# Date 2008-01-16 Time 01:50:12 PST -0800 (1200477012.16 s)
#phil __OFF__

Command line arguments: "../576.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9578
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 576

-------------------------------------------------------------------------------
  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, 85.9581, 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: 3.27, per 1000 atoms: 1.16


================================== 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, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99049
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964168

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9905

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, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99049
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964168

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2583 [2122/2150]  1911   211   9.9%
  bin  2:  4.2583 -  3.3930 [2038/2057]  1832   206  10.1%
  bin  3:  3.3930 -  2.9679 [2025/2045]  1823   202  10.0%
  bin  4:  2.9679 -  2.6983 [1986/2011]  1791   195   9.8%
  bin  5:  2.6983 -  2.5059 [1988/2008]  1788   200  10.1%
  bin  6:  2.5059 -  2.3587 [1969/2015]  1774   195   9.9%
  bin  7:  2.3587 -  2.2410 [1961/1993]  1764   197  10.0%
  bin  8:  2.2410 -  2.1438 [1959/1995]  1758   201  10.3%
  bin  9:  2.1438 -  2.0615 [1944/1974]  1753   191   9.8%
  bin 10:  2.0615 -  1.9905 [1597/2005]  1436   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/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: 24
        2.42 -     3.04: 2178
        3.04 -     3.66: 4682
        3.66 -     4.28: 8978
        4.28 -     4.90: 12363
  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
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.120 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.126 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.157 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.183 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28220 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_576/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 85.95805 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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4576   r_free= 0.4434   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.257473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7490 0.99   1380  154 0.3743 0.3620      6.5451      6.5344|
|  2:  4.7490 -  3.7898 0.99   1329  146 0.3669 0.3885      6.7179      6.7654|
|  3:  3.7898 -  3.3167 0.99   1305  147 0.4073 0.3713      6.6384      6.6171|
|  4:  3.3167 -  3.0162 0.99   1293  138 0.4375 0.3794      6.4943      6.3781|
|  5:  3.0162 -  2.8015 0.99   1282  146 0.4824 0.4892      6.3639      6.3968|
|  6:  2.8015 -  2.6373 0.98   1282  142 0.4830 0.5103      6.2614      6.2144|
|  7:  2.6373 -  2.5059 0.99   1274  141 0.4819 0.4600      6.2312      6.1232|
|  8:  2.5059 -  2.3973 0.98   1267  142 0.5019 0.4451       6.178      6.1576|
|  9:  2.3973 -  2.3053 0.98   1275  146 0.5175 0.5207      6.1176      6.1402|
| 10:  2.3053 -  2.2260 0.97   1233  132 0.5167 0.5149      6.1204      6.1019|
| 11:  2.2260 -  2.1566 0.99   1274  144 0.5043 0.4512      6.0236       6.056|
| 12:  2.1566 -  2.0952 0.98   1272  133 0.5253 0.5129      5.9858      6.0056|
| 13:  2.0952 -  2.0401 0.97   1227  139 0.5098 0.5258      5.8859       5.885|
| 14:  2.0401 -  1.9905 0.73    937  109 0.5408 0.5009      5.8593      5.7424|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7490  1380   154  0.70  33.99   0.81     0.72      68599.14|
|  2:  4.7490 -  3.7898  1329   146  0.74  31.88   0.90     0.78      88142.76|
|  3:  3.7898 -  3.3167  1305   147  0.67  38.21   0.85     0.76      91102.30|
|  4:  3.3167 -  3.0162  1293   138  0.60  43.51   0.82     0.67      77429.56|
|  5:  3.0162 -  2.8015  1282   146  0.51  51.41   0.76     0.58      69306.27|
|  6:  2.8015 -  2.6373  1282   142  0.49  53.05   0.74     0.54      59985.42|
|  7:  2.6373 -  2.5059  1274   141  0.48  53.44   0.75     0.54      55492.53|
|  8:  2.5059 -  2.3973  1267   142  0.48  53.75   0.75     0.54      48711.08|
|  9:  2.3973 -  2.3053  1275   146  0.44  57.11   0.72     0.51      46936.21|
| 10:  2.3053 -  2.2260  1233   132  0.43  57.44   0.74     0.49      44831.47|
| 11:  2.2260 -  2.1566  1274   144  0.39  61.04   0.77     0.46      43638.78|
| 12:  2.1566 -  2.0952  1272   133  0.36  62.88   0.76     0.45      41692.00|
| 13:  2.0952 -  2.0401  1227   139  0.35  64.09   0.74     0.41      35825.45|
| 14:  2.0401 -  1.9905   937   109  0.36  63.04   0.72     0.40      27865.94|
|alpha:            min =        0.40 max =            0.78 mean =         0.57|
|beta:             min =    27865.94 max =        91102.30 mean =     58014.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.31|
|phase err.(test): min =        0.00 max =           89.98 mean =        51.24|
|-----------------------------------------------------------------------------|

============================== 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 = 10.193734             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.665   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.871229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.212   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1509 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2619 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3898 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5065 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6571 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7700 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.851 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.780 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4648   r_free= 0.4536   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.260498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4497   r_free= 0.4373   ksol= 0.34   Bsol= 20.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.81,11.10,7.61,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.249964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.778855              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.187   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.879781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4497      final r-factor (work) = 0.3510          |
| start r-factor (free) = 0.4373      final r-factor (free) = 0.3706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.4830 = 9.78 * 0.50 * 6.2650 + 1.00 * 53.8509                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1088 = 9.78 * 0.50 * 6.1306 + 1.00 * 0.1338                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3510      final r-factor (work) = 0.2955          |
| start r-factor (free) = 0.3706      final r-factor (free) = 0.3319          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4083 = 0.88 * 1.00 * 6.1306 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2954 = 0.88 * 1.00 * 6.0027 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.59   11.69    None  None   None       |
|    all(noH): 2823   0      0.00    78.59   11.69    None  None   None       |
|    Sol.    : 438    0      0.00    78.59   26.65    None  None   None       |
|    Mac.    : 2385   0      0.00    71.86   8.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.859: 1409   |   5:    39.295 -  47.154:   66        |
|      1:     7.859 -  15.718:  693   |   6:    47.154 -  55.013:   34        |
|      2:    15.718 -  23.577:  315   |   7:    55.013 -  62.872:   10        |
|      3:    23.577 -  31.436:  187   |   8:    62.872 -  70.730:    4        |
|      4:    31.436 -  39.295:  101   |   9:    70.730 -  78.589:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2955 r_free = 0.3319             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2949 r_free = 0.3315             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2949   r_free= 0.3315   ksol= 0.34   Bsol= 20.00   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.81,11.10,7.61,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.964246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2924   r_free= 0.3259   ksol= 0.32   Bsol= 40.35   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,7.25,4.94,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.964649                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.564374              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2924      final r-factor (work) = 0.2119          |
