# Date 2008-01-16 Time 02:04:15 PST -0800 (1200477855.32 s)
#phil __OFF__

Command line arguments: "../683.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10317
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 683

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, 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: (70.25, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96136
Completeness in resolution range: 0.940513
Completeness with d_max=infinity: 0.937677

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9109
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96136
Completeness in resolution range: 0.940513
Completeness with d_max=infinity: 0.937677

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9113 -  4.1972 [2193/2222]  1974   219  10.0%
  bin  2:  4.1972 -  3.3438 [2091/2114]  1884   207   9.9%
  bin  3:  3.3438 -  2.9247 [2065/2090]  1852   213  10.3%
  bin  4:  2.9247 -  2.6590 [2068/2084]  1870   198   9.6%
  bin  5:  2.6590 -  2.4693 [2034/2072]  1824   210  10.3%
  bin  6:  2.4693 -  2.3243 [2041/2074]  1840   201   9.8%
  bin  7:  2.3243 -  2.2083 [2008/2045]  1806   202  10.1%
  bin  8:  2.2083 -  2.1124 [2003/2045]  1804   199   9.9%
  bin  9:  2.1124 -  2.0313 [2011/2049]  1807   204  10.1%
  bin 10:  2.0313 -  1.9614 [1075/2033]   969   106   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/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:
        1.68 -     2.32: 25
        2.32 -     2.97: 1741
        2.97 -     3.61: 4580
        3.61 -     4.26: 9202
        4.26 -     4.90: 12905
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.676 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.785 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.822 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.985 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28448 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_683/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4647   r_free= 0.4656   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.266591                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6814 0.99   1418  161 0.3818 0.3723      6.5675      6.5735|
|  2:  4.6814 -  3.7350 0.99   1368  145 0.3758 0.3939      6.7463        6.75|
|  3:  3.7350 -  3.2686 0.99   1336  154 0.4190 0.4016      6.6361      6.6785|
|  4:  3.2686 -  2.9723 0.99   1338  149 0.4379 0.4453      6.4888      6.4756|
|  5:  2.9723 -  2.7607 0.98   1320  145 0.4832 0.5229      6.3529      6.3698|
|  6:  2.7607 -  2.5988 0.99   1312  143 0.4868 0.5296       6.258      6.1903|
|  7:  2.5988 -  2.4693 0.99   1312  150 0.5030 0.4096      6.2512      6.1417|
|  8:  2.4693 -  2.3622 0.99   1300  145 0.5147 0.5307      6.1494      6.1864|
|  9:  2.3622 -  2.2716 0.99   1306  146 0.5247 0.5074      6.1235      6.1192|
| 10:  2.2716 -  2.1935 0.98   1304  141 0.5210 0.5331      6.1019      6.1139|
| 11:  2.1935 -  2.1251 0.98   1280  138 0.5189 0.5114      6.0257      6.0413|
| 12:  2.1251 -  2.0645 1.00   1278  148 0.5261 0.5884      5.9597      6.0027|
| 13:  2.0645 -  2.0103 0.95   1275  145 0.5348 0.4981      5.8691      5.8378|
| 14:  2.0103 -  1.9614 0.36    483   49 0.5558 0.5851      5.8627      5.7404|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6814  1418   161  0.71  33.24   0.81     0.73      66272.18|
|  2:  4.6814 -  3.7350  1368   145  0.72  33.52   0.89     0.78      95487.72|
|  3:  3.7350 -  3.2686  1336   154  0.62  42.23   0.85     0.74     104544.62|
|  4:  3.2686 -  2.9723  1338   149  0.53  49.11   0.82     0.63      94691.38|
|  5:  2.9723 -  2.7607  1320   145  0.44  56.56   0.75     0.54      80888.16|
|  6:  2.7607 -  2.5988  1312   143  0.43  57.20   0.76     0.51      66668.17|
|  7:  2.5988 -  2.4693  1312   150  0.45  55.90   0.74     0.50      57503.04|
|  8:  2.4693 -  2.3622  1300   145  0.43  57.80   0.72     0.50      52441.12|
|  9:  2.3622 -  2.2716  1306   146  0.38  61.80   0.74     0.45      51849.72|
| 10:  2.2716 -  2.1935  1304   141  0.32  66.04   0.77     0.39      51914.21|
| 11:  2.1935 -  2.1251  1280   138  0.28  69.48   0.76     0.34      49562.20|
| 12:  2.1251 -  2.0645  1278   148  0.25  71.28   0.75     0.32      47000.63|
| 13:  2.0645 -  2.0103  1275   145  0.25  71.16   0.73     0.33      39499.62|
| 14:  2.0103 -  1.9614   483    49  0.31  66.66   0.72     0.37      31336.74|
|alpha:            min =        0.32 max =            0.78 mean =         0.52|
|beta:             min =    31336.74 max =       104544.62 mean =     65413.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.76|
|phase err.(test): min =        0.00 max =           89.90 mean =        56.05|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.004060             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.845   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.094948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.782   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      696 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2658 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3937 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5084 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6585 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7780 |
|-----------------------------------------------------------------------------|
|-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 |       53.519 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.916 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    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 = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4716   r_free= 0.4730   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.269168                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4565   r_free= 0.4560   ksol= 0.35   Bsol= 14.55   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.74,9.18,9.11,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.265669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.326550             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.110   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.003018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.998   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4565      final r-factor (work) = 0.3736          |
| start r-factor (free) = 0.4560      final r-factor (free) = 0.3971          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.8806 = 10.33 * 0.50 * 6.2676 + 1.00 * 53.5192                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.9660 = 10.33 * 0.50 * 6.1645 + 1.00 * 0.1369                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3736      final r-factor (work) = 0.3263          |
| start r-factor (free) = 0.3971      final r-factor (free) = 0.3723          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1974 = 1.00 * 1.00 * 6.1645 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0994 = 1.00 * 1.00 * 6.0665 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.90   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    67.90   12.37    None  None   None       |
|    Sol.    : 438    0      0.00    67.90   26.82    None  None   None       |
|    Mac.    : 2385   0      0.00    59.53   9.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.790: 1143   |   5:    33.948 -  40.737:   98        |
|      1:     6.790 -  13.579:  755   |   6:    40.737 -  47.527:   62        |
|      2:    13.579 -  20.369:  386   |   7:    47.527 -  54.316:   24        |
|      3:    20.369 -  27.158:  226   |   8:    54.316 -  61.106:   13        |
|      4:    27.158 -  33.948:  111   |   9:    61.106 -  67.895:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3263 r_free = 0.3723             target_work(ml) = 6.043         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3260 r_free = 0.3726             target_work(ml) = 6.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3260   r_free= 0.3726   ksol= 0.35   Bsol= 14.55   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.74,9.18,9.11,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.042134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3227   r_free= 0.3671   ksol= 0.33   Bsol= 37.03   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,5.41,6.00,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.041592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.756690              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.471748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.726  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3227      final r-factor (work) = 0.2306          |
