# Date 2008-01-16 Time 01:50:32 PST -0800 (1200477032.18 s)
#phil __OFF__

Command line arguments: "../579.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19138
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 579

-------------------------------------------------------------------------------
  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, 47.6339, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99067
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951523

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9907

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, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99067
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951523

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2590 [2165/2193]  1947   218  10.1%
  bin  2:  4.2590 -  3.3934 [2058/2077]  1855   203   9.9%
  bin  3:  3.3934 -  2.9683 [2050/2070]  1845   205  10.0%
  bin  4:  2.9683 -  2.6986 [2021/2046]  1820   201   9.9%
  bin  5:  2.6986 -  2.5061 [2015/2034]  1806   209  10.4%
  bin  6:  2.5061 -  2.3590 [1999/2046]  1804   195   9.8%
  bin  7:  2.3590 -  2.2412 [1992/2024]  1796   196   9.8%
  bin  8:  2.2412 -  2.1440 [1994/2030]  1790   204  10.2%
  bin  9:  2.1440 -  2.0616 [1953/1983]  1754   199  10.2%
  bin 10:  2.0616 -  1.9907 [1342/2020]  1213   129   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2164
        3.04 -     3.66: 4644
        3.66 -     4.28: 8898
        4.28 -     4.90: 12297
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.016 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.116 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.195 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.195 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28019 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_579/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/model_refine_001.geo

CPU time processing inputs: 9.03


============================ 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 47.63395 87.2539 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: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4679   r_free= 0.4532   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.268406                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7500 0.99   1401  157 0.3749 0.3656       6.556      6.5447|
|  2:  4.7500 -  3.7903 0.99   1346  151 0.3810 0.4152      6.7429      6.8444|
|  3:  3.7903 -  3.3171 0.99   1324  147 0.4273 0.3822      6.6584      6.6046|
|  4:  3.3171 -  3.0165 0.99   1309  136 0.4490 0.4113       6.502      6.4189|
|  5:  3.0165 -  2.8018 0.99   1307  150 0.5016 0.4852      6.3687      6.3854|
|  6:  2.8018 -  2.6376 0.98   1297  143 0.4947 0.5283      6.2672      6.2028|
|  7:  2.6376 -  2.5061 0.99   1289  152 0.4918 0.4599      6.2282      6.1179|
|  8:  2.5061 -  2.3975 0.98   1308  136 0.5130 0.4320      6.1845      6.1473|
|  9:  2.3975 -  2.3055 0.98   1280  146 0.5218 0.5516      6.1108      6.1648|
| 10:  2.3055 -  2.2262 0.97   1259  139 0.5412 0.4672      6.1271      6.0964|
| 11:  2.2262 -  2.1568 0.99   1287  146 0.5151 0.4875      6.0156      6.0328|
| 12:  2.1568 -  2.0954 0.98   1277  139 0.5232 0.5279      5.9703      6.0001|
| 13:  2.0954 -  2.0403 0.97   1251  136 0.5227 0.5219      5.8906      5.8225|
| 14:  2.0403 -  1.9907 0.54    695   81 0.5453 0.4997       5.875      5.7707|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.7500  1401   157  0.71  33.34   0.81     0.72      66195.42|
|  2:  4.7500 -  3.7903  1346   151  0.73  33.00   0.89     0.77      94411.49|
|  3:  3.7903 -  3.3171  1324   147  0.64  40.34   0.83     0.73      98849.00|
|  4:  3.3171 -  3.0165  1309   136  0.57  45.93   0.80     0.64      83762.57|
|  5:  3.0165 -  2.8018  1307   150  0.49  52.99   0.74     0.56      70697.40|
|  6:  2.8018 -  2.6376  1297   143  0.47  54.73   0.73     0.53      62460.99|
|  7:  2.6376 -  2.5061  1289   152  0.45  55.74   0.75     0.51      57249.38|
|  8:  2.5061 -  2.3975  1308   136  0.46  54.96   0.74     0.53      50947.95|
|  9:  2.3975 -  2.3055  1280   146  0.44  57.05   0.70     0.52      47908.70|
| 10:  2.3055 -  2.2262  1259   139  0.42  58.22   0.74     0.50      44683.81|
| 11:  2.2262 -  2.1568  1287   146  0.39  60.53   0.73     0.47      43311.18|
| 12:  2.1568 -  2.0954  1277   139  0.36  62.89   0.77     0.46      41004.05|
| 13:  2.0954 -  2.0403  1251   136  0.34  64.35   0.72     0.41      36014.68|
| 14:  2.0403 -  1.9907   695    81  0.33  65.46   0.71     0.35      28071.25|
|alpha:            min =        0.35 max =            0.77 mean =         0.56|
|beta:             min =    28071.25 max =        98849.00 mean =     60376.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.14|
|phase err.(test): min =        0.00 max =           89.97 mean =        52.36|
|-----------------------------------------------------------------------------|