| start r-factor (free) = 0.3259      final r-factor (free) = 0.2547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8309 = 4.56 * 0.50 * 6.0020 + 1.00 * 0.1332                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3186 = 4.56 * 0.50 * 5.8046 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2119      final r-factor (work) = 0.1929          |
| start r-factor (free) = 0.2547      final r-factor (free) = 0.2369          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4248 = 0.42 * 1.00 * 5.8046 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3513 = 0.42 * 1.00 * 5.6341 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.54   11.90    None  None   None       |
|    all(noH): 2823   0      0.00    76.54   11.90    None  None   None       |
|    Sol.    : 438    0      1.19    74.60   31.68    None  None   None       |
|    Mac.    : 2385   0      0.00    76.54   8.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.654: 1480   |   5:    38.270 -  45.923:  100        |
|      1:     7.654 -  15.308:  694   |   6:    45.923 -  53.577:   62        |
|      2:    15.308 -  22.962:  220   |   7:    53.577 -  61.231:   23        |
|      3:    22.962 -  30.616:  134   |   8:    61.231 -  68.885:    7        |
|      4:    30.616 -  38.270:   96   |   9:    68.885 -  76.539:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1929 r_free = 0.2369             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1927 r_free = 0.2372             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1927   r_free= 0.2372   ksol= 0.32   Bsol= 40.35   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.69,7.25,4.94,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.605391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1911   r_free= 0.2370   ksol= 0.33   Bsol= 51.82   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,4.51,3.88,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.603932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.907043              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.529  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223250              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.547  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2370      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2700 = 2.91 * 0.50 * 5.6405 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0300 = 2.91 * 0.50 * 5.4816 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1433      final r-factor (work) = 0.1339          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2368 = 0.22 * 1.00 * 5.4816 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2024 = 0.22 * 1.00 * 5.2976 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.17   11.91    None  None   None       |
|    all(noH): 2823   0      0.00    75.17   11.91    None  None   None       |
|    Sol.    : 438    0      1.03    68.85   33.30    None  None   None       |
|    Mac.    : 2385   0      0.00    75.17   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.517: 1527   |   5:    37.586 -  45.103:   96        |
|      1:     7.517 -  15.034:  677   |   6:    45.103 -  52.620:   67        |
|      2:    15.034 -  22.552:  175   |   7:    52.620 -  60.137:   33        |
|      3:    22.552 -  30.069:  110   |   8:    60.137 -  67.654:   12        |
|      4:    30.069 -  37.586:  120   |   9:    67.654 -  75.171:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1339 r_free = 0.1687             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1685             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1685   ksol= 0.33   Bsol= 51.82   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,4.51,3.88,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.268211                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1339   r_free= 0.1685   ksol= 0.33   Bsol= 49.36   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.08,3.42,3.49,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.269710                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.017503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.751  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.333175              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.931   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1339      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4099 = 2.02 * 0.50 * 5.3011 + 1.00 * 0.0624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3287 = 2.02 * 0.50 * 5.2219 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7511 = 0.33 * 1.00 * 5.2219 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7384 = 0.33 * 1.00 * 5.1853 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.21   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    77.21   11.97    None  None   None       |
|    Sol.    : 438    0      1.10    69.53   34.17    None  None   None       |
|    Mac.    : 2385   0      0.00    77.21   7.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.721: 1598   |   5:    38.606 -  46.328:  101        |
|      1:     7.721 -  15.443:  627   |   6:    46.328 -  54.049:   70        |
|      2:    15.443 -  23.164:  159   |   7:    54.049 -  61.770:   32        |
|      3:    23.164 -  30.885:  117   |   8:    61.770 -  69.492:   13        |
|      4:    30.885 -  38.606:  101   |   9:    69.492 -  77.213:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1599             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1599             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1599   ksol= 0.33   Bsol= 49.36   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.08,3.42,3.49,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1599   ksol= 0.33   Bsol= 49.36   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,3.22,3.53,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.265653              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.759  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.014  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9347 = 2.27 * 0.50 * 5.1850 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9165 = 2.27 * 0.50 * 5.1642 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8430 = 0.35 * 1.00 * 5.1642 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8391 = 0.35 * 1.00 * 5.1527 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.55   11.86    None  None   None       |
|    all(noH): 2823   0      0.00    77.55   11.86    None  None   None       |
|    Sol.    : 438    0      0.66    69.53   34.08    None  None   None       |
|    Mac.    : 2385   0      0.00    77.55   7.78     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.755: 1634   |   5:    38.777 -  46.532:   94        |
|      1:     7.755 -  15.511:  590   |   6:    46.532 -  54.287:   72        |
|      2:    15.511 -  23.266:  162   |   7:    54.287 -  62.043:   28        |
|      3:    23.266 -  31.021:  120   |   8:    62.043 -  69.798:   14        |
|      4:    31.021 -  38.777:  105   |   9:    69.798 -  77.553:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1572             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1573             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1573   ksol= 0.33   Bsol= 49.36   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.13,3.22,3.53,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.154258                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7490 0.99   1380  154 0.1018 0.1271      5.3939      5.5151|
|  2:  4.7490 -  3.7898 0.99   1329  146 0.0876 0.1122      5.4526      5.6661|
|  3:  3.7898 -  3.3167 0.99   1305  147 0.1056 0.1493      5.4853      5.8747|
|  4:  3.3167 -  3.0162 0.99   1293  138 0.1223 0.1555      5.4578      5.6182|
|  5:  3.0162 -  2.8015 0.99   1282  146 0.1326 0.1620      5.3461      5.4841|
|  6:  2.8015 -  2.6373 0.98   1282  142 0.1281 0.1974      5.2462      5.5081|
|  7:  2.6373 -  2.5059 0.99   1274  141 0.1254 0.1698      5.1762      5.3768|
