# Date 2008-01-16 Time 01:46:37 PST -0800 (1200476797.17 s)
#phil __OFF__

Command line arguments: "../562.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1778
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 562

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 84.6622, 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: 3.38, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96136
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96136
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1968 [2183/2211]  1965   218  10.0%
  bin  2:  4.1968 -  3.3436 [2080/2103]  1872   208  10.0%
  bin  3:  3.3436 -  2.9247 [2058/2083]  1848   210  10.2%
  bin  4:  2.9247 -  2.6589 [2049/2065]  1851   198   9.7%
  bin  5:  2.6589 -  2.4693 [2035/2073]  1826   209  10.3%
  bin  6:  2.4693 -  2.3243 [2022/2055]  1828   194   9.6%
  bin  7:  2.3243 -  2.2082 [1992/2029]  1788   204  10.2%
  bin  8:  2.2082 -  2.1124 [2000/2042]  1800   200  10.0%
  bin  9:  2.1124 -  2.0313 [2007/2045]  1807   200  10.0%
  bin 10:  2.0313 -  1.9614 [1163/2022]  1045   118  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/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:
        1.70 -     2.34: 30
        2.34 -     2.98: 1838
        2.98 -     3.62: 4619
        3.62 -     4.26: 9221
        4.26 -     4.90: 12828
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.704 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.770 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.780 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.832 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28531 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_562/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/model_refine_001.geo

CPU time processing inputs: 9.56


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4677   r_free= 0.4687   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.268877                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.3830 0.3704      6.5703      6.5422|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.3800 0.3947      6.7493      6.7763|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.4192 0.4068      6.6424       6.691|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.4411 0.4461      6.4878      6.4756|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.4848 0.5200      6.3647      6.3713|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.4912 0.5440      6.2574      6.1998|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.5081 0.4156      6.2495      6.1503|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.5173 0.5189      6.1639      6.1771|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.5245 0.5266       6.122      6.1334|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.5234 0.5387      6.1076      6.1105|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.5216 0.5166      6.0342      6.0446|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.5269 0.5875      5.9652      6.0004|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.5412 0.5191      5.8716      5.8474|
| 14:  2.0103 -  1.9614 0.43    557   66 0.5499 0.5321      5.8652      5.7341|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.70  34.03   0.81     0.72      69048.10|
|  2:  4.6809 -  3.7348  1365   147  0.71  34.12   0.90     0.78      98702.75|
|  3:  3.7348 -  3.2685  1325   155  0.61  42.69   0.85     0.73     107091.30|
|  4:  3.2685 -  2.9722  1330   146  0.53  49.54   0.82     0.63      95686.05|
|  5:  2.9722 -  2.7606  1317   147  0.44  56.77   0.75     0.53      81341.11|
|  6:  2.7606 -  2.5988  1303   143  0.42  57.98   0.75     0.50      67728.97|
|  7:  2.5988 -  2.4693  1310   148  0.43  57.56   0.74     0.49      59820.88|
|  8:  2.4693 -  2.3622  1289   141  0.41  58.88   0.73     0.48      54321.55|
|  9:  2.3622 -  2.2716  1298   145  0.37  62.27   0.74     0.44      52583.21|
| 10:  2.2716 -  2.1935  1292   140  0.32  66.14   0.77     0.39      51979.81|
| 11:  2.1935 -  2.1251  1274   142  0.26  70.60   0.76     0.32      50567.27|
| 12:  2.1251 -  2.0645  1293   144  0.24  72.34   0.75     0.30      48202.62|
| 13:  2.0645 -  2.0103  1265   138  0.26  70.75   0.73     0.34      38986.04|
| 14:  2.0103 -  1.9614   557    66  0.40  60.33   0.73     0.45      27184.86|
|alpha:            min =        0.30 max =            0.78 mean =         0.51|
|beta:             min =    27184.86 max =       107091.30 mean =     66464.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.24|
|phase err.(test): min =        0.00 max =           89.92 mean =        56.54|
|-----------------------------------------------------------------------------|

============================== 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 = 12.132932             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.162   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.140364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.520   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2670 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3942 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5094 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6614 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7794 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.400 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.982 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4745   r_free= 0.4760   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.271391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4595   r_free= 0.4600   ksol= 0.35   Bsol= 13.96   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.68,9.04,8.98,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.266466                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.602357             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.275   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.064687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.293   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4595      final r-factor (work) = 0.3777          |
| start r-factor (free) = 0.4600      final r-factor (free) = 0.3999          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.6380 = 10.60 * 0.50 * 6.2699 + 1.00 * 53.4001                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8511 = 10.60 * 0.50 * 6.1709 + 1.00 * 0.1380                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3777      final r-factor (work) = 0.3306          |
| start r-factor (free) = 0.3999      final r-factor (free) = 0.3743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5844 = 1.06 * 1.00 * 6.1709 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4825 = 1.06 * 1.00 * 6.0745 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.76   12.49    None  None   None       |
|    all(noH): 2823   0      0.00    68.76   12.49    None  None   None       |
|    Sol.    : 438    0      0.00    68.76   27.04    None  None   None       |
|    Mac.    : 2385   0      0.00    62.18   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.876: 1157   |   5:    34.378 -  41.254:   87        |
|      1:     6.876 -  13.751:  735   |   6:    41.254 -  48.129:   52        |
|      2:    13.751 -  20.627:  387   |   7:    48.129 -  55.005:   34        |
|      3:    20.627 -  27.502:  224   |   8:    55.005 -  61.880:   13        |
|      4:    27.502 -  34.378:  127   |   9:    61.880 -  68.756:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3306 r_free = 0.3743             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3301 r_free = 0.3742             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3301   r_free= 0.3742   ksol= 0.35   Bsol= 13.96   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.68,9.04,8.98,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.050218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3269   r_free= 0.3687   ksol= 0.33   Bsol= 33.96   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,5.36,5.94,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.049718                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.943781              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.845   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.086  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3269      final r-factor (work) = 0.2210          |
