " CB  SER A  62 " =    1.020
peak=    3.326 closest distance to " O   ASP A 124 " =    1.085
peak=    3.321 closest distance to " CB  MET A  47 " =    1.080
peak=    3.317 closest distance to " O   ASN A 209 " =    1.543
peak=    3.314 closest distance to " O   HOH Z  61 " =    1.665
peak=    3.313 closest distance to " NE2 GLN A  58 " =    4.308
peak=    3.309 closest distance to " CB  ALA A  10 " =    0.932
peak=    3.305 closest distance to " N   TYR A  15 " =    1.096
peak=    3.301 closest distance to " O   HOH Z 385 " =    3.814
peak=    3.300 closest distance to " O   HOH Z 248 " =    1.065
peak=    3.295 closest distance to " O   HOH Z  71 " =    1.263
peak=    3.293 closest distance to " O   HOH Z 273 " =    2.882
peak=    3.292 closest distance to " CA  LEU A 101 " =    1.316
peak=    3.291 closest distance to " CB  ASN A 110 " =    1.128
peak=    3.288 closest distance to " OG1 THR A 264 " =    0.758
peak=    3.288 closest distance to " O   HOH Z 176 " =    1.337
peak=    3.287 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.285 closest distance to " O   HOH Z 346 " =    1.572
peak=    3.285 closest distance to " O   GLY A 302 " =    2.223
peak=    3.281 closest distance to " CB  LEU A 300 " =    0.923
peak=    3.278 closest distance to " O   HOH Z 184 " =    1.501
peak=    3.277 closest distance to " CA  ALA A 295 " =    1.122
peak=    3.276 closest distance to " CG  GLN A  77 " =    0.897
peak=    3.276 closest distance to " CA  ALA A 158 " =    1.191
peak=    3.274 closest distance to " CG  GLN A  88 " =    1.130
peak=    3.271 closest distance to " CB  PHE A  16 " =    1.084
peak=    3.270 closest distance to " O   HOH Z  10 " =    1.749
peak=    3.269 closest distance to " O   PHE A 192 " =    1.365
peak=    3.260 closest distance to " CA  ILE A 106 " =    0.821
peak=    3.260 closest distance to " C   GLN A  73 " =    1.058
peak=    3.260 closest distance to " CG1AVAL A 121 " =    0.837
peak=    3.258 closest distance to " CD  GLN A  77 " =    1.222
peak=    3.253 closest distance to " CA  ARG A 139 " =    0.966
peak=    3.251 closest distance to " O   HOH Z  53 " =    2.400
peak=    3.246 closest distance to " CD  ARG A  24 " =    1.035
peak=    3.245 closest distance to " O   HOH Z 188 " =    2.985
peak=    3.244 closest distance to " O   HOH Z 110 " =    1.653
peak=    3.242 closest distance to " O   HOH Z 371 " =    2.852
peak=    3.240 closest distance to " CD1 LEU A 281 " =    0.921
peak=    3.239 closest distance to " CA  ALA A 291 " =    0.896
peak=    3.237 closest distance to " O   HOH Z  88 " =    2.957
peak=    3.237 closest distance to " O   HOH Z 258 " =    1.302
peak=    3.230 closest distance to " C   ALA A 299 " =    0.933
peak=    3.228 closest distance to " CB  ALA A 104 " =    0.767
peak=    3.221 closest distance to " CB  GLN A  88 " =    1.358
peak=    3.219 closest distance to " CB  SER A  26 " =    1.653
peak=    3.217 closest distance to " O   HOH Z 115 " =    1.458
peak=    3.217 closest distance to " CB  ALA A  43 " =    0.819
peak=    3.215 closest distance to " O   HOH Z  27 " =    1.047
peak=    3.208 closest distance to " CD1 ILE A 199 " =    0.984
peak=    3.208 closest distance to " O  BHOH Z 338 " =    2.402
peak=    3.208 closest distance to " O   HOH Z 172 " =    5.237
peak=    3.202 closest distance to " NE1 TRP A  92 " =    1.748
peak=    3.201 closest distance to " O   MET A 105 " =    1.841
peak=    3.197 closest distance to " O   HOH Z 328 " =    1.588
peak=    3.190 closest distance to " NH2AARG A 145 " =    2.409
peak=    3.187 closest distance to " N   ASN A 127 " =    1.337
peak=    3.186 closest distance to " CG  ARG A 159 " =    0.977
peak=    3.184 closest distance to " O   HOH Z 425 " =    2.125
peak=    3.181 closest distance to " O   HOH Z 148 " =    1.503
peak=    3.177 closest distance to " O   THR A 182 " =    1.476
peak=    3.176 closest distance to " NE AARG A 275 " =    1.396
peak=    3.173 closest distance to " N   TYR A 247 " =    1.200