|  8:  2.5059 -  2.3973 0.98   1267  142 0.1184 0.1721      5.0918        5.36|
|  9:  2.3973 -  2.3053 0.98   1275  146 0.1203 0.1843        5.04      5.3352|
| 10:  2.3053 -  2.2260 0.97   1233  132 0.1153 0.1743      4.9922      5.1909|
| 11:  2.2260 -  2.1566 0.99   1274  144 0.1145 0.1709      4.9363      5.2767|
| 12:  2.1566 -  2.0952 0.98   1272  133 0.1095 0.1721      4.8665      5.1852|
| 13:  2.0952 -  2.0401 0.97   1227  139 0.1144 0.1647      4.7971      5.0218|
| 14:  2.0401 -  1.9905 0.73    937  109 0.1067 0.1669       4.688      4.9286|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7490  1380   154  0.94   8.87   0.98     0.96       7100.67|
|  2:  4.7490 -  3.7898  1329   146  0.95   8.14   1.01     0.99       9172.88|
|  3:  3.7898 -  3.3167  1305   147  0.93  11.35   1.02     1.01      10773.63|
|  4:  3.3167 -  3.0162  1293   138  0.92  13.53   1.00     0.98      10194.05|
|  5:  3.0162 -  2.8015  1282   146  0.90  16.06   0.99     0.96       8521.16|
|  6:  2.8015 -  2.6373  1282   142  0.90  16.39   0.98     0.95       7424.76|
|  7:  2.6373 -  2.5059  1274   141  0.90  15.64   0.98     0.95       6252.49|
|  8:  2.5059 -  2.3973  1267   142  0.91  15.14   0.99     0.96       5507.05|
|  9:  2.3973 -  2.3053  1275   146  0.90  16.04   1.00     0.97       5057.80|
| 10:  2.3053 -  2.2260  1233   132  0.90  15.88   1.00     0.97       4674.97|
| 11:  2.2260 -  2.1566  1274   144  0.90  15.92   0.99     0.96       4322.03|
| 12:  2.1566 -  2.0952  1272   133  0.92  14.84   1.00     0.98       3821.62|
| 13:  2.0952 -  2.0401  1227   139  0.91  15.66   0.99     0.98       3353.75|
| 14:  2.0401 -  1.9905   937   109  0.91  15.43   0.97     0.93       2685.52|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2685.52 max =        10773.63 mean =      6456.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.12|
|phase err.(test): min =        0.00 max =           89.11 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1573   ksol= 0.33   Bsol= 52.45   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.21,0.59,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.154298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1573   ksol= 0.33   Bsol= 52.45   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.21,0.59,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.154298                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7490 0.99   1380  154 0.1018 0.1273      5.3946      5.5161|
|  2:  4.7490 -  3.7898 0.99   1329  146 0.0877 0.1122       5.453      5.6661|
|  3:  3.7898 -  3.3167 0.99   1305  147 0.1057 0.1494      5.4855      5.8752|
|  4:  3.3167 -  3.0162 0.99   1293  138 0.1223 0.1555      5.4578      5.6182|
|  5:  3.0162 -  2.8015 0.99   1282  146 0.1326 0.1620      5.3459      5.4838|
|  6:  2.8015 -  2.6373 0.98   1282  142 0.1281 0.1972       5.246      5.5074|
|  7:  2.6373 -  2.5059 0.99   1274  141 0.1254 0.1700      5.1761      5.3772|
|  8:  2.5059 -  2.3973 0.98   1267  142 0.1184 0.1720      5.0918      5.3598|
|  9:  2.3973 -  2.3053 0.98   1275  146 0.1202 0.1842        5.04      5.3351|
| 10:  2.3053 -  2.2260 0.97   1233  132 0.1153 0.1744      4.9923      5.1915|
| 11:  2.2260 -  2.1566 0.99   1274  144 0.1145 0.1708      4.9362      5.2766|
| 12:  2.1566 -  2.0952 0.98   1272  133 0.1094 0.1721      4.8665      5.1856|
| 13:  2.0952 -  2.0401 0.97   1227  139 0.1144 0.1646       4.797      5.0216|
| 14:  2.0401 -  1.9905 0.73    937  109 0.1067 0.1669      4.6878      4.9279|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7490  1380   154  0.94   8.88   0.98     0.96       7112.90|
|  2:  4.7490 -  3.7898  1329   146  0.95   8.15   1.01     1.00       9182.30|
|  3:  3.7898 -  3.3167  1305   147  0.93  11.36   1.02     1.01      10778.97|
|  4:  3.3167 -  3.0162  1293   138  0.92  13.53   1.00     0.98      10193.47|
|  5:  3.0162 -  2.8015  1282   146  0.90  16.06   0.99     0.96       8513.96|
|  6:  2.8015 -  2.6373  1282   142  0.90  16.38   0.98     0.95       7419.55|
|  7:  2.6373 -  2.5059  1274   141  0.90  15.65   0.99     0.96       6250.59|
|  8:  2.5059 -  2.3973  1267   142  0.91  15.15   0.99     0.96       5507.92|
|  9:  2.3973 -  2.3053  1275   146  0.90  16.04   1.00     0.97       5059.22|
| 10:  2.3053 -  2.2260  1233   132  0.90  15.88   1.00     0.97       4675.12|
| 11:  2.2260 -  2.1566  1274   144  0.90  15.92   1.00     0.96       4322.19|
| 12:  2.1566 -  2.0952  1272   133  0.92  14.84   1.00     0.99       3821.96|
| 13:  2.0952 -  2.0401  1227   139  0.91  15.66   1.00     0.99       3352.23|
| 14:  2.0401 -  1.9905   937   109  0.91  15.43   0.98     0.94       2682.59|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2682.59 max =        10778.97 mean =      6457.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.12|
|phase err.(test): min =        0.00 max =           89.11 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.10    80.65   14.96    None  None   None       |
|    all(noH): 2823   0      3.10    80.65   14.96    None  None   None       |
|    Sol.    : 438    0      3.76    72.63   37.18    None  None   None       |
|    Mac.    : 2385   0      3.10    80.65   10.88    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:     3.098 -  10.853: 1634   |   5:    41.875 -  49.630:   94        |
|      1:    10.853 -  18.609:  590   |   6:    49.630 -  57.385:   72        |
|      2:    18.609 -  26.364:  162   |   7:    57.385 -  65.141:   28        |
|      3:    26.364 -  34.119:  120   |   8:    65.141 -  72.896:   14        |
|      4:    34.119 -  41.875:  105   |   9:    72.896 -  80.651:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.272 - 4.915
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 329
   mapped sites are within: 0.702 - 4.915

peak=   10.710 closest distance to " CB  VAL A 230 " =    1.458
peak=    6.919 closest distance to " CG2 VAL A 296 " =    1.110
peak=    6.092 closest distance to " CG  LEU A   5 " =    1.204
peak=    5.517 closest distance to " NH2 ARG A  56 " =    2.260
peak=    5.461 closest distance to " CB  VAL A 296 " =    1.081
peak=    5.417 closest distance to " CG  LEU A 228 " =    1.204
peak=    5.253 closest distance to " CB  GLN A 223 " =    1.382
peak=    5.185 closest distance to " CG  PRO A  54 " =    1.284
peak=    5.167 closest distance to " CB  SER A  63 " =    1.183
peak=    5.104 closest distance to " CD1AILE A 234 " =    1.050
peak=    4.944 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.865 closest distance to " CB  GLN A 183 " =    1.314
peak=    4.827 closest distance to " O   SER A  87 " =    2.269
peak=    4.704 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.684 closest distance to " CB  PRO A  54 " =    0.909
peak=    4.656 closest distance to " O   HOH Z 232 " =    2.319
peak=    4.599 closest distance to " CG  PRO A 213 " =    1.260
peak=    4.590 closest distance to " O   HOH Z 402 " =    1.534
peak=    4.538 closest distance to " CD2 LEU A   5 " =    1.118
peak=    4.538 closest distance to " O   HOH Z 403 " =    1.693
peak=    4.485 closest distance to " CB  TYR A 169 " =    0.702
peak=    4.450 closest distance to " CG  PRO A 198 " =    1.198
peak=    4.416 closest distance to " O   HOH Z 423 " =    1.848
peak=    4.392 closest distance to " CG  PRO A 280 " =    0.729
peak=    4.373 closest distance to " CB  VAL A 230 " =    1.217
peak=    4.332 closest distance to " CB  SER A   3 " =    1.272
peak=    4.319 closest distance to " NE2 GLN A  11 " =    1.066
peak=    4.314 closest distance to " O   HOH Z 236 " =    1.826
peak=    4.263 closest distance to " CA  TYR A  30 " =    0.911
peak=    4.249 closest distance to " O   HOH Z 126 " =    1.923
peak=    4.247 closest distance to " O   HOH Z 234 " =    3.589
peak=    4.244 closest distance to " O   HOH Z 298 " =    1.840
peak=    4.239 closest distance to " C   PRO A 198 " =    1.495
peak=    4.236 closest distance to " O   HOH Z  44 " =    2.310
peak=    4.201 closest distance to " CG  PRO A  90 " =    1.184
peak=    4.200 closest distance to " O   HOH Z 142 " =    1.577
peak=    4.196 closest distance to " O   HOH Z  80 " =    1.866
peak=    4.192 closest distance to " O   HOH Z 193 " =    1.839
peak=    4.155 closest distance to " CB  ASN A 148 " =    1.362
peak=    4.155 closest distance to " O   HOH Z 368 " =    2.237