| start r-factor (free) = 0.3687      final r-factor (free) = 0.2731          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2894 = 8.94 * 0.50 * 6.0716 + 1.00 * 0.1380                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4619 = 8.94 * 0.50 * 5.8984 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2210      final r-factor (work) = 0.1928          |
| start r-factor (free) = 0.2731      final r-factor (free) = 0.2442          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9107 = 0.49 * 1.00 * 5.8984 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7919 = 0.49 * 1.00 * 5.6596 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.60   12.75    None  None   None       |
|    all(noH): 2823   0      0.00    70.60   12.75    None  None   None       |
|    Sol.    : 438    0      1.20    69.54   33.28    None  None   None       |
|    Mac.    : 2385   0      0.00    70.60   8.97     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 -   7.060: 1292   |   5:    35.301 -  42.361:  103        |
|      1:     7.060 -  14.120:  784   |   6:    42.361 -  49.421:   87        |
|      2:    14.120 -  21.180:  235   |   7:    49.421 -  56.481:   40        |
|      3:    21.180 -  28.241:  138   |   8:    56.481 -  63.541:   22        |
|      4:    28.241 -  35.301:  113   |   9:    63.541 -  70.601:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1928 r_free = 0.2442             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1926 r_free = 0.2443             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1926   r_free= 0.2443   ksol= 0.33   Bsol= 33.96   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,5.36,5.94,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.604320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1895   r_free= 0.2421   ksol= 0.32   Bsol= 37.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,3.17,3.36,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.600746                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.291576              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.262  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.576773              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1895      final r-factor (work) = 0.1484          |
| start r-factor (free) = 0.2421      final r-factor (free) = 0.1960          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5817 = 2.29 * 0.50 * 5.6702 + 1.00 * 0.0849                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3611 = 2.29 * 0.50 * 5.5033 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1392          |
| start r-factor (free) = 0.1960      final r-factor (free) = 0.1868          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1889 = 0.58 * 1.00 * 5.5033 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1026 = 0.58 * 1.00 * 5.3534 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.55   13.16    None  None   None       |
|    all(noH): 2823   0      0.00    83.55   13.16    None  None   None       |
|    Sol.    : 438    0      2.15    74.36   36.68    None  None   None       |
|    Mac.    : 2385   0      0.00    83.55   8.85     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 -   8.355: 1540   |   5:    41.777 -  50.133:  110        |
|      1:     8.355 -  16.711:  669   |   6:    50.133 -  58.488:   64        |
|      2:    16.711 -  25.066:  175   |   7:    58.488 -  66.843:   31        |
|      3:    25.066 -  33.422:   99   |   8:    66.843 -  75.199:    9        |
|      4:    33.422 -  41.777:  121   |   9:    75.199 -  83.554:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1392 r_free = 0.1868             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1391 r_free = 0.1869             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1391   r_free= 0.1869   ksol= 0.32   Bsol= 37.90   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,3.17,3.36,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.328693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1872   ksol= 0.32   Bsol= 40.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,2.65,2.71,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331080                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.466495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.372602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.708  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1394      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3392 = 3.47 * 0.50 * 5.3563 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1955 = 3.47 * 0.50 * 5.2644 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9741 = 0.37 * 1.00 * 5.2644 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9425 = 0.37 * 1.00 * 5.1843 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.53   12.89    None  None   None       |
|    all(noH): 2823   0      0.00    85.53   12.89    None  None   None       |
|    Sol.    : 438    0      1.52    76.65   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    85.53   8.65     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 -   8.553: 1626   |   5:    42.763 -  51.316:   97        |
|      1:     8.553 -  17.105:  623   |   6:    51.316 -  59.869:   60        |
|      2:    17.105 -  25.658:  161   |   7:    59.869 -  68.422:   26        |
|      3:    25.658 -  34.211:  105   |   8:    68.422 -  76.974:    7        |
|      4:    34.211 -  42.763:  113   |   9:    76.974 -  85.527:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1610             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1610             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1610   ksol= 0.32   Bsol= 40.90   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,2.65,2.71,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1609   ksol= 0.32   Bsol= 40.14   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,2.65,2.71,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.176125              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.589  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.199095              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.668  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7116 = 2.18 * 0.50 * 5.1840 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6838 = 2.18 * 0.50 * 5.1686 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0398 = 0.20 * 1.00 * 5.1686 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0398 = 0.20 * 1.00 * 5.1677 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.62   12.45    None  None   None       |
|    all(noH): 2823   0      0.00    82.62   12.45    None  None   None       |
|    Sol.    : 438    0      1.62    74.82   33.96    None  None   None       |
|    Mac.    : 2385   0      0.00    82.62   8.50     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 -   8.262: 1597   |   5:    41.309 -  49.571:   88        |
|      1:     8.262 -  16.524:  653   |   6:    49.571 -  57.833:   54        |
|      2:    16.524 -  24.786:  166   |   7:    57.833 -  66.095:   19        |
|      3:    24.786 -  33.048:  119   |   8:    66.095 -  74.357:    5        |
|      4:    33.048 -  41.309:  115   |   9:    74.357 -  82.619:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1592             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1592             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1592   ksol= 0.32   Bsol= 40.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,2.65,2.71,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.165437                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.1008 0.1292      5.3881      5.5344|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.0877 0.1145      5.4477      5.6718|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.1077 0.1552      5.4827      5.8421|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.1258 0.1499      5.4684      5.6154|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.1334 0.1690      5.3405      5.4811|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.1273 0.2070      5.2412      5.5308|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.1266 0.1713       5.184      5.4324|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.1195 0.1638      5.0879      5.2736|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.1204 0.1816      5.0462      5.3145|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.1172 0.1816      4.9903      5.2512|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.1160 0.1730       4.937      5.2558|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.1117 0.1637      4.8638       5.098|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.1193 0.1856      4.7977      5.0845|