peak=    3.172 closest distance to " O   HOH Z   4 " =    1.487
peak=    3.171 closest distance to " CD  ARG A 195 " =    3.445
peak=    3.169 closest distance to " CD  GLU A 152 " =    0.756
peak=    3.168 closest distance to " CG1 VAL A 153 " =    0.975
peak=    3.164 closest distance to " N   GLU A   2 " =    1.537
peak=    3.163 closest distance to " O   THR A 251 " =    1.172
peak=    3.162 closest distance to " OG  SER A  62 " =    3.125
peak=    3.159 closest distance to " CA  ASN A 217 " =    1.185
peak=    3.157 closest distance to " O   PHE A  61 " =    1.354
peak=    3.154 closest distance to " OE1 GLU A 236 " =    1.369
peak=    3.152 closest distance to " O   HOH Z 128 " =    2.146
peak=    3.149 closest distance to " O   PRO A  90 " =    1.610
peak=    3.149 closest distance to " CZ3 TRP A 177 " =    1.084
peak=    3.145 closest distance to " CA  THR A 221 " =    0.945
peak=    3.142 closest distance to " CD  GLU A 236 " =    1.092
peak=    3.142 closest distance to " CG2 ILE A 120 " =    1.300
peak=    3.141 closest distance to " CA  ALA A 129 " =    1.321
peak=    3.137 closest distance to " O   HOH Z 132 " =    2.475
peak=    3.136 closest distance to " O   HOH Z 172 " =    2.842
peak=    3.134 closest distance to " N   SER A  97 " =    0.800
peak=    3.133 closest distance to " CG1 VAL A 257 " =    1.289
peak=    3.131 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.128 closest distance to " CA  SER A 210 " =    1.435
peak=    3.125 closest distance to " CD2 LEU A 297 " =    0.917
peak=    3.120 closest distance to " O   HOH Z 218 " =    1.857
peak=    3.119 closest distance to " CB  SER A  22 " =    0.988
peak=    3.115 closest distance to " OG  SER A 135 " =    1.331
peak=    3.108 closest distance to " O   THR A 220 " =    1.333
peak=    3.107 closest distance to " CA  THR A 264 " =    0.784
peak=    3.105 closest distance to " CB  ASN A 215 " =    1.283
peak=    3.104 closest distance to " OD1 ASN A  69 " =    2.606
peak=    3.103 closest distance to " CD1 LEU A 167 " =    1.218
peak=    3.095 closest distance to " CA  ALA A 180 " =    1.291
peak=    3.095 closest distance to " CE2 PHE A  16 " =    0.980
peak=    3.090 closest distance to " O   HOH Z 251 " =    1.663
peak=    3.086 closest distance to " OG ASER A 212 " =    1.814
peak=    3.086 closest distance to " OD1 ASN A  60 " =    1.035
peak=    3.080 closest distance to " O   HOH Z 394 " =    3.527
peak=    3.076 closest distance to " CD  LYS A 166 " =    1.393
peak=    3.067 closest distance to " O   HOH Z 238 " =    1.560
peak=    3.051 closest distance to " CB  GLU A 175 " =    0.990
peak=    3.043 closest distance to " CA  ASP A 149 " =    1.312
peak=    3.025 closest distance to " OE2 GLU A  53 " =    1.143

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 230         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 5.527
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 227 from: 230
   mapped sites are within: 0.754 - 5.527

peak=   -5.109 closest distance to " CD  ARG A 138 " =    1.196
peak=   -4.397 closest distance to " CZ2 TRP A  92 " =    2.871
peak=   -4.325 closest distance to " CD  ARG A  14 " =    3.158
peak=   -4.294 closest distance to " OG BSER A 134 " =    1.525
peak=   -4.285 closest distance to " O   PRO A 198 " =    1.240
peak=   -4.244 closest distance to " CG2 VAL A 202 " =    2.701
peak=   -4.226 closest distance to " CG2 VAL A 230 " =    0.867
peak=   -4.158 closest distance to " CB  ASP A  27 " =    2.487
peak=   -4.157 closest distance to " CD  ARG A 156 " =    1.986
peak=   -4.076 closest distance to " CB  VAL A 230 " =    1.055
peak=   -4.069 closest distance to " CB  PRO A 243 " =    2.650
peak=   -4.021 closest distance to " O   HOH Z  39 " =    0.930
peak=   -4.006 closest distance to " O   HOH Z 389 " =    1.496
peak=   -3.932 closest distance to " O   HOH Z 411 " =    5.198
peak=   -3.910 closest distance to " CG  ARG A 219 " =    2.467
peak=   -3.885 closest distance to " O   HOH Z 131 " =    4.007