============================== 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 = 10.898543             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.565   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.967975              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.043   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1490 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2599 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3875 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5018 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6528 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7692 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.096 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.723 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    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: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4745   r_free= 0.4576   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.271535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4607   r_free= 0.4458   ksol= 0.32   Bsol= 15.09   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.65,10.77,9.17,0.00,0.00,0.00); trace/3= 8.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.260616                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.144742             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.869   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.904183              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.493   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4607      final r-factor (work) = 0.3633          |
| start r-factor (free) = 0.4458      final r-factor (free) = 0.3795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.9156 = 10.14 * 0.50 * 6.2731 + 1.00 * 54.0960                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3247 = 10.14 * 0.50 * 6.1487 + 1.00 * 0.1360                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3633      final r-factor (work) = 0.3112          |
| start r-factor (free) = 0.3795      final r-factor (free) = 0.3560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5740 = 0.90 * 1.00 * 6.1487 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4682 = 0.90 * 1.00 * 6.0308 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.72   12.41    None  None   None       |
|    all(noH): 2823   0      0.00    86.72   12.41    None  None   None       |
|    Sol.    : 438    0      0.00    86.72   27.30    None  None   None       |
|    Mac.    : 2385   0      0.00    71.87   9.68     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 -   8.672: 1406   |   5:    43.361 -  52.033:   46        |
|      1:     8.672 -  17.344:  751   |   6:    52.033 -  60.705:   24        |
|      2:    17.344 -  26.017:  304   |   7:    60.705 -  69.377:    7        |
|      3:    26.017 -  34.689:  176   |   8:    69.377 -  78.050:    2        |
|      4:    34.689 -  43.361:  104   |   9:    78.050 -  86.722:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3112 r_free = 0.3560             target_work(ml) = 6.004         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3106 r_free = 0.3561             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3106   r_free= 0.3561   ksol= 0.32   Bsol= 15.09   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.65,10.77,9.17,0.00,0.00,0.00); trace/3= 8.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.002825                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3065   r_free= 0.3511   ksol= 0.32   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,6.57,5.37,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.003234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.576457              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.189   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.384226              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.791  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3065      final r-factor (work) = 0.2081          |
| start r-factor (free) = 0.3511      final r-factor (free) = 0.2543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9994 = 8.58 * 0.50 * 6.0313 + 1.00 * 0.1360                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.1100 = 8.58 * 0.50 * 5.8348 + 1.00 * 0.0890                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2081      final r-factor (work) = 0.1839          |
| start r-factor (free) = 0.2543      final r-factor (free) = 0.2282          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2573 = 0.38 * 1.00 * 5.8348 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1810 = 0.38 * 1.00 * 5.6020 + 1.00 * 0.0285                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.45   12.19    None  None   None       |
|    all(noH): 2823   0      0.00    81.45   12.19    None  None   None       |
|    Sol.    : 438    0      0.78    81.45   32.58    None  None   None       |
|    Mac.    : 2385   0      0.00    68.98   8.44     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 -   8.145: 1541   |   5:    40.727 -  48.872:   95        |
|      1:     8.145 -  16.291:  662   |   6:    48.872 -  57.018:   47        |
|      2:    16.291 -  24.436:  208   |   7:    57.018 -  65.163:   23        |
|      3:    24.436 -  32.582:  133   |   8:    65.163 -  73.309:    3        |
|      4:    32.582 -  40.727:  109   |   9:    73.309 -  81.454:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1839 r_free = 0.2282             target_work(ml) = 5.558         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1837 r_free = 0.2288             target_work(ml) = 5.558         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1837   r_free= 0.2288   ksol= 0.32   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,6.57,5.37,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.558320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1821   r_free= 0.2277   ksol= 0.32   Bsol= 62.16   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.91,4.04,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.557272                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.774798              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.699  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.019106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.589   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1821      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.2277      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4836 = 4.77 * 0.50 * 5.6104 + 1.00 * 0.0893                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0706 = 4.77 * 0.50 * 5.4418 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1368      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5589 = 1.02 * 1.00 * 5.4418 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3803 = 1.02 * 1.00 * 5.2622 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.38   12.79    None  None   None       |
|    all(noH): 2823   0      0.00    80.38   12.79    None  None   None       |
|    Sol.    : 438    0      0.76    78.48   37.26    None  None   None       |
|    Mac.    : 2385   0      0.00    80.38   8.30     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 -   8.038: 1568   |   5:    40.191 -  48.229:   96        |
|      1:     8.038 -  16.077:  641   |   6:    48.229 -  56.268:   67        |
|      2:    16.077 -  24.115:  173   |   7:    56.268 -  64.306:   51        |
|      3:    24.115 -  32.153:  106   |   8:    64.306 -  72.344:   23        |
|      4:    32.153 -  40.191:   88   |   9:    72.344 -  80.382:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1266 r_free = 0.1708             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1264 r_free = 0.1707             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1707   ksol= 0.32   Bsol= 62.16   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.91,4.04,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.241752                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1708   ksol= 0.33   Bsol= 62.16   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.24,3.84,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.242448                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.937219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.836  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.575  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8084 = 2.94 * 0.50 * 5.2629 + 1.00 * 0.0792                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7321 = 2.94 * 0.50 * 5.2131 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6284 = 0.31 * 1.00 * 5.2131 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6121 = 0.31 * 1.00 * 5.1872 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.56   12.40    None  None   None       |
|    all(noH): 2823   0      0.00    80.56   12.40    None  None   None       |
|    Sol.    : 438    0      0.43    76.90   36.10    None  None   None       |