| start r-factor (free) = 0.3671      final r-factor (free) = 0.2871          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5918 = 5.76 * 0.50 * 6.0642 + 1.00 * 0.1369                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0687 = 5.76 * 0.50 * 5.9042 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2306      final r-factor (work) = 0.2087          |
| start r-factor (free) = 0.2871      final r-factor (free) = 0.2618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7999 = 0.47 * 1.00 * 5.9042 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7130 = 0.47 * 1.00 * 5.7212 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.73   12.65    None  None   None       |
|    all(noH): 2823   0      0.00    68.73   12.65    None  None   None       |
|    Sol.    : 438    0      1.56    68.73   32.36    None  None   None       |
|    Mac.    : 2385   0      0.00    66.31   9.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.873: 1230   |   5:    34.364 -  41.237:  119        |
|      1:     6.873 -  13.746:  807   |   6:    41.237 -  48.109:   74        |
|      2:    13.746 -  20.618:  256   |   7:    48.109 -  54.982:   50        |
|      3:    20.618 -  27.491:  148   |   8:    54.982 -  61.855:   14        |
|      4:    27.491 -  34.364:  116   |   9:    61.855 -  68.728:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2087 r_free = 0.2618             target_work(ml) = 5.680         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2085 r_free = 0.2619             target_work(ml) = 5.680         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2085   r_free= 0.2619   ksol= 0.33   Bsol= 37.03   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,5.41,6.00,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.679939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2064   r_free= 0.2604   ksol= 0.32   Bsol= 37.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,3.26,3.50,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.678295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.555305              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.066  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.752196              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.895   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2064      final r-factor (work) = 0.1565          |
| start r-factor (free) = 0.2604      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3941 = 2.56 * 0.50 * 5.7291 + 1.00 * 0.0742                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1692 = 2.56 * 0.50 * 5.5652 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1565      final r-factor (work) = 0.1442          |
| start r-factor (free) = 0.2033      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2009 = 0.75 * 1.00 * 5.5652 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0878 = 0.75 * 1.00 * 5.3891 + 1.00 * 0.0341                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.55   13.42    None  None   None       |
|    all(noH): 2823   0      0.00    87.55   13.42    None  None   None       |
|    Sol.    : 438    0      2.46    77.36   37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    87.55   9.00     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:     0.000 -   8.755: 1572   |   5:    43.773 -  52.527:   99        |
|      1:     8.755 -  17.509:  646   |   6:    52.527 -  61.282:   68        |
|      2:    17.509 -  26.264:  176   |   7:    61.282 -  70.036:   24        |
|      3:    26.264 -  35.018:  103   |   8:    70.036 -  78.791:   10        |
|      4:    35.018 -  43.773:  121   |   9:    78.791 -  87.546:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1442 r_free = 0.1925             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1439 r_free = 0.1925             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1439   r_free= 0.1925   ksol= 0.32   Bsol= 37.03   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,3.26,3.50,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.360518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1925   ksol= 0.31   Bsol= 37.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.57,2.66,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.361164                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.781352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.689   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.704792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8615 = 1.78 * 0.50 * 5.3922 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7829 = 1.78 * 0.50 * 5.3079 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7591 = 0.70 * 1.00 * 5.3079 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7151 = 0.70 * 1.00 * 5.2399 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.40   13.36    None  None   None       |
|    all(noH): 2823   0      0.00    94.40   13.36    None  None   None       |
|    Sol.    : 438    0      1.72    79.12   37.62    None  None   None       |
|    Mac.    : 2385   0      0.00    94.40   8.90     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.440: 1706   |   5:    47.200 -  56.639:   89        |
|      1:     9.440 -  18.880:  573   |   6:    56.639 -  66.079:   46        |
|      2:    18.880 -  28.320:  151   |   7:    66.079 -  75.519:   19        |
|      3:    28.320 -  37.760:  109   |   8:    75.519 -  84.959:    7        |
|      4:    37.760 -  47.200:  120   |   9:    84.959 -  94.399:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1695             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1695             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1695   ksol= 0.31   Bsol= 37.03   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.57,2.66,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.231248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1696   ksol= 0.32   Bsol= 41.48   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.45,2.54,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.231176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.438185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.632891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.718  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8229 = 1.44 * 0.50 * 5.2394 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8009 = 1.44 * 0.50 * 5.2146 + 1.00 * 0.0512                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3155 = 0.63 * 1.00 * 5.2146 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3045 = 0.63 * 1.00 * 5.1983 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.71   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    98.71   13.13    None  None   None       |
|    Sol.    : 438    0      1.51    79.66   36.91    None  None   None       |
|    Mac.    : 2385   0      0.00    98.71   8.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.871: 1774   |   5:    49.355 -  59.226:   70        |
|      1:     9.871 -  19.742:  535   |   6:    59.226 -  69.097:   32        |
|      2:    19.742 -  29.613:  154   |   7:    69.097 -  78.968:   16        |
|      3:    29.613 -  39.484:  121   |   8:    78.968 -  88.839:    5        |
|      4:    39.484 -  49.355:  113   |   9:    88.839 -  98.710:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1637             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1637             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1637   ksol= 0.32   Bsol= 41.48   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.45,2.54,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197286                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6814 0.99   1418  161 0.0980 0.1234      5.3708      5.5163|
|  2:  4.6814 -  3.7350 0.99   1368  145 0.0890 0.1153      5.4512      5.6778|
|  3:  3.7350 -  3.2686 0.99   1336  154 0.1103 0.1583       5.507      5.8554|
|  4:  3.2686 -  2.9723 0.99   1338  149 0.1311 0.1565      5.5015      5.6674|
|  5:  2.9723 -  2.7607 0.98   1320  145 0.1402 0.1775      5.3712      5.5045|