peak=   -3.882 closest distance to " O   HOH Z 275 " =    1.824
peak=   -3.826 closest distance to " OG  SER A  97 " =    2.278
peak=   -3.791 closest distance to " C   HIS A 108 " =    1.197
peak=   -3.783 closest distance to " N   THR A 157 " =    1.568
peak=   -3.776 closest distance to " CD2 TYR A 293 " =    1.891
peak=   -3.763 closest distance to " O   HOH Z 231 " =    1.952
peak=   -3.735 closest distance to " CB  GLN A  55 " =    1.200
peak=   -3.718 closest distance to " CB  PHE A 130 " =    1.225
peak=   -3.706 closest distance to " O   HOH Z 147 " =    1.975
peak=   -3.659 closest distance to " CG2 THR A  52 " =    3.148
peak=   -3.652 closest distance to " SD  MET A 105 " =    1.010
peak=   -3.651 closest distance to " CD2 LEU A 237 " =    2.802
peak=   -3.637 closest distance to " CD2 LEU A   5 " =    0.944
peak=   -3.637 closest distance to " CG1 VAL A 112 " =    2.582
peak=   -3.635 closest distance to " O   PRO A 163 " =    1.813
peak=   -3.630 closest distance to " O   HOH Z   9 " =    1.982
peak=   -3.629 closest distance to " CB  TRP A  85 " =    2.420
peak=   -3.625 closest distance to " CB  ALA A  43 " =    2.737
peak=   -3.616 closest distance to " CG2 VAL A 296 " =    1.700
peak=   -3.613 closest distance to " O   HOH Z 394 " =    1.591
peak=   -3.612 closest distance to " O   GLY A  17 " =    1.197
peak=   -3.601 closest distance to " CD1 LEU A 101 " =    2.247
peak=   -3.593 closest distance to " O   HOH Z  52 " =    1.870
peak=   -3.585 closest distance to " CB  ALA A   9 " =    2.549
peak=   -3.580 closest distance to " O   HOH Z 100 " =    1.078
peak=   -3.567 closest distance to " CG2 THR A 178 " =    2.365
peak=   -3.560 closest distance to " OG  SER A  87 " =    1.466
peak=   -3.560 closest distance to " CA  HIS A 207 " =    1.098
peak=   -3.558 closest distance to " CE2 TYR A  30 " =    2.653
peak=   -3.557 closest distance to " O   HOH Z 286 " =    1.616
peak=   -3.554 closest distance to " OG  SER A  28 " =    2.148
peak=   -3.553 closest distance to " O   HOH Z 134 " =    1.786
peak=   -3.553 closest distance to " CD2 HIS A 207 " =    2.269
peak=   -3.549 closest distance to " OG ASER A 134 " =    1.222
peak=   -3.549 closest distance to " O   HOH Z  11 " =    1.728
peak=   -3.540 closest distance to " O   ALA A  84 " =    1.737
peak=   -3.532 closest distance to " OG  SER A  62 " =    4.312
peak=   -3.531 closest distance to " CG  ARG A 138 " =    0.775
peak=   -3.529 closest distance to " CG2BVAL A  41 " =    2.627
peak=   -3.528 closest distance to " O   HOH Z  60 " =    1.710
peak=   -3.528 closest distance to " O   HOH Z  69 " =    1.912
peak=   -3.520 closest distance to " O   HOH Z 364 " =    2.723
peak=   -3.518 closest distance to " O   HOH Z 219 " =    4.960
peak=   -3.516 closest distance to " O   HOH Z 350 " =    1.682
peak=   -3.512 closest distance to " OH  TYR A 247 " =    1.650
peak=   -3.510 closest distance to " O   HOH Z 276 " =    1.230
peak=   -3.496 closest distance to " ND2 ASN A 187 " =    1.488
peak=   -3.493 closest distance to " O   HOH Z 201 " =    1.669
peak=   -3.492 closest distance to " O   HOH Z 216 " =    1.457
peak=   -3.491 closest distance to " O   HOH Z 185 " =    2.210
peak=   -3.490 closest distance to " N   ASP A 270 " =    1.405
peak=   -3.486 closest distance to " O   HOH Z 183 " =    1.411
peak=   -3.483 closest distance to " O   HOH Z 292 " =    1.636
peak=   -3.482 closest distance to " O   HOH Z 359 " =    3.188
peak=   -3.476 closest distance to " O   SER A  22 " =    2.679
peak=   -3.474 closest distance to " O   HOH Z 295 " =    1.729
peak=   -3.472 closest distance to " C   GLU A 236 " =    0.955
peak=   -3.470 closest distance to " CG  TRP A 266 " =    1.693
peak=   -3.469 closest distance to " O   HOH Z 126 " =    1.781
peak=   -3.469 closest distance to " O   HOH Z 111 " =    1.675
peak=   -3.466 closest distance to " CD  LYS A 166 " =    2.505
peak=   -3.465 closest distance to " CB  ALA A 227 " =    2.440