peak=    4.104 closest distance to " CB  GLU A 277 " =    3.608
peak=    4.094 closest distance to " CB  TRP A 179 " =    1.332
peak=    4.092 closest distance to " O   HOH Z  48 " =    1.662
peak=    4.083 closest distance to " O   HOH Z 316 " =    3.028
peak=    4.075 closest distance to " CB  ARG A  79 " =    1.377
peak=    4.069 closest distance to " O   HOH Z  97 " =    1.970
peak=    4.067 closest distance to " CA  ALA A  21 " =    1.183
peak=    4.065 closest distance to " O   HOH Z 303 " =    2.184
peak=    4.065 closest distance to " O   HOH Z 124 " =    1.341
peak=    4.061 closest distance to " O   HOH Z  48 " =    1.624
peak=    4.043 closest distance to " O   HOH Z 272 " =    1.918
peak=    4.034 closest distance to " CB  ASN A  39 " =    0.804
peak=    4.034 closest distance to " O   HOH Z  59 " =    2.365
peak=    4.029 closest distance to " CD2 LEU A 228 " =    1.167
peak=    4.021 closest distance to " O   HOH Z 369 " =    2.214
peak=    4.008 closest distance to " O   HOH Z  85 " =    1.382
peak=    3.997 closest distance to " O   HOH Z  63 " =    1.995
peak=    3.988 closest distance to " O   HOH Z 389 " =    1.927
peak=    3.985 closest distance to " O   HOH Z  54 " =    1.576
peak=    3.985 closest distance to " O   HOH Z 247 " =    1.396
peak=    3.968 closest distance to " CG1 ILE A  33 " =    1.283
peak=    3.968 closest distance to " CG  PRO A 243 " =    1.135
peak=    3.960 closest distance to " CB  ARG A 190 " =    1.690
peak=    3.948 closest distance to " O   HOH Z 134 " =    1.551
peak=    3.939 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.935 closest distance to " OD1 ASN A  69 " =    2.576
peak=    3.926 closest distance to " O   HOH Z 130 " =    2.847
peak=    3.915 closest distance to " CZ  PHE A 218 " =    1.178
peak=    3.913 closest distance to " CB  TRP A 266 " =    0.963
peak=    3.903 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.893 closest distance to " O   HOH Z 346 " =    1.529
peak=    3.889 closest distance to " O   HOH Z 214 " =    2.612
peak=    3.884 closest distance to " CB  GLU A 128 " =    1.132
peak=    3.875 closest distance to " CD  LYS A 166 " =    1.324
peak=    3.871 closest distance to " CG1BVAL A  72 " =    1.748
peak=    3.863 closest distance to " CA  ALA A  51 " =    0.961
peak=    3.839 closest distance to " ND2 ASN A 187 " =    1.618
peak=    3.838 closest distance to " O   HOH Z 189 " =    2.553
peak=    3.831 closest distance to " CE1 HIS A 108 " =    1.143
peak=    3.828 closest distance to " O   TRP A 274 " =    1.959
peak=    3.809 closest distance to " O   HOH Z 248 " =    1.697
peak=    3.787 closest distance to " O   HOH Z 102 " =    1.292
peak=    3.785 closest distance to " O   HOH Z  40 " =    1.882
peak=    3.777 closest distance to " CG2 THR A 221 " =    1.156
peak=    3.774 closest distance to " O   HOH Z 345 " =    2.952
peak=    3.764 closest distance to " O   HOH Z  15 " =    2.135
peak=    3.758 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.751 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.743 closest distance to " O   HOH Z 245 " =    1.412
peak=    3.739 closest distance to " O   HOH Z 344 " =    2.942
peak=    3.738 closest distance to " O   HOH Z 419 " =    1.786
peak=    3.736 closest distance to " CB  ARG A 139 " =    0.902
peak=    3.734 closest distance to " O   HOH Z 193 " =    2.149
peak=    3.720 closest distance to " O   HOH Z 411 " =    3.776
peak=    3.719 closest distance to " O   HOH Z  21 " =    1.807
peak=    3.713 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.696 closest distance to " O   HOH Z 130 " =    2.257
peak=    3.695 closest distance to " O   HOH Z  43 " =    2.270
peak=    3.692 closest distance to " OG BSER A 164 " =    2.240
peak=    3.685 closest distance to " CG  GLN A  58 " =    2.752
peak=    3.682 closest distance to " O   HOH Z  97 " =    2.499
peak=    3.681 closest distance to " CA  VAL A  41 " =    0.821
peak=    3.680 closest distance to " O   HOH Z 357 " =    2.020
peak=    3.674 closest distance to " O   HOH Z 383 " =    1.905
peak=    3.674 closest distance to " O   HOH Z 203 " =    1.748
peak=    3.674 closest distance to " CD2 TRP A 179 " =    1.340
peak=    3.671 closest distance to " O   HOH Z 371 " =    3.268
peak=    3.668 closest distance to " O   HOH Z 426 " =    1.514
peak=    3.663 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.658 closest distance to " CA  LYS A 117 " =    1.243
peak=    3.654 closest distance to " OG1 THR A 294 " =    2.284
peak=    3.651 closest distance to " CA  ASP A 191 " =    0.868
peak=    3.646 closest distance to " O   HOH Z 427 " =    2.945
peak=    3.643 closest distance to " CB  ASN A 187 " =    1.516
peak=    3.640 closest distance to " NZ  LYS A 117 " =    3.015
peak=    3.637 closest distance to " O   HOH Z 265 " =    2.374
peak=    3.623 closest distance to " CG2 ILE A  20 " =    1.435
peak=    3.621 closest distance to " OD2 ASP A 286 " =    2.860
peak=    3.619 closest distance to " CB  ARG A  79 " =    0.887
peak=    3.614 closest distance to " O   HOH Z 250 " =    1.432
peak=    3.606 closest distance to " O   HOH Z 365 " =    2.928
peak=    3.600 closest distance to " CB  ALA A 248 " =    1.363
peak=    3.595 closest distance to " CB BVAL A  41 " =    0.996
peak=    3.585 closest distance to " CB  MET A  40 " =    0.846
peak=    3.584 closest distance to " CA  ARG A 195 " =    1.183
peak=    3.583 closest distance to " CG1 VAL A 153 " =    1.010
peak=    3.580 closest distance to " NZ  LYS A 166 " =    3.082
peak=    3.579 closest distance to " CB  ASP A 140 " =    0.824
peak=    3.577 closest distance to " O   HOH Z 433 " =    1.411
peak=    3.575 closest distance to " CB  ALA A   9 " =    1.623
peak=    3.570 closest distance to " O   HOH Z 108 " =    2.662
peak=    3.568 closest distance to " CE1 TYR A 186 " =    1.291
peak=    3.561 closest distance to " O   HOH Z 128 " =    1.940
peak=    3.561 closest distance to " O   ASP A 124 " =    1.290
peak=    3.559 closest distance to " O   HOH Z 126 " =    1.597
peak=    3.557 closest distance to " OD2 ASP A 298 " =    3.898
peak=    3.555 closest distance to " O   HOH Z 327 " =    1.595
peak=    3.554 closest distance to " CB  HIS A 108 " =    0.832
peak=    3.549 closest distance to " CA  ALA A 295 " =    1.032
peak=    3.544 closest distance to " O   HOH Z  88 " =    2.613
peak=    3.539 closest distance to " N   ASN A  39 " =    1.191
peak=    3.538 closest distance to " CD1 LEU A  96 " =    0.745
peak=    3.532 closest distance to " CD1 LEU A 300 " =    1.141
peak=    3.530 closest distance to " CB  THR A  31 " =    1.636
peak=    3.528 closest distance to " CB  ALA A 295 " =    1.179
peak=    3.526 closest distance to " CB  ALA A 291 " =    1.338
peak=    3.521 closest distance to " O   HOH Z 132 " =    2.755
peak=    3.520 closest distance to " O   HOH Z  78 " =    1.691
peak=    3.520 closest distance to " NH1BARG A 190 " =    2.146
peak=    3.512 closest distance to " CB  VAL A 202 " =    1.459
peak=    3.512 closest distance to " O   HOH Z 250 " =    1.481
peak=    3.512 closest distance to " N   SER A 135 " =    1.341
peak=    3.508 closest distance to " O   HOH Z 329 " =    3.906
peak=    3.506 closest distance to " O   HOH Z 126 " =    1.892
peak=    3.505 closest distance to " O   HOH Z 273 " =    2.896
peak=    3.500 closest distance to " O   HOH Z 189 " =    2.687
peak=    3.493 closest distance to " O   HOH Z 128 " =    1.967
peak=    3.489 closest distance to " CG  MET A 185 " =    1.090
peak=    3.487 closest distance to " O   HOH Z 155 " =    3.110
peak=    3.485 closest distance to " O   HOH Z 147 " =    1.816
peak=    3.485 closest distance to " O   HOH Z 422 " =    2.678
peak=    3.483 closest distance to " NZ  LYS A  76 " =    1.488
peak=    3.481 closest distance to " CB  ALA A 100 " =    1.240
peak=    3.479 closest distance to " O   HOH Z 197 " =    2.574
peak=    3.471 closest distance to " O   ALA A 165 " =    1.419
peak=    3.455 closest distance to " O   HOH Z 261 " =    2.205
peak=    3.453 closest distance to " CA  ARG A  36 " =    1.091
peak=    3.446 closest distance to " NH2BARG A 145 " =    2.233
peak=    3.446 closest distance to " CB  LEU A 143 " =    1.172
peak=    3.439 closest distance to " OE1 GLU A   2 " =    1.983
peak=    3.436 closest distance to " O   HOH Z 435 " =    1.891