|  6:  2.7607 -  2.5988 0.99   1312  143 0.1322 0.2150      5.2799      5.5639|
|  7:  2.5988 -  2.4693 0.99   1312  150 0.1319 0.1738      5.2166      5.4439|
|  8:  2.4693 -  2.3622 0.99   1300  145 0.1250 0.1780      5.1194      5.3397|
|  9:  2.3622 -  2.2716 0.99   1306  146 0.1246 0.1887      5.0804      5.3307|
| 10:  2.2716 -  2.1935 0.98   1304  141 0.1210 0.1864      5.0359      5.2995|
| 11:  2.1935 -  2.1251 0.98   1280  138 0.1231 0.1830       4.978      5.2996|
| 12:  2.1251 -  2.0645 1.00   1278  148 0.1190 0.1786      4.9088      5.1354|
| 13:  2.0645 -  2.0103 0.95   1275  145 0.1254 0.1819      4.8423      5.0782|
| 14:  2.0103 -  1.9614 0.36    483   49 0.1195 0.1978      4.7604      5.0441|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6814  1418   161  0.94   8.74   0.98     0.96       6932.22|
|  2:  4.6814 -  3.7350  1368   145  0.95   8.00   1.02     1.00       8878.72|
|  3:  3.7350 -  3.2686  1336   154  0.93  11.85   1.03     1.03      11131.95|
|  4:  3.2686 -  2.9723  1338   149  0.91  14.56   1.01     0.98      10996.18|
|  5:  2.9723 -  2.7607  1320   145  0.89  17.16   0.99     0.97       9146.16|
|  6:  2.7607 -  2.5988  1312   143  0.89  17.20   0.99     0.97       8164.42|
|  7:  2.5988 -  2.4693  1312   150  0.90  16.40   0.99     0.96       6772.77|
|  8:  2.4693 -  2.3622  1300   145  0.90  16.68   1.00     0.96       6081.22|
|  9:  2.3622 -  2.2716  1306   146  0.89  16.98   1.00     0.98       5560.57|
| 10:  2.2716 -  2.1935  1304   141  0.90  16.47   1.00     0.96       5117.87|
| 11:  2.1935 -  2.1251  1280   138  0.89  17.20   1.00     0.96       4710.83|
| 12:  2.1251 -  2.0645  1278   148  0.91  15.67   1.00     0.99       4142.66|
| 13:  2.0645 -  2.0103  1275   145  0.89  17.74   1.00     1.00       3734.96|
| 14:  2.0103 -  1.9614   483    49  0.89  17.15   0.99     0.96       3155.79|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     3155.79 max =        11131.95 mean =      6958.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.96|
|phase err.(test): min =        0.00 max =           87.97 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1644   ksol= 0.32   Bsol= 45.48   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.20,0.29,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200024                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1644   ksol= 0.32   Bsol= 45.48   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.20,0.29,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200024                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6814 0.99   1418  161 0.0978 0.1267      5.3824      5.5349|
|  2:  4.6814 -  3.7350 0.99   1368  145 0.0907 0.1161      5.4677       5.693|
|  3:  3.7350 -  3.2686 0.99   1336  154 0.1111 0.1582      5.5148      5.8529|
|  4:  3.2686 -  2.9723 0.99   1338  149 0.1319 0.1580      5.5044      5.6731|
|  5:  2.9723 -  2.7607 0.98   1320  145 0.1404 0.1769      5.3725       5.504|
|  6:  2.7607 -  2.5988 0.99   1312  143 0.1320 0.2145      5.2789      5.5606|
|  7:  2.5988 -  2.4693 0.99   1312  150 0.1319 0.1744      5.2161      5.4493|
|  8:  2.4693 -  2.3622 0.99   1300  145 0.1248 0.1775      5.1191      5.3383|
|  9:  2.3622 -  2.2716 0.99   1306  146 0.1245 0.1888      5.0799      5.3309|
| 10:  2.2716 -  2.1935 0.98   1304  141 0.1208 0.1866      5.0346      5.2998|
| 11:  2.1935 -  2.1251 0.98   1280  138 0.1228 0.1827      4.9774      5.2988|
| 12:  2.1251 -  2.0645 1.00   1278  148 0.1189 0.1788      4.9085      5.1361|
| 13:  2.0645 -  2.0103 0.95   1275  145 0.1253 0.1815      4.8416       5.077|
| 14:  2.0103 -  1.9614 0.36    483   49 0.1195 0.1977      4.7596      5.0426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9113 -  4.6814  1418   161  0.94   9.06   0.98     0.96       7302.64|
|  2:  4.6814 -  3.7350  1368   145  0.95   8.25   1.02     1.00       9201.39|
|  3:  3.7350 -  3.2686  1336   154  0.93  12.01   1.03     1.03      11356.44|
|  4:  3.2686 -  2.9723  1338   149  0.91  14.61   1.01     0.98      11039.16|
|  5:  2.9723 -  2.7607  1320   145  0.89  17.21   1.00     0.97       9158.83|
|  6:  2.7607 -  2.5988  1312   143  0.89  17.25   0.99     0.97       8176.46|
|  7:  2.5988 -  2.4693  1312   150  0.90  16.43   0.99     0.96       6785.26|
|  8:  2.4693 -  2.3622  1300   145  0.90  16.69   1.00     0.96       6089.97|
|  9:  2.3622 -  2.2716  1306   146  0.89  16.99   1.00     0.98       5561.31|
| 10:  2.2716 -  2.1935  1304   141  0.90  16.45   1.00     0.96       5106.83|
| 11:  2.1935 -  2.1251  1280   138  0.89  17.21   1.00     0.96       4710.54|
| 12:  2.1251 -  2.0645  1278   148  0.91  15.67   1.00     0.99       4142.99|
| 13:  2.0645 -  2.0103  1275   145  0.89  17.74   1.00     1.00       3732.35|
| 14:  2.0103 -  1.9614   483    49  0.89  17.15   0.99     0.96       3150.53|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     3150.53 max =        11356.44 mean =      7036.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.03|
|phase err.(test): min =        0.00 max =           88.54 mean =        14.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.786)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.25    100.96  15.39    None  None   None       |
|    all(noH): 2823   0      2.25    100.96  15.39    None  None   None       |
|    Sol.    : 438    0      3.77    81.91   39.16    None  None   None       |
|    Mac.    : 2385   0      2.25    100.96  11.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.254 -  12.125: 1774   |   5:    51.608 -  61.479:   70        |
|      1:    12.125 -  21.996:  535   |   6:    61.479 -  71.350:   32        |
|      2:    21.996 -  31.866:  154   |   7:    71.350 -  81.221:   16        |
|      3:    31.866 -  41.737:  121   |   8:    81.221 -  91.092:    5        |
|      4:    41.737 -  51.608:  113   |   9:    91.092 - 100.963:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.404 - 5.945
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 347
   mapped sites are within: 0.745 - 5.945

peak=   10.243 closest distance to " CB  VAL A 230 " =    1.426
peak=    9.289 closest distance to " CG2 VAL A 296 " =    1.291
peak=    6.036 closest distance to " CG  LEU A   5 " =    1.343
peak=    5.916 closest distance to " O   HOH Z 279 " =    1.266
peak=    5.907 closest distance to " NH2 ARG A  56 " =    2.256
peak=    5.750 closest distance to " O   HOH Z 124 " =    1.622
peak=    5.595 closest distance to " CD2 LEU A   5 " =    1.210
peak=    5.311 closest distance to " CB  GLN A 223 " =    1.400
peak=    5.302 closest distance to " O   HOH Z 278 " =    1.166
peak=    5.300 closest distance to " CD1AILE A 234 " =    1.078
peak=    5.166 closest distance to " O   HOH Z 272 " =    1.909
peak=    5.081 closest distance to " CG  PRO A 198 " =    1.248
peak=    5.046 closest distance to " O   HOH Z 247 " =    1.406
peak=    5.035 closest distance to " CG  PRO A  54 " =    1.259
peak=    4.959 closest distance to " CB  ARG A 275 " =    0.876
peak=    4.950 closest distance to " O   HOH Z 132 " =    1.224
peak=    4.921 closest distance to " CB  PRO A  54 " =    0.898
peak=    4.865 closest distance to " O   HOH Z 120 " =    1.127
peak=    4.828 closest distance to " O   HOH Z  48 " =    1.740
peak=    4.723 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.692 closest distance to " O   HOH Z  11 " =    1.342
peak=    4.674 closest distance to " CD2 LEU A 228 " =    1.238
peak=    4.615 closest distance to " NH1 ARG A 138 " =    1.076
peak=    4.603 closest distance to " CB  GLN A 183 " =    1.331
peak=    4.584 closest distance to " O   HOH Z 193 " =    1.769
peak=    4.579 closest distance to " CB  SER A  63 " =    1.260
peak=    4.527 closest distance to " NE2 GLN A  11 " =    1.083
peak=    4.492 closest distance to " CG  LEU A 228 " =    1.241
peak=    4.407 closest distance to " O   HOH Z 126 " =    1.932
peak=    4.393 closest distance to " O   HOH Z  97 " =    1.882
peak=    4.342 closest distance to " O   HOH Z 232 " =    2.187
peak=    4.341 closest distance to " O   HOH Z  59 " =    2.326
peak=    4.336 closest distance to " CB  VAL A 230 " =    1.222
peak=    4.334 closest distance to " O   HOH Z 411 " =    3.578
peak=    4.328 closest distance to " O   SER A  87 " =    2.278
peak=    4.309 closest distance to " CB  TYR A 169 " =    0.968
peak=    4.304 closest distance to " O   HOH Z 403 " =    1.746