peak=   -3.464 closest distance to " CB  ALA A   7 " =    2.059
peak=   -3.461 closest distance to " O   PHE A 218 " =    1.438
peak=   -3.460 closest distance to " CG2 ILE A 151 " =    2.611
peak=   -3.457 closest distance to " N   ALA A  43 " =    2.494
peak=   -3.454 closest distance to " O   ILE A  49 " =    1.743
peak=   -3.453 closest distance to " O   HOH Z 198 " =    2.027
peak=   -3.443 closest distance to " CD2 TYR A 116 " =    2.350
peak=   -3.443 closest distance to " OE1 GLU A 277 " =    2.179
peak=   -3.440 closest distance to " OE1 GLN A  88 " =    1.134
peak=   -3.439 closest distance to " CZ2 TRP A 274 " =    0.965
peak=   -3.434 closest distance to " CA  ASN A 127 " =    1.084
peak=   -3.433 closest distance to " CB  PRO A 163 " =    2.318
peak=   -3.433 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.429 closest distance to " O   HOH Z 368 " =    1.658
peak=   -3.428 closest distance to " CG2AVAL A  41 " =    2.825
peak=   -3.418 closest distance to " O   HOH Z 318 " =    2.051
peak=   -3.412 closest distance to " O   HOH Z 351 " =    1.650
peak=   -3.409 closest distance to " O   HOH Z 111 " =    4.659
peak=   -3.408 closest distance to " CE3 TRP A 150 " =    2.514
peak=   -3.408 closest distance to " O   HOH Z 102 " =    1.585
peak=   -3.408 closest distance to " O   HOH Z  43 " =    1.764
peak=   -3.406 closest distance to " ND2 ASN A 285 " =    2.170
peak=   -3.403 closest distance to " O   ARG A 145 " =    1.334
peak=   -3.402 closest distance to " CD1 LEU A 255 " =    2.924
peak=   -3.402 closest distance to " CB  TYR A  15 " =    2.205
peak=   -3.400 closest distance to " O   HOH Z 359 " =    1.635
peak=   -3.384 closest distance to " O   ALA A  10 " =    1.625
peak=   -3.383 closest distance to " CZ  PHE A 130 " =    1.071
peak=   -3.382 closest distance to " O   HOH Z 377 " =    1.911
peak=   -3.380 closest distance to " CD  GLN A  77 " =    1.449
peak=   -3.379 closest distance to " CG  LEU A   5 " =    0.972
peak=   -3.374 closest distance to " CA  ALA A 158 " =    1.293
peak=   -3.370 closest distance to " CA  GLY A 241 " =    3.061
peak=   -3.369 closest distance to " O   HOH Z  73 " =    2.227
peak=   -3.369 closest distance to " NE2 GLN A 223 " =    1.675
peak=   -3.368 closest distance to " C   MET A 188 " =    1.464
peak=   -3.359 closest distance to " CE BMET A  47 " =    1.252
peak=   -3.357 closest distance to " O   HOH Z  44 " =    1.021
peak=   -3.354 closest distance to " CG1 VAL A 250 " =    2.586
peak=   -3.352 closest distance to " O   HOH Z 177 " =    2.630
peak=   -3.351 closest distance to " O   TRP A  70 " =    1.444
peak=   -3.351 closest distance to " CG  LEU A 281 " =    1.869
peak=   -3.348 closest distance to " O   HOH Z 298 " =    2.811
peak=   -3.346 closest distance to " OE1 GLN A 183 " =    1.652
peak=   -3.345 closest distance to " OE2 GLU A 152 " =    1.233
peak=   -3.344 closest distance to " NH2 ARG A 219 " =    1.752
peak=   -3.340 closest distance to " O   ASP A  27 " =    1.747
peak=   -3.337 closest distance to " O   HOH Z 427 " =    1.785
peak=   -3.331 closest distance to " O   SER A 135 " =    1.416
peak=   -3.325 closest distance to " CG1 VAL A  78 " =    2.465
peak=   -3.324 closest distance to " C   ASN A 148 " =    1.698
peak=   -3.323 closest distance to " CA  TYR A  68 " =    1.122
peak=   -3.322 closest distance to " O   HOH Z 112 " =    1.326
peak=   -3.318 closest distance to " O   HOH Z 143 " =    1.356
peak=   -3.318 closest distance to " CB  VAL A 189 " =    2.341
peak=   -3.314 closest distance to " C   ASN A 285 " =    2.326
peak=   -3.304 closest distance to " NH2AARG A 275 " =    5.384
peak=   -3.303 closest distance to " O   HOH Z 134 " =    4.419
peak=   -3.303 closest distance to " O   HOH Z 368 " =    1.534
peak=   -3.302 closest distance to " O   HOH Z 238 " =    0.843
peak=   -3.301 closest distance to " CB  HIS A  81 " =    1.040
peak=   -3.299 closest distance to " NE1 TRP A 177 " =    2.087
peak=   -3.297 closest distance to " CG1BVAL A  72 " =    2.268