|    Mac.    : 2385   0      0.00    80.56   8.05     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 -   8.056: 1638   |   5:    40.282 -  48.338:   85        |
|      1:     8.056 -  16.113:  595   |   6:    48.338 -  56.394:   71        |
|      2:    16.113 -  24.169:  169   |   7:    56.394 -  64.451:   45        |
|      3:    24.169 -  32.225:  105   |   8:    64.451 -  72.507:   16        |
|      4:    32.225 -  40.282:   90   |   9:    72.507 -  80.563:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1605             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1605             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1605   ksol= 0.33   Bsol= 62.16   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.24,3.84,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1604   ksol= 0.33   Bsol= 62.16   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,3.05,3.88,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176841                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.619599              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.095  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.998550              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.883  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8697 = 2.62 * 0.50 * 5.1868 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8452 = 2.62 * 0.50 * 5.1697 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1739 = 1.00 * 1.00 * 5.1697 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1648 = 1.00 * 1.00 * 5.1589 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.93   12.38    None  None   None       |
|    all(noH): 2823   0      0.00    84.93   12.38    None  None   None       |
|    Sol.    : 438    0      1.15    77.45   36.20    None  None   None       |
|    Mac.    : 2385   0      0.00    84.93   8.01     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 -   8.494: 1707   |   5:    42.467 -  50.961:   77        |
|      1:     8.494 -  16.987:  545   |   6:    50.961 -  59.454:   71        |
|      2:    16.987 -  25.480:  164   |   7:    59.454 -  67.948:   30        |
|      3:    25.480 -  33.974:  107   |   8:    67.948 -  76.441:   16        |
|      4:    33.974 -  42.467:  101   |   9:    76.441 -  84.935:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1594             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1594             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1594   ksol= 0.33   Bsol= 62.16   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,3.05,3.88,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165353                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7500 0.99   1401  157 0.0999 0.1301       5.395      5.5562|
|  2:  4.7500 -  3.7903 0.99   1346  151 0.0859 0.1080      5.4358      5.6402|
|  3:  3.7903 -  3.3171 0.99   1324  147 0.1059 0.1489      5.4727      5.8509|
|  4:  3.3171 -  3.0165 0.99   1309  136 0.1217 0.1553      5.4542      5.5902|
|  5:  3.0165 -  2.8018 0.99   1307  150 0.1364 0.1709      5.3588      5.5276|
|  6:  2.8018 -  2.6376 0.98   1297  143 0.1272 0.2175      5.2441      5.5621|
|  7:  2.6376 -  2.5061 0.99   1289  152 0.1282 0.1635      5.1931      5.3347|
|  8:  2.5061 -  2.3975 0.98   1308  136 0.1176 0.1702      5.1046      5.3731|
|  9:  2.3975 -  2.3055 0.98   1280  146 0.1209 0.1955      5.0492      5.3685|
| 10:  2.3055 -  2.2262 0.97   1259  139 0.1176 0.1619      5.0047      5.1808|
| 11:  2.2262 -  2.1568 0.99   1287  146 0.1158 0.1878      4.9559      5.2874|
| 12:  2.1568 -  2.0954 0.98   1277  139 0.1117 0.1722       4.876      5.1958|
| 13:  2.0954 -  2.0403 0.97   1251  136 0.1104 0.1733      4.7881      5.0399|
| 14:  2.0403 -  1.9907 0.54    695   81 0.1063 0.1673      4.7049      4.9339|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.7500  1401   157  0.94   9.22   0.97     0.95       7464.66|
|  2:  4.7500 -  3.7903  1346   151  0.95   8.02   1.00     0.99       9058.92|
|  3:  3.7903 -  3.3171  1324   147  0.93  11.22   1.02     1.01      10377.19|
|  4:  3.3171 -  3.0165  1309   136  0.92  13.54   1.00     0.98      10290.56|
|  5:  3.0165 -  2.8018  1307   150  0.89  16.53   0.99     0.96       8788.58|
|  6:  2.8018 -  2.6376  1297   143  0.89  17.05   0.97     0.94       7621.35|
|  7:  2.6376 -  2.5061  1289   152  0.90  16.14   0.98     0.95       6616.84|
|  8:  2.5061 -  2.3975  1308   136  0.91  15.48   0.98     0.95       5753.28|
|  9:  2.3975 -  2.3055  1280   146  0.90  16.50   1.00     0.96       5276.40|
| 10:  2.3055 -  2.2262  1259   139  0.89  16.73   0.98     0.95       4846.60|
| 11:  2.2262 -  2.1568  1287   146  0.90  16.58   0.98     0.94       4565.53|
| 12:  2.1568 -  2.0954  1277   139  0.91  15.63   1.00     0.98       3991.64|
| 13:  2.0954 -  2.0403  1251   136  0.90  16.12   0.98     0.97       3403.28|
| 14:  2.0403 -  1.9907   695    81  0.91  15.41   0.96     0.91       2763.27|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2763.27 max =        10377.19 mean =      6653.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.49|
|phase err.(test): min =        0.00 max =           87.83 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1594   ksol= 0.33   Bsol= 61.61   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.01,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1594   ksol= 0.33   Bsol= 61.61   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.01,0.90,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165287                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7500 0.99   1401  157 0.0997 0.1300      5.3929      5.5547|
|  2:  4.7500 -  3.7903 0.99   1346  151 0.0858 0.1077      5.4341       5.638|
|  3:  3.7903 -  3.3171 0.99   1324  147 0.1058 0.1488       5.472      5.8512|
|  4:  3.3171 -  3.0165 0.99   1309  136 0.1218 0.1555      5.4547      5.5906|
|  5:  3.0165 -  2.8018 0.99   1307  150 0.1366 0.1710      5.3598      5.5284|
|  6:  2.8018 -  2.6376 0.98   1297  143 0.1273 0.2176      5.2446      5.5624|
|  7:  2.6376 -  2.5061 0.99   1289  152 0.1283 0.1635      5.1936      5.3353|
|  8:  2.5061 -  2.3975 0.98   1308  136 0.1177 0.1703      5.1049      5.3733|
|  9:  2.3975 -  2.3055 0.98   1280  146 0.1209 0.1953      5.0495      5.3683|
| 10:  2.3055 -  2.2262 0.97   1259  139 0.1176 0.1621      5.0051      5.1819|
| 11:  2.2262 -  2.1568 0.99   1287  146 0.1158 0.1878       4.956      5.2873|
| 12:  2.1568 -  2.0954 0.98   1277  139 0.1117 0.1722       4.876      5.1964|
| 13:  2.0954 -  2.0403 0.97   1251  136 0.1104 0.1731      4.7881      5.0394|
| 14:  2.0403 -  1.9907 0.54    695   81 0.1063 0.1671      4.7049      4.9335|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9794 -  4.7500  1401   157  0.94   9.19   0.97     0.95       7433.86|
|  2:  4.7500 -  3.7903  1346   151  0.95   8.01   1.01     0.99       9023.53|
|  3:  3.7903 -  3.3171  1324   147  0.93  11.20   1.02     1.02      10353.38|
|  4:  3.3171 -  3.0165  1309   136  0.92  13.54   1.00     0.99      10301.05|
|  5:  3.0165 -  2.8018  1307   150  0.89  16.54   1.00     0.96       8803.21|
|  6:  2.8018 -  2.6376  1297   143  0.89  17.06   0.98     0.95       7630.24|
|  7:  2.6376 -  2.5061  1289   152  0.90  16.15   0.99     0.96       6622.69|
|  8:  2.5061 -  2.3975  1308   136  0.91  15.49   0.99     0.96       5757.28|
|  9:  2.3975 -  2.3055  1280   146  0.90  16.51   1.00     0.96       5280.41|
| 10:  2.3055 -  2.2262  1259   139  0.89  16.74   0.99     0.95       4850.19|
| 11:  2.2262 -  2.1568  1287   146  0.90  16.59   0.99     0.94       4568.04|
| 12:  2.1568 -  2.0954  1277   139  0.91  15.63   1.01     0.99       3993.09|
| 13:  2.0954 -  2.0403  1251   136  0.90  16.12   0.99     0.98       3402.87|
| 14:  2.0403 -  1.9907   695    81  0.91  15.41   0.96     0.92       2762.35|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2762.35 max =        10353.38 mean =      6650.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.49|
|phase err.(test): min =        0.00 max =           87.73 mean =        13.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.102)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.15    88.08   15.53    None  None   None       |
|    all(noH): 2823   0      3.15    88.08   15.53    None  None   None       |
|    Sol.    : 438    0      4.30    80.60   39.34    None  None   None       |
|    Mac.    : 2385   0      3.15    88.08   11.15    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:     3.146 -  11.639: 1707   |   5:    45.613 -  54.107:   77        |
|      1:    11.639 -  20.133:  545   |   6:    54.107 -  62.600:   71        |
|      2:    20.133 -  28.626:  164   |   7:    62.600 -  71.094:   30        |
|      3:    28.626 -  37.120:  107   |   8:    71.094 -  79.587:   16        |
|      4:    37.120 -  45.613:  101   |   9:    79.587 -  88.081:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.294 - 5.471
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 316
   mapped sites are within: 0.718 - 5.471