peak=    4.302 closest distance to " O   HOH Z 368 " =    2.167
peak=    4.286 closest distance to " O   HOH Z  80 " =    1.679
peak=    4.276 closest distance to " CA  ALA A  21 " =    1.282
peak=    4.273 closest distance to " CG  PRO A 280 " =    0.787
peak=    4.257 closest distance to " O   HOH Z 234 " =    3.838
peak=    4.248 closest distance to " O   HOH Z 316 " =    2.695
peak=    4.242 closest distance to " O   HOH Z 130 " =    2.793
peak=    4.226 closest distance to " O   HOH Z 128 " =    1.935
peak=    4.215 closest distance to " O   HOH Z 263 " =    1.495
peak=    4.205 closest distance to " CB  GLU A 128 " =    1.117
peak=    4.204 closest distance to " O   HOH Z 423 " =    1.840
peak=    4.189 closest distance to " CB  TRP A 179 " =    1.270
peak=    4.183 closest distance to " CB  SER A   3 " =    1.338
peak=    4.174 closest distance to " O   HOH Z 142 " =    1.589
peak=    4.164 closest distance to " CG1BVAL A  72 " =    1.604
peak=    4.140 closest distance to " CB  ASN A 148 " =    1.309
peak=    4.136 closest distance to " O   HOH Z 371 " =    3.276
peak=    4.131 closest distance to " O   HOH Z 426 " =    1.455
peak=    4.130 closest distance to " O   PRO A 198 " =    1.535
peak=    4.122 closest distance to " O   HOH Z   4 " =    1.482
peak=    4.101 closest distance to " O   HOH Z 394 " =    1.523
peak=    4.088 closest distance to " O   HOH Z 427 " =    2.932
peak=    4.072 closest distance to " O   HOH Z  40 " =    1.649
peak=    4.071 closest distance to " CB  GLU A 152 " =    1.135
peak=    4.057 closest distance to " CA  VAL A  41 " =    0.835
peak=    4.041 closest distance to " O   HOH Z 346 " =    1.477
peak=    4.027 closest distance to " O   HOH Z 369 " =    2.231
peak=    4.020 closest distance to " O   HOH Z 189 " =    2.526
peak=    4.019 closest distance to " O   HOH Z 298 " =    1.936
peak=    3.994 closest distance to " CA  TYR A  30 " =    1.032
peak=    3.964 closest distance to " CG2 THR A 221 " =    1.069
peak=    3.959 closest distance to " O   HOH Z 260 " =    1.243
peak=    3.956 closest distance to " O   HOH Z 389 " =    1.807
peak=    3.956 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.953 closest distance to " O   HOH Z  44 " =    2.407
peak=    3.944 closest distance to " CG1 ILE A  33 " =    1.363
peak=    3.943 closest distance to " O   HOH Z 134 " =    1.574
peak=    3.940 closest distance to " O   HOH Z  85 " =    1.303
peak=    3.940 closest distance to " O   HOH Z  20 " =    1.606
peak=    3.932 closest distance to " O   HOH Z 345 " =    3.040
peak=    3.918 closest distance to " O   HOH Z 344 " =    2.828
peak=    3.915 closest distance to " NH2 ARG A 156 " =    1.139
peak=    3.897 closest distance to " O   HOH Z  78 " =    1.689
peak=    3.897 closest distance to " CD  ARG A 269 " =    1.029
peak=    3.895 closest distance to " O   HOH Z 102 " =    1.276
peak=    3.894 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.885 closest distance to " O   HOH Z 214 " =    2.381
peak=    3.880 closest distance to " O   HOH Z 202 " =    1.107
peak=    3.871 closest distance to " CG  PRO A 243 " =    1.178
peak=    3.863 closest distance to " O   HOH Z  15 " =    2.230
peak=    3.861 closest distance to " O   HOH Z 236 " =    1.708
peak=    3.853 closest distance to " OE1 GLN A  11 " =    1.759
peak=    3.850 closest distance to " O   HOH Z 112 " =    1.575
peak=    3.812 closest distance to " CB  PRO A 198 " =    1.045
peak=    3.811 closest distance to " O   TRP A 274 " =    1.850
peak=    3.803 closest distance to " O   HOH Z 133 " =    1.691
peak=    3.798 closest distance to " OD2 ASP A 286 " =    2.763
peak=    3.790 closest distance to " O   HOH Z  44 " =    1.857
peak=    3.789 closest distance to " CB  LEU A 228 " =    1.416
peak=    3.788 closest distance to " OD1 ASN A  69 " =    2.595
peak=    3.784 closest distance to " O   HOH Z  63 " =    1.567
peak=    3.773 closest distance to " CG AARG A 275 " =    1.078
peak=    3.771 closest distance to " O   HOH Z 303 " =    2.145
peak=    3.762 closest distance to " O   HOH Z 280 " =    3.040
peak=    3.761 closest distance to " CD  LYS A 119 " =    1.811
peak=    3.748 closest distance to " O   HOH Z 108 " =    2.259
peak=    3.734 closest distance to " CB  VAL A 265 " =    1.215
peak=    3.733 closest distance to " O   THR A  31 " =    1.513
peak=    3.731 closest distance to " CA  ASP A 191 " =    0.855
peak=    3.714 closest distance to " O   HOH Z 395 " =    1.416
peak=    3.708 closest distance to " ND2 ASN A 187 " =    1.740
peak=    3.702 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.701 closest distance to " O   HOH Z 406 " =    1.654
peak=    3.698 closest distance to " CA  LYS A 117 " =    1.302
peak=    3.697 closest distance to " CD  ARG A 159 " =    0.764
peak=    3.693 closest distance to " O   HOH Z 276 " =    1.306
peak=    3.690 closest distance to " CB  SER A 141 " =    1.119
peak=    3.686 closest distance to " O   HOH Z 108 " =    1.139
peak=    3.681 closest distance to " CA  ASP A 140 " =    1.243
peak=    3.680 closest distance to " O   HOH Z 227 " =    1.709
peak=    3.678 closest distance to " NZ  LYS A  76 " =    1.265
peak=    3.678 closest distance to " CB  GLU A 277 " =    3.633
peak=    3.674 closest distance to " O   HOH Z  97 " =    2.570
peak=    3.647 closest distance to " CB BVAL A  41 " =    1.194
peak=    3.640 closest distance to " O   HOH Z  88 " =    3.143
peak=    3.639 closest distance to " CA  LEU A 282 " =    1.064
peak=    3.632 closest distance to " CG1 VAL A 153 " =    0.995
peak=    3.626 closest distance to " CB  VAL A 296 " =    1.006
peak=    3.617 closest distance to " O   HOH Z 374 " =    2.465
peak=    3.615 closest distance to " O   HOH Z 295 " =    1.568
peak=    3.610 closest distance to " CE1 TYR A 186 " =    1.285
peak=    3.607 closest distance to " OE1 GLN A  58 " =    5.945
peak=    3.599 closest distance to " OE1 GLU A   2 " =    2.163
peak=    3.598 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.596 closest distance to " O   HOH Z 273 " =    2.749
peak=    3.595 closest distance to " O   HOH Z 284 " =    1.335
peak=    3.595 closest distance to " CG BARG A 102 " =    1.842
peak=    3.585 closest distance to " O   HOH Z 357 " =    2.113
peak=    3.583 closest distance to " CB  VAL A 202 " =    1.626
peak=    3.581 closest distance to " O   GLN A 278 " =    1.387
peak=    3.573 closest distance to " CA  THR A 221 " =    0.893
peak=    3.570 closest distance to " O   HOH Z  66 " =    2.003
peak=    3.560 closest distance to " O   HOH Z  54 " =    1.513
peak=    3.557 closest distance to " CA  GLN A 194 " =    1.136
peak=    3.556 closest distance to " CA  ARG A  36 " =    1.070
peak=    3.549 closest distance to " CG  ARG A 138 " =    0.913
peak=    3.549 closest distance to " O   HOH Z 155 " =    1.518
peak=    3.545 closest distance to " O   HOH Z 261 " =    1.795
peak=    3.543 closest distance to " O   HOH Z 261 " =    1.613
peak=    3.540 closest distance to " O   HOH Z 197 " =    1.993
peak=    3.537 closest distance to " CA  VAL A 126 " =    1.022
peak=    3.534 closest distance to " CB  ALA A   9 " =    1.530
peak=    3.529 closest distance to " CG  ARG A  66 " =    0.934
peak=    3.528 closest distance to " O   HOH Z 422 " =    2.616
peak=    3.523 closest distance to " O   HOH Z 136 " =    1.355
peak=    3.523 closest distance to " O   HOH Z 408 " =    1.532
peak=    3.522 closest distance to " O   HOH Z 280 " =    1.594
peak=    3.521 closest distance to " CD  LYS A 166 " =    1.371
peak=    3.519 closest distance to " O   HOH Z  37 " =    1.203
peak=    3.515 closest distance to " CG  MET A 188 " =    1.394
peak=    3.512 closest distance to " O   HOH Z 132 " =    3.025
peak=    3.510 closest distance to " O   HOH Z 329 " =    3.591
peak=    3.506 closest distance to " CD BLYS A 290 " =    0.966
peak=    3.503 closest distance to " O   HOH Z 366 " =    2.882
peak=    3.498 closest distance to " O   HOH Z  78 " =    1.821
peak=    3.497 closest distance to " CD1 LEU A 300 " =    1.149
peak=    3.494 closest distance to " O   HOH Z 116 " =    1.719
peak=    3.487 closest distance to " O   HOH Z 383 " =    2.016
peak=    3.483 closest distance to " O   MET A 105 " =    1.862
peak=    3.478 closest distance to " CB  ARG A 139 " =    0.830
peak=    3.477 closest distance to " O   HOH Z 133 " =    2.157
peak=    3.476 closest distance to " CE  LYS A 119 " =    1.135