peak=   -3.296 closest distance to " CG1 VAL A 112 " =    2.935
peak=   -3.294 closest distance to " CG  PRO A 163 " =    2.483
peak=   -3.294 closest distance to " CB  ALA A 248 " =    2.130
peak=   -3.290 closest distance to " O   HOH Z 139 " =    0.947
peak=   -3.289 closest distance to " CD  LYS A 289 " =    2.323
peak=   -3.288 closest distance to " C   LEU A 222 " =    1.144
peak=   -3.288 closest distance to " NH2 ARG A  79 " =    2.203
peak=   -3.287 closest distance to " N   ALA A 244 " =    1.294
peak=   -3.286 closest distance to " CD  PRO A 213 " =    2.117
peak=   -3.286 closest distance to " O   HOH Z 256 " =    1.418
peak=   -3.285 closest distance to " N   GLN A 223 " =    2.026
peak=   -3.284 closest distance to " CG  ARG A 259 " =    2.434
peak=   -3.282 closest distance to " O   HOH Z 389 " =    2.278
peak=   -3.281 closest distance to " CG2BVAL A  72 " =    2.329
peak=   -3.280 closest distance to " CG2 ILE A  20 " =    2.704
peak=   -3.278 closest distance to " O   SER A 271 " =    2.099
peak=   -3.276 closest distance to " CE3 TRP A  70 " =    1.580
peak=   -3.276 closest distance to " O   HOH Z  68 " =    1.364
peak=   -3.274 closest distance to " CE2 PHE A 218 " =    2.482
peak=   -3.268 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.267 closest distance to " O   HOH Z 243 " =    2.042
peak=   -3.263 closest distance to " O   HOH Z  53 " =    1.658
peak=   -3.261 closest distance to " O   HOH Z 426 " =    1.641
peak=   -3.257 closest distance to " O   HOH Z 186 " =    1.332
peak=   -3.257 closest distance to " ND2 ASN A 249 " =    2.483
peak=   -3.253 closest distance to " O   HOH Z 166 " =    1.927
peak=   -3.238 closest distance to " O   HOH Z 407 " =    3.015
peak=   -3.233 closest distance to " ND2 ASN A 173 " =    1.828
peak=   -3.226 closest distance to " CB  PRO A 213 " =    2.249
peak=   -3.225 closest distance to " O   HOH Z 163 " =    2.061
peak=   -3.217 closest distance to " CE1 PHE A 218 " =    1.511
peak=   -3.217 closest distance to " CG  GLN A  58 " =    1.258
peak=   -3.213 closest distance to " O   GLY A 203 " =    2.598
peak=   -3.212 closest distance to " O   HOH Z  52 " =    1.976
peak=   -3.209 closest distance to " OH  TYR A 172 " =    1.855
peak=   -3.207 closest distance to " OE1 GLN A 278 " =    1.222
peak=   -3.207 closest distance to " OD2 ASP A  50 " =    1.676
peak=   -3.206 closest distance to " O   HOH Z  24 " =    1.242
peak=   -3.203 closest distance to " ND2 ASN A  39 " =    1.783
peak=   -3.203 closest distance to " CG  LEU A 282 " =    2.520
peak=   -3.202 closest distance to " OG  SER A 245 " =    1.436
peak=   -3.202 closest distance to " CB  CYS A 201 " =    2.124
peak=   -3.199 closest distance to " CG1 VAL A 197 " =    2.545
peak=   -3.195 closest distance to " ND2 ASN A  45 " =    1.212
peak=   -3.189 closest distance to " CB  PRO A  54 " =    2.549
peak=   -3.189 closest distance to " O   HOH Z 191 " =    5.527
peak=   -3.188 closest distance to " O   HOH Z  52 " =    0.898
peak=   -3.186 closest distance to " N   ASP A 191 " =    1.162
peak=   -3.184 closest distance to " O   HOH Z 357 " =    2.108
peak=   -3.180 closest distance to " OD1 ASP A 191 " =    1.826
peak=   -3.174 closest distance to " O   HOH Z 105 " =    2.019
peak=   -3.170 closest distance to " NZ  LYS A 166 " =    1.256
peak=   -3.170 closest distance to " O   HOH Z 108 " =    1.467
peak=   -3.169 closest distance to " CA  GLY A  98 " =    1.939
peak=   -3.163 closest distance to " CD1 LEU A 282 " =    2.709
peak=   -3.160 closest distance to " O   HOH Z 165 " =    2.205
peak=   -3.159 closest distance to " CE2 TRP A  70 " =    2.438
peak=   -3.158 closest distance to " CB  ASP A 132 " =    2.379
peak=   -3.156 closest distance to " OG  SER A  63 " =    1.242
peak=   -3.153 closest distance to " CB  TYR A  68 " =    1.205
peak=   -3.146 closest distance to " CD  GLU A  44 " =    1.054
peak=   -3.143 closest distance to " O   ASP A 238 " =    1.605