peak=   10.285 closest distance to " CG2 VAL A 230 " =    1.351
peak=    6.383 closest distance to " CG  LEU A   5 " =    1.187
peak=    6.091 closest distance to " NH2 ARG A  56 " =    2.294
peak=    5.665 closest distance to " CB  VAL A 296 " =    1.157
peak=    5.578 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.363 closest distance to " CB  GLN A 223 " =    1.411
peak=    5.193 closest distance to " CG  PRO A  54 " =    1.261
peak=    4.999 closest distance to " CB  VAL A 230 " =    1.210
peak=    4.943 closest distance to " O   HOH Z 210 " =    0.990
peak=    4.864 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.841 closest distance to " CG2 VAL A 296 " =    0.993
peak=    4.800 closest distance to " CD2 LEU A   5 " =    1.161
peak=    4.797 closest distance to " O   HOH Z 232 " =    2.318
peak=    4.782 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.736 closest distance to " CB  SER A  63 " =    1.192
peak=    4.669 closest distance to " CG1 VAL A 296 " =    1.151
peak=    4.595 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.550 closest distance to " O   HOH Z  44 " =    2.266
peak=    4.536 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.523 closest distance to " CB  PRO A  54 " =    0.950
peak=    4.505 closest distance to " CB  ARG A 190 " =    1.693
peak=    4.477 closest distance to " CZ  PHE A 218 " =    1.200
peak=    4.423 closest distance to " O   SER A  87 " =    2.219
peak=    4.408 closest distance to " O   HOH Z 234 " =    3.665
peak=    4.348 closest distance to " CG  PRO A 213 " =    1.237
peak=    4.344 closest distance to " CB  GLU A 152 " =    1.165
peak=    4.342 closest distance to " C   PRO A 198 " =    1.499
peak=    4.341 closest distance to " O   HOH Z 403 " =    1.733
peak=    4.319 closest distance to " CG  PRO A 198 " =    1.201
peak=    4.296 closest distance to " O   HOH Z 142 " =    1.571
peak=    4.273 closest distance to " CG  PRO A 243 " =    1.154
peak=    4.240 closest distance to " O   HOH Z  59 " =    2.331
peak=    4.229 closest distance to " O   HOH Z 265 " =    2.105
peak=    4.204 closest distance to " O   HOH Z  63 " =    2.126
peak=    4.191 closest distance to " CB  ARG A  79 " =    1.440
peak=    4.170 closest distance to " O   HOH Z 248 " =    1.608
peak=    4.150 closest distance to " OG BSER A 164 " =    2.144
peak=    4.137 closest distance to " O   HOH Z 346 " =    1.554
peak=    4.131 closest distance to " O   HOH Z 193 " =    1.709
peak=    4.084 closest distance to " O   HOH Z 412 " =    3.736
peak=    4.071 closest distance to " CA  ALA A  51 " =    0.974
peak=    4.068 closest distance to " O   HOH Z 369 " =    2.358
peak=    4.067 closest distance to " O   HOH Z 423 " =    1.870
peak=    4.066 closest distance to " O   HOH Z 126 " =    1.879
peak=    4.054 closest distance to " O   HOH Z  43 " =    1.993
peak=    4.034 closest distance to " CB  ASN A 148 " =    1.386
peak=    4.034 closest distance to " O   HOH Z 365 " =    2.386
peak=    4.031 closest distance to " O   HOH Z 280 " =    2.916
peak=    4.030 closest distance to " CD2 LEU A 228 " =    1.195
peak=    4.029 closest distance to " O   HOH Z 287 " =    1.913
peak=    4.018 closest distance to " O   HOH Z 422 " =    2.659
peak=    4.004 closest distance to " O   HOH Z 427 " =    3.011
peak=    3.996 closest distance to " CA  ARG A  36 " =    1.071
peak=    3.981 closest distance to " O   HOH Z 303 " =    2.186
peak=    3.975 closest distance to " CB  GLU A 128 " =    1.174
peak=    3.972 closest distance to " OD1 ASN A  69 " =    2.532
peak=    3.970 closest distance to " O   HOH Z  97 " =    1.986
peak=    3.969 closest distance to " CB  VAL A 202 " =    1.478
peak=    3.949 closest distance to " O   HOH Z 126 " =    1.600
peak=    3.942 closest distance to " O   HOH Z 189 " =    2.559
peak=    3.930 closest distance to " CA  ALA A 295 " =    1.029
peak=    3.926 closest distance to " O   HOH Z 298 " =    1.792
peak=    3.918 closest distance to " CB AVAL A  41 " =    1.082
peak=    3.902 closest distance to " CG  MET A 185 " =    1.200
peak=    3.893 closest distance to " CD2 TRP A 179 " =    1.313
peak=    3.892 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.891 closest distance to " CD  LYS A 166 " =    1.324
peak=    3.879 closest distance to " O   HOH Z 402 " =    1.475
peak=    3.878 closest distance to " O   HOH Z 214 " =    2.538
peak=    3.874 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.864 closest distance to " CB  GLU A 277 " =    3.669
peak=    3.845 closest distance to " O   HOH Z 251 " =    1.444
peak=    3.843 closest distance to " O   HOH Z 158 " =    3.137
peak=    3.824 closest distance to " O   HOH Z 154 " =    1.458
peak=    3.810 closest distance to " O   HOH Z  97 " =    2.350
peak=    3.805 closest distance to " CB  TRP A 266 " =    1.055
peak=    3.805 closest distance to " O   HOH Z  49 " =    1.049
peak=    3.794 closest distance to " O   HOH Z 261 " =    2.129
peak=    3.791 closest distance to " CG1 ILE A  33 " =    1.205
peak=    3.791 closest distance to " CB  GLU A  46 " =    1.019
peak=    3.787 closest distance to " O   HOH Z  40 " =    2.052
peak=    3.778 closest distance to " O   HOH Z 316 " =    3.083
peak=    3.763 closest distance to " CB  ASP A 140 " =    1.068
peak=    3.757 closest distance to " CG  ARG A  66 " =    2.537
peak=    3.754 closest distance to " ND2 ASN A 187 " =    1.470
peak=    3.750 closest distance to " O   HOH Z 359 " =    1.571
peak=    3.750 closest distance to " ND2 ASN A 249 " =    1.918
peak=    3.749 closest distance to " O   HOH Z 285 " =    2.659
peak=    3.746 closest distance to " O   HOH Z 272 " =    1.940
peak=    3.741 closest distance to " CA  ARG A 195 " =    1.213
peak=    3.719 closest distance to " O   HOH Z 193 " =    2.051
peak=    3.710 closest distance to " NE2 GLN A  77 " =    3.332
peak=    3.709 closest distance to " CA  VAL A  41 " =    0.844
peak=    3.707 closest distance to " CD  ARG A 269 " =    1.007
peak=    3.705 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.705 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.703 closest distance to " O   HOH Z  80 " =    1.864
peak=    3.677 closest distance to " CB  ALA A   9 " =    1.665
peak=    3.665 closest distance to " O   HOH Z 327 " =    1.569
peak=    3.658 closest distance to " O   HOH Z 417 " =    3.034
peak=    3.657 closest distance to " CE  LYS A  76 " =    0.862
peak=    3.636 closest distance to " CB  SER A  26 " =    1.829
peak=    3.634 closest distance to " O   HOH Z  48 " =    1.648
peak=    3.634 closest distance to " NH2 ARG A 156 " =    1.144
peak=    3.632 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.632 closest distance to " NZ  LYS A  48 " =    1.209
peak=    3.631 closest distance to " O   HOH Z 383 " =    2.069
peak=    3.628 closest distance to " O   HOH Z 357 " =    2.055
peak=    3.616 closest distance to " O   HOH Z 145 " =    2.384
peak=    3.616 closest distance to " N   ASN A  39 " =    1.261
peak=    3.613 closest distance to " CB  ARG A  79 " =    0.933
peak=    3.610 closest distance to " O   HOH Z 371 " =    3.140
peak=    3.606 closest distance to " O   TRP A 274 " =    1.883
peak=    3.605 closest distance to " CB  SER A   3 " =    1.292
peak=    3.601 closest distance to " O   HOH Z  35 " =    2.357
peak=    3.597 closest distance to " O   HOH Z  21 " =    1.772
peak=    3.595 closest distance to " CB  ALA A 248 " =    1.348
peak=    3.594 closest distance to " CB  THR A  31 " =    1.528
peak=    3.593 closest distance to " O   HOH Z 426 " =    1.449
peak=    3.590 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.590 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.589 closest distance to " CB  VAL A 265 " =    1.277
peak=    3.588 closest distance to " O   HOH Z  85 " =    1.278
peak=    3.587 closest distance to " O   HOH Z  54 " =    1.585
peak=    3.587 closest distance to " O   ALA A 165 " =    1.471
peak=    3.583 closest distance to " O   HOH Z 147 " =    1.845
peak=    3.574 closest distance to " O   HOH Z  78 " =    1.638
peak=    3.573 closest distance to " O   HOH Z 271 " =    2.549
peak=    3.572 closest distance to " CG1 ILE A  49 " =    1.585
peak=    3.566 closest distance to " CD  LYS A  76 " =    2.036
peak=    3.565 closest distance to " CD1 LEU A  96 " =    0.728
peak=    3.564 closest distance to " CZ  PHE A  38 " =    1.178
peak=    3.564 closest distance to " CB  ASN A 142 " =    1.227
peak=    3.549 closest distance to " CG2 THR A 221 " =    1.209
peak=    3.548 closest distance to " O   HOH Z 180 " =    2.221
peak=    3.541 closest distance to " CB  GLN A  88 " =    1.214
peak=    3.539 closest distance to " CG  GLN A  58 " =    2.874
peak=    3.535 closest distance to " OD2 ASP A 298 " =    3.791
peak=    3.532 closest distance to " O   HOH Z 130 " =    2.358
peak=    3.532 closest distance to " CB  THR A  52 " =    0.873
peak=    3.531 closest distance to " CG1BVAL A  72 " =    1.808
peak=    3.521 closest distance to " O   HOH Z 407 " =    2.674
peak=    3.514 closest distance to " N   ASP A 162 " =    1.241
peak=    3.511 closest distance to " O   HOH Z 134 " =    1.441
peak=    3.505 closest distance to " O   HOH Z 437 " =    1.946
peak=    3.505 closest distance to " O   HOH Z 102 " =    1.310
peak=    3.503 closest distance to " O   HOH Z 203 " =    1.822
peak=    3.502 closest distance to " CB  ASN A 187 " =    1.362
peak=    3.499 closest distance to " OE1 GLU A   2 " =    1.869
peak=    3.499 closest distance to " O  BHOH Z 338 " =    2.355
peak=    3.497 closest distance to " CB  MET A  40 " =    0.971
peak=    3.494 closest distance to " O   HOH Z 197 " =    2.607
peak=    3.491 closest distance to " CB  ASN A  39 " =    0.861
peak=    3.488 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.485 closest distance to " O   HOH Z 258 " =    2.211