peak=    3.475 closest distance to " NH2BARG A 145 " =    2.303
peak=    3.473 closest distance to " N   ASN A  39 " =    1.225
peak=    3.469 closest distance to " O   SER A  26 " =    1.634
peak=    3.469 closest distance to " CB  ALA A 291 " =    1.295
peak=    3.466 closest distance to " O   HOH Z 214 " =    1.021
peak=    3.464 closest distance to " O   HOH Z 280 " =    2.336
peak=    3.460 closest distance to " CB  ARG A  79 " =    1.377
peak=    3.454 closest distance to " O   HOH Z 145 " =    2.493
peak=    3.453 closest distance to " CA  ALA A 248 " =    1.213
peak=    3.451 closest distance to " O   ALA A 158 " =    1.306
peak=    3.451 closest distance to " CA  ASN A 176 " =    1.036
peak=    3.449 closest distance to " OG1 THR A 294 " =    2.231
peak=    3.447 closest distance to " O   HOH Z 236 " =    1.795
peak=    3.447 closest distance to " CA  GLY A 211 " =    1.263
peak=    3.446 closest distance to " NZ  LYS A 166 " =    2.966
peak=    3.443 closest distance to " O   GLY A  23 " =    2.419
peak=    3.441 closest distance to " O   GLY A  91 " =    1.395
peak=    3.425 closest distance to " O   HOH Z  21 " =    1.802
peak=    3.421 closest distance to " CA  ALA A  51 " =    1.051
peak=    3.419 closest distance to " O   HOH Z 425 " =    1.350
peak=    3.417 closest distance to " CA  ALA A 160 " =    0.840
peak=    3.413 closest distance to " CD2 HIS A  81 " =    1.131
peak=    3.413 closest distance to " O   HOH Z  67 " =    1.728
peak=    3.410 closest distance to " O   HOH Z  40 " =    2.019
peak=    3.407 closest distance to " CB  SER A 216 " =    0.783
peak=    3.406 closest distance to " NE2 GLN A  58 " =    4.242
peak=    3.405 closest distance to " NH1 ARG A  14 " =    1.064
peak=    3.403 closest distance to " O   HOH Z 150 " =    1.783
peak=    3.403 closest distance to " O   HOH Z 203 " =    1.632
peak=    3.401 closest distance to " CB  GLN A  88 " =    1.191
peak=    3.400 closest distance to " OG  SER A  22 " =    2.764
peak=    3.399 closest distance to " O   HOH Z  85 " =    1.058
peak=    3.397 closest distance to " O   HOH Z 327 " =    2.596
peak=    3.396 closest distance to " C   ALA A 299 " =    0.949
peak=    3.390 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.386 closest distance to " OH  TYR A  30 " =    1.084
peak=    3.384 closest distance to " O   HOH Z 155 " =    2.790
peak=    3.384 closest distance to " O   HOH Z  66 " =    2.158
peak=    3.383 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.382 closest distance to " O   HOH Z 423 " =    3.270
peak=    3.381 closest distance to " O   HOH Z 185 " =    1.657
peak=    3.379 closest distance to " O   HOH Z 193 " =    2.142
peak=    3.378 closest distance to " O   HOH Z 126 " =    2.020
peak=    3.378 closest distance to " CB  SER A 273 " =    0.817
peak=    3.377 closest distance to " O   HOH Z 352 " =    1.292
peak=    3.375 closest distance to " CB  ARG A 190 " =    1.757
peak=    3.366 closest distance to " OG BSER A 164 " =    2.227
peak=    3.364 closest distance to " O   HOH Z 163 " =    1.418
peak=    3.364 closest distance to " CG  GLN A  58 " =    2.520
peak=    3.363 closest distance to " CA  LEU A 101 " =    1.467
peak=    3.361 closest distance to " NH2BARG A 102 " =    0.924
peak=    3.361 closest distance to " O   HOH Z 332 " =    1.570
peak=    3.360 closest distance to " O   HOH Z 419 " =    1.627
peak=    3.360 closest distance to " O   HOH Z 303 " =    1.655
peak=    3.359 closest distance to " O   HOH Z 359 " =    2.076
peak=    3.355 closest distance to " O   HOH Z 137 " =    1.649
peak=    3.352 closest distance to " CA  ALA A 295 " =    1.113
peak=    3.348 closest distance to " CG2 ILE A 120 " =    1.382
peak=    3.346 closest distance to " O   HOH Z 114 " =    1.110
peak=    3.346 closest distance to " O   HOH Z 128 " =    2.009
peak=    3.345 closest distance to " CA  GLY A  80 " =    1.052
peak=    3.344 closest distance to " CE1 HIS A 108 " =    1.157
peak=    3.337 closest distance to " CA  LYS A 290 " =    1.244
peak=    3.336 closest distance to " O   HOH Z 433 " =    1.417
peak=    3.332 closest distance to " CB  LEU A 143 " =    1.161
peak=    3.330 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.330 closest distance to " CG  GLN A  88 " =    1.068
peak=    3.324 closest distance to " O   HOH Z 221 " =    1.327
peak=    3.323 closest distance to " O   ASP A 124 " =    1.204
peak=    3.315 closest distance to " OG BSER A 258 " =    3.429
peak=    3.310 closest distance to " OD1 ASP A 286 " =    1.729
peak=    3.309 closest distance to " O   HOH Z 336 " =    1.894
peak=    3.308 closest distance to " CD2 LEU A 255 " =    1.122
peak=    3.308 closest distance to " O   HOH Z 192 " =    1.428
peak=    3.308 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.306 closest distance to " OD1 ASN A 217 " =    1.748
peak=    3.305 closest distance to " OG  SER A  97 " =    2.537
peak=    3.304 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.302 closest distance to " O   HOH Z 154 " =    1.291
peak=    3.301 closest distance to " O   HOH Z  50 " =    1.919
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.293 closest distance to " O   HOH Z 267 " =    2.089
peak=    3.292 closest distance to " NH2 ARG A  79 " =    1.387
peak=    3.292 closest distance to " O   HOH Z 227 " =    1.569
peak=    3.284 closest distance to " O   HOH Z 130 " =    1.140
peak=    3.282 closest distance to " CB  ALA A 295 " =    1.304
peak=    3.281 closest distance to " OD2 ASP A 298 " =    4.008
peak=    3.280 closest distance to " O   HOH Z  30 " =    1.163
peak=    3.278 closest distance to " O   HOH Z 411 " =    1.860
peak=    3.276 closest distance to " O   HOH Z 118 " =    1.360
peak=    3.273 closest distance to " NH1AARG A 145 " =    1.015
peak=    3.272 closest distance to " CD1 LEU A  96 " =    0.758
peak=    3.268 closest distance to " CD1 ILE A  33 " =    1.645
peak=    3.265 closest distance to " CD1 TRP A 266 " =    1.147
peak=    3.262 closest distance to " CG2 VAL A 257 " =    0.810
peak=    3.262 closest distance to " CA  THR A 264 " =    0.780
peak=    3.260 closest distance to " CD2 LEU A 297 " =    0.851
peak=    3.256 closest distance to " OD1 ASP A 231 " =    1.905
peak=    3.252 closest distance to " CG1BVAL A 121 " =    1.159
peak=    3.250 closest distance to " CB  ILE A 199 " =    0.928
peak=    3.247 closest distance to " OD2 ASP A 200 " =    1.368
peak=    3.243 closest distance to " O   HOH Z  48 " =    2.141
peak=    3.236 closest distance to " CA  THR A 246 " =    1.189
peak=    3.236 closest distance to " O   HOH Z 326 " =    1.424
peak=    3.230 closest distance to " O   HOH Z 156 " =    2.410
peak=    3.228 closest distance to " O   HOH Z 387 " =    2.888
peak=    3.227 closest distance to " N   ALA A 256 " =    0.883
peak=    3.225 closest distance to " O   HOH Z 279 " =    2.169
peak=    3.223 closest distance to " O   HOH Z 290 " =    1.078
peak=    3.219 closest distance to " N   ILE A  33 " =    1.119
peak=    3.219 closest distance to " NE1 TRP A 274 " =    0.898
peak=    3.215 closest distance to " CE  MET A  93 " =    1.372
peak=    3.214 closest distance to " CA  ASP A 162 " =    1.171
peak=    3.212 closest distance to " CA  MET A  40 " =    1.081
peak=    3.206 closest distance to " O   HOH Z 414 " =    1.504
peak=    3.204 closest distance to " CG2 THR A 220 " =    0.859
peak=    3.202 closest distance to " CD2 TRP A 179 " =    1.366
peak=    3.194 closest distance to " CA  ARG A 195 " =    1.116
peak=    3.192 closest distance to " CB  GLU A 236 " =    1.256
peak=    3.190 closest distance to " CZ  PHE A 192 " =    1.110
peak=    3.187 closest distance to " OD1 ASP A 238 " =    0.830
peak=    3.187 closest distance to " CB  LEU A 255 " =    0.767
peak=    3.183 closest distance to " N   GLN A 278 " =    1.088
peak=    3.175 closest distance to " OG  SER A 206 " =    1.300
peak=    3.175 closest distance to " O   HOH Z 211 " =    2.462
peak=    3.171 closest distance to " O   HOH Z 192 " =    1.151
peak=    3.171 closest distance to " O   ALA A   1 " =    1.725
peak=    3.171 closest distance to " O   HOH Z 166 " =    1.536
peak=    3.171 closest distance to " CB  SER A  62 " =    0.755
peak=    3.169 closest distance to " CG2 VAL A 174 " =    1.250
peak=    3.168 closest distance to " O   HOH Z 361 " =    3.241
peak=    3.167 closest distance to " O   HOH Z 434 " =    3.095