peak=   -3.131 closest distance to " O   HOH Z 281 " =    2.599
peak=   -3.124 closest distance to " CG  GLN A  88 " =    0.754
peak=   -3.122 closest distance to " CD1 PHE A  61 " =    2.978
peak=   -3.121 closest distance to " CE  MET A 188 " =    2.265
peak=   -3.117 closest distance to " CA  SER A 135 " =    1.403
peak=   -3.109 closest distance to " O   CYS A 260 " =    1.479
peak=   -3.107 closest distance to " O   HOH Z 193 " =    1.305
peak=   -3.106 closest distance to " O   PRO A 243 " =    2.506
peak=   -3.101 closest distance to " O   HOH Z  52 " =    0.993
peak=   -3.101 closest distance to " O   TYR A 186 " =    1.732
peak=   -3.100 closest distance to " C   ASN A 176 " =    1.348
peak=   -3.098 closest distance to " CB  ALA A 291 " =    2.046
peak=   -3.098 closest distance to " O   GLN A 240 " =    2.063
peak=   -3.098 closest distance to " OG BSER A 134 " =    1.991
peak=   -3.097 closest distance to " O   ALA A  51 " =    1.402
peak=   -3.086 closest distance to " O   HOH Z 251 " =    4.795
peak=   -3.073 closest distance to " CD2 PHE A  16 " =    2.509
peak=   -3.073 closest distance to " O   HOH Z 144 " =    0.987
peak=   -3.070 closest distance to " NE2 GLN A  77 " =    1.468
peak=   -3.064 closest distance to " CG2 VAL A 189 " =    1.975
peak=   -3.061 closest distance to " O   HOH Z 200 " =    3.421
peak=   -3.055 closest distance to " CB  GLN A  11 " =    1.661
peak=   -3.047 closest distance to " N   VAL A 232 " =    2.135
peak=   -3.034 closest distance to " OE1 GLN A 223 " =    2.052

================= 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    :  0.4934 0.4796   6.294688e+00   6.274969e+00
   1_bss:  0.4861 0.4677   6.289887e+00   6.269052e+00
   1_xyz:  0.4078 0.4303   6.192911e+00   6.216449e+00
   1_adp:  0.3650 0.4215   6.127064e+00   6.206452e+00
   1_occ:  0.3646 0.4223   6.126660e+00   6.207130e+00
   2_bss:  0.3611 0.4179   6.128032e+00   6.206244e+00
   2_xyz:  0.2788 0.3410   5.920882e+00   6.062172e+00
   2_adp:  0.2518 0.3183   5.850777e+00   6.008125e+00
   2_occ:  0.2516 0.3179   5.850140e+00   6.007364e+00
   3_bss:  0.2499 0.3170   5.850833e+00   6.008341e+00
   3_xyz:  0.1845 0.2398   5.576809e+00   5.778873e+00
   3_adp:  0.1672 0.2237   5.497455e+00   5.715758e+00
   3_occ:  0.1671 0.2235   5.496899e+00   5.715492e+00
   4_bss:  0.1667 0.2222   5.495801e+00   5.713394e+00
   4_xyz:  0.1432 0.1962   5.368654e+00   5.594937e+00
   4_adp:  0.1373 0.1898   5.332823e+00   5.558775e+00
   4_occ:  0.1372 0.1897   5.332352e+00   5.558301e+00
   5_bss:  0.1377 0.1901   5.333384e+00   5.558494e+00
   5_xyz:  0.1288 0.1795   5.276143e+00   5.508577e+00
   5_adp:  0.1265 0.1783   5.263355e+00   5.499998e+00
   5_occ:  0.1264 0.1783   5.263125e+00   5.499826e+00
   5_bss:  0.1264 0.1782   5.263246e+00   5.499964e+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:  0.330  12.076   7.161   8.590  10.808   0.000   0.000   0.000
   1_xyz:  0.330  12.076   7.161   8.590  10.808   0.000   0.000   0.000
   1_adp:  0.330  12.076   7.161   8.590  10.808   0.000   0.000   0.000
   1_occ:  0.330  12.076   7.161   8.590  10.808   0.000   0.000   0.000
   2_bss:  0.342  50.000   3.817   4.524   6.803   0.000   0.000   0.000
   2_xyz:  0.342  50.000   3.817   4.524   6.803   0.000   0.000   0.000
   2_adp:  0.342  50.000   3.817   4.524   6.803   0.000   0.000   0.000
   2_occ:  0.342  50.000   3.817   4.524   6.803   0.000   0.000   0.000
   3_bss:  0.339  61.030   2.043   2.217   4.320   0.000   0.000   0.000
   3_xyz:  0.339  61.030   2.043   2.217   4.320   0.000   0.000   0.000
   3_adp:  0.339  61.030   2.043   2.217   4.320   0.000   0.000   0.000
   3_occ:  0.339  61.030   2.043   2.217   4.320   0.000   0.000   0.000
   4_bss:  0.334  61.030   1.263   1.170   3.299   0.000   0.000   0.000
   4_xyz:  0.334  61.030   1.263   1.170   3.299   0.000   0.000   0.000
   4_adp:  0.334  61.030   1.263   1.170   3.299   0.000   0.000   0.000
   4_occ:  0.334  61.030   1.263   1.170   3.299   0.000   0.000   0.000