peak=    3.432 closest distance to " O   HOH Z 227 " =    1.525
peak=    3.418 closest distance to " CG  ARG A  66 " =    0.969
peak=    3.416 closest distance to " O   HOH Z 109 " =    2.515
peak=    3.411 closest distance to " CA  VAL A 126 " =    1.030
peak=    3.408 closest distance to " O   HOH Z  68 " =    1.754
peak=    3.404 closest distance to " CA  TYR A 116 " =    1.339
peak=    3.397 closest distance to " O   HOH Z 417 " =    3.158
peak=    3.395 closest distance to " O   HOH Z 409 " =    3.660
peak=    3.392 closest distance to " O   HOH Z 414 " =    1.555
peak=    3.388 closest distance to " O   HOH Z 420 " =    1.886
peak=    3.386 closest distance to " O   HOH Z 416 " =    2.731
peak=    3.382 closest distance to " O   HOH Z 423 " =    3.293
peak=    3.381 closest distance to " O   HOH Z 438 " =    2.064
peak=    3.380 closest distance to " O   HOH Z 291 " =    1.526
peak=    3.378 closest distance to " CG1 ILE A  49 " =    1.570
peak=    3.368 closest distance to " CD2 LEU A 297 " =    0.877
peak=    3.367 closest distance to " CG AARG A 275 " =    1.242
peak=    3.365 closest distance to " O   HOH Z 406 " =    1.522
peak=    3.364 closest distance to " CA  ASP A 162 " =    1.116
peak=    3.364 closest distance to " O   HOH Z 263 " =    1.636
peak=    3.361 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.359 closest distance to " C   ALA A 299 " =    0.953
peak=    3.356 closest distance to " CE  LYS A 119 " =    1.012
peak=    3.348 closest distance to " O   HOH Z 261 " =    1.929
peak=    3.347 closest distance to " O   HOH Z 261 " =    1.987
peak=    3.340 closest distance to " CZ  PHE A 192 " =    1.039
peak=    3.336 closest distance to " CB  THR A 157 " =    1.203
peak=    3.335 closest distance to " CB  TYR A 247 " =    0.997
peak=    3.334 closest distance to " CB  SER A  26 " =    1.703
peak=    3.330 closest distance to " O   HOH Z 280 " =    2.624
peak=    3.328 closest distance to " CB  GLU A  46 " =    1.039
peak=    3.324 closest distance to " O   HOH Z 421 " =    1.759
peak=    3.324 closest distance to " O   HOH Z 425 " =    2.026
peak=    3.323 closest distance to " O   HOH Z 163 " =    1.489
peak=    3.316 closest distance to " CD  LYS A 119 " =    2.051
peak=    3.315 closest distance to " CA  ASP A 140 " =    1.194
peak=    3.315 closest distance to " CB  PRO A 198 " =    1.012
peak=    3.315 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.182
peak=    3.310 closest distance to " CB  GLN A 278 " =    0.865
peak=    3.306 closest distance to " CB  SER A 141 " =    0.999
peak=    3.305 closest distance to " OG  SER A 245 " =    1.570
peak=    3.301 closest distance to " O   HOH Z 345 " =    1.615
peak=    3.301 closest distance to " CG1 VAL A 296 " =    1.153
peak=    3.298 closest distance to " O   HOH Z 123 " =    2.147
peak=    3.291 closest distance to " CB  TRP A 150 " =    1.486
peak=    3.290 closest distance to " O   HOH Z  20 " =    1.380
peak=    3.286 closest distance to " CD1 LEU A 222 " =    0.710
peak=    3.285 closest distance to " O   HOH Z 258 " =    2.311
peak=    3.283 closest distance to " CA  LEU A 282 " =    1.131
peak=    3.278 closest distance to " CB  THR A  52 " =    1.040
peak=    3.276 closest distance to " OG BSER A 134 " =    2.893
peak=    3.275 closest distance to " O   HOH Z  83 " =    1.559
peak=    3.274 closest distance to " CE  LYS A  76 " =    0.820
peak=    3.272 closest distance to " OG  SER A 276 " =    1.309
peak=    3.270 closest distance to " CA  GLN A 194 " =    1.219
peak=    3.270 closest distance to " O   HOH Z 227 " =    2.132
peak=    3.266 closest distance to " O   HOH Z 133 " =    2.506
peak=    3.259 closest distance to " O   MET A 105 " =    1.833
peak=    3.256 closest distance to " O   HOH Z 180 " =    2.189
peak=    3.256 closest distance to " CA  THR A 264 " =    0.773
peak=    3.253 closest distance to " O   HOH Z 327 " =    2.934
peak=    3.252 closest distance to " CA  ASN A 176 " =    1.107
peak=    3.251 closest distance to " CB  ASN A 142 " =    1.145
peak=    3.246 closest distance to " O   HOH Z 281 " =    4.799
peak=    3.242 closest distance to " NH2 ARG A  79 " =    1.270
peak=    3.242 closest distance to " O   HOH Z 411 " =    1.802
peak=    3.242 closest distance to " CG2 ILE A 106 " =    0.803
peak=    3.240 closest distance to " CG2 ILE A 234 " =    0.912
peak=    3.236 closest distance to " CB  ALA A  71 " =    1.270
peak=    3.235 closest distance to " O   HOH Z 374 " =    2.655
peak=    3.233 closest distance to " O   HOH Z  88 " =    3.027
peak=    3.230 closest distance to " O   HOH Z 271 " =    1.549
peak=    3.230 closest distance to " CG2 ILE A 234 " =    2.034
peak=    3.229 closest distance to " O   HOH Z 154 " =    1.383
peak=    3.228 closest distance to " O   HOH Z  44 " =    1.843
peak=    3.227 closest distance to " O   HOH Z 185 " =    1.682
peak=    3.227 closest distance to " CB  ARG A 259 " =    1.900
peak=    3.223 closest distance to " O   HOH Z 128 " =    1.585
peak=    3.221 closest distance to " O   HOH Z 313 " =    1.710
peak=    3.220 closest distance to " O   HOH Z 404 " =    2.259
peak=    3.220 closest distance to " N   ASP A 162 " =    1.364
peak=    3.220 closest distance to " CG  MET A 185 " =    1.029
peak=    3.217 closest distance to " CB  LEU A 228 " =    1.339
peak=    3.217 closest distance to " CD2 HIS A  81 " =    1.077
peak=    3.215 closest distance to " OD1 ASP A 286 " =    1.786
peak=    3.212 closest distance to " O   HOH Z  66 " =    2.159
peak=    3.212 closest distance to " CG BARG A 275 " =    1.339
peak=    3.210 closest distance to " C   SER A  32 " =    1.028
peak=    3.205 closest distance to " O   ASP A 124 " =    1.761
peak=    3.203 closest distance to " OH  TYR A 116 " =    1.173
peak=    3.203 closest distance to " CG BARG A 102 " =    1.780
peak=    3.202 closest distance to " OG  SER A  22 " =    2.761
peak=    3.202 closest distance to " OE1 GLN A  11 " =    1.851
peak=    3.201 closest distance to " O   ALA A 158 " =    1.290
peak=    3.201 closest distance to " O   GLY A  91 " =    1.358
peak=    3.198 closest distance to " O   HOH Z  48 " =    2.962
peak=    3.198 closest distance to " CG2 VAL A 197 " =    1.038
peak=    3.198 closest distance to " CA  LYS A 290 " =    1.299
peak=    3.196 closest distance to " O   HOH Z 280 " =    3.237
peak=    3.191 closest distance to " CD BLYS A 290 " =    1.044
peak=    3.189 closest distance to " CD1 LEU A 101 " =    1.177
peak=    3.188 closest distance to " O   HOH Z 197 " =    1.929
peak=    3.187 closest distance to " O   HOH Z 251 " =    1.345
peak=    3.187 closest distance to " ND2 ASN A 110 " =    1.587
peak=    3.186 closest distance to " CA  ASN A 215 " =    1.138
peak=    3.184 closest distance to " O   HOH Z 336 " =    1.792
peak=    3.184 closest distance to " O   HOH Z 130 " =    1.051
peak=    3.182 closest distance to " CD1 ILE A  33 " =    1.584
peak=    3.179 closest distance to " CD1 ILE A 106 " =    1.058
peak=    3.179 closest distance to " O   HOH Z 112 " =    1.621
peak=    3.177 closest distance to " CB  SER A 273 " =    0.837
peak=    3.176 closest distance to " O   HOH Z 145 " =    2.588
peak=    3.175 closest distance to " O   HOH Z 171 " =    3.882
peak=    3.175 closest distance to " O   HOH Z  90 " =    3.456
peak=    3.174 closest distance to " CA  ALA A  84 " =    1.298
peak=    3.170 closest distance to " ND1 HIS A  81 " =    1.611
peak=    3.169 closest distance to " CB  ALA A 242 " =    0.921
peak=    3.168 closest distance to " N   ARG A 190 " =    1.044
peak=    3.167 closest distance to " CA  ILE A 106 " =    0.737
peak=    3.165 closest distance to " O   HOH Z  96 " =    2.122
peak=    3.165 closest distance to " CG  LEU A 167 " =    1.134
peak=    3.163 closest distance to " CD2 TYR A  30 " =    0.906
peak=    3.160 closest distance to " NH2AARG A 275 " =    3.699
peak=    3.158 closest distance to " N   VAL A 126 " =    1.472
peak=    3.150 closest distance to " O   HOH Z 387 " =    2.649
peak=    3.141 closest distance to " CB  GLN A 103 " =    0.878
peak=    3.138 closest distance to " CZ2 TRP A 179 " =    1.812
peak=    3.137 closest distance to " O   HOH Z 368 " =    3.525
peak=    3.137 closest distance to " CZ3 TRP A  85 " =    0.993
peak=    3.137 closest distance to " CA  ALA A 158 " =    1.242