peak=    3.165 closest distance to " NH2BARG A 190 " =    1.839
peak=    3.162 closest distance to " CG2 ILE A  20 " =    1.463
peak=    3.160 closest distance to " CB  ARG A 102 " =    0.753
peak=    3.159 closest distance to " CG  GLN A  77 " =    0.745
peak=    3.158 closest distance to " CD1 LEU A 222 " =    0.825
peak=    3.155 closest distance to " O   HOH Z 244 " =    1.647
peak=    3.155 closest distance to " O   HOH Z 417 " =    1.962
peak=    3.151 closest distance to " NH1 ARG A 269 " =    0.845
peak=    3.148 closest distance to " O   HOH Z  54 " =    2.422
peak=    3.145 closest distance to " CG  GLN A  11 " =    1.514
peak=    3.145 closest distance to " O   HOH Z 261 " =    1.964
peak=    3.144 closest distance to " CG2 ILE A 106 " =    0.882
peak=    3.143 closest distance to " O   HOH Z 271 " =    1.843
peak=    3.141 closest distance to " OH  TYR A 116 " =    1.124
peak=    3.133 closest distance to " O   HOH Z 217 " =    1.190
peak=    3.133 closest distance to " CB  TYR A  30 " =    1.484
peak=    3.132 closest distance to " O   HOH Z 416 " =    2.891
peak=    3.132 closest distance to " CG  LEU A 167 " =    1.077
peak=    3.126 closest distance to " OG1 THR A 221 " =    1.341
peak=    3.121 closest distance to " CB  ALA A 256 " =    0.928
peak=    3.118 closest distance to " CH2 TRP A 150 " =    1.066
peak=    3.118 closest distance to " CD2 TYR A 186 " =    1.060
peak=    3.116 closest distance to " CB  ALA A 100 " =    1.282
peak=    3.115 closest distance to " CD  ARG A 138 " =    1.019
peak=    3.115 closest distance to " CB  ALA A 137 " =    1.171
peak=    3.115 closest distance to " O   HOH Z 197 " =    2.726
peak=    3.113 closest distance to " CB  THR A  31 " =    1.589
peak=    3.113 closest distance to " CD2 TYR A  30 " =    0.851
peak=    3.112 closest distance to " O   HOH Z 334 " =    1.376
peak=    3.111 closest distance to " O   HOH Z 281 " =    4.310
peak=    3.109 closest distance to " CA  ASN A 217 " =    1.364
peak=    3.109 closest distance to " CG  MET A  93 " =    1.064
peak=    3.100 closest distance to " O   HOH Z 420 " =    5.509
peak=    3.095 closest distance to " CG  GLN A  77 " =    2.303
peak=    3.090 closest distance to " CB  THR A 157 " =    0.973
peak=    3.088 closest distance to " O   HOH Z   1 " =    1.905
peak=    3.087 closest distance to " CG  MET A 185 " =    1.231
peak=    3.075 closest distance to " CB  VAL A 268 " =    0.826
peak=    3.073 closest distance to " OD1 ASN A  45 " =    1.347
peak=    3.062 closest distance to " CA  ALA A 158 " =    1.082
peak=    3.049 closest distance to " CB  GLN A  58 " =    0.757
peak=    3.027 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.005 closest distance to " CG2 VAL A 202 " =    1.168

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.742 - 5.270
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.742 - 5.270

peak=   -5.197 closest distance to " CG2 VAL A 230 " =    0.851
peak=   -4.453 closest distance to " OG ASER A 134 " =    1.166
peak=   -4.334 closest distance to " O   HOH Z  92 " =    1.242
peak=   -4.334 closest distance to " O   HOH Z 210 " =    0.742
peak=   -4.218 closest distance to " O   HOH Z 266 " =    4.415
peak=   -4.171 closest distance to " O   ILE A 109 " =    2.634
peak=   -4.151 closest distance to " O   HOH Z 166 " =    1.753
peak=   -4.147 closest distance to " OXT GLY A 302 " =    2.904
peak=   -4.136 closest distance to " O   HOH Z  13 " =    1.312
peak=   -4.121 closest distance to " CA  SER A 164 " =    2.024
peak=   -4.109 closest distance to " CD  ARG A 156 " =    2.010
peak=   -4.068 closest distance to " OD1 ASN A  39 " =    2.235
peak=   -4.042 closest distance to " NH2 ARG A  66 " =    1.445
peak=   -3.960 closest distance to " CE2 TYR A  30 " =    2.770
peak=   -3.954 closest distance to " O   HOH Z 423 " =    2.304
peak=   -3.907 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.876 closest distance to " O   HOH Z 290 " =    1.025
peak=   -3.848 closest distance to " O   HOH Z  11 " =    1.619
peak=   -3.843 closest distance to " O   HOH Z 407 " =    3.007
peak=   -3.833 closest distance to " CG2 THR A   4 " =    1.879
peak=   -3.824 closest distance to " O   HOH Z  43 " =    1.612
peak=   -3.821 closest distance to " O   HOH Z 231 " =    1.866
peak=   -3.798 closest distance to " O   HOH Z  71 " =    1.070
peak=   -3.797 closest distance to " CE  MET A 105 " =    2.109
peak=   -3.784 closest distance to " C   HIS A 108 " =    1.196
peak=   -3.780 closest distance to " C   ALA A 158 " =    1.183
peak=   -3.779 closest distance to " ND2 ASN A  45 " =    1.061
peak=   -3.773 closest distance to " N   SER A 276 " =    1.393
peak=   -3.770 closest distance to " SG  CYS A 254 " =    3.174
peak=   -3.767 closest distance to " O   HOH Z 351 " =    1.421
peak=   -3.752 closest distance to " CB  ALA A 248 " =    1.955
peak=   -3.752 closest distance to " O   SER A 271 " =    2.056
peak=   -3.740 closest distance to " O   HOH Z 266 " =    4.569
peak=   -3.731 closest distance to " O   HOH Z 165 " =    2.045
peak=   -3.728 closest distance to " O   VAL A  67 " =    2.774
peak=   -3.708 closest distance to " CG  ASP A  50 " =    2.372
peak=   -3.704 closest distance to " CA  GLY A 203 " =    2.141
peak=   -3.689 closest distance to " O   HOH Z 151 " =    1.437
peak=   -3.676 closest distance to " CG  ASP A 231 " =    0.837
peak=   -3.659 closest distance to " CD1 LEU A 101 " =    2.560
peak=   -3.649 closest distance to " O   ASN A 187 " =    1.458
peak=   -3.645 closest distance to " N   THR A 235 " =    1.209
peak=   -3.632 closest distance to " O   HOH Z 221 " =    1.282
peak=   -3.631 closest distance to " O   HOH Z 126 " =    1.866
peak=   -3.629 closest distance to " CD2 LEU A 300 " =    2.848
peak=   -3.627 closest distance to " NH2AARG A 275 " =    5.063
peak=   -3.617 closest distance to " O   HOH Z 145 " =    1.523
peak=   -3.613 closest distance to " O   HOH Z  52 " =    1.906
peak=   -3.612 closest distance to " CG  GLU A  53 " =    1.401
peak=   -3.601 closest distance to " CD  LYS A 289 " =    2.529
peak=   -3.595 closest distance to " CD  ARG A 139 " =    1.664
peak=   -3.594 closest distance to " CD2 LEU A 237 " =    2.518
peak=   -3.592 closest distance to " N   GLN A  58 " =    1.843
peak=   -3.589 closest distance to " O   HOH Z 350 " =    1.901
peak=   -3.577 closest distance to " CG  LYS A 193 " =    2.250
peak=   -3.576 closest distance to " OD1 ASN A 249 " =    1.159
peak=   -3.567 closest distance to " CD1 PHE A  59 " =    1.926
peak=   -3.567 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.563 closest distance to " CB  SER A 134 " =    1.780
peak=   -3.554 closest distance to " O   HOH Z  19 " =    2.216
peak=   -3.546 closest distance to " O   HOH Z 150 " =    1.396
peak=   -3.546 closest distance to " C   THR A 279 " =    1.236
peak=   -3.545 closest distance to " O   HOH Z 198 " =    2.144
peak=   -3.541 closest distance to " O   HOH Z 103 " =    1.891
peak=   -3.521 closest distance to " O   HOH Z 222 " =    1.270
peak=   -3.518 closest distance to " O   HOH Z 193 " =    1.661
peak=   -3.512 closest distance to " OG BSER A 134 " =    1.214
peak=   -3.512 closest distance to " CG2 ILE A 263 " =    2.370
peak=   -3.509 closest distance to " O   ALA A 161 " =    1.551
peak=   -3.505 closest distance to " O   HOH Z 265 " =    1.849
peak=   -3.505 closest distance to " CH2 TRP A 179 " =    1.302
peak=   -3.503 closest distance to " O   HOH Z 292 " =    4.323
peak=   -3.501 closest distance to " OXT GLY A 302 " =    3.344
peak=   -3.494 closest distance to " O   HOH Z 196 " =    2.374
peak=   -3.494 closest distance to " O   ALA A 256 " =    1.420
peak=   -3.493 closest distance to " OG  SER A  62 " =    1.478
peak=   -3.473 closest distance to " O   VAL A  67 " =    2.537
peak=   -3.467 closest distance to " O   HOH Z 191 " =    5.270
peak=   -3.466 closest distance to " CD1 LEU A 228 " =    2.307
peak=   -3.465 closest distance to " O   HOH Z 377 " =    1.237
peak=   -3.461 closest distance to " N   ALA A 248 " =    1.739
peak=   -3.454 closest distance to " NH2 ARG A  79 " =    1.899
peak=   -3.453 closest distance to " OE1 GLN A 223 " =    2.439
peak=   -3.448 closest distance to " CZ  TYR A 169 " =    1.811
peak=   -3.446 closest distance to " O   HOH Z 252 " =    4.265
peak=   -3.445 closest distance to " CG  PRO A 243 " =    1.637
peak=   -3.437 closest distance to " CD2 LEU A 167 " =    1.725