peak=    3.482 closest distance to " CB  ARG A 139 " =    0.918
peak=    3.479 closest distance to " O   HOH Z 366 " =    2.850
peak=    3.479 closest distance to " O   ASP A 124 " =    1.406
peak=    3.477 closest distance to " CA  LYS A 117 " =    1.278
peak=    3.475 closest distance to " CA  TYR A 116 " =    1.319
peak=    3.471 closest distance to " O   HOH Z 313 " =    1.741
peak=    3.464 closest distance to " CA  ASP A 191 " =    1.009
peak=    3.464 closest distance to " CG2 ILE A  20 " =    1.363
peak=    3.455 closest distance to " O   HOH Z 126 " =    1.770
peak=    3.452 closest distance to " O   HOH Z 128 " =    1.473
peak=    3.452 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.451 closest distance to " O   ASN A  74 " =    1.650
peak=    3.438 closest distance to " OG1 THR A 294 " =    2.414
peak=    3.437 closest distance to " O   HOH Z 393 " =    3.820
peak=    3.435 closest distance to " CE1 HIS A 108 " =    1.138
peak=    3.434 closest distance to " O   HOH Z 345 " =    1.627
peak=    3.429 closest distance to " CD2 LEU A 297 " =    0.911
peak=    3.427 closest distance to " O   HOH Z 245 " =    1.371
peak=    3.410 closest distance to " CA  LYS A 181 " =    1.060
peak=    3.409 closest distance to " O   HOH Z 273 " =    2.942
peak=    3.406 closest distance to " O   HOH Z 406 " =    1.496
peak=    3.402 closest distance to " OG BSER A 134 " =    2.837
peak=    3.398 closest distance to " CB  ASN A 285 " =    0.947
peak=    3.397 closest distance to " C   ILE A 106 " =    1.850
peak=    3.394 closest distance to " NZ  LYS A 117 " =    3.095
peak=    3.390 closest distance to " CA  ASN A 176 " =    1.240
peak=    3.387 closest distance to " O   HOH Z 420 " =    5.471
peak=    3.384 closest distance to " CB  THR A 157 " =    1.177
peak=    3.378 closest distance to " CA  VAL A 125 " =    1.241
peak=    3.378 closest distance to " O   HOH Z 199 " =    1.637
peak=    3.374 closest distance to " C   ALA A 299 " =    0.944
peak=    3.372 closest distance to " O   HOH Z 353 " =    2.702
peak=    3.371 closest distance to " NH1AARG A 145 " =    1.291
peak=    3.371 closest distance to " O   HOH Z 299 " =    4.260
peak=    3.368 closest distance to " O   HOH Z 421 " =    1.661
peak=    3.367 closest distance to " O   HOH Z 357 " =    2.537
peak=    3.365 closest distance to " CB  TRP A 150 " =    1.458
peak=    3.364 closest distance to " CA  ILE A 106 " =    0.756
peak=    3.361 closest distance to " CD BLYS A 290 " =    0.991
peak=    3.357 closest distance to " CA  ALA A 160 " =    0.879
peak=    3.357 closest distance to " CZ3 TRP A  85 " =    0.970
peak=    3.356 closest distance to " CB  HIS A 108 " =    0.792
peak=    3.351 closest distance to " O   HOH Z 369 " =    1.410
peak=    3.347 closest distance to " O   HOH Z 128 " =    1.979
peak=    3.346 closest distance to " O   HOH Z 404 " =    2.365
peak=    3.344 closest distance to " O   HOH Z  88 " =    2.591
peak=    3.341 closest distance to " O   HOH Z 425 " =    1.994
peak=    3.339 closest distance to " CB  TYR A 247 " =    1.003
peak=    3.335 closest distance to " N   VAL A 126 " =    1.498
peak=    3.334 closest distance to " O   HOH Z 189 " =    2.824
peak=    3.329 closest distance to " CB  PRO A  90 " =    1.170
peak=    3.327 closest distance to " CD1 ILE A 199 " =    0.981
peak=    3.324 closest distance to " CB  ALA A 295 " =    1.140
peak=    3.322 closest distance to " ND2 ASN A 249 " =    0.936
peak=    3.322 closest distance to " O   HOH Z 391 " =    3.016
peak=    3.320 closest distance to " O   HOH Z 171 " =    2.703
peak=    3.313 closest distance to " O   HOH Z 133 " =    2.648
peak=    3.313 closest distance to " O   HOH Z 344 " =    2.962
peak=    3.313 closest distance to " CA  ALA A 158 " =    1.384
peak=    3.311 closest distance to " CG2 ILE A 120 " =    1.149
peak=    3.311 closest distance to " CB  ALA A 291 " =    1.304
peak=    3.308 closest distance to " O   HOH Z 355 " =    1.890
peak=    3.299 closest distance to " O   HOH Z 435 " =    1.936
peak=    3.299 closest distance to " CD2 TYR A 186 " =    1.029
peak=    3.298 closest distance to " O   HOH Z 419 " =    1.694
peak=    3.296 closest distance to " CA  THR A 264 " =    0.718
peak=    3.293 closest distance to " O   HOH Z 112 " =    1.708
peak=    3.291 closest distance to " C   TYR A 214 " =    1.511
peak=    3.287 closest distance to " CA  ASN A 217 " =    1.152
peak=    3.285 closest distance to " CB  ASN A 215 " =    1.175
peak=    3.283 closest distance to " OH  TYR A 116 " =    1.191
peak=    3.281 closest distance to " CD  PRO A  54 " =    0.980
peak=    3.273 closest distance to " CB  GLN A 103 " =    0.978
peak=    3.272 closest distance to " OE1 GLN A  11 " =    1.825
peak=    3.264 closest distance to " O   HOH Z 294 " =    1.558
peak=    3.263 closest distance to " O   HOH Z  15 " =    2.232
peak=    3.262 closest distance to " O   HOH Z 420 " =    1.858
peak=    3.260 closest distance to " O   HOH Z 411 " =    1.756
peak=    3.259 closest distance to " CA  ALA A  84 " =    1.326
peak=    3.259 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.258 closest distance to " O   ALA A 158 " =    1.297
peak=    3.254 closest distance to " O   HOH Z 116 " =    2.804
peak=    3.252 closest distance to " O   HOH Z 109 " =    2.474
peak=    3.249 closest distance to " CA  ASN A 215 " =    1.111
peak=    3.247 closest distance to " CB  ASN A 110 " =    1.242
peak=    3.242 closest distance to " N   SER A 135 " =    1.371
peak=    3.241 closest distance to " CZ3 TRP A 266 " =    1.123
peak=    3.233 closest distance to " CB  SER A 273 " =    0.861
peak=    3.227 closest distance to " CA  ASP A 140 " =    1.187
peak=    3.226 closest distance to " O   HOH Z 368 " =    3.551
peak=    3.222 closest distance to " CG2 VAL A 257 " =    0.819
peak=    3.220 closest distance to " CZ  PHE A 192 " =    1.052
peak=    3.215 closest distance to " NH2BARG A 190 " =    1.839
peak=    3.215 closest distance to " O   HOH Z  44 " =    1.851
peak=    3.215 closest distance to " O   HOH Z  83 " =    1.545
peak=    3.214 closest distance to " N   SER A 288 " =    1.728
peak=    3.213 closest distance to " CA  SER A  87 " =    0.981
peak=    3.211 closest distance to " O   HOH Z 227 " =    2.002
peak=    3.205 closest distance to " CG1 ILE A 151 " =    1.141
peak=    3.205 closest distance to " CB  GLN A 278 " =    0.897
peak=    3.204 closest distance to " OG1 THR A 294 " =    1.637
peak=    3.204 closest distance to " CB  LEU A  83 " =    0.770
peak=    3.203 closest distance to " O   HOH Z 361 " =    3.048
peak=    3.199 closest distance to " O   HOH Z 425 " =    1.275
peak=    3.195 closest distance to " OG  SER A  22 " =    2.794
peak=    3.193 closest distance to " O   HOH Z 329 " =    4.145
peak=    3.181 closest distance to " O   HOH Z 380 " =    1.800
peak=    3.181 closest distance to " NH2AARG A 275 " =    3.473
peak=    3.177 closest distance to " O   HOH Z 193 " =    1.636
peak=    3.177 closest distance to " O   HOH Z  66 " =    2.286
peak=    3.173 closest distance to " CA  LYS A 290 " =    1.169
peak=    3.173 closest distance to " O   HOH Z 173 " =    2.493
peak=    3.171 closest distance to " ND1 HIS A  81 " =    1.691
peak=    3.168 closest distance to " CA  ASP A 162 " =    1.117
peak=    3.167 closest distance to " O   HOH Z 305 " =    3.656
peak=    3.166 closest distance to " CZ3 TRP A 274 " =    4.548
peak=    3.165 closest distance to " CG  MET A 185 " =    1.061
peak=    3.164 closest distance to " O   HOH Z 409 " =    3.551
peak=    3.162 closest distance to " O   HOH Z 227 " =    1.532
peak=    3.159 closest distance to " O   HOH Z  68 " =    2.125
peak=    3.157 closest distance to " N   PHE A 130 " =    1.291
peak=    3.156 closest distance to " CD  ARG A  66 " =    2.129
peak=    3.156 closest distance to " OG  SER A 245 " =    1.532
peak=    3.153 closest distance to " O   HOH Z 132 " =    2.746
peak=    3.153 closest distance to " CA  ALA A 233 " =    1.623
peak=    3.141 closest distance to " N   ASP A 231 " =    1.713
peak=    3.141 closest distance to " CG2 ILE A 234 " =    0.913
peak=    3.138 closest distance to " CB  ALA A 100 " =    1.226
peak=    3.138 closest distance to " CG2 VAL A 197 " =    1.123
peak=    3.134 closest distance to " O   HOH Z 128 " =    2.179
peak=    3.132 closest distance to " O   HOH Z 345 " =    3.098
peak=    3.132 closest distance to " O   HOH Z  94 " =    2.485
peak=    3.128 closest distance to " CG2 THR A 220 " =    0.723
peak=    3.128 closest distance to " O   HOH Z 139 " =    4.784
peak=    3.123 closest distance to " O   HOH Z 172 " =    3.406
peak=    3.122 closest distance to " O   HOH Z 279 " =    2.148
peak=    3.119 closest distance to " CG1 ILE A  20 " =    1.285
peak=    3.117 closest distance to " O   ILE A  20 " =    2.212
peak=    3.110 closest distance to " CA  SER A  32 " =    1.625
peak=    3.104 closest distance to " NE2 HIS A 207 " =    1.199
peak=    3.102 closest distance to " O   HOH Z 188 " =    1.938
peak=    3.089 closest distance to " O   HOH Z 301 " =    1.900
peak=    3.085 closest distance to " CG  LEU A 281 " =    1.077
peak=    3.071 closest distance to " CD  ARG A  66 " =    2.562
peak=    3.063 closest distance to " CB  LYS A 117 " =    1.124
peak=    3.063 closest distance to " CB  PHE A 204 " =    0.841
peak=    3.059 closest distance to " CA  MET A 105 " =    0.976
peak=    3.047 closest distance to " O   HOH Z 213 " =    2.383
peak=    3.044 closest distance to " O   SER A 164 " =    1.200
peak=    3.044 closest distance to " CD2 TYR A  30 " =    1.010
peak=    3.041 closest distance to " O   HOH Z  78 " =    1.879
peak=    3.041 closest distance to " CG2BVAL A  72 " =    1.771
peak=    3.026 closest distance to " O   GLN A 278 " =    1.501
peak=    3.019 closest distance to " O   HOH Z 438 " =    2.791