| 14:  2.0103 -  1.9614 0.43    557   66 0.1121 0.1656      4.7179      4.8871|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.94   8.92   0.98     0.97       7154.57|
|  2:  4.6809 -  3.7348  1365   147  0.95   8.05   1.02     1.00       9010.03|
|  3:  3.7348 -  3.2685  1325   155  0.93  11.65   1.03     1.02      10731.48|
|  4:  3.2685 -  2.9722  1330   146  0.91  14.22   1.01     0.98      10504.09|
|  5:  2.9722 -  2.7606  1317   147  0.89  16.47   0.99     0.96       8540.89|
|  6:  2.7606 -  2.5988  1303   143  0.90  16.45   0.99     0.96       7491.04|
|  7:  2.5988 -  2.4693  1310   148  0.90  15.72   0.99     0.96       6383.16|
|  8:  2.4693 -  2.3622  1289   141  0.90  15.85   1.00     0.97       5639.27|
|  9:  2.3622 -  2.2716  1298   145  0.91  15.77   1.01     0.99       5138.60|
| 10:  2.2716 -  2.1935  1292   140  0.90  15.90   1.01     0.97       4620.48|
| 11:  2.1935 -  2.1251  1274   142  0.90  16.26   1.01     0.98       4295.63|
| 12:  2.1251 -  2.0645  1293   144  0.92  14.64   1.01     1.00       3761.05|
| 13:  2.0645 -  2.0103  1265   138  0.90  16.70   1.02     1.02       3389.05|
| 14:  2.0103 -  1.9614   557    66  0.90  15.95   1.00     0.96       2822.31|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2822.31 max =        10731.48 mean =      6583.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.34|
|phase err.(test): min =        0.00 max =           88.17 mean =        13.84|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1594   ksol= 0.32   Bsol= 42.35   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.25,0.36,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1594   ksol= 0.32   Bsol= 42.35   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.61,0.25,0.36,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166620                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.0989 0.1308      5.3887      5.5357|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.0892 0.1158      5.4601      5.6842|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.1080 0.1552      5.4862      5.8377|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.1266 0.1497      5.4706      5.6121|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.1335 0.1687      5.3416      5.4816|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.1273 0.2074       5.241      5.5297|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.1264 0.1717      5.1836      5.4335|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.1195 0.1636      5.0873      5.2742|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.1202 0.1811      5.0455      5.3132|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.1171 0.1823      4.9889      5.2526|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.1158 0.1726      4.9364      5.2552|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.1115 0.1639      4.8635      5.0986|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.1192 0.1854      4.7976      5.0842|
| 14:  2.0103 -  1.9614 0.43    557   66 0.1120 0.1645      4.7173       4.885|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.94   9.04   0.98     0.96       7289.50|
|  2:  4.6809 -  3.7348  1365   147  0.95   8.21   1.02     1.00       9141.68|
|  3:  3.7348 -  3.2685  1325   155  0.93  11.67   1.03     1.02      10821.18|
|  4:  3.2685 -  2.9722  1330   146  0.91  14.19   1.00     0.98      10464.89|
|  5:  2.9722 -  2.7606  1317   147  0.89  16.48   0.99     0.96       8554.43|
|  6:  2.7606 -  2.5988  1303   143  0.90  16.50   0.98     0.96       7501.78|
|  7:  2.5988 -  2.4693  1310   148  0.90  15.73   0.99     0.96       6403.31|
|  8:  2.4693 -  2.3622  1289   141  0.90  15.86   1.00     0.97       5634.13|
|  9:  2.3622 -  2.2716  1298   145  0.90  15.78   1.01     0.98       5143.98|
| 10:  2.2716 -  2.1935  1292   140  0.90  15.90   1.00     0.97       4612.02|
| 11:  2.1935 -  2.1251  1274   142  0.90  16.27   1.00     0.97       4295.94|
| 12:  2.1251 -  2.0645  1293   144  0.92  14.63   1.00     0.99       3760.21|
| 13:  2.0645 -  2.0103  1265   138  0.90  16.70   1.01     1.01       3388.16|
| 14:  2.0103 -  1.9614   557    66  0.90  15.93   1.00     0.96       2817.68|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2817.68 max =        10821.18 mean =      6610.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.36|
|phase err.(test): min =        0.00 max =           88.10 mean =        13.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.21    84.83   14.66    None  None   None       |
|    all(noH): 2823   0      2.21    84.83   14.66    None  None   None       |
|    Sol.    : 438    0      3.84    77.03   36.18    None  None   None       |
|    Mac.    : 2385   0      2.21    84.83   10.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.213 -  10.475: 1597   |   5:    43.522 -  51.784:   88        |
|      1:    10.475 -  18.737:  653   |   6:    51.784 -  60.046:   54        |
|      2:    18.737 -  26.999:  166   |   7:    60.046 -  68.308:   19        |
|      3:    26.999 -  35.260:  119   |   8:    68.308 -  76.570:    5        |
|      4:    35.260 -  43.522:  115   |   9:    76.570 -  84.832:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.397 - 5.989
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 333
   mapped sites are within: 0.722 - 5.989

peak=   10.109 closest distance to " CG2 VAL A 230 " =    1.445
peak=    7.301 closest distance to " CG2 VAL A 296 " =    1.113
peak=    6.191 closest distance to " CG  LEU A   5 " =    1.314
peak=    6.181 closest distance to " NH2 ARG A  56 " =    2.195
peak=    5.632 closest distance to " O   HOH Z 124 " =    1.584
peak=    5.353 closest distance to " CD2 LEU A   5 " =    1.245
peak=    5.289 closest distance to " O   HOH Z 272 " =    1.925
peak=    5.238 closest distance to " CG  PRO A  54 " =    1.271
peak=    5.234 closest distance to " O   HOH Z 278 " =    1.197
peak=    5.183 closest distance to " CB  VAL A 296 " =    1.113
peak=    5.119 closest distance to " CB  GLN A 223 " =    1.374
peak=    4.974 closest distance to " CB  ARG A 275 " =    0.882
peak=    4.915 closest distance to " CB  SER A  63 " =    1.181
peak=    4.846 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.837 closest distance to " CG  LEU A 228 " =    1.246
peak=    4.786 closest distance to " O   HOH Z 193 " =    1.764
peak=    4.729 closest distance to " O   HOH Z 132 " =    1.160
peak=    4.695 closest distance to " NE2 GLN A  11 " =    1.113
peak=    4.619 closest distance to " O   HOH Z  48 " =    1.671
peak=    4.601 closest distance to " O   HOH Z 126 " =    1.899
peak=    4.597 closest distance to " CB  SER A   3 " =    1.311
peak=    4.580 closest distance to " O   SER A  87 " =    2.188
peak=    4.555 closest distance to " O   HOH Z 368 " =    2.212
peak=    4.532 closest distance to " O   HOH Z 234 " =    3.806
peak=    4.527 closest distance to " C   PRO A 198 " =    1.518
peak=    4.518 closest distance to " CD2 LEU A 228 " =    1.235
peak=    4.485 closest distance to " O   HOH Z  97 " =    1.881
peak=    4.467 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.444 closest distance to " O   HOH Z 423 " =    1.880
peak=    4.442 closest distance to " CB  PRO A  54 " =    0.853
peak=    4.442 closest distance to " O   HOH Z  11 " =    1.324
peak=    4.432 closest distance to " O   HOH Z 209 " =    2.395
peak=    4.382 closest distance to " CB  GLU A 152 " =    1.136
peak=    4.343 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.334 closest distance to " O   HOH Z  59 " =    2.257
peak=    4.334 closest distance to " O   HOH Z  80 " =    1.627
peak=    4.314 closest distance to " O   HOH Z 142 " =    1.608
peak=    4.295 closest distance to " CG1BVAL A  72 " =    1.569