   5_bss:  0.327  64.306   1.252   1.007   3.139   0.000   0.000   0.000
   5_xyz:  0.327  64.306   1.252   1.007   3.139   0.000   0.000   0.000
   5_adp:  0.327  64.306   1.252   1.007   3.139   0.000   0.000   0.000
   5_occ:  0.327  64.306   1.252   1.007   3.139   0.000   0.000   0.000
   5_bss:  0.327  66.274  -0.477  -0.789   1.266  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.370 0.4011  0.4736    71907.497
   1_bss:  58.894 0.4064  0.6194    70450.397
   1_xyz:  50.537 0.5120  0.7594    54491.675
   1_adp:  47.945 0.5448  0.8796    51883.352
   1_occ:  48.052 0.5435  0.8765    52086.534
   2_bss:  47.722 0.5475  0.7766    51634.306
   2_xyz:  36.892 0.6774  0.9307    31936.714
   2_adp:  33.257 0.7206  0.9623    27343.811
   2_occ:  33.241 0.7208  0.9617    27268.677
   3_bss:  33.205 0.7213  0.8916    27348.793
   3_xyz:  23.851 0.8225  0.9826    14952.074
   3_adp:  21.827 0.8435  0.9906    12968.598
   3_occ:  21.827 0.8435  0.9903    12936.286
   4_bss:  21.738 0.8442  0.9579    12839.193
   4_xyz:  18.748 0.8733  0.9715     9934.473
   4_adp:  17.925 0.8812  0.9655     9262.726
   4_occ:  17.913 0.8813  0.9655     9246.518
   5_bss:  17.924 0.8812  0.9617     9268.763
   5_xyz:  16.724 0.8919  0.9689     8225.435
   5_adp:  16.418 0.8948  0.9622     8042.466
   5_occ:  16.413 0.8948  0.9621     8034.911
   5_bss:  16.416 0.8948  0.9678     8038.512
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.4070e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.4070e+01
   1_xyz:   1.753  0.014  0.111 18.557  0.006  4.109   1.5047e-01
   1_adp:   1.753  0.014  0.111 18.557  0.006  4.109   1.5047e-01
   1_occ:   1.753  0.014  0.111 18.557  0.006  4.109   1.5047e-01
   2_bss:   1.753  0.014  0.111 18.557  0.006  4.109   1.5047e-01
   2_xyz:   1.230  0.009  0.087 16.695  0.005  4.108   9.1674e-02
   2_adp:   1.230  0.009  0.087 16.695  0.005  4.108   9.1674e-02
   2_occ:   1.230  0.009  0.087 16.695  0.005  4.108   9.1674e-02
   3_bss:   1.230  0.009  0.087 16.695  0.005  4.108   9.1674e-02
   3_xyz:   1.100  0.008  0.083 15.913  0.004  4.127   7.0946e-02
   3_adp:   1.100  0.008  0.083 15.913  0.004  4.127   7.0946e-02
   3_occ:   1.100  0.008  0.083 15.913  0.004  4.127   7.0946e-02
   4_bss:   1.100  0.008  0.083 15.913  0.004  4.127   7.0946e-02
   4_xyz:   0.936  0.007  0.072 15.560  0.003  4.133   5.7985e-02
   4_adp:   0.936  0.007  0.072 15.560  0.003  4.133   5.7985e-02
   4_occ:   0.936  0.007  0.072 15.560  0.003  4.133   5.7985e-02
   5_bss:   0.936  0.007  0.072 15.560  0.003  4.133   5.7985e-02
   5_xyz:   0.941  0.006  0.073 15.403  0.003  4.116   5.6846e-02
   5_adp:   0.941  0.006  0.073 15.403  0.003  4.116   5.6846e-02
   5_occ:   0.941  0.006  0.073 15.403  0.003  4.116   5.6846e-02
   5_bss:   0.941  0.006  0.073 15.403  0.003  4.116   5.6846e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0095e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0095e+00
   1_xyz:  14.178  0.181  0.445 85.465  0.031  2.159   1.0579e-01
   1_adp:  14.178  0.181  0.445 85.465  0.031  2.159   1.0579e-01
   1_occ:  14.178  0.181  0.445 85.465  0.031  2.159   1.0579e-01
   2_bss:  14.178  0.181  0.445 85.465  0.031  2.159   1.0579e-01
   2_xyz:   6.851  0.074  0.291 85.936  0.037  2.201   5.4474e-02
   2_adp:   6.851  0.074  0.291 85.936  0.037  2.201   5.4474e-02
   2_occ:   6.851  0.074  0.291 85.936  0.037  2.201   5.4474e-02
   3_bss:   6.851  0.074  0.291 85.936  0.037  2.201   5.4474e-02
   3_xyz:   7.016  0.078  0.386 89.978  0.032  2.255   5.0951e-02
   3_adp:   7.016  0.078  0.386 89.978  0.032  2.255   5.0951e-02
   3_occ:   7.016  0.078  0.386 89.978  0.032  2.255   5.0951e-02
   4_bss:   7.016  0.078  0.386 89.978  0.032  2.255   5.0951e-02
   4_xyz:   7.128  0.046  0.298 80.732  0.039  2.374   7.0510e-02
   4_adp:   7.128  0.046  0.298 80.732  0.039  2.374   7.0510e-02
   4_occ:   7.128  0.046  0.298 80.732  0.039  2.374   7.0510e-02
   5_bss:   7.128  0.046  0.298 80.732  0.039  2.374   7.0510e-02