peak=   -3.434 closest distance to " O   HOH Z 234 " =    4.256
peak=   -3.434 closest distance to " CA  ASN A 127 " =    0.951
peak=   -3.433 closest distance to " CD  GLN A  88 " =    2.207
peak=   -3.432 closest distance to " O   HOH Z 202 " =    0.755
peak=   -3.427 closest distance to " O   HOH Z 435 " =    2.659
peak=   -3.417 closest distance to " OE2 GLU A   2 " =    1.668
peak=   -3.410 closest distance to " C   ASN A 285 " =    2.395
peak=   -3.407 closest distance to " ND2 ASN A  39 " =    1.334
peak=   -3.407 closest distance to " CA  GLY A 133 " =    1.902
peak=   -3.402 closest distance to " CG2 VAL A 112 " =    2.572
peak=   -3.399 closest distance to " CG1 VAL A 296 " =    1.294
peak=   -3.397 closest distance to " O   HOH Z 118 " =    2.804
peak=   -3.396 closest distance to " CB  ASN A  39 " =    2.078
peak=   -3.393 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.390 closest distance to " O   HOH Z  38 " =    1.639
peak=   -3.387 closest distance to " NE2 GLN A  88 " =    1.021
peak=   -3.387 closest distance to " O   HOH Z 283 " =    1.792
peak=   -3.384 closest distance to " CD  ARG A 195 " =    5.041
peak=   -3.380 closest distance to " O   HOH Z 360 " =    2.541
peak=   -3.377 closest distance to " O  BHOH Z 338 " =    1.482
peak=   -3.375 closest distance to " CG  TRP A 266 " =    1.777
peak=   -3.370 closest distance to " O   HOH Z  17 " =    1.244
peak=   -3.369 closest distance to " C   ARG A  79 " =    2.633
peak=   -3.368 closest distance to " ND2 ASN A  60 " =    1.445
peak=   -3.368 closest distance to " CD2 TYR A 293 " =    2.154
peak=   -3.365 closest distance to " O   HOH Z 308 " =    1.752
peak=   -3.365 closest distance to " O   LEU A 228 " =    2.391
peak=   -3.364 closest distance to " O   HOH Z  98 " =    1.937
peak=   -3.362 closest distance to " N   ALA A  43 " =    2.490
peak=   -3.361 closest distance to " O   ALA A 100 " =    2.376
peak=   -3.360 closest distance to " OD1 ASP A 200 " =    1.277
peak=   -3.358 closest distance to " O   PRO A 198 " =    1.240
peak=   -3.354 closest distance to " CE3 TRP A 150 " =    2.271
peak=   -3.353 closest distance to " CA  VAL A 197 " =    1.025
peak=   -3.350 closest distance to " O   HOH Z 341 " =    1.171
peak=   -3.342 closest distance to " CB  CYS A 254 " =    2.400
peak=   -3.331 closest distance to " NE1 TRP A 266 " =    2.266
peak=   -3.329 closest distance to " CB  ALA A  51 " =    1.848
peak=   -3.323 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.323 closest distance to " O   HOH Z 184 " =    1.385
peak=   -3.315 closest distance to " O   HOH Z  63 " =    0.844
peak=   -3.314 closest distance to " O   HOH Z 388 " =    1.918
peak=   -3.311 closest distance to " CD2 PHE A  61 " =    1.864
peak=   -3.308 closest distance to " OD2 ASP A  50 " =    1.386
peak=   -3.304 closest distance to " CG  GLU A 277 " =    1.114
peak=   -3.292 closest distance to " CZ  TYR A 172 " =    1.720
peak=   -3.283 closest distance to " OG  SER A  32 " =    1.074
peak=   -3.263 closest distance to " OG  SER A 206 " =    1.700
peak=   -3.254 closest distance to " CG  MET A 105 " =    0.865
peak=   -3.253 closest distance to " ND2BASN A 224 " =    1.735
peak=   -3.245 closest distance to " O   HOH Z 377 " =    1.999
peak=   -3.243 closest distance to " O   HOH Z 297 " =    2.878
peak=   -3.240 closest distance to " O   HOH Z  15 " =    1.605
peak=   -3.240 closest distance to " NH2 ARG A  66 " =    1.470
peak=   -3.238 closest distance to " O   HOH Z 431 " =    1.965
peak=   -3.235 closest distance to " CD1 TRP A 179 " =    1.096
peak=   -3.233 closest distance to " CB  PHE A 283 " =    2.773
peak=   -3.230 closest distance to " O   ASP A 270 " =    1.718
peak=   -3.228 closest distance to " O   HOH Z 185 " =    2.106
peak=   -3.217 closest distance to " O   VAL A  67 " =    1.879
peak=   -3.211 closest distance to " CE  MET A  93 " =    1.259
peak=   -3.207 closest distance to " O   HOH Z 295 " =    1.429
peak=   -3.205 closest distance to " C   GLU A  46 " =    1.058
peak=   -3.203 closest distance to " O   HOH Z 426 " =    1.733
peak=   -3.196 closest distance to " CD1 TYR A 247 " =    2.280
peak=   -3.194 closest distance to " O   ALA A  51 " =    1.509
peak=   -3.187 closest distance to " O   GLY A 211 " =    1.451
peak=   -3.186 closest distance to " O   MET A  40 " =    2.670
peak=   -3.185 closest distance to " CD  GLN A  88 " =    0.855
peak=   -3.183 closest distance to " O   HOH Z  44 " =    1.973
peak=   -3.182 closest distance to " O   HOH Z 396 " =    1.669
peak=   -3.180 closest distance to " O   VAL A 197 " =    1.227
peak=   -3.179 closest distance to " O   HOH Z 193 " =    2.229
peak=   -3.177 closest distance to " O   HOH Z 134 " =    2.537
peak=   -3.175 closest distance to " CG  PHE A  59 " =    2.190
peak=   -3.172 closest distance to " NE2 GLN A 194 " =    2.336
peak=   -3.170 closest distance to " O   HOH Z 189 " =    1.757
peak=   -3.166 closest distance to " C   GLY A  91 " =    1.308
peak=   -3.165 closest distance to " O   HOH Z  48 " =    1.468
peak=   -3.164 closest distance to " O   HOH Z 241 " =    1.447
peak=   -3.157 closest distance to " O   HOH Z 437 " =    1.834
peak=   -3.153 closest distance to " OG  SER A  26 " =    1.259
peak=   -3.151 closest distance to " CB  GLN A  11 " =    1.948
peak=   -3.151 closest distance to " OD1 ASN A 148 " =    1.575
peak=   -3.147 closest distance to " O   PRO A 198 " =    1.344
peak=   -3.141 closest distance to " O   HOH Z 208 " =    1.327
peak=   -3.136 closest distance to " O   HOH Z  97 " =    1.525
peak=   -3.128 closest distance to " O   GLY A 196 " =    0.994
peak=   -3.121 closest distance to " NE2 GLN A  73 " =    1.588
peak=   -3.111 closest distance to " O   HOH Z 387 " =    3.754
peak=   -3.107 closest distance to " O   HOH Z 353 " =    2.269
peak=   -3.104 closest distance to " O   HOH Z 227 " =    1.092
peak=   -3.102 closest distance to " O   HOH Z  12 " =    3.528
peak=   -3.083 closest distance to " CA  TYR A  30 " =    1.004
peak=   -3.077 closest distance to " O   LEU A 167 " =    1.635
peak=   -3.065 closest distance to " CB  ASP A 124 " =    2.079
peak=   -3.049 closest distance to " C   LEU A 143 " =    1.190
peak=   -3.037 closest distance to " CA  ARG A  66 " =    1.888
peak=   -3.032 closest distance to " CG1 VAL A 112 " =    2.673
peak=   -3.004 closest distance to " CB  ALA A 291 " =    2.205

================= 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    :  0.4647 0.4656   6.266591e+00   6.259760e+00
   1_bss:  0.4565 0.4560   6.265669e+00   6.249775e+00
   1_xyz:  0.3736 0.3971   6.134287e+00   6.176537e+00
   1_adp:  0.3263 0.3723   6.042527e+00   6.135860e+00
   1_occ:  0.3260 0.3726   6.042134e+00   6.135869e+00
   2_bss:  0.3227 0.3671   6.041592e+00   6.132991e+00
   2_xyz:  0.2306 0.2871   5.767582e+00   5.932225e+00
   2_adp:  0.2087 0.2618   5.680283e+00   5.856514e+00
   2_occ:  0.2085 0.2619   5.679939e+00   5.856735e+00
   3_bss:  0.2064 0.2604   5.678295e+00   5.854044e+00
   3_xyz:  0.1565 0.2033   5.426845e+00   5.637142e+00
   3_adp:  0.1442 0.1925   5.361019e+00   5.580372e+00
   3_occ:  0.1439 0.1925   5.360518e+00   5.580430e+00
   4_bss:  0.1440 0.1925   5.361164e+00   5.579788e+00
   4_xyz:  0.1273 0.1721   5.249664e+00   5.474750e+00
   4_adp:  0.1244 0.1695   5.231777e+00   5.459529e+00
   4_occ:  0.1242 0.1695   5.231248e+00   5.459347e+00
   5_bss:  0.1242 0.1696   5.231176e+00   5.459596e+00
   5_xyz:  0.1190 0.1642   5.200833e+00   5.433920e+00
   5_adp:  0.1183 0.1637   5.197356e+00   5.432391e+00
   5_occ:  0.1183 0.1637   5.197286e+00   5.432680e+00
   5_bss:  0.1186 0.1644   5.200024e+00   5.435501e+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:  0.349  14.549   6.738   9.180   9.106   0.000   0.000   0.000
   1_xyz:  0.349  14.549   6.738   9.180   9.106   0.000   0.000   0.000
   1_adp:  0.349  14.549   6.738   9.180   9.106   0.000   0.000   0.000
   1_occ:  0.349  14.549   6.738   9.180   9.106   0.000   0.000   0.000
   2_bss:  0.334  37.029   3.275   5.410   5.995   0.000   0.000   0.000
   2_xyz:  0.334  37.029   3.275   5.410   5.995   0.000   0.000   0.000
   2_adp:  0.334  37.029   3.275   5.410   5.995   0.000   0.000   0.000
   2_occ:  0.334  37.029   3.275   5.410   5.995   0.000   0.000   0.000
   3_bss:  0.318  37.029   2.012   3.255   3.499   0.000   0.000   0.000