peak=    4.260 closest distance to " CB  VAL A 230 " =    1.236
peak=    4.243 closest distance to " O   HOH Z 247 " =    1.327
peak=    4.232 closest distance to " O   HOH Z  85 " =    1.475
peak=    4.230 closest distance to " O   HOH Z 403 " =    1.737
peak=    4.216 closest distance to " CA  ALA A  21 " =    1.221
peak=    4.205 closest distance to " O   HOH Z 316 " =    2.860
peak=    4.200 closest distance to " O   HOH Z 402 " =    1.444
peak=    4.200 closest distance to " O   HOH Z 411 " =    3.616
peak=    4.155 closest distance to " O   HOH Z 128 " =    2.020
peak=    4.151 closest distance to " OD1 ASN A  69 " =    2.629
peak=    4.132 closest distance to " O   HOH Z 232 " =    2.246
peak=    4.120 closest distance to " CB  TYR A 169 " =    0.843
peak=    4.111 closest distance to " O   HOH Z 426 " =    1.462
peak=    4.090 closest distance to " ND2 ASN A 187 " =    1.635
peak=    4.088 closest distance to " O   HOH Z  40 " =    1.641
peak=    4.088 closest distance to " O   HOH Z 371 " =    3.282
peak=    4.082 closest distance to " CB  TRP A 179 " =    1.297
peak=    4.073 closest distance to " CG  PRO A 243 " =    1.156
peak=    4.052 closest distance to " CB  GLU A 277 " =    3.553
peak=    4.052 closest distance to " O   HOH Z 345 " =    2.957
peak=    4.040 closest distance to " O   HOH Z 303 " =    2.023
peak=    4.034 closest distance to " O   HOH Z 346 " =    1.507
peak=    4.020 closest distance to " O   HOH Z 263 " =    1.482
peak=    4.018 closest distance to " CG  ARG A  66 " =    2.792
peak=    4.014 closest distance to " O   HOH Z 298 " =    1.905
peak=    4.006 closest distance to " O   HOH Z 189 " =    2.489
peak=    3.998 closest distance to " CB  GLU A 128 " =    1.070
peak=    3.983 closest distance to " O   HOH Z 344 " =    2.762
peak=    3.983 closest distance to " O   HOH Z 102 " =    1.281
peak=    3.979 closest distance to " CB  ASN A 148 " =    1.287
peak=    3.974 closest distance to " O   TRP A 274 " =    1.924
peak=    3.964 closest distance to " O   HOH Z 214 " =    2.294
peak=    3.955 closest distance to " CG  PRO A 280 " =    0.745
peak=    3.951 closest distance to " OD2 ASP A 286 " =    2.759
peak=    3.948 closest distance to " O   HOH Z 279 " =    1.153
peak=    3.929 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.926 closest distance to " CG2 VAL A 296 " =    1.730
peak=    3.920 closest distance to " O   HOH Z 389 " =    1.857
peak=    3.909 closest distance to " O   HOH Z 137 " =    1.743
peak=    3.879 closest distance to " O   HOH Z  54 " =    1.520
peak=    3.870 closest distance to " O   HOH Z  78 " =    1.660
peak=    3.869 closest distance to " O   HOH Z 369 " =    2.099
peak=    3.849 closest distance to " CB  ASN A  39 " =    0.830
peak=    3.848 closest distance to " O   HOH Z  63 " =    1.809
peak=    3.846 closest distance to " O   HOH Z 265 " =    2.498
peak=    3.840 closest distance to " O   HOH Z 406 " =    1.624
peak=    3.837 closest distance to " O   HOH Z 128 " =    1.986
peak=    3.821 closest distance to " CA  TYR A  30 " =    1.021
peak=    3.814 closest distance to " O   HOH Z 133 " =    1.555
peak=    3.791 closest distance to " O   HOH Z  61 " =    1.600
peak=    3.784 closest distance to " CB  VAL A 202 " =    1.531
peak=    3.776 closest distance to " O   HOH Z 227 " =    1.629
peak=    3.775 closest distance to " O   HOH Z  97 " =    2.576
peak=    3.771 closest distance to " O   HOH Z  66 " =    2.286
peak=    3.768 closest distance to " CA  ASP A 191 " =    0.864
peak=    3.761 closest distance to " OE1 GLU A   2 " =    2.169
peak=    3.753 closest distance to " O   HOH Z 280 " =    2.959
peak=    3.753 closest distance to " CA  LYS A 117 " =    1.316
peak=    3.750 closest distance to " O   HOH Z 394 " =    1.535
peak=    3.740 closest distance to " CB  PRO A 198 " =    1.000
peak=    3.737 closest distance to " CA  ASP A 140 " =    1.214
peak=    3.737 closest distance to " O   HOH Z 236 " =    1.834
peak=    3.737 closest distance to " O   HOH Z 416 " =    2.695
peak=    3.736 closest distance to " O   HOH Z 427 " =    2.861
peak=    3.723 closest distance to " O   HOH Z 322 " =    2.158
peak=    3.713 closest distance to " O   HOH Z 273 " =    2.687
peak=    3.708 closest distance to " O   HOH Z 203 " =    1.699
peak=    3.706 closest distance to " CA  VAL A  41 " =    0.804
peak=    3.705 closest distance to " CD  ARG A 269 " =    1.054
peak=    3.703 closest distance to " O   HOH Z  20 " =    1.398
peak=    3.697 closest distance to " CB  ARG A  79 " =    1.375
peak=    3.693 closest distance to " O   HOH Z  15 " =    2.103
peak=    3.691 closest distance to " CB  ARG A 139 " =    0.890
peak=    3.680 closest distance to " NZ  LYS A  76 " =    1.209
peak=    3.674 closest distance to " CG2 THR A 221 " =    1.184
peak=    3.669 closest distance to " N   ASN A  39 " =    1.173
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.735
peak=    3.665 closest distance to " O   HOH Z 419 " =    1.674
peak=    3.661 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.660 closest distance to " CB  ALA A 248 " =    1.395
peak=    3.651 closest distance to " O   HOH Z 366 " =    2.835
peak=    3.650 closest distance to " O   HOH Z 134 " =    1.525
peak=    3.648 closest distance to " O   HOH Z 108 " =    2.406
peak=    3.647 closest distance to " CG  ARG A  66 " =    1.006
peak=    3.635 closest distance to " O   HOH Z 136 " =    1.340
peak=    3.628 closest distance to " CB  SER A 141 " =    1.047
peak=    3.625 closest distance to " CG AARG A 275 " =    1.072
peak=    3.619 closest distance to " O   HOH Z 112 " =    1.600
peak=    3.619 closest distance to " OE1 GLN A  11 " =    1.815
peak=    3.618 closest distance to " CG1 ILE A  33 " =    1.334
peak=    3.617 closest distance to " O   HOH Z 155 " =    1.554
peak=    3.616 closest distance to " O   HOH Z 276 " =    1.299
peak=    3.612 closest distance to " CD2 HIS A  81 " =    1.170
peak=    3.606 closest distance to " C   ALA A 299 " =    0.941
peak=    3.604 closest distance to " O   HOH Z 245 " =    1.447
peak=    3.596 closest distance to " CD  LYS A 166 " =    1.385
peak=    3.585 closest distance to " CA  ASN A 176 " =    1.026
peak=    3.585 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.583 closest distance to " CD  LYS A 119 " =    1.914
peak=    3.582 closest distance to " O   HOH Z 357 " =    2.025
peak=    3.571 closest distance to " O   HOH Z 260 " =    1.318
peak=    3.570 closest distance to " CA  ARG A  36 " =    1.087
peak=    3.569 closest distance to " OG BSER A 164 " =    2.237
peak=    3.566 closest distance to " O   HOH Z 420 " =    2.018
peak=    3.566 closest distance to " CB  GLN A  88 " =    1.167
peak=    3.563 closest distance to " O   HOH Z 280 " =    1.625
peak=    3.562 closest distance to " O   HOH Z 197 " =    2.659
peak=    3.562 closest distance to " CB  SER A  26 " =    1.651
peak=    3.557 closest distance to " O   HOH Z 313 " =    1.759
peak=    3.553 closest distance to " OG1 THR A 294 " =    2.308
peak=    3.553 closest distance to " OD1 ASP A 286 " =    1.718
peak=    3.552 closest distance to " O   HOH Z 414 " =    1.618
peak=    3.549 closest distance to " O   HOH Z  67 " =    1.737
peak=    3.547 closest distance to " CB  ARG A 190 " =    1.719
peak=    3.546 closest distance to " CB  ALA A   9 " =    1.553
peak=    3.544 closest distance to " NH2BARG A 145 " =    2.143
peak=    3.541 closest distance to " O   HOH Z  88 " =    3.063
peak=    3.531 closest distance to " CA  ALA A  51 " =    0.995
peak=    3.530 closest distance to " CE1 TYR A 186 " =    1.237
peak=    3.528 closest distance to " O   HOH Z   4 " =    1.642
peak=    3.527 closest distance to " O   HOH Z 261 " =    2.019
peak=    3.522 closest distance to " CA  GLY A 211 " =    1.187
peak=    3.520 closest distance to " CD  GLN A  58 " =    5.989
peak=    3.519 closest distance to " C   ALA A   1 " =    1.739
peak=    3.517 closest distance to " O   HOH Z 374 " =    2.508
peak=    3.507 closest distance to " O   MET A 105 " =    1.865
peak=    3.506 closest distance to " CG1 VAL A 296 " =    1.121
peak=    3.500 closest distance to " O   HOH Z 303 " =    1.693
peak=    3.500 closest distance to " CZ AARG A 102 " =    1.840
peak=    3.498 closest distance to " O   HOH Z 329 " =    3.680