   5_xyz:   7.308  0.044  0.320 81.743  0.036  2.377   5.0658e-02
   5_adp:   7.308  0.044  0.320 81.743  0.036  2.377   5.0658e-02
   5_occ:   7.308  0.044  0.320 81.743  0.036  2.377   5.0658e-02
   5_bss:   7.308  0.044  0.320 81.743  0.036  2.377   5.0658e-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:  77.27   0.00  14.92  65.54   0.00  12.83  77.27   0.00  26.32
   1_occ:  77.27   0.00  14.92  65.54   0.00  12.83  77.27   0.00  26.32
   2_bss:  77.27   0.00  14.92  65.54   0.00  12.83  77.27   0.00  26.32
   2_xyz:  77.27   0.00  14.92  65.54   0.00  12.83  77.27   0.00  26.32
   2_adp:  88.25   0.00  14.16  66.13   0.00  10.62  88.25   0.00  33.42
   2_occ:  88.25   0.00  14.16  66.13   0.00  10.62  88.25   0.00  33.42
   3_bss:  88.25   0.00  14.16  66.13   0.00  10.62  88.25   0.00  33.42
   3_xyz:  88.25   0.00  14.16  66.13   0.00  10.62  88.25   0.00  33.42
   3_adp:  90.85   0.00  14.22  70.09   0.00   9.94  90.85   1.52  37.53
   3_occ:  90.85   0.00  14.22  70.09   0.00   9.94  90.85   1.52  37.53
   4_bss:  90.85   0.00  14.22  70.09   0.00   9.94  90.85   1.52  37.53
   4_xyz:  90.85   0.00  14.22  70.09   0.00   9.94  90.85   1.52  37.53
   4_adp:  91.28   0.00  14.46  77.35   0.00   9.66  91.28   2.70  40.60
   4_occ:  91.28   0.00  14.46  77.35   0.00   9.66  91.28   2.70  40.60
   5_bss:  91.28   0.00  14.46  77.35   0.00   9.66  91.28   2.70  40.60
   5_xyz:  91.28   0.00  14.46  77.35   0.00   9.66  91.28   2.70  40.60
   5_adp: 109.45   0.00  14.73  91.29   0.00   9.64 109.45   2.81  42.42
   5_occ: 109.45   0.00  14.73  91.29   0.00   9.64 109.45   2.81  42.42
   5_bss: 111.42   1.97  16.69  93.26   1.97  11.61 111.42   4.78  44.39
------------------------------------------------------------------------
 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:    1.272    0.017    0.414
   1_adp:    1.272    0.017    0.414
   1_occ:    1.272    0.017    0.414
   2_bss:    1.272    0.017    0.414
   2_xyz:    1.729    0.025    0.593
   2_adp:    1.729    0.025    0.593
   2_occ:    1.729    0.025    0.593
   3_bss:    1.729    0.025    0.593
   3_xyz:    1.581    0.043    0.694
   3_adp:    1.581    0.043    0.694
   3_occ:    1.581    0.043    0.694
   4_bss:    1.581    0.043    0.694
   4_xyz:    1.743    0.049    0.738
   4_adp:    1.743    0.049    0.738
   4_occ:    1.743    0.049    0.738
   5_bss:    1.743    0.049    0.738
   5_xyz:    1.826    0.059    0.761
   5_adp:    1.826    0.059    0.761
   5_occ:    1.826    0.059    0.761
   5_bss:    1.826    0.059    0.761
------------------------------------------------------------------------

CPU time actual refinement: 324.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/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_878/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_878/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.14 
  Macro-tasks:
    bulk solvent and scale       = 41.40  
    individual site refinement   = 134.56 
    weights calculation          = 31.56  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.17 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 97.78  
    alpha_beta                      = 8.37   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 108.61 
    fmodel                         = 7.05   
    r_factors                      = 0.26   
    phase_errors                   = 10.42  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 236.24 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.584 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    623 calls, 97.53 s
gradients_fft:          568 calls, 95.30 s

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

# Date 2008-01-16 Time 02:38:45 PST -0800 (1200479925.39 s)
Start R-work = 0.4934, R-free = 0.4796 (no bulk solvent and anisotropic scale)
Final R-work = 0.1427, R-free = 0.1940 (no bulk solvent and anisotropic scale)

Start R-work = 0.4861, R-free = 0.4677
Final R-work = 0.1264, R-free = 0.1782