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.849 - 5.657
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.849 - 5.657

peak=   -5.392 closest distance to " CG2 VAL A 230 " =    0.849
peak=   -4.608 closest distance to " SG  CYS A 254 " =    3.332
peak=   -4.536 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.399 closest distance to " O   HOH Z 266 " =    5.232
peak=   -4.349 closest distance to " O   HOH Z 166 " =    1.628
peak=   -4.345 closest distance to " CD  GLN A  58 " =    1.065
peak=   -4.304 closest distance to " O   HOH Z 196 " =    2.172
peak=   -4.259 closest distance to " CB  PRO A 243 " =    2.719
peak=   -4.225 closest distance to " CG2BVAL A  41 " =    2.734
peak=   -4.161 closest distance to " O   HOH Z 283 " =    2.152
peak=   -4.090 closest distance to " OG  SER A  97 " =    2.327
peak=   -4.085 closest distance to " O   HOH Z 210 " =    0.934
peak=   -4.080 closest distance to " OXT GLY A 302 " =    2.842
peak=   -4.065 closest distance to " CB  PHE A 192 " =    1.990
peak=   -4.065 closest distance to " CD1 LEU A 101 " =    2.409
peak=   -4.029 closest distance to " O   HOH Z  13 " =    1.723
peak=   -4.028 closest distance to " CA  ASP A 298 " =    1.051
peak=   -3.979 closest distance to " C   HIS A 108 " =    1.190
peak=   -3.963 closest distance to " CH2 TRP A 179 " =    1.226
peak=   -3.944 closest distance to " O   PRO A 163 " =    2.197
peak=   -3.937 closest distance to " CG1 VAL A 250 " =    2.746
peak=   -3.915 closest distance to " CB  ALA A 161 " =    2.621
peak=   -3.900 closest distance to " O   HOH Z 351 " =    1.596
peak=   -3.834 closest distance to " CG1 VAL A 112 " =    2.674
peak=   -3.831 closest distance to " OE1 GLN A 223 " =    2.227
peak=   -3.830 closest distance to " O   HOH Z 394 " =    1.630
peak=   -3.826 closest distance to " CA  VAL A  67 " =    2.936
peak=   -3.821 closest distance to " CG  ASP A 231 " =    0.870
peak=   -3.814 closest distance to " CD1 PHE A  59 " =    1.974
peak=   -3.809 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.782 closest distance to " CE3 TRP A 150 " =    2.232
peak=   -3.778 closest distance to " OG BSER A 134 " =    1.337
peak=   -3.776 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.773 closest distance to " CB  ALA A 248 " =    2.101
peak=   -3.767 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -3.747 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.710 closest distance to " CB  ALA A 248 " =    2.288
peak=   -3.699 closest distance to " CG2 ILE A  49 " =    2.735
peak=   -3.699 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.687 closest distance to " CG1 VAL A 296 " =    1.127
peak=   -3.686 closest distance to " O   HOH Z 231 " =    2.206
peak=   -3.685 closest distance to " O   HOH Z  37 " =    1.950
peak=   -3.676 closest distance to " O   HOH Z  11 " =    1.878
peak=   -3.673 closest distance to " O   HOH Z 290 " =    1.182
peak=   -3.659 closest distance to " O   VAL A 189 " =    2.627
peak=   -3.655 closest distance to " O   SER A 271 " =    2.011
peak=   -3.655 closest distance to " CE BMET A  47 " =    2.099
peak=   -3.654 closest distance to " CB  ASP A 171 " =    2.274
peak=   -3.648 closest distance to " O   HOH Z 177 " =    1.753
peak=   -3.634 closest distance to " ND2 ASN A 249 " =    2.338
peak=   -3.627 closest distance to " ND2 ASN A 187 " =    1.603
peak=   -3.627 closest distance to " NE2 GLN A  88 " =    1.920
peak=   -3.621 closest distance to " CG2 ILE A 263 " =    2.369
peak=   -3.620 closest distance to " CD  ARG A 139 " =    1.589
peak=   -3.620 closest distance to " CD  LYS A 289 " =    2.469
peak=   -3.609 closest distance to " CB  PHE A 208 " =    2.368
peak=   -3.603 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.601 closest distance to " NE2 GLN A  88 " =    1.061
peak=   -3.598 closest distance to " CG  ARG A 269 " =    2.304
peak=   -3.588 closest distance to " O   HOH Z  10 " =    1.639
peak=   -3.570 closest distance to " NH2AARG A 275 " =    5.033
peak=   -3.539 closest distance to " O   HOH Z 264 " =    1.752
peak=   -3.537 closest distance to " N   SER A 276 " =    1.372
peak=   -3.534 closest distance to " O   ARG A  24 " =    2.084
peak=   -3.533 closest distance to " CG  GLU A  53 " =    1.571
peak=   -3.521 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.513 closest distance to " OD1 ASN A 148 " =    1.448
peak=   -3.489 closest distance to " O   HOH Z  52 " =    1.698
peak=   -3.477 closest distance to " NE2 GLN A 194 " =    1.837
peak=   -3.473 closest distance to " CB  ALA A 291 " =    2.301
peak=   -3.466 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.460 closest distance to " O   HOH Z 136 " =    2.393
peak=   -3.450 closest distance to " O   HOH Z   6 " =    1.729
peak=   -3.445 closest distance to " C   SER A 206 " =    1.492
peak=   -3.442 closest distance to " O   HOH Z  44 " =    2.232
peak=   -3.439 closest distance to " O   HOH Z 114 " =    3.255
peak=   -3.439 closest distance to " O   HOH Z 123 " =    2.510
peak=   -3.433 closest distance to " ND2 ASN A  69 " =    1.820
peak=   -3.430 closest distance to " CD1 ILE A 151 " =    2.389
peak=   -3.427 closest distance to " O   HOH Z 234 " =    4.286
peak=   -3.424 closest distance to " ND2 ASN A  45 " =    1.156
peak=   -3.419 closest distance to " CA  GLY A 241 " =    2.371
peak=   -3.419 closest distance to " N   ALA A 226 " =    2.028
peak=   -3.418 closest distance to " O   ASN A  45 " =    1.893
peak=   -3.418 closest distance to " O   HOH Z 285 " =    1.631
peak=   -3.417 closest distance to " CD2 LEU A 300 " =    2.527
peak=   -3.415 closest distance to " OD1 ASN A 249 " =    2.458
peak=   -3.415 closest distance to " ND2 ASN A  45 " =    2.021
peak=   -3.413 closest distance to " O   GLY A  75 " =    1.976
peak=   -3.412 closest distance to " O   ILE A 234 " =    1.219
peak=   -3.412 closest distance to " C   LEU A 143 " =    1.036
peak=   -3.412 closest distance to " CG  TRP A 266 " =    1.901
peak=   -3.408 closest distance to " CB  PRO A 163 " =    2.555
peak=   -3.396 closest distance to " O   HOH Z 191 " =    5.657
peak=   -3.391 closest distance to " CA  GLY A 133 " =    2.342
peak=   -3.389 closest distance to " O   HOH Z 426 " =    1.806
peak=   -3.388 closest distance to " O   HOH Z 193 " =    1.621
peak=   -3.383 closest distance to " O   HOH Z 166 " =    1.962
peak=   -3.379 closest distance to " O   HOH Z 252 " =    3.867
peak=   -3.360 closest distance to " CG  GLU A 277 " =    1.156