peak=    3.129 closest distance to " CA  GLY A 267 " =    0.753
peak=    3.127 closest distance to " O   HOH Z 256 " =    2.324
peak=    3.127 closest distance to " CG  GLN A  77 " =    2.104
peak=    3.123 closest distance to " CG2AVAL A 121 " =    2.128
peak=    3.122 closest distance to " O   HOH Z 162 " =    1.835
peak=    3.119 closest distance to " CZ2 TRP A 274 " =    1.572
peak=    3.112 closest distance to " CB  ALA A  84 " =    0.705
peak=    3.109 closest distance to " O   HOH Z  46 " =    1.420
peak=    3.108 closest distance to " O   HOH Z 298 " =    4.223
peak=    3.101 closest distance to " CA  ASN A 217 " =    1.321
peak=    3.101 closest distance to " CB  ASN A 215 " =    1.131
peak=    3.097 closest distance to " O   HOH Z 251 " =    1.633
peak=    3.096 closest distance to " O   HOH Z 166 " =    1.342
peak=    3.091 closest distance to " O   HOH Z 298 " =    4.915
peak=    3.086 closest distance to " O   HOH Z 353 " =    2.802
peak=    3.086 closest distance to " CG2 THR A  42 " =    0.820
peak=    3.084 closest distance to " O   HOH Z 260 " =    1.498
peak=    3.081 closest distance to " CB  MET A  47 " =    1.157
peak=    3.064 closest distance to " O   HOH Z 305 " =    3.589
peak=    3.049 closest distance to " CG2 VAL A 202 " =    1.175
peak=    3.042 closest distance to " O   THR A  31 " =    1.573
peak=    3.041 closest distance to " O   HOH Z 367 " =    3.388
peak=    3.037 closest distance to " O   HOH Z 207 " =    2.265

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.590
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.732 - 5.590

peak=   -5.819 closest distance to " CG2 VAL A 230 " =    0.732
peak=   -4.513 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.498 closest distance to " CG2BVAL A  41 " =    2.618
peak=   -4.477 closest distance to " O   HOH Z 266 " =    4.820
peak=   -4.353 closest distance to " O   PRO A 163 " =    2.157
peak=   -4.304 closest distance to " O   HOH Z 196 " =    2.202
peak=   -4.300 closest distance to " SG  CYS A 254 " =    3.229
peak=   -4.293 closest distance to " CG  ASP A 231 " =    0.885
peak=   -4.283 closest distance to " O   HOH Z 166 " =    1.777
peak=   -4.211 closest distance to " O   HOH Z 290 " =    0.962
peak=   -4.193 closest distance to " CD  GLN A  58 " =    1.127
peak=   -4.162 closest distance to " CD1 LEU A 101 " =    2.462
peak=   -4.073 closest distance to " O   HOH Z 351 " =    1.598
peak=   -4.068 closest distance to " C   HIS A 108 " =    1.171
peak=   -4.064 closest distance to " O   HOH Z  13 " =    1.644
peak=   -4.050 closest distance to " CH2 TRP A 179 " =    1.234
peak=   -4.035 closest distance to " OXT GLY A 302 " =    2.763
peak=   -4.033 closest distance to " CE2 TYR A  30 " =    2.770
peak=   -3.898 closest distance to " OG BSER A 134 " =    1.280
peak=   -3.894 closest distance to " OG  SER A  97 " =    2.334
peak=   -3.891 closest distance to " O   HOH Z 426 " =    1.885
peak=   -3.883 closest distance to " CB  ALA A 161 " =    2.628
peak=   -3.867 closest distance to " CB  PRO A 243 " =    2.668
peak=   -3.818 closest distance to " O   HOH Z 165 " =    1.940
peak=   -3.802 closest distance to " O   HOH Z  37 " =    1.859
peak=   -3.786 closest distance to " O   VAL A  67 " =    2.759
peak=   -3.781 closest distance to " CD1 PHE A  59 " =    1.920
peak=   -3.751 closest distance to " O   HOH Z 394 " =    1.636
peak=   -3.747 closest distance to " CB  ALA A 248 " =    2.263
peak=   -3.742 closest distance to " OE1 GLN A 223 " =    2.217
peak=   -3.711 closest distance to " O   HOH Z 407 " =    3.055
peak=   -3.710 closest distance to " CD1 ILE A 263 " =    2.770
peak=   -3.709 closest distance to " CB  ALA A 248 " =    2.014
peak=   -3.706 closest distance to " N   ALA A 226 " =    2.064
peak=   -3.693 closest distance to " N   THR A 235 " =    1.274
peak=   -3.691 closest distance to " ND2 ASN A 187 " =    1.605
peak=   -3.686 closest distance to " CD2 LEU A 300 " =    2.744
peak=   -3.681 closest distance to " OG ASER A 134 " =    1.278
peak=   -3.667 closest distance to " O   HOH Z 283 " =    1.938
peak=   -3.665 closest distance to " O   HOH Z 292 " =    4.468
peak=   -3.657 closest distance to " O   HOH Z 114 " =    3.388
peak=   -3.653 closest distance to " O   HOH Z 231 " =    2.083
peak=   -3.653 closest distance to " O   VAL A 125 " =    2.303
peak=   -3.643 closest distance to " O   HOH Z  44 " =    2.178
peak=   -3.629 closest distance to " NH2 ARG A  66 " =    1.511
peak=   -3.624 closest distance to " CD  LYS A 289 " =    2.453
peak=   -3.618 closest distance to " N   ALA A  43 " =    2.639
peak=   -3.618 closest distance to " O   HOH Z 311 " =    3.633
peak=   -3.618 closest distance to " OD1 ASN A 148 " =    1.464
peak=   -3.614 closest distance to " O   HOH Z 136 " =    2.241
peak=   -3.604 closest distance to " CB  PHE A 192 " =    1.828
peak=   -3.599 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.590 closest distance to " CD1 LEU A  25 " =    2.506
peak=   -3.584 closest distance to " O   HOH Z 123 " =    2.363
peak=   -3.579 closest distance to " NE2 GLN A  88 " =    2.025
peak=   -3.578 closest distance to " C   THR A 279 " =    1.111
peak=   -3.576 closest distance to " O   HOH Z 234 " =    4.122
peak=   -3.574 closest distance to " O   HOH Z 166 " =    1.894
peak=   -3.564 closest distance to " CG2 VAL A 296 " =    1.133
peak=   -3.555 closest distance to " O   HOH Z 185 " =    2.448
peak=   -3.551 closest distance to " CE BMET A  47 " =    1.834
peak=   -3.551 closest distance to " O   VAL A 189 " =    2.577
peak=   -3.549 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.549 closest distance to " ND2 ASN A  45 " =    1.025
peak=   -3.548 closest distance to " O   HOH Z  11 " =    1.861
peak=   -3.547 closest distance to " NE2 GLN A  88 " =    1.014
peak=   -3.542 closest distance to " O   HOH Z  52 " =    1.571
peak=   -3.530 closest distance to " O   HOH Z  10 " =    1.559
peak=   -3.517 closest distance to " O   HOH Z 353 " =    2.197
peak=   -3.514 closest distance to " O   HOH Z  60 " =    2.272
peak=   -3.502 closest distance to " CG  GLU A  53 " =    1.593
peak=   -3.495 closest distance to " O   SER A 271 " =    2.054
peak=   -3.494 closest distance to " N   GLN A  58 " =    1.751
peak=   -3.487 closest distance to " O   SER A 210 " =    1.883
peak=   -3.476 closest distance to " ND2 ASN A  69 " =    1.691
peak=   -3.475 closest distance to " O   HOH Z 150 " =    1.890
peak=   -3.469 closest distance to " CB  ALA A 291 " =    2.248
peak=   -3.468 closest distance to " NE1 TRP A 266 " =    2.420
peak=   -3.458 closest distance to " C   ALA A 158 " =    1.265
peak=   -3.455 closest distance to " CE3 TRP A 150 " =    2.244
peak=   -3.447 closest distance to " NH2AARG A 275 " =    4.931
peak=   -3.440 closest distance to " CZ  TYR A 169 " =    1.741
peak=   -3.434 closest distance to " OG  SER A   3 " =    1.677
peak=   -3.428 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.416 closest distance to " NE2 GLN A 194 " =    1.767
peak=   -3.415 closest distance to " O   ALA A   1 " =    1.849
peak=   -3.406 closest distance to " OG BSER A 134 " =    1.830
peak=   -3.405 closest distance to " C   SER A 206 " =    1.507
peak=   -3.397 closest distance to " CG  TRP A 266 " =    2.016
peak=   -3.396 closest distance to " ND2 ASN A  39 " =    1.176
peak=   -3.395 closest distance to " NE2 GLN A 103 " =    1.764
peak=   -3.391 closest distance to " O   HOH Z  15 " =    1.478
peak=   -3.390 closest distance to " O   HOH Z 177 " =    1.735
peak=   -3.388 closest distance to " CD1 TRP A 179 " =    1.087
peak=   -3.383 closest distance to " C   LEU A 143 " =    0.959
peak=   -3.380 closest distance to " NH2 ARG A  79 " =    2.005
peak=   -3.380 closest distance to " CB  PRO A 163 " =    2.676
peak=   -3.380 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.378 closest distance to " O   HOH Z 126 " =    1.920
peak=   -3.376 closest distance to " O   HOH Z 166 " =    1.729
peak=   -3.375 closest distance to " CD  ARG A 139 " =    1.647
peak=   -3.371 closest distance to " O   HOH Z 348 " =    1.832
peak=   -3.369 closest distance to " O   HOH Z 423 " =    2.198
peak=   -3.367 closest distance to " CZ3 TRP A 274 " =    1.002
peak=   -3.366 closest distance to " OG  SER A  26 " =    1.249
peak=   -3.366 closest distance to " NH2 ARG A 159 " =    2.334