peak=    3.484 closest distance to " O   HOH Z  43 " =    2.324
peak=    3.482 closest distance to " O   HOH Z 280 " =    2.406
peak=    3.482 closest distance to " CD1 LEU A 300 " =    1.116
peak=    3.480 closest distance to " O   HOH Z 193 " =    2.121
peak=    3.465 closest distance to " O   HOH Z 408 " =    1.539
peak=    3.464 closest distance to " O   HOH Z 344 " =    1.875
peak=    3.460 closest distance to " O   ASP A 124 " =    1.217
peak=    3.455 closest distance to " O   HOH Z 326 " =    1.490
peak=    3.446 closest distance to " O   HOH Z 154 " =    1.386
peak=    3.442 closest distance to " O   THR A  31 " =    1.440
peak=    3.441 closest distance to " O   HOH Z 132 " =    3.179
peak=    3.437 closest distance to " CB  ALA A   1 " =    1.315
peak=    3.433 closest distance to " O   HOH Z 261 " =    2.056
peak=    3.430 closest distance to " O   HOH Z 227 " =    1.693
peak=    3.428 closest distance to " O   HOH Z  21 " =    1.817
peak=    3.423 closest distance to " CA  VAL A 126 " =    0.894
peak=    3.422 closest distance to " CG  GLN A  58 " =    2.598
peak=    3.420 closest distance to " CB  SER A  62 " =    0.778
peak=    3.419 closest distance to " CG1 VAL A 153 " =    0.992
peak=    3.417 closest distance to " O   GLY A  91 " =    1.307
peak=    3.417 closest distance to " O   HOH Z  49 " =    2.462
peak=    3.410 closest distance to " CB BVAL A  41 " =    1.090
peak=    3.403 closest distance to " CA  ALA A 295 " =    1.057
peak=    3.402 closest distance to " CA  THR A 221 " =    0.870
peak=    3.398 closest distance to " O   HOH Z 116 " =    1.718
peak=    3.396 closest distance to " OG  SER A  22 " =    2.744
peak=    3.390 closest distance to " N   ARG A 190 " =    1.079
peak=    3.389 closest distance to " CG2 ILE A  20 " =    1.480
peak=    3.382 closest distance to " O   HOH Z 383 " =    1.960
peak=    3.381 closest distance to " NE2 GLN A  58 " =    4.271
peak=    3.378 closest distance to " O   HOH Z 236 " =    1.623
peak=    3.376 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.374 closest distance to " CD BLYS A 290 " =    1.089
peak=    3.374 closest distance to " O   HOH Z 126 " =    1.656
peak=    3.367 closest distance to " O   HOH Z 421 " =    1.603
peak=    3.367 closest distance to " CB  ALA A 291 " =    1.298
peak=    3.364 closest distance to " O   HOH Z 148 " =    3.120
peak=    3.364 closest distance to " CD2 TRP A 179 " =    1.355
peak=    3.364 closest distance to " O   HOH Z 209 " =    2.317
peak=    3.363 closest distance to " OD1 ASP A 231 " =    1.876
peak=    3.363 closest distance to " O   HOH Z 295 " =    1.510
peak=    3.359 closest distance to " CE1 HIS A 108 " =    1.147
peak=    3.355 closest distance to " CA  GLN A 194 " =    1.135
peak=    3.351 closest distance to " CD1 ILE A  33 " =    1.652
peak=    3.349 closest distance to " O   HOH Z 141 " =    1.556
peak=    3.347 closest distance to " CA  ASP A 162 " =    1.081
peak=    3.346 closest distance to " O   HOH Z 261 " =    1.596
peak=    3.346 closest distance to " O   HOH Z 417 " =    2.099
peak=    3.345 closest distance to " O   HOH Z 411 " =    1.743
peak=    3.343 closest distance to " O   HOH Z 417 " =    3.298
peak=    3.342 closest distance to " CA  ARG A 195 " =    1.104
peak=    3.340 closest distance to " OG  SER A  97 " =    2.544
peak=    3.335 closest distance to " O   HOH Z 281 " =    4.325
peak=    3.332 closest distance to " O   SER A  26 " =    1.666
peak=    3.332 closest distance to " O   HOH Z  48 " =    2.229
peak=    3.315 closest distance to " O   HOH Z 359 " =    1.970
peak=    3.310 closest distance to " O   HOH Z  50 " =    1.427
peak=    3.308 closest distance to " O   HOH Z 185 " =    1.602
peak=    3.303 closest distance to " O   HOH Z 133 " =    2.315
peak=    3.302 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.300 closest distance to " CG  GLN A  77 " =    2.244
peak=    3.298 closest distance to " O   ALA A 158 " =    1.312
peak=    3.298 closest distance to " O   HOH Z 118 " =    1.181
peak=    3.295 closest distance to " O   HOH Z 367 " =    3.423
peak=    3.294 closest distance to " O   HOH Z 248 " =    1.704
peak=    3.290 closest distance to " O   HOH Z 255 " =    1.518
peak=    3.286 closest distance to " NH2 ARG A  79 " =    1.349
peak=    3.275 closest distance to " CB  ALA A 295 " =    1.204
peak=    3.275 closest distance to " O   HOH Z 284 " =    1.511
peak=    3.272 closest distance to " CB  LEU A 143 " =    1.161
peak=    3.268 closest distance to " NZ  LYS A 166 " =    2.901
peak=    3.266 closest distance to " O   HOH Z 171 " =    2.629
peak=    3.265 closest distance to " O   HOH Z 197 " =    1.951
peak=    3.265 closest distance to " CG  MET A 185 " =    1.184
peak=    3.264 closest distance to " O   HOH Z 180 " =    2.123
peak=    3.264 closest distance to " O   HOH Z 362 " =    3.530
peak=    3.262 closest distance to " O   HOH Z 267 " =    2.082
peak=    3.261 closest distance to " O   HOH Z 158 " =    3.089
peak=    3.261 closest distance to " O   HOH Z 192 " =    1.613
peak=    3.260 closest distance to " O   HOH Z 345 " =    1.688
peak=    3.257 closest distance to " O   HOH Z 128 " =    1.832
peak=    3.255 closest distance to " CG2 ILE A 120 " =    1.349
peak=    3.252 closest distance to " O   HOH Z  96 " =    2.153
peak=    3.247 closest distance to " O   HOH Z 250 " =    1.559
peak=    3.247 closest distance to " O   HOH Z 130 " =    1.187
peak=    3.245 closest distance to " O   HOH Z   9 " =    2.100
peak=    3.242 closest distance to " CD2 TYR A  30 " =    0.827
peak=    3.235 closest distance to " O   HOH Z 155 " =    2.826
peak=    3.233 closest distance to " O   SER A 164 " =    1.230
peak=    3.233 closest distance to " O   HOH Z 163 " =    1.397
peak=    3.229 closest distance to " CB  ALA A  71 " =    1.204
peak=    3.229 closest distance to " CB  ALA A 100 " =    1.227
peak=    3.223 closest distance to " O   HOH Z 292 " =    1.628
peak=    3.223 closest distance to " O   HOH Z 173 " =    2.372
peak=    3.222 closest distance to " CB  TRP A 266 " =    0.982
peak=    3.221 closest distance to " CA  TYR A 116 " =    1.404
peak=    3.220 closest distance to " CB  GLN A 205 " =    1.174
peak=    3.220 closest distance to " O   HOH Z 358 " =    2.359
peak=    3.215 closest distance to " CG2AVAL A 121 " =    2.135
peak=    3.215 closest distance to " CG  MET A 188 " =    1.362
peak=    3.207 closest distance to " O   HOH Z  90 " =    3.292
peak=    3.207 closest distance to " CA  ASN A 217 " =    1.411
peak=    3.206 closest distance to " CB  TRP A 150 " =    1.533
peak=    3.204 closest distance to " O   HOH Z 327 " =    1.710
peak=    3.203 closest distance to " OD2 ASP A 298 " =    3.994
peak=    3.202 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.201 closest distance to " OD1 ASN A  60 " =    1.485
peak=    3.201 closest distance to " O   HOH Z 215 " =    1.633
peak=    3.199 closest distance to " NH1 ARG A  14 " =    1.090
peak=    3.195 closest distance to " CB  SER A 273 " =    0.759
peak=    3.194 closest distance to " CB  THR A  31 " =    1.632
peak=    3.194 closest distance to " CG  MET A 185 " =    1.087
peak=    3.190 closest distance to " CA  THR A 264 " =    0.770
peak=    3.190 closest distance to " O   HOH Z 423 " =    3.322
peak=    3.189 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.189 closest distance to " O   HOH Z 387 " =    2.688
peak=    3.187 closest distance to " O   HOH Z 166 " =    1.555
peak=    3.186 closest distance to " CE  LYS A 119 " =    1.084
peak=    3.183 closest distance to " O   HOH Z 244 " =    1.640
peak=    3.181 closest distance to " N   TRP A 177 " =    1.813
peak=    3.181 closest distance to " O   HOH Z 150 " =    1.727
peak=    3.180 closest distance to " O   HOH Z  30 " =    2.096
peak=    3.177 closest distance to " O   ALA A 165 " =    1.316
peak=    3.169 closest distance to " O   HOH Z 135 " =    1.756
peak=    3.166 closest distance to " O   GLY A  91 " =    1.791
peak=    3.163 closest distance to " O   HOH Z 108 " =    1.061
peak=    3.161 closest distance to " N   ARG A 156 " =    1.314
peak=    3.156 closest distance to " CB  LEU A   5 " =    1.193
peak=    3.154 closest distance to " O   HOH Z 151 " =    1.736
peak=    3.153 closest distance to " CD  ARG A 195 " =    3.425
peak=    3.148 closest distance to " NH2BARG A 190 " =    1.811