peak=   -3.360 closest distance to " NE2 GLN A 103 " =    1.799
peak=   -3.359 closest distance to " CD2 LEU A 167 " =    1.807
peak=   -3.353 closest distance to " O   HOH Z 407 " =    2.949
peak=   -3.353 closest distance to " O   HOH Z 166 " =    1.670
peak=   -3.351 closest distance to " O   HOH Z 198 " =    2.318
peak=   -3.350 closest distance to " O   HOH Z 311 " =    3.747
peak=   -3.349 closest distance to " N   THR A 235 " =    1.279
peak=   -3.348 closest distance to " CA  SER A  62 " =    2.592
peak=   -3.346 closest distance to " N   ALA A  43 " =    2.645
peak=   -3.346 closest distance to " O   HOH Z  88 " =    4.454
peak=   -3.344 closest distance to " O   HOH Z  71 " =    1.856
peak=   -3.342 closest distance to " CA  GLY A 241 " =    3.093
peak=   -3.341 closest distance to " C   ILE A 239 " =    2.081
peak=   -3.340 closest distance to " ND2BASN A 224 " =    1.793
peak=   -3.339 closest distance to " O   SER A 210 " =    1.826
peak=   -3.327 closest distance to " O   ALA A 161 " =    1.759
peak=   -3.324 closest distance to " O   HOH Z 102 " =    1.591
peak=   -3.320 closest distance to " O   HOH Z 422 " =    1.545
peak=   -3.315 closest distance to " O   HOH Z 222 " =    1.585
peak=   -3.312 closest distance to " N   THR A  52 " =    1.667
peak=   -3.312 closest distance to " O   ALA A   1 " =    1.773
peak=   -3.307 closest distance to " O   HOH Z 236 " =    1.504
peak=   -3.305 closest distance to " C   THR A 279 " =    1.128
peak=   -3.301 closest distance to " ND2 ASN A  45 " =    1.486
peak=   -3.299 closest distance to " CB  TRP A  85 " =    2.565
peak=   -3.287 closest distance to " O   HOH Z 165 " =    1.986
peak=   -3.281 closest distance to " O   HOH Z  60 " =    2.213
peak=   -3.281 closest distance to " O   VAL A 125 " =    2.361
peak=   -3.274 closest distance to " O   HOH Z 174 " =    2.244
peak=   -3.266 closest distance to " CG1 VAL A 112 " =    2.834
peak=   -3.266 closest distance to " NH2 ARG A  79 " =    2.078
peak=   -3.264 closest distance to " O   GLY A  17 " =    1.180
peak=   -3.262 closest distance to " CG  ASP A  50 " =    2.240
peak=   -3.262 closest distance to " N   MET A 188 " =    1.886
peak=   -3.257 closest distance to " O   HOH Z 211 " =    1.631
peak=   -3.255 closest distance to " CG2 VAL A 189 " =    2.114
peak=   -3.255 closest distance to " ND2 ASN A  39 " =    1.207
peak=   -3.249 closest distance to " CD1 LEU A  25 " =    2.485
peak=   -3.249 closest distance to " O   HOH Z 150 " =    2.133
peak=   -3.239 closest distance to " O   ALA A  34 " =    2.426
peak=   -3.232 closest distance to " CB  SER A 210 " =    1.149
peak=   -3.229 closest distance to " OG1 THR A  82 " =    1.422
peak=   -3.226 closest distance to " O   SER A   3 " =    1.179
peak=   -3.226 closest distance to " CG  ARG A 219 " =    2.586
peak=   -3.225 closest distance to " O   HOH Z 350 " =    2.187
peak=   -3.222 closest distance to " O   HOH Z 392 " =    1.770
peak=   -3.221 closest distance to " CD  GLN A 223 " =    0.919
peak=   -3.221 closest distance to " CZ2 TRP A 274 " =    1.074
peak=   -3.221 closest distance to " O   HOH Z  90 " =    1.703
peak=   -3.215 closest distance to " NE2 GLN A  58 " =    2.468
peak=   -3.215 closest distance to " O   HOH Z 244 " =    1.423
peak=   -3.214 closest distance to " N   ASP A 171 " =    2.197
peak=   -3.210 closest distance to " O   HOH Z 423 " =    2.291
peak=   -3.205 closest distance to " O   HOH Z 313 " =    1.202
peak=   -3.199 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.188 closest distance to " O   HOH Z 110 " =    1.479
peak=   -3.179 closest distance to " O   PHE A 218 " =    1.607
peak=   -3.178 closest distance to " CG1 VAL A  78 " =    2.552
peak=   -3.178 closest distance to " NH2 ARG A  66 " =    1.801
peak=   -3.177 closest distance to " CG1 VAL A 230 " =    1.919
peak=   -3.176 closest distance to " CD  PRO A 243 " =    2.073
peak=   -3.173 closest distance to " CD  ARG A 195 " =    5.179
peak=   -3.166 closest distance to " OG BSER A 134 " =    1.879
peak=   -3.164 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.161 closest distance to " CB  PHE A  16 " =    2.468
peak=   -3.159 closest distance to " O   HOH Z 353 " =    2.189
peak=   -3.159 closest distance to " N   ASN A  60 " =    1.289
peak=   -3.159 closest distance to " O   HOH Z 372 " =    2.464
peak=   -3.156 closest distance to " OG  SER A  26 " =    1.305
peak=   -3.154 closest distance to " CG  ASN A 252 " =    1.470
peak=   -3.153 closest distance to " C   MET A 188 " =    1.457
peak=   -3.138 closest distance to " CG2 VAL A 296 " =    1.340
peak=   -3.137 closest distance to " O   HOH Z 395 " =    1.466
peak=   -3.135 closest distance to " O   HOH Z 208 " =    1.897
peak=   -3.134 closest distance to " O   HOH Z 174 " =    4.071
peak=   -3.132 closest distance to " O   HOH Z 131 " =    4.046
peak=   -3.132 closest distance to " CE  MET A 105 " =    2.306
peak=   -3.126 closest distance to " O   HOH Z 139 " =    3.200
peak=   -3.124 closest distance to " O   PRO A 198 " =    1.357
peak=   -3.124 closest distance to " CE2 PHE A  61 " =    2.526
peak=   -3.124 closest distance to " O   HOH Z 431 " =    2.095
peak=   -3.122 closest distance to " OG  SER A 206 " =    1.668
peak=   -3.114 closest distance to " O   HOH Z 177 " =    1.379
peak=   -3.114 closest distance to " N   TYR A  68 " =    3.054
peak=   -3.109 closest distance to " O   HOH Z 154 " =    1.582
peak=   -3.107 closest distance to " CD  GLN A 223 " =    1.320
peak=   -3.106 closest distance to " O   HOH Z 111 " =    1.423
peak=   -3.104 closest distance to " O   ASN A 187 " =    1.629
peak=   -3.102 closest distance to " CB  ASN A  69 " =    1.275
peak=   -3.101 closest distance to " O   HOH Z 171 " =    2.143
peak=   -3.100 closest distance to " O   HOH Z 377 " =    1.692
peak=   -3.100 closest distance to " CD2 TYR A 247 " =    2.199
peak=   -3.086 closest distance to " O   VAL A 174 " =    2.107
peak=   -3.079 closest distance to " O   HOH Z 251 " =    5.208
peak=   -3.078 closest distance to " CD1 ILE A 199 " =    2.441
peak=   -3.072 closest distance to " OD1 ASN A 173 " =    1.427
peak=   -3.071 closest distance to " OD1 ASN A 301 " =    2.030
peak=   -3.061 closest distance to " CB  GLN A  11 " =    1.861
peak=   -3.053 closest distance to " O   HOH Z 238 " =    1.184
peak=   -3.041 closest distance to " CZ  PHE A  38 " =    2.007
peak=   -3.035 closest distance to " O   ASP A 171 " =    1.985
peak=   -3.029 closest distance to " O   HOH Z 284 " =    2.206