peak=   -3.362 closest distance to " N   THR A 157 " =    1.557
peak=   -3.349 closest distance to " O   GLY A 196 " =    1.077
peak=   -3.346 closest distance to " CD  GLN A 223 " =    0.737
peak=   -3.344 closest distance to " O   HOH Z 193 " =    1.836
peak=   -3.344 closest distance to " CB  ASP A 132 " =    2.354
peak=   -3.341 closest distance to " O   HOH Z  71 " =    1.438
peak=   -3.341 closest distance to " O   GLY A  80 " =    2.546
peak=   -3.340 closest distance to " CG  ARG A 269 " =    2.249
peak=   -3.338 closest distance to " O   HOH Z 171 " =    2.014
peak=   -3.337 closest distance to " N   THR A  52 " =    1.630
peak=   -3.337 closest distance to " O   HOH Z 389 " =    1.788
peak=   -3.333 closest distance to " O   HOH Z  17 " =    1.252
peak=   -3.332 closest distance to " OXT GLY A 302 " =    3.491
peak=   -3.328 closest distance to " O   HOH Z 222 " =    1.532
peak=   -3.326 closest distance to " O   HOH Z 191 " =    5.590
peak=   -3.324 closest distance to " O   ALA A 161 " =    1.695
peak=   -3.320 closest distance to " CB  PHE A 208 " =    2.337
peak=   -3.319 closest distance to " CE  MET A 105 " =    2.082
peak=   -3.317 closest distance to " CG  ASP A  50 " =    2.303
peak=   -3.315 closest distance to " O   HOH Z 369 " =    2.291
peak=   -3.313 closest distance to " CD1 PHE A  59 " =    2.204
peak=   -3.312 closest distance to " CE2 PHE A 218 " =    2.670
peak=   -3.303 closest distance to " OG1 THR A  82 " =    1.420
peak=   -3.302 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.297 closest distance to " NZ  LYS A 119 " =    3.632
peak=   -3.290 closest distance to " CD  GLN A 223 " =    1.221
peak=   -3.290 closest distance to " CG1 VAL A 296 " =    1.250
peak=   -3.289 closest distance to " C   MET A 188 " =    1.621
peak=   -3.288 closest distance to " CD1 LEU A 228 " =    2.206
peak=   -3.285 closest distance to " N   SER A 276 " =    1.436
peak=   -3.279 closest distance to " CD2 LEU A 167 " =    1.725
peak=   -3.277 closest distance to " CG1 VAL A 112 " =    2.752
peak=   -3.277 closest distance to " CB  TRP A  85 " =    2.567
peak=   -3.271 closest distance to " CB  ALA A 291 " =    2.274
peak=   -3.271 closest distance to " N   LEU A 281 " =    1.821
peak=   -3.269 closest distance to " OG  SER A  62 " =    1.555
peak=   -3.268 closest distance to " CD2 TYR A 293 " =    2.015
peak=   -3.261 closest distance to " O   SER A 258 " =    1.952
peak=   -3.260 closest distance to " O   HOH Z 377 " =    2.084
peak=   -3.258 closest distance to " CG  ARG A 219 " =    2.607
peak=   -3.255 closest distance to " O   HOH Z 414 " =    1.896
peak=   -3.254 closest distance to " O   SER A  95 " =    1.710
peak=   -3.249 closest distance to " OG  SER A 206 " =    1.548
peak=   -3.248 closest distance to " CA  GLY A 241 " =    2.403
peak=   -3.247 closest distance to " O   PHE A 218 " =    1.719
peak=   -3.242 closest distance to " CG2 THR A 221 " =    2.366
peak=   -3.238 closest distance to " O   HOH Z 211 " =    1.646
peak=   -3.236 closest distance to " O   HOH Z 174 " =    4.292
peak=   -3.233 closest distance to " O   HOH Z   6 " =    1.942
peak=   -3.230 closest distance to " CB  GLN A  11 " =    1.879
peak=   -3.227 closest distance to " N   SER A   3 " =    2.106
peak=   -3.227 closest distance to " O   HOH Z  43 " =    1.848
peak=   -3.224 closest distance to " CG  GLU A 277 " =    1.101
peak=   -3.224 closest distance to " CB  TYR A  15 " =    2.187
peak=   -3.219 closest distance to " N   ASP A 171 " =    2.276
peak=   -3.218 closest distance to " O   ASN A  45 " =    1.896
peak=   -3.217 closest distance to " O   HOH Z 131 " =    4.156
peak=   -3.207 closest distance to " O   HOH Z 150 " =    2.240
peak=   -3.203 closest distance to " O   HOH Z 252 " =    3.899
peak=   -3.202 closest distance to " ND2 ASN A  45 " =    1.716
peak=   -3.201 closest distance to " O   HOH Z 422 " =    1.525
peak=   -3.198 closest distance to " CD2 LEU A 237 " =    2.730
peak=   -3.197 closest distance to " CG  PRO A 243 " =    1.727
peak=   -3.196 closest distance to " O   HOH Z 264 " =    1.769
peak=   -3.196 closest distance to " O   ALA A  10 " =    1.809
peak=   -3.194 closest distance to " O   HOH Z 285 " =    1.538
peak=   -3.188 closest distance to " O   TRP A  92 " =    1.912
peak=   -3.188 closest distance to " CG  MET A 105 " =    0.891
peak=   -3.181 closest distance to " O   GLY A  80 " =    2.435
peak=   -3.177 closest distance to " CG1 VAL A  78 " =    2.513
peak=   -3.174 closest distance to " CB  ASP A 286 " =    1.976
peak=   -3.172 closest distance to " O   HOH Z 431 " =    2.121
peak=   -3.169 closest distance to " C   ASP A 270 " =    1.143
peak=   -3.169 closest distance to " C   GLN A 205 " =    1.951
peak=   -3.168 closest distance to " OE2 GLU A   2 " =    1.783
peak=   -3.167 closest distance to " O   HOH Z 174 " =    2.177
peak=   -3.166 closest distance to " O   HOH Z 292 " =    2.855
peak=   -3.164 closest distance to " O   HOH Z 313 " =    1.210
peak=   -3.156 closest distance to " NE2 GLN A  58 " =    2.658
peak=   -3.155 closest distance to " O   HOH Z  90 " =    1.695
peak=   -3.148 closest distance to " C   ASP A 231 " =    2.591
peak=   -3.138 closest distance to " OG BSER A 210 " =    2.178
peak=   -3.135 closest distance to " O   HOH Z 372 " =    2.325
peak=   -3.129 closest distance to " CG  LEU A  83 " =    1.913
peak=   -3.125 closest distance to " CD  ARG A 195 " =    5.117
peak=   -3.124 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.123 closest distance to " O   HOH Z 412 " =    4.928
peak=   -3.122 closest distance to " CG  LEU A 228 " =    1.052
peak=   -3.118 closest distance to " O   HOH Z 236 " =    1.406
peak=   -3.118 closest distance to " O  BHOH Z 338 " =    1.537
peak=   -3.114 closest distance to " O   HOH Z 313 " =    2.057
peak=   -3.100 closest distance to " OD1 ASN A 301 " =    1.998
peak=   -3.096 closest distance to " CE  LYS A 166 " =    3.066
peak=   -3.084 closest distance to " CG  PHE A 283 " =    2.731
peak=   -3.080 closest distance to " O   HOH Z 437 " =    1.609
peak=   -3.071 closest distance to " O   HOH Z 250 " =    1.312
peak=   -3.071 closest distance to " O   HOH Z 392 " =    1.691
peak=   -3.071 closest distance to " O   HOH Z 111 " =    1.431
peak=   -3.068 closest distance to " O   HOH Z 407 " =    1.667

================= 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    :  0.4576 0.4434   6.257473e+00   6.236719e+00
   1_bss:  0.4497 0.4373   6.249964e+00   6.226202e+00
   1_xyz:  0.3510 0.3706   6.091481e+00   6.123979e+00
   1_adp:  0.2955 0.3319   5.965297e+00   6.052943e+00
   1_occ:  0.2949 0.3315   5.964246e+00   6.052978e+00
   2_bss:  0.2924 0.3259   5.964649e+00   6.049849e+00
   2_xyz:  0.2119 0.2547   5.681767e+00   5.833392e+00
   2_adp:  0.1929 0.2369   5.605426e+00   5.772744e+00
   2_occ:  0.1927 0.2372   5.605391e+00   5.773394e+00
   3_bss:  0.1911 0.2370   5.603932e+00   5.770918e+00
   3_xyz:  0.1433 0.1797   5.330761e+00   5.521693e+00
   3_adp:  0.1339 0.1687   5.269186e+00   5.463088e+00
   3_occ:  0.1338 0.1685   5.268211e+00   5.462331e+00
   4_bss:  0.1339 0.1685   5.269710e+00   5.462813e+00
   4_xyz:  0.1212 0.1604   5.195918e+00   5.412392e+00
   4_adp:  0.1188 0.1599   5.183393e+00   5.407357e+00
   4_occ:  0.1187 0.1599   5.183218e+00   5.407445e+00
   5_bss:  0.1187 0.1599   5.183030e+00   5.407358e+00
   5_xyz:  0.1136 0.1570   5.155633e+00   5.392055e+00
   5_adp:  0.1132 0.1572   5.154216e+00   5.393403e+00
   5_occ:  0.1132 0.1573   5.154258e+00   5.393780e+00
   5_bss:  0.1131 0.1573   5.154298e+00   5.393835e+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:  0.337  20.001   6.810  11.098   7.612   0.000   0.000   0.000
   1_xyz:  0.337  20.001   6.810  11.098   7.612   0.000   0.000   0.000
   1_adp:  0.337  20.001   6.810  11.098   7.612   0.000   0.000   0.000
   1_occ:  0.337  20.001   6.810  11.098   7.612   0.000   0.000   0.000
   2_bss:  0.325  40.349   3.691   7.251   4.941   0.000   0.000   0.000
   2_xyz:  0.325  40.349   3.691   7.251   4.941   0.000   0.000   0.000
   2_adp:  0.325  40.349   3.691   7.251   4.941   0.000   0.000   0.000
   2_occ:  0.325  40.349   3.691   7.251   4.941   0.000   0.000   0.000
   3_bss:  0.330  51.821   2.487   4.511   3.885   0.000   0.000   0.000