peak=    3.148 closest distance to " O   HOH Z  44 " =    1.789
peak=    3.144 closest distance to " CB  GLN A 103 " =    0.857
peak=    3.143 closest distance to " CB  ALA A 242 " =    0.903
peak=    3.142 closest distance to " OD1 ASP A 238 " =    1.100
peak=    3.141 closest distance to " O   HOH Z 337 " =    3.752
peak=    3.136 closest distance to " O   HOH Z  10 " =    1.708
peak=    3.135 closest distance to " O   GLN A 278 " =    1.259
peak=    3.127 closest distance to " O   ALA A   1 " =    1.481
peak=    3.126 closest distance to " O   HOH Z 250 " =    1.361
peak=    3.124 closest distance to " O   HOH Z 207 " =    2.229
peak=    3.113 closest distance to " O   HOH Z  94 " =    1.878
peak=    3.110 closest distance to " NH1 ARG A 138 " =    1.247
peak=    3.102 closest distance to " O   HOH Z 251 " =    1.734
peak=    3.095 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.081 closest distance to " CG  MET A  93 " =    1.062
peak=    3.074 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.071 closest distance to " O   HOH Z 227 " =    2.212
peak=    3.068 closest distance to " CA  ALA A  84 " =    1.369
peak=    3.066 closest distance to " CE  MET A  93 " =    1.328
peak=    3.066 closest distance to " CB  MET A  47 " =    1.243
peak=    3.063 closest distance to " CB  GLN A 278 " =    0.794
peak=    3.061 closest distance to " CZ2 TRP A 274 " =    1.660
peak=    3.059 closest distance to " OH  TYR A 116 " =    1.100
peak=    3.052 closest distance to " CA  ARG A  56 " =    1.581
peak=    3.050 closest distance to " CA  SER A  87 " =    0.896
peak=    3.040 closest distance to " CH2 TRP A 274 " =    2.104
peak=    3.021 closest distance to " CB  ASN A 215 " =    1.078
peak=    3.013 closest distance to " O   HOH Z  20 " =    1.897
peak=    3.011 closest distance to " OD1 ASN A  45 " =    1.340

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.630 - 5.269
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 200
   mapped sites are within: 0.708 - 5.269

peak=   -5.755 closest distance to " CG2 VAL A 230 " =    0.746
peak=   -4.419 closest distance to " O   HOH Z 290 " =    0.933
peak=   -4.377 closest distance to " O   PRO A 163 " =    2.092
peak=   -4.375 closest distance to " O   HOH Z 266 " =    4.410
peak=   -4.350 closest distance to " O   HOH Z  13 " =    1.344
peak=   -4.242 closest distance to " CD  ARG A 156 " =    1.988
peak=   -4.167 closest distance to " CB  ALA A 161 " =    2.520
peak=   -4.141 closest distance to " C   HIS A 108 " =    1.183
peak=   -4.073 closest distance to " O   HOH Z 166 " =    1.733
peak=   -4.070 closest distance to " OG ASER A 134 " =    1.302
peak=   -4.047 closest distance to " CE2 TYR A  30 " =    2.822
peak=   -4.004 closest distance to " SG  CYS A 254 " =    3.169
peak=   -3.965 closest distance to " OXT GLY A 302 " =    2.805
peak=   -3.898 closest distance to " O   HOH Z 351 " =    1.410
peak=   -3.892 closest distance to " CD1 LEU A 101 " =    2.544
peak=   -3.866 closest distance to " CG2 THR A   4 " =    1.900
peak=   -3.830 closest distance to " N   GLN A  58 " =    1.807
peak=   -3.818 closest distance to " CD2 LEU A 300 " =    2.837
peak=   -3.794 closest distance to " C   ALA A 158 " =    1.225
peak=   -3.770 closest distance to " O   HOH Z  17 " =    1.231
peak=   -3.766 closest distance to " O   HOH Z  11 " =    1.618
peak=   -3.765 closest distance to " O   HOH Z  43 " =    1.678
peak=   -3.760 closest distance to " OG BSER A 134 " =    1.728
peak=   -3.759 closest distance to " O   HOH Z  71 " =    1.060
peak=   -3.757 closest distance to " O   VAL A  67 " =    2.600
peak=   -3.752 closest distance to " CG  ASP A  50 " =    2.402
peak=   -3.744 closest distance to " C   THR A 279 " =    1.183
peak=   -3.732 closest distance to " CE  MET A 105 " =    1.963
peak=   -3.730 closest distance to " O   HOH Z 407 " =    3.028
peak=   -3.724 closest distance to " O   HOH Z  52 " =    1.708
peak=   -3.721 closest distance to " N   ALA A 226 " =    1.991
peak=   -3.717 closest distance to " O   HOH Z 423 " =    2.281
peak=   -3.710 closest distance to " O   HOH Z 231 " =    1.784
peak=   -3.710 closest distance to " N   SER A 276 " =    1.319
peak=   -3.709 closest distance to " CG  ASP A 231 " =    0.857
peak=   -3.698 closest distance to " CB  ALA A 248 " =    1.937
peak=   -3.693 closest distance to " O   GLY A  80 " =    2.465
peak=   -3.685 closest distance to " O   ALA A 161 " =    1.596
peak=   -3.668 closest distance to " O   HOH Z  92 " =    1.446
peak=   -3.667 closest distance to " ND2 ASN A  45 " =    1.011
peak=   -3.663 closest distance to " O   GLY A 196 " =    1.021
peak=   -3.655 closest distance to " O   HOH Z 150 " =    1.525
peak=   -3.655 closest distance to " O   HOH Z 118 " =    3.009
peak=   -3.651 closest distance to " O   HOH Z  63 " =    0.864
peak=   -3.633 closest distance to " OG  SER A  62 " =    1.291
peak=   -3.632 closest distance to " CD2 LEU A 237 " =    2.677
peak=   -3.627 closest distance to " OXT GLY A 302 " =    3.413
peak=   -3.627 closest distance to " OD1 ASN A  39 " =    2.179
peak=   -3.624 closest distance to " NE2 GLN A  88 " =    1.012
peak=   -3.620 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.614 closest distance to " NH2 ARG A  66 " =    1.562
peak=   -3.608 closest distance to " NH2AARG A 275 " =    4.982
peak=   -3.608 closest distance to " CH2 TRP A 179 " =    1.326
peak=   -3.601 closest distance to " CG  LYS A 193 " =    2.279
peak=   -3.596 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.580 closest distance to " O   VAL A  67 " =    2.625
peak=   -3.563 closest distance to " CD  LYS A 289 " =    2.529
peak=   -3.563 closest distance to " O   HOH Z 196 " =    2.155
peak=   -3.562 closest distance to " CG1 VAL A 296 " =    1.216
peak=   -3.558 closest distance to " O   HOH Z 151 " =    1.538
peak=   -3.541 closest distance to " O   HOH Z 283 " =    1.825
peak=   -3.532 closest distance to " CB  ASN A  39 " =    2.115
peak=   -3.527 closest distance to " CB  PRO A 243 " =    2.588
peak=   -3.522 closest distance to " CD  ARG A 139 " =    1.661
peak=   -3.515 closest distance to " O   HOH Z 165 " =    1.973
peak=   -3.506 closest distance to " O   HOH Z  44 " =    2.107
peak=   -3.503 closest distance to " O   HOH Z 234 " =    4.280
peak=   -3.500 closest distance to " OG BSER A 134 " =    1.228
peak=   -3.497 closest distance to " O   HOH Z 353 " =    2.191
peak=   -3.492 closest distance to " CG  GLU A 277 " =    1.104
peak=   -3.492 closest distance to " CZ  TYR A 169 " =    1.827
peak=   -3.492 closest distance to " CG  GLU A  53 " =    1.469
peak=   -3.490 closest distance to " OE1 GLN A 223 " =    2.398
peak=   -3.487 closest distance to " O   HOH Z 292 " =    4.356
peak=   -3.483 closest distance to " OG  SER A  97 " =    2.342
peak=   -3.481 closest distance to " CD1 LEU A 228 " =    2.267
peak=   -3.448 closest distance to " O   HOH Z 426 " =    1.722
peak=   -3.440 closest distance to " N   THR A 235 " =    1.312
peak=   -3.437 closest distance to " O   HOH Z 265 " =    1.944
peak=   -3.435 closest distance to " O   HOH Z 252 " =    4.085
peak=   -3.432 closest distance to " O   HOH Z 435 " =    2.708
peak=   -3.427 closest distance to " O   SER A 271 " =    2.054
peak=   -3.424 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.409 closest distance to " O   HOH Z  38 " =    1.740
peak=   -3.407 closest distance to " OG  SER A  26 " =    1.172
peak=   -3.401 closest distance to " O   HOH Z 311 " =    3.488
peak=   -3.401 closest distance to " O   HOH Z 193 " =    1.904
peak=   -3.397 closest distance to " CD2 TYR A 293 " =    2.094
peak=   -3.395 closest distance to " O   ASN A 187 " =    1.483
peak=   -3.394 closest distance to " N   ALA A 248 " =    1.664
peak=   -3.392 closest distance to " O  BHOH Z 338 " =    1.434
peak=   -3.391 closest distance to " O   HOH Z 411 " =    1.550
peak=   -3.387 closest distance to " O   HOH Z 103 " =    1.953
peak=   -3.387 closest distance to " CG  LEU A 101 " =    2.508
peak=   -3.384 closest distance to " CD  GLN A  88 " =    2.092
peak=   -3.383 closest distance to " O   ALA A 256 " =    1.514
peak=   -3.374 closest distance to " O   PHE A  59 " =    2.365
peak=   -3.371 closest distance to " O   HOH Z 202 " =    0.708
peak=   -3.365 closest distance to " CB  CYS A 254 " =    2.510