================= 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    :  0.4679 0.4532   6.268406e+00   6.246653e+00
   1_bss:  0.4607 0.4458   6.260616e+00   6.240113e+00
   1_xyz:  0.3633 0.3795   6.114932e+00   6.138567e+00
   1_adp:  0.3112 0.3560   6.003803e+00   6.088826e+00
   1_occ:  0.3106 0.3561   6.002825e+00   6.089318e+00
   2_bss:  0.3065 0.3511   6.003234e+00   6.087845e+00
   2_xyz:  0.2081 0.2543   5.662269e+00   5.829666e+00
   2_adp:  0.1839 0.2282   5.558449e+00   5.737916e+00
   2_occ:  0.1837 0.2288   5.558320e+00   5.739252e+00
   3_bss:  0.1821 0.2277   5.557272e+00   5.736400e+00
   3_xyz:  0.1368 0.1774   5.298457e+00   5.508671e+00
   3_adp:  0.1266 0.1708   5.242422e+00   5.468573e+00
   3_occ:  0.1264 0.1707   5.241752e+00   5.468239e+00
   4_bss:  0.1265 0.1708   5.242448e+00   5.468128e+00
   4_xyz:  0.1171 0.1636   5.188955e+00   5.425317e+00
   4_adp:  0.1166 0.1605   5.177135e+00   5.407749e+00
   4_occ:  0.1164 0.1605   5.176950e+00   5.408030e+00
   5_bss:  0.1164 0.1604   5.176841e+00   5.407958e+00
   5_xyz:  0.1145 0.1583   5.164118e+00   5.398561e+00
   5_adp:  0.1135 0.1594   5.165387e+00   5.407521e+00
   5_occ:  0.1135 0.1594   5.165353e+00   5.407678e+00
   5_bss:  0.1134 0.1594   5.165287e+00   5.407626e+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:  0.320  15.090   6.652  10.773   9.170   0.000   0.000   0.000
   1_xyz:  0.320  15.090   6.652  10.773   9.170   0.000   0.000   0.000
   1_adp:  0.320  15.090   6.652  10.773   9.170   0.000   0.000   0.000
   1_occ:  0.320  15.090   6.652  10.773   9.170   0.000   0.000   0.000
   2_bss:  0.317  50.001   3.064   6.573   5.371   0.000   0.000   0.000
   2_xyz:  0.317  50.001   3.064   6.573   5.371   0.000   0.000   0.000
   2_adp:  0.317  50.001   3.064   6.573   5.371   0.000   0.000   0.000
   2_occ:  0.317  50.001   3.064   6.573   5.371   0.000   0.000   0.000
   3_bss:  0.318  62.162   2.096   3.912   4.045   0.000   0.000   0.000
   3_xyz:  0.318  62.162   2.096   3.912   4.045   0.000   0.000   0.000
   3_adp:  0.318  62.162   2.096   3.912   4.045   0.000   0.000   0.000
   3_occ:  0.318  62.162   2.096   3.912   4.045   0.000   0.000   0.000
   4_bss:  0.332  62.162   2.021   3.243   3.844   0.000   0.000   0.000
   4_xyz:  0.332  62.162   2.021   3.243   3.844   0.000   0.000   0.000
   4_adp:  0.332  62.162   2.021   3.243   3.844   0.000   0.000   0.000
   4_occ:  0.332  62.162   2.021   3.243   3.844   0.000   0.000   0.000
   5_bss:  0.332  62.162   2.091   3.046   3.882   0.000   0.000   0.000
   5_xyz:  0.332  62.162   2.091   3.046   3.882   0.000   0.000   0.000
   5_adp:  0.332  62.162   2.091   3.046   3.882   0.000   0.000   0.000
   5_occ:  0.332  62.162   2.091   3.046   3.882   0.000   0.000   0.000
   5_bss:  0.326  61.611  -0.895  -0.008   0.902   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.159 0.4947  0.5581    60369.261
   1_bss:  51.769 0.4984  0.7346    58835.637
   1_xyz:  42.260 0.6145  0.8782    40448.800
   1_adp:  37.804 0.6687  0.9741    34579.234
   1_occ:  37.816 0.6686  0.9733    34600.015
   2_bss:  37.519 0.6721  0.8555    34267.227
   2_xyz:  25.976 0.8005  0.9834    16962.681
   2_adp:  22.836 0.8337  1.0027    13770.480
   2_occ:  22.859 0.8335  1.0022    13798.780
   3_bss:  22.704 0.8351  0.9470    13703.333
   3_xyz:  16.804 0.8908  0.9796     8113.295
   3_adp:  15.876 0.8991  0.9787     7517.179
   3_occ:  15.869 0.8992  0.9787     7514.160
   4_bss:  15.873 0.8992  0.9681     7523.299
   4_xyz:  14.857 0.9082  0.9709     6892.481
   4_adp:  14.441 0.9118  0.9681     6696.519
   4_occ:  14.444 0.9118  0.9680     6698.341
   5_bss:  14.440 0.9118  0.9673     6699.533
   5_xyz:  14.253 0.9133  0.9680     6558.723
   5_adp:  14.434 0.9119  0.9620     6649.837
   5_occ:  14.434 0.9119  0.9619     6652.053
   5_bss:  14.435 0.9118  0.9666     6649.122
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4096e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4096e+01
   1_xyz:   1.661  0.013  0.108 17.879  0.006  4.112   1.3599e-01
   1_adp:   1.661  0.013  0.108 17.879  0.006  4.112   1.3599e-01
   1_occ:   1.661  0.013  0.108 17.879  0.006  4.112   1.3599e-01
   2_bss:   1.661  0.013  0.108 17.879  0.006  4.112   1.3599e-01
   2_xyz:   1.259  0.010  0.080 16.165  0.005  4.131   8.9016e-02
   2_adp:   1.259  0.010  0.080 16.165  0.005  4.131   8.9016e-02
   2_occ:   1.259  0.010  0.080 16.165  0.005  4.131   8.9016e-02
   3_bss:   1.259  0.010  0.080 16.165  0.005  4.131   8.9016e-02
   3_xyz:   1.146  0.010  0.087 15.993  0.004  4.131   7.8860e-02
   3_adp:   1.146  0.010  0.087 15.993  0.004  4.131   7.8860e-02
   3_occ:   1.146  0.010  0.087 15.993  0.004  4.131   7.8860e-02
   4_bss:   1.146  0.010  0.087 15.993  0.004  4.131   7.8860e-02
   4_xyz:   1.125  0.010  0.089 15.677  0.004  4.129   7.6018e-02
   4_adp:   1.125  0.010  0.089 15.677  0.004  4.129   7.6018e-02
   4_occ:   1.125  0.010  0.089 15.677  0.004  4.129   7.6018e-02
   5_bss:   1.125  0.010  0.089 15.677  0.004  4.129   7.6018e-02
   5_xyz:   1.108  0.010  0.088 15.504  0.004  4.130   7.3914e-02
   5_adp:   1.108  0.010  0.088 15.504  0.004  4.130   7.3914e-02
   5_occ:   1.108  0.010  0.088 15.504  0.004  4.130   7.3914e-02
   5_bss:   1.108  0.010  0.088 15.504  0.004  4.130   7.3914e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0136e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0136e+00
   1_xyz:  15.429  0.158  0.500 86.175  0.037  2.306   1.0255e-01
   1_adp:  15.429  0.158  0.500 86.175  0.037  2.306   1.0255e-01
   1_occ:  15.429  0.158  0.500 86.175  0.037  2.306   1.0255e-01
   2_bss:  15.429  0.158  0.500 86.175  0.037  2.306   1.0255e-01
   2_xyz:   8.231  0.094  0.320 86.008  0.039  2.050   6.7901e-02
   2_adp:   8.231  0.094  0.320 86.008  0.039  2.050   6.7901e-02
   2_occ:   8.231  0.094  0.320 86.008  0.039  2.050   6.7901e-02
   3_bss:   8.231  0.094  0.320 86.008  0.039  2.050   6.7901e-02
   3_xyz:   7.849  0.056  0.468 85.257  0.048  2.216   5.9707e-02
   3_adp:   7.849  0.056  0.468 85.257  0.048  2.216   5.9707e-02
   3_occ:   7.849  0.056  0.468 85.257  0.048  2.216   5.9707e-02
   4_bss:   7.849  0.056  0.468 85.257  0.048  2.216   5.9707e-02
   4_xyz:   8.037  0.051  0.523 83.226  0.040  2.244   7.5994e-02
   4_adp:   8.037  0.051  0.523 83.226  0.040  2.244   7.5994e-02
   4_occ:   8.037  0.051  0.523 83.226  0.040  2.244   7.5994e-02
   5_bss:   8.037  0.051  0.523 83.226  0.040  2.244   7.5994e-02
   5_xyz:   8.074  0.057  0.522 81.695  0.039  2.279   4.9677e-02
   5_adp:   8.074  0.057  0.522 81.695  0.039  2.279   4.9677e-02
   5_occ:   8.074  0.057  0.522 81.695  0.039  2.279   4.9677e-02
   5_bss:   8.074  0.057  0.522 81.695  0.039  2.279   4.9677e-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:  86.72   0.00  12.41  71.87   0.00   9.68  86.72   0.00  27.30
   1_occ:  86.72   0.00  12.41  71.87   0.00   9.68  86.72   0.00  27.30
   2_bss:  86.72   0.00  12.41  71.87   0.00   9.68  86.72   0.00  27.30
   2_xyz:  86.72   0.00  12.41  71.87   0.00   9.68  86.72   0.00  27.30
   2_adp:  81.45   0.00  12.19  68.98   0.00   8.44  81.45   0.78  32.58
   2_occ:  81.45   0.00  12.19  68.98   0.00   8.44  81.45   0.78  32.58
   3_bss:  81.45   0.00  12.19  68.98   0.00   8.44  81.45   0.78  32.58
   3_xyz:  81.45   0.00  12.19  68.98   0.00   8.44  81.45   0.78  32.58
   3_adp:  80.38   0.00  12.79  80.38   0.00   8.30  78.48   0.76  37.26
   3_occ:  80.38   0.00  12.79  80.38   0.00   8.30  78.48   0.76  37.26
   4_bss:  80.38   0.00  12.79  80.38   0.00   8.30  78.48   0.76  37.26
   4_xyz:  80.38   0.00  12.79  80.38   0.00   8.30  78.48   0.76  37.26
   4_adp:  80.56   0.00  12.40  80.56   0.00   8.05  76.90   0.43  36.10
   4_occ:  80.56   0.00  12.40  80.56   0.00   8.05  76.90   0.43  36.10
   5_bss:  80.56   0.00  12.40  80.56   0.00   8.05  76.90   0.43  36.10
   5_xyz:  80.56   0.00  12.40  80.56   0.00   8.05  76.90   0.43  36.10
   5_adp:  84.93   0.00  12.38  84.93   0.00   8.01  77.45   1.15  36.20
   5_occ:  84.93   0.00  12.38  84.93   0.00   8.01  77.45   1.15  36.20
   5_bss:  88.08   3.15  15.53  88.08   3.15  11.15  80.60   4.30  39.34
------------------------------------------------------------------------
 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:    1.233    0.018    0.411
   1_adp:    1.233    0.018    0.411
   1_occ:    1.233    0.018    0.411
   2_bss:    1.233    0.018    0.411
   2_xyz:    1.612    0.034    0.587
   2_adp:    1.612    0.034    0.587
   2_occ:    1.612    0.034    0.587
   3_bss:    1.612    0.034    0.587
   3_xyz:    1.569    0.063    0.655
   3_adp:    1.569    0.063    0.655
   3_occ:    1.569    0.063    0.655
   4_bss:    1.569    0.063    0.655
   4_xyz:    1.641    0.051    0.679
   4_adp:    1.641    0.051    0.679
   4_occ:    1.641    0.051    0.679
   5_bss:    1.641    0.051    0.679
   5_xyz:    1.734    0.052    0.689
   5_adp:    1.734    0.052    0.689
   5_occ:    1.734    0.052    0.689
   5_bss:    1.734    0.052    0.689
------------------------------------------------------------------------

CPU time actual refinement: 319.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/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_579/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_579/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.00 
  Macro-tasks:
    bulk solvent and scale       = 40.87  
    individual site refinement   = 124.81 
    weights calculation          = 31.97  
    collect and process          = 6.53   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 204.30 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 96.67  
    alpha_beta                      = 8.26   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 106.60 
    fmodel                         = 6.80   
    r_factors                      = 0.20   
    phase_errors                   = 10.90  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 232.55 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.587 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    627 calls, 96.34 s
gradients_fft:          573 calls, 94.01 s

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

# Date 2008-01-16 Time 01:56:04 PST -0800 (1200477364.37 s)
Start R-work = 0.4679, R-free = 0.4532 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1749 (no bulk solvent and anisotropic scale)

Start R-work = 0.4607, R-free = 0.4458
Final R-work = 0.1134, R-free = 0.1594