   3_xyz:  0.330  51.821   2.487   4.511   3.885   0.000   0.000   0.000
   3_adp:  0.330  51.821   2.487   4.511   3.885   0.000   0.000   0.000
   3_occ:  0.330  51.821   2.487   4.511   3.885   0.000   0.000   0.000
   4_bss:  0.327  49.357   2.076   3.422   3.487   0.000   0.000   0.000
   4_xyz:  0.327  49.357   2.076   3.422   3.487   0.000   0.000   0.000
   4_adp:  0.327  49.357   2.076   3.422   3.487   0.000   0.000   0.000
   4_occ:  0.327  49.357   2.076   3.422   3.487   0.000   0.000   0.000
   5_bss:  0.327  49.357   2.132   3.219   3.534   0.000   0.000   0.000
   5_xyz:  0.327  49.357   2.132   3.219   3.534   0.000   0.000   0.000
   5_adp:  0.327  49.357   2.132   3.219   3.534   0.000   0.000   0.000
   5_occ:  0.327  49.357   2.132   3.219   3.534   0.000   0.000   0.000
   5_bss:  0.327  52.455  -0.802   0.208   0.595   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.302 0.5055  0.5669    58007.149
   1_bss:  51.220 0.5045  0.7275    55915.237
   1_xyz:  41.306 0.6259  0.8844    38564.970
   1_adp:  35.066 0.7012  0.9941    30332.002
   1_occ:  35.048 0.7014  0.9933    30285.478
   2_bss:  34.777 0.7044  0.8902    29887.574
   2_xyz:  26.112 0.7992  0.9852    17181.176
   2_adp:  23.835 0.8236  1.0028    14903.245
   2_occ:  23.861 0.8233  1.0024    14925.484
   3_bss:  23.731 0.8247  0.9461    14832.272
   3_xyz:  16.990 0.8892  0.9890     8259.094
   3_adp:  15.573 0.9020  0.9954     7370.210
   3_occ:  15.555 0.9022  0.9955     7359.129
   4_bss:  15.553 0.9022  0.9731     7381.569
   4_xyz:  14.486 0.9113  0.9747     6682.748
   4_adp:  14.359 0.9125  0.9713     6646.127
   4_occ:  14.356 0.9126  0.9712     6651.449
   5_bss:  14.349 0.9126  0.9704     6650.452
   5_xyz:  14.037 0.9150  0.9720     6438.260
   5_adp:  14.062 0.9149  0.9675     6449.339
   5_occ:  14.065 0.9149  0.9674     6455.559
   5_bss:  14.066 0.9149  0.9722     6456.489
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3851e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3851e+01
   1_xyz:   1.647  0.013  0.108 17.878  0.007  4.122   1.3383e-01
   1_adp:   1.647  0.013  0.108 17.878  0.007  4.122   1.3383e-01
   1_occ:   1.647  0.013  0.108 17.878  0.007  4.122   1.3383e-01
   2_bss:   1.647  0.013  0.108 17.878  0.007  4.122   1.3383e-01
   2_xyz:   1.107  0.007  0.076 16.153  0.004  4.126   7.1442e-02
   2_adp:   1.107  0.007  0.076 16.153  0.004  4.126   7.1442e-02
   2_occ:   1.107  0.007  0.076 16.153  0.004  4.126   7.1442e-02
   3_bss:   1.107  0.007  0.076 16.153  0.004  4.126   7.1442e-02
   3_xyz:   1.025  0.007  0.078 15.155  0.004  4.112   6.2401e-02
   3_adp:   1.025  0.007  0.078 15.155  0.004  4.112   6.2401e-02
   3_occ:   1.025  0.007  0.078 15.155  0.004  4.112   6.2401e-02
   4_bss:   1.025  0.007  0.078 15.155  0.004  4.112   6.2401e-02
   4_xyz:   1.016  0.007  0.081 15.166  0.004  4.116   6.1027e-02
   4_adp:   1.016  0.007  0.081 15.166  0.004  4.116   6.1027e-02
   4_occ:   1.016  0.007  0.081 15.166  0.004  4.116   6.1027e-02
   5_bss:   1.016  0.007  0.081 15.166  0.004  4.116   6.1027e-02
   5_xyz:   1.059  0.008  0.086 15.157  0.004  4.119   6.6353e-02
   5_adp:   1.059  0.008  0.086 15.157  0.004  4.119   6.6353e-02
   5_occ:   1.059  0.008  0.086 15.157  0.004  4.119   6.6353e-02
   5_bss:   1.059  0.008  0.086 15.157  0.004  4.119   6.6353e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9815e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9815e+00
   1_xyz:  14.985  0.156  0.523 86.331  0.044  2.316   1.0049e-01
   1_adp:  14.985  0.156  0.523 86.331  0.044  2.316   1.0049e-01
   1_occ:  14.985  0.156  0.523 86.331  0.044  2.316   1.0049e-01
   2_bss:  14.985  0.156  0.523 86.331  0.044  2.316   1.0049e-01
   2_xyz:   6.845  0.073  0.260 82.652  0.026  2.147   6.6794e-02
   2_adp:   6.845  0.073  0.260 82.652  0.026  2.147   6.6794e-02
   2_occ:   6.845  0.073  0.260 82.652  0.026  2.147   6.6794e-02
   3_bss:   6.845  0.073  0.260 82.652  0.026  2.147   6.6794e-02
   3_xyz:   6.744  0.056  0.470 81.139  0.039  2.347   4.6755e-02
   3_adp:   6.744  0.056  0.470 81.139  0.039  2.347   4.6755e-02
   3_occ:   6.744  0.056  0.470 81.139  0.039  2.347   4.6755e-02
   4_bss:   6.744  0.056  0.470 81.139  0.039  2.347   4.6755e-02
   4_xyz:   7.156  0.040  0.547 83.320  0.037  2.282   4.0250e-02
   4_adp:   7.156  0.040  0.547 83.320  0.037  2.282   4.0250e-02
   4_occ:   7.156  0.040  0.547 83.320  0.037  2.282   4.0250e-02
   5_bss:   7.156  0.040  0.547 83.320  0.037  2.282   4.0250e-02
   5_xyz:   7.649  0.043  0.632 81.391  0.035  2.314   4.3894e-02
   5_adp:   7.649  0.043  0.632 81.391  0.035  2.314   4.3894e-02
   5_occ:   7.649  0.043  0.632 81.391  0.035  2.314   4.3894e-02
   5_bss:   7.649  0.043  0.632 81.391  0.035  2.314   4.3894e-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:  78.59   0.00  11.69  71.86   0.00   8.95  78.59   0.00  26.65
   1_occ:  78.59   0.00  11.69  71.86   0.00   8.95  78.59   0.00  26.65
   2_bss:  78.59   0.00  11.69  71.86   0.00   8.95  78.59   0.00  26.65
   2_xyz:  78.59   0.00  11.69  71.86   0.00   8.95  78.59   0.00  26.65
   2_adp:  76.54   0.00  11.90  76.54   0.00   8.27  74.60   1.19  31.68
   2_occ:  76.54   0.00  11.90  76.54   0.00   8.27  74.60   1.19  31.68
   3_bss:  76.54   0.00  11.90  76.54   0.00   8.27  74.60   1.19  31.68
   3_xyz:  76.54   0.00  11.90  76.54   0.00   8.27  74.60   1.19  31.68
   3_adp:  75.17   0.00  11.91  75.17   0.00   7.98  68.85   1.03  33.30
   3_occ:  75.17   0.00  11.91  75.17   0.00   7.98  68.85   1.03  33.30
   4_bss:  75.17   0.00  11.91  75.17   0.00   7.98  68.85   1.03  33.30
   4_xyz:  75.17   0.00  11.91  75.17   0.00   7.98  68.85   1.03  33.30
   4_adp:  77.21   0.00  11.97  77.21   0.00   7.89  69.53   1.10  34.17
   4_occ:  77.21   0.00  11.97  77.21   0.00   7.89  69.53   1.10  34.17
   5_bss:  77.21   0.00  11.97  77.21   0.00   7.89  69.53   1.10  34.17
   5_xyz:  77.21   0.00  11.97  77.21   0.00   7.89  69.53   1.10  34.17
   5_adp:  77.55   0.00  11.86  77.55   0.00   7.78  69.53   0.66  34.08
   5_occ:  77.55   0.00  11.86  77.55   0.00   7.78  69.53   0.66  34.08
   5_bss:  80.65   3.10  14.96  80.65   3.10  10.88  72.63   3.76  37.18
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.165    0.020    0.411
   1_adp:    1.165    0.020    0.411
   1_occ:    1.165    0.020    0.411
   2_bss:    1.165    0.020    0.411
   2_xyz:    1.653    0.026    0.557
   2_adp:    1.653    0.026    0.557
   2_occ:    1.653    0.026    0.557
   3_bss:    1.653    0.026    0.557
   3_xyz:    1.646    0.062    0.620
   3_adp:    1.646    0.062    0.620
   3_occ:    1.646    0.062    0.620
   4_bss:    1.646    0.062    0.620
   4_xyz:    1.740    0.036    0.648
   4_adp:    1.740    0.036    0.648
   4_occ:    1.740    0.036    0.648
   5_bss:    1.740    0.036    0.648
   5_xyz:    1.832    0.064    0.666
   5_adp:    1.832    0.064    0.666
   5_occ:    1.832    0.064    0.666
   5_bss:    1.832    0.064    0.666
------------------------------------------------------------------------

CPU time actual refinement: 337.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/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_576/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_576/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.32 
  Macro-tasks:
    bulk solvent and scale       = 41.90  
    individual site refinement   = 141.00 
    weights calculation          = 31.63  
    collect and process          = 6.57   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.21 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 103.39 
    alpha_beta                      = 8.21   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 115.45 
    fmodel                         = 7.88   
    r_factors                      = 0.17   
    phase_errors                   = 10.76  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 249.06 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.643 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    680 calls, 103.03 s
gradients_fft:          624 calls, 101.24 s

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

# Date 2008-01-16 Time 01:56:02 PST -0800 (1200477362.73 s)
Start R-work = 0.4576, R-free = 0.4434 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.4497, R-free = 0.4373
Final R-work = 0.1131, R-free = 0.1573