peak=   -3.361 closest distance to " O   SER A 146 " =    0.871
peak=   -3.353 closest distance to " O   HOH Z 222 " =    1.367
peak=   -3.347 closest distance to " O   HOH Z 191 " =    5.269
peak=   -3.338 closest distance to " O   VAL A 197 " =    1.298
peak=   -3.336 closest distance to " CA  ASP A 298 " =    1.069
peak=   -3.332 closest distance to " CG  PHE A  59 " =    2.193
peak=   -3.330 closest distance to " O   HOH Z 354 " =    2.546
peak=   -3.327 closest distance to " CB  GLN A  11 " =    1.846
peak=   -3.324 closest distance to " CG2 VAL A 296 " =    1.085
peak=   -3.324 closest distance to " C   MET A 188 " =    1.625
peak=   -3.317 closest distance to " C   ASN A 285 " =    2.248
peak=   -3.314 closest distance to " O   HOH Z  47 " =    1.351
peak=   -3.314 closest distance to " O   HOH Z 377 " =    1.984
peak=   -3.312 closest distance to " CA  GLY A 133 " =    1.974
peak=   -3.307 closest distance to " O   PRO A 198 " =    1.225
peak=   -3.306 closest distance to " O   HOH Z  19 " =    2.329
peak=   -3.306 closest distance to " O   HOH Z  10 " =    1.511
peak=   -3.305 closest distance to " O   ALA A  51 " =    1.495
peak=   -3.305 closest distance to " CG  LEU A 228 " =    0.912
peak=   -3.299 closest distance to " C   VAL A 265 " =    0.814
peak=   -3.298 closest distance to " O   HOH Z 132 " =    0.804
peak=   -3.287 closest distance to " O   HOH Z  48 " =    1.284
peak=   -3.286 closest distance to " CE3 TRP A 150 " =    2.027
peak=   -3.285 closest distance to " NE2 GLN A 103 " =    1.649
peak=   -3.282 closest distance to " CB  PRO A 163 " =    2.728
peak=   -3.278 closest distance to " O   HOH Z 113 " =    2.087
peak=   -3.277 closest distance to " O   MET A  40 " =    2.742
peak=   -3.269 closest distance to " NE1 TRP A 266 " =    2.351
peak=   -3.268 closest distance to " O   HOH Z 308 " =    1.778
peak=   -3.266 closest distance to " CD1 TYR A 247 " =    2.304
peak=   -3.265 closest distance to " O   TRP A  92 " =    1.869
peak=   -3.264 closest distance to " O   HOH Z 313 " =    1.121
peak=   -3.263 closest distance to " O   ASP A 191 " =    1.407
peak=   -3.262 closest distance to " CB  ALA A 291 " =    2.325
peak=   -3.259 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.258 closest distance to " N   HIS A 115 " =    2.094
peak=   -3.257 closest distance to " CG  TRP A 266 " =    1.803
peak=   -3.254 closest distance to " O   VAL A  67 " =    1.876
peak=   -3.246 closest distance to " ND2 ASN A  60 " =    1.418
peak=   -3.242 closest distance to " OE2 GLU A   2 " =    1.682
peak=   -3.242 closest distance to " CD2 TRP A 274 " =    1.201
peak=   -3.242 closest distance to " CB  ALA A  51 " =    1.877
peak=   -3.236 closest distance to " CD  ARG A 195 " =    5.119
peak=   -3.235 closest distance to " CD  GLN A  58 " =    1.265
peak=   -3.235 closest distance to " O   HOH Z 266 " =    4.509
peak=   -3.230 closest distance to " CD2 LEU A 167 " =    1.728
peak=   -3.226 closest distance to " O   ALA A 160 " =    1.421
peak=   -3.225 closest distance to " CZ3 TRP A 274 " =    1.186
peak=   -3.220 closest distance to " N   THR A 157 " =    1.486
peak=   -3.216 closest distance to " O   HOH Z 175 " =    4.578
peak=   -3.200 closest distance to " O   HOH Z 126 " =    1.911
peak=   -3.199 closest distance to " NE2 GLN A  58 " =    1.175
peak=   -3.196 closest distance to " O   HOH Z  19 " =    1.793
peak=   -3.191 closest distance to " CB  PHE A 192 " =    1.867
peak=   -3.188 closest distance to " NE2 GLN A 194 " =    1.694
peak=   -3.187 closest distance to " N   ALA A  43 " =    2.445
peak=   -3.183 closest distance to " O   SER A 210 " =    1.874
peak=   -3.177 closest distance to " NZ  LYS A 119 " =    3.469
peak=   -3.175 closest distance to " O   HOH Z  60 " =    2.380
peak=   -3.175 closest distance to " ND2 ASN A  39 " =    1.232
peak=   -3.173 closest distance to " O   LYS A 117 " =    1.618
peak=   -3.173 closest distance to " O   HOH Z 250 " =    1.419
peak=   -3.171 closest distance to " O   HOH Z 310 " =    3.579
peak=   -3.169 closest distance to " O   ASP A 270 " =    1.824
peak=   -3.159 closest distance to " OG1 THR A  82 " =    1.329
peak=   -3.159 closest distance to " OD1 ASN A 249 " =    1.147
peak=   -3.155 closest distance to " CA  ASN A 127 " =    1.061
peak=   -3.151 closest distance to " O   HOH Z 264 " =    1.824
peak=   -3.150 closest distance to " OD1 ASN A 148 " =    1.576
peak=   -3.145 closest distance to " OD1 ASP A 200 " =    1.241
peak=   -3.133 closest distance to " CD2 LEU A 237 " =    2.814
peak=   -3.130 closest distance to " O   HOH Z 231 " =    1.164
peak=   -3.129 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.127 closest distance to " O   HOH Z 414 " =    1.577
peak=   -3.125 closest distance to " CB  PHE A 283 " =    2.781
peak=   -3.125 closest distance to " CE  LYS A 166 " =    3.004
peak=   -3.124 closest distance to " OG BSER A 210 " =    2.125
peak=   -3.121 closest distance to " CD1 ILE A 263 " =    2.409
peak=   -3.120 closest distance to " O   LEU A 167 " =    1.613
peak=   -3.118 closest distance to " O   HOH Z 339 " =    1.800
peak=   -3.113 closest distance to " O   GLY A 262 " =    2.119
peak=   -3.111 closest distance to " C   SER A 206 " =    1.610
peak=   -3.102 closest distance to " CB  ASP A 124 " =    2.079
peak=   -3.096 closest distance to " CG1 VAL A 112 " =    2.598
peak=   -3.094 closest distance to " OD2 ASP A 171 " =    2.275
peak=   -3.094 closest distance to " CB  VAL A 296 " =    1.088
peak=   -3.090 closest distance to " OD1 ASN A 301 " =    2.004
peak=   -3.088 closest distance to " CG  ARG A 269 " =    2.267
peak=   -3.087 closest distance to " O   VAL A 174 " =    1.972
peak=   -3.074 closest distance to " O   ALA A 100 " =    2.398
peak=   -3.070 closest distance to " O   HOH Z 100 " =    0.876
peak=   -3.047 closest distance to " CD  ARG A 259 " =    2.482
peak=   -3.046 closest distance to " O   HOH Z 396 " =    1.625
peak=   -3.041 closest distance to " ND2 ASN A 252 " =    1.690
peak=   -3.039 closest distance to " CB  PHE A 208 " =    2.278
peak=   -3.035 closest distance to " O   HOH Z 297 " =    2.796
peak=   -3.010 closest distance to " O   HOH Z  97 " =    1.585

================= 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    :  0.4677 0.4687   6.268877e+00   6.259701e+00
   1_bss:  0.4595 0.4600   6.266466e+00   6.246482e+00
   1_xyz:  0.3777 0.3999   6.140578e+00   6.176637e+00
   1_adp:  0.3306 0.3743   6.050741e+00   6.136478e+00
   1_occ:  0.3301 0.3742   6.050218e+00   6.136344e+00
   2_bss:  0.3269 0.3687   6.049718e+00   6.133415e+00
   2_xyz:  0.2210 0.2731   5.723441e+00   5.892676e+00
   2_adp:  0.1928 0.2442   5.604813e+00   5.795084e+00
   2_occ:  0.1926 0.2443   5.604320e+00   5.795024e+00
   3_bss:  0.1895 0.2421   5.600746e+00   5.790720e+00
   3_xyz:  0.1484 0.1960   5.381821e+00   5.596374e+00
   3_adp:  0.1392 0.1868   5.328908e+00   5.547961e+00
   3_occ:  0.1391 0.1869   5.328693e+00   5.548051e+00
   4_bss:  0.1394 0.1872   5.331080e+00   5.549507e+00
   4_xyz:  0.1187 0.1647   5.194782e+00   5.430590e+00
   4_adp:  0.1158 0.1610   5.173827e+00   5.412098e+00
   4_occ:  0.1157 0.1610   5.173375e+00   5.411962e+00
   5_bss:  0.1157 0.1609   5.173483e+00   5.411985e+00
   5_xyz:  0.1137 0.1597   5.164135e+00   5.404583e+00
   5_adp:  0.1145 0.1592   5.165814e+00   5.402107e+00
   5_occ:  0.1144 0.1592   5.165437e+00   5.402069e+00
   5_bss:  0.1145 0.1594   5.166620e+00   5.402500e+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:  0.351  13.962   6.679   9.044   8.978   0.000   0.000   0.000
   1_xyz:  0.351  13.962   6.679   9.044   8.978   0.000   0.000   0.000
   1_adp:  0.351  13.962   6.679   9.044   8.978   0.000   0.000   0.000
   1_occ:  0.351  13.962   6.679   9.044   8.978   0.000   0.000   0.000
   2_bss:  0.330  33.959   3.199   5.358   5.936   0.000   0.000   0.000
   2_xyz:  0.330  33.959   3.199   5.358   5.936   0.000   0.000   0.000
   2_adp:  0.330  33.959   3.199   5.358   5.936   0.000   0.000   0.000
   2_occ:  0.330  33.959   3.199   5.358   5.936   0.000   0.000   0.000
   3_bss:  0.316  37.904   1.928   3.173   3.357   0.000   0.000   0.000
   3_xyz:  0.316  37.904   1.928   3.173   3.357   0.000   0.000   0.000
   3_adp:  0.316  37.904   1.928   3.173   3.357   0.000   0.000   0.000