   3_xyz:  0.318  37.029   2.012   3.255   3.499   0.000   0.000   0.000
   3_adp:  0.318  37.029   2.012   3.255   3.499   0.000   0.000   0.000
   3_occ:  0.318  37.029   2.012   3.255   3.499   0.000   0.000   0.000
   4_bss:  0.310  37.029   1.666   2.575   2.658   0.000   0.000   0.000
   4_xyz:  0.310  37.029   1.666   2.575   2.658   0.000   0.000   0.000
   4_adp:  0.310  37.029   1.666   2.575   2.658   0.000   0.000   0.000
   4_occ:  0.310  37.029   1.666   2.575   2.658   0.000   0.000   0.000
   5_bss:  0.317  41.478   1.720   2.455   2.544   0.000   0.000   0.000
   5_xyz:  0.317  41.478   1.720   2.455   2.544   0.000   0.000   0.000
   5_adp:  0.317  41.478   1.720   2.455   2.544   0.000   0.000   0.000
   5_occ:  0.317  41.478   1.720   2.455   2.544   0.000   0.000   0.000
   5_bss:  0.318  45.480  -0.481   0.195   0.286   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.790 0.4474  0.5197    65414.722
   1_bss:  55.731 0.4453  0.6520    62414.951
   1_xyz:  46.105 0.5662  0.8214    45955.097
   1_adp:  41.520 0.6231  0.9323    39354.565
   1_occ:  41.564 0.6226  0.9310    39417.051
   2_bss:  41.186 0.6271  0.8319    38863.502
   2_xyz:  29.756 0.7595  0.9808    21795.512
   2_adp:  26.364 0.7970  1.0130    18045.352
   2_occ:  26.388 0.7967  1.0125    18060.171
   3_bss:  26.265 0.7980  0.9443    17943.202
   3_xyz:  19.587 0.8652  0.9888    10618.101
   3_adp:  18.135 0.8794  0.9934     9480.093
   3_occ:  18.133 0.8794  0.9931     9482.695
   4_bss:  18.115 0.8796  0.9708     9479.600
   4_xyz:  15.949 0.8986  0.9805     7608.607
   4_adp:  15.520 0.9026  0.9804     7383.857
   4_occ:  15.511 0.9027  0.9803     7383.845
   5_bss:  15.511 0.9027  0.9785     7396.034
   5_xyz:  14.978 0.9072  0.9795     6987.780
   5_adp:  14.902 0.9079  0.9771     6954.746
   5_occ:  14.904 0.9079  0.9769     6959.218
   5_bss:  14.974 0.9074  0.9769     7036.666
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3519e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3519e+01
   1_xyz:   1.673  0.013  0.108 18.088  0.007  4.111   1.3694e-01
   1_adp:   1.673  0.013  0.108 18.088  0.007  4.111   1.3694e-01
   1_occ:   1.673  0.013  0.108 18.088  0.007  4.111   1.3694e-01
   2_bss:   1.673  0.013  0.108 18.088  0.007  4.111   1.3694e-01
   2_xyz:   1.100  0.008  0.075 15.933  0.005  4.113   7.4248e-02
   2_adp:   1.100  0.008  0.075 15.933  0.005  4.113   7.4248e-02
   2_occ:   1.100  0.008  0.075 15.933  0.005  4.113   7.4248e-02
   3_bss:   1.100  0.008  0.075 15.933  0.005  4.113   7.4248e-02
   3_xyz:   0.993  0.006  0.072 15.298  0.004  4.125   5.8772e-02
   3_adp:   0.993  0.006  0.072 15.298  0.004  4.125   5.8772e-02
   3_occ:   0.993  0.006  0.072 15.298  0.004  4.125   5.8772e-02
   4_bss:   0.993  0.006  0.072 15.298  0.004  4.125   5.8772e-02
   4_xyz:   0.944  0.006  0.072 15.325  0.003  4.127   5.5229e-02
   4_adp:   0.944  0.006  0.072 15.325  0.003  4.127   5.5229e-02
   4_occ:   0.944  0.006  0.072 15.325  0.003  4.127   5.5229e-02
   5_bss:   0.944  0.006  0.072 15.325  0.003  4.127   5.5229e-02
   5_xyz:   0.912  0.005  0.071 14.974  0.003  4.120   5.1198e-02
   5_adp:   0.912  0.005  0.071 14.974  0.003  4.120   5.1198e-02
   5_occ:   0.912  0.005  0.071 14.974  0.003  4.120   5.1198e-02
   5_bss:   0.912  0.005  0.071 14.974  0.003  4.120   5.1198e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9374e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9374e+00
   1_xyz:  14.685  0.163  0.490 87.964  0.057  2.188   9.8068e-02
   1_adp:  14.685  0.163  0.490 87.964  0.057  2.188   9.8068e-02
   1_occ:  14.685  0.163  0.490 87.964  0.057  2.188   9.8068e-02
   2_bss:  14.685  0.163  0.490 87.964  0.057  2.188   9.8068e-02
   2_xyz:   6.894  0.077  0.269 82.380  0.037  2.243   6.8822e-02
   2_adp:   6.894  0.077  0.269 82.380  0.037  2.243   6.8822e-02
   2_occ:   6.894  0.077  0.269 82.380  0.037  2.243   6.8822e-02
   3_bss:   6.894  0.077  0.269 82.380  0.037  2.243   6.8822e-02
   3_xyz:   6.831  0.042  0.375 85.359  0.041  2.403   8.0339e-02
   3_adp:   6.831  0.042  0.375 85.359  0.041  2.403   8.0339e-02
   3_occ:   6.831  0.042  0.375 85.359  0.041  2.403   8.0339e-02
   4_bss:   6.831  0.042  0.375 85.359  0.041  2.403   8.0339e-02
   4_xyz:   6.724  0.034  0.410 80.194  0.027  2.392   3.4842e-02
   4_adp:   6.724  0.034  0.410 80.194  0.027  2.392   3.4842e-02
   4_occ:   6.724  0.034  0.410 80.194  0.027  2.392   3.4842e-02
   5_bss:   6.724  0.034  0.410 80.194  0.027  2.392   3.4842e-02
   5_xyz:   6.336  0.040  0.389 83.494  0.026  2.395   2.6510e-02
   5_adp:   6.336  0.040  0.389 83.494  0.026  2.395   2.6510e-02
   5_occ:   6.336  0.040  0.389 83.494  0.026  2.395   2.6510e-02
   5_bss:   6.336  0.040  0.389 83.494  0.026  2.395   2.6510e-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:  67.90   0.00  12.37  59.53   0.00   9.72  67.90   0.00  26.82
   1_occ:  67.90   0.00  12.37  59.53   0.00   9.72  67.90   0.00  26.82
   2_bss:  67.90   0.00  12.37  59.53   0.00   9.72  67.90   0.00  26.82
   2_xyz:  67.90   0.00  12.37  59.53   0.00   9.72  67.90   0.00  26.82
   2_adp:  68.73   0.00  12.65  66.31   0.00   9.03  68.73   1.56  32.36
   2_occ:  68.73   0.00  12.65  66.31   0.00   9.03  68.73   1.56  32.36
   3_bss:  68.73   0.00  12.65  66.31   0.00   9.03  68.73   1.56  32.36
   3_xyz:  68.73   0.00  12.65  66.31   0.00   9.03  68.73   1.56  32.36
   3_adp:  87.55   0.00  13.42  87.55   0.00   9.00  77.36   2.46  37.50
   3_occ:  87.55   0.00  13.42  87.55   0.00   9.00  77.36   2.46  37.50
   4_bss:  87.55   0.00  13.42  87.55   0.00   9.00  77.36   2.46  37.50
   4_xyz:  87.55   0.00  13.42  87.55   0.00   9.00  77.36   2.46  37.50
   4_adp:  94.40   0.00  13.36  94.40   0.00   8.90  79.12   1.72  37.62
   4_occ:  94.40   0.00  13.36  94.40   0.00   8.90  79.12   1.72  37.62
   5_bss:  94.40   0.00  13.36  94.40   0.00   8.90  79.12   1.72  37.62
   5_xyz:  94.40   0.00  13.36  94.40   0.00   8.90  79.12   1.72  37.62
   5_adp:  98.71   0.00  13.13  98.71   0.00   8.77  79.66   1.51  36.91
   5_occ:  98.71   0.00  13.13  98.71   0.00   8.77  79.66   1.51  36.91
   5_bss: 100.96   2.25  15.39 100.96   2.25  11.02  81.91   3.77  39.16
------------------------------------------------------------------------
 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:    1.202    0.017    0.411
   1_adp:    1.202    0.017    0.411
   1_occ:    1.202    0.017    0.411
   2_bss:    1.202    0.017    0.411
   2_xyz:    1.587    0.031    0.567
   2_adp:    1.587    0.031    0.567
   2_occ:    1.587    0.031    0.567
   3_bss:    1.587    0.031    0.567
   3_xyz:    1.512    0.057    0.628
   3_adp:    1.512    0.057    0.628
   3_occ:    1.512    0.057    0.628
   4_bss:    1.512    0.057    0.628
   4_xyz:    1.699    0.036    0.664
   4_adp:    1.699    0.036    0.664
   4_occ:    1.699    0.036    0.664
   5_bss:    1.699    0.036    0.664
   5_xyz:    1.771    0.047    0.679
   5_adp:    1.771    0.047    0.679
   5_occ:    1.771    0.047    0.679
   5_bss:    1.771    0.047    0.679
------------------------------------------------------------------------

CPU time actual refinement: 349.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/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_683/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_683/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.69 
  Macro-tasks:
    bulk solvent and scale       = 40.56  
    individual site refinement   = 152.90 
    weights calculation          = 32.64  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 232.74 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 109.14 
    alpha_beta                      = 8.31   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.87 
    fmodel                         = 7.26   
    r_factors                      = 0.26   
    phase_errors                   = 10.42  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 261.18 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.822 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    661 calls, 108.78 s
gradients_fft:          606 calls, 107.57 s

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

# Date 2008-01-16 Time 02:10:18 PST -0800 (1200478218.10 s)
Start R-work = 0.4647, R-free = 0.4656 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4565, R-free = 0.4560
Final R-work = 0.1186, R-free = 0.1644