   3_occ:  0.316  37.904   1.928   3.173   3.357   0.000   0.000   0.000
   4_bss:  0.319  40.899   1.655   2.647   2.706   0.000   0.000   0.000
   4_xyz:  0.319  40.899   1.655   2.647   2.706   0.000   0.000   0.000
   4_adp:  0.319  40.899   1.655   2.647   2.706   0.000   0.000   0.000
   4_occ:  0.319  40.899   1.655   2.647   2.706   0.000   0.000   0.000
   5_bss:  0.321  40.137   1.655   2.647   2.706   0.000   0.000   0.000
   5_xyz:  0.321  40.137   1.655   2.647   2.706   0.000   0.000   0.000
   5_adp:  0.321  40.137   1.655   2.647   2.706   0.000   0.000   0.000
   5_occ:  0.321  40.137   1.655   2.647   2.706   0.000   0.000   0.000
   5_bss:  0.323  42.349  -0.608   0.252   0.356   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.273 0.4414  0.5131    66467.791
   1_bss:  56.471 0.4359  0.6351    63459.462
   1_xyz:  46.658 0.5595  0.8103    46794.046
   1_adp:  42.001 0.6174  0.9218    40189.916
   1_occ:  42.027 0.6171  0.9205    40204.451
   2_bss:  41.658 0.6215  0.8234    39625.832
   2_xyz:  28.292 0.7751  0.9948    19655.542
   2_adp:  24.388 0.8175  1.0284    15573.513
   2_occ:  24.397 0.8174  1.0277    15568.023
   3_bss:  24.245 0.8188  0.9569    15407.887
   3_xyz:  18.672 0.8738  0.9889     9720.066
   3_adp:  17.448 0.8855  0.9927     8835.046
   3_occ:  17.450 0.8855  0.9927     8842.534
   4_bss:  17.473 0.8854  0.9753     8896.097
   4_xyz:  15.072 0.9059  0.9852     6995.525
   4_adp:  14.607 0.9101  0.9855     6749.308
   4_occ:  14.600 0.9101  0.9854     6749.924
   5_bss:  14.600 0.9101  0.9854     6750.372
   5_xyz:  14.377 0.9122  0.9847     6615.526
   5_adp:  14.291 0.9130  0.9839     6582.157
   5_occ:  14.286 0.9130  0.9838     6583.998
   5_bss:  14.313 0.9128  0.9789     6611.247
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3400e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3400e+01
   1_xyz:   1.679  0.013  0.108 18.105  0.007  4.109   1.3801e-01
   1_adp:   1.679  0.013  0.108 18.105  0.007  4.109   1.3801e-01
   1_occ:   1.679  0.013  0.108 18.105  0.007  4.109   1.3801e-01
   2_bss:   1.679  0.013  0.108 18.105  0.007  4.109   1.3801e-01
   2_xyz:   1.201  0.009  0.084 16.383  0.005  4.114   8.4874e-02
   2_adp:   1.201  0.009  0.084 16.383  0.005  4.114   8.4874e-02
   2_occ:   1.201  0.009  0.084 16.383  0.005  4.114   8.4874e-02
   3_bss:   1.201  0.009  0.084 16.383  0.005  4.114   8.4874e-02
   3_xyz:   0.939  0.005  0.069 15.395  0.004  4.123   5.5457e-02
   3_adp:   0.939  0.005  0.069 15.395  0.004  4.123   5.5457e-02
   3_occ:   0.939  0.005  0.069 15.395  0.004  4.123   5.5457e-02
   4_bss:   0.939  0.005  0.069 15.395  0.004  4.123   5.5457e-02
   4_xyz:   1.110  0.008  0.087 15.701  0.004  4.119   7.1082e-02
   4_adp:   1.110  0.008  0.087 15.701  0.004  4.119   7.1082e-02
   4_occ:   1.110  0.008  0.087 15.701  0.004  4.119   7.1082e-02
   5_bss:   1.110  0.008  0.087 15.701  0.004  4.119   7.1082e-02
   5_xyz:   1.006  0.007  0.078 15.264  0.004  4.117   6.0072e-02
   5_adp:   1.006  0.007  0.078 15.264  0.004  4.117   6.0072e-02
   5_occ:   1.006  0.007  0.078 15.264  0.004  4.117   6.0072e-02
   5_bss:   1.006  0.007  0.078 15.264  0.004  4.117   6.0072e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9215e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9215e+00
   1_xyz:  14.763  0.166  0.492 89.122  0.057  2.199   9.8659e-02
   1_adp:  14.763  0.166  0.492 89.122  0.057  2.199   9.8659e-02
   1_occ:  14.763  0.166  0.492 89.122  0.057  2.199   9.8659e-02
   2_bss:  14.763  0.166  0.492 89.122  0.057  2.199   9.8659e-02
   2_xyz:   7.053  0.109  0.294 88.821  0.044  2.237   6.8524e-02
   2_adp:   7.053  0.109  0.294 88.821  0.044  2.237   6.8524e-02
   2_occ:   7.053  0.109  0.294 88.821  0.044  2.237   6.8524e-02
   3_bss:   7.053  0.109  0.294 88.821  0.044  2.237   6.8524e-02
   3_xyz:   6.623  0.040  0.366 81.909  0.041  2.391   4.1805e-02
   3_adp:   6.623  0.040  0.366 81.909  0.041  2.391   4.1805e-02
   3_occ:   6.623  0.040  0.366 81.909  0.041  2.391   4.1805e-02
   4_bss:   6.623  0.040  0.366 81.909  0.041  2.391   4.1805e-02
   4_xyz:   7.116  0.049  0.621 82.063  0.031  2.315   5.4791e-02
   4_adp:   7.116  0.049  0.621 82.063  0.031  2.315   5.4791e-02
   4_occ:   7.116  0.049  0.621 82.063  0.031  2.315   5.4791e-02
   5_bss:   7.116  0.049  0.621 82.063  0.031  2.315   5.4791e-02
   5_xyz:   6.903  0.035  0.545 82.237  0.031  2.345   4.0087e-02
   5_adp:   6.903  0.035  0.545 82.237  0.031  2.345   4.0087e-02
   5_occ:   6.903  0.035  0.545 82.237  0.031  2.345   4.0087e-02
   5_bss:   6.903  0.035  0.545 82.237  0.031  2.345   4.0087e-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:  68.76   0.00  12.49  62.18   0.00   9.82  68.76   0.00  27.04
   1_occ:  68.76   0.00  12.49  62.18   0.00   9.82  68.76   0.00  27.04
   2_bss:  68.76   0.00  12.49  62.18   0.00   9.82  68.76   0.00  27.04
   2_xyz:  68.76   0.00  12.49  62.18   0.00   9.82  68.76   0.00  27.04
   2_adp:  70.60   0.00  12.75  70.60   0.00   8.97  69.54   1.20  33.28
   2_occ:  70.60   0.00  12.75  70.60   0.00   8.97  69.54   1.20  33.28
   3_bss:  70.60   0.00  12.75  70.60   0.00   8.97  69.54   1.20  33.28
   3_xyz:  70.60   0.00  12.75  70.60   0.00   8.97  69.54   1.20  33.28
   3_adp:  83.55   0.00  13.16  83.55   0.00   8.85  74.36   2.15  36.68
   3_occ:  83.55   0.00  13.16  83.55   0.00   8.85  74.36   2.15  36.68
   4_bss:  83.55   0.00  13.16  83.55   0.00   8.85  74.36   2.15  36.68
   4_xyz:  83.55   0.00  13.16  83.55   0.00   8.85  74.36   2.15  36.68
   4_adp:  85.53   0.00  12.89  85.53   0.00   8.65  76.65   1.52  36.00
   4_occ:  85.53   0.00  12.89  85.53   0.00   8.65  76.65   1.52  36.00
   5_bss:  85.53   0.00  12.89  85.53   0.00   8.65  76.65   1.52  36.00
   5_xyz:  85.53   0.00  12.89  85.53   0.00   8.65  76.65   1.52  36.00
   5_adp:  82.62   0.00  12.45  82.62   0.00   8.50  74.82   1.62  33.96
   5_occ:  82.62   0.00  12.45  82.62   0.00   8.50  74.82   1.62  33.96
   5_bss:  84.83   2.21  14.66  84.83   2.21  10.71  77.03   3.84  36.18
------------------------------------------------------------------------
 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:    1.205    0.022    0.411
   1_adp:    1.205    0.022    0.411
   1_occ:    1.205    0.022    0.411
   2_bss:    1.205    0.022    0.411
   2_xyz:    1.536    0.043    0.606
   2_adp:    1.536    0.043    0.606
   2_occ:    1.536    0.043    0.606
   3_bss:    1.536    0.043    0.606
   3_xyz:    1.523    0.028    0.639
   3_adp:    1.523    0.028    0.639
   3_occ:    1.523    0.028    0.639
   4_bss:    1.523    0.028    0.639
   4_xyz:    1.613    0.055    0.685
   4_adp:    1.613    0.055    0.685
   4_occ:    1.613    0.055    0.685
   5_bss:    1.613    0.055    0.685
   5_xyz:    1.693    0.064    0.691
   5_adp:    1.693    0.064    0.691
   5_occ:    1.693    0.064    0.691
   5_bss:    1.693    0.064    0.691
------------------------------------------------------------------------

CPU time actual refinement: 341.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/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_562/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_562/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.63 
  Macro-tasks:
    bulk solvent and scale       = 40.82  
    individual site refinement   = 143.75 
    weights calculation          = 33.12  
    collect and process          = 6.49   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 224.32 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 105.68 
    alpha_beta                      = 8.23   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 117.15 
    fmodel                         = 7.19   
    r_factors                      = 0.27   
    phase_errors                   = 10.33  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 252.77 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.787 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    641 calls, 105.34 s
gradients_fft:          587 calls, 103.22 s

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

# Date 2008-01-16 Time 01:52:32 PST -0800 (1200477152.53 s)
Start R-work = 0.4677, R-free = 0.4687 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.4595, R-free = 0.4600
Final R-work = 0.1145, R-free = 0.1594