# Date 2008-01-16 Time 01:33:10 PST -0800 (1200475990.24 s)
#phil __OFF__

Command line arguments: "../466.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11252
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 466

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.8686, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.98061
Completeness in resolution range: 0.954118
Completeness with d_max=infinity: 0.951153

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9586
                             d_min =   1.9806

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.98061
Completeness in resolution range: 0.954118
Completeness with d_max=infinity: 0.951153

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9590 -  4.2378 [2162/2190]  1946   216  10.0%
  bin  2:  4.2378 -  3.3764 [2065/2088]  1858   207  10.0%
  bin  3:  3.3764 -  2.9533 [2046/2071]  1841   205  10.0%
  bin  4:  2.9533 -  2.6850 [2023/2039]  1822   201   9.9%
  bin  5:  2.6850 -  2.4935 [2005/2042]  1798   207  10.3%
  bin  6:  2.4935 -  2.3471 [2000/2034]  1809   191   9.6%
  bin  7:  2.3471 -  2.2299 [1983/2020]  1784   199  10.0%
  bin  8:  2.2299 -  2.1331 [1984/2026]  1784   200  10.1%
  bin  9:  2.1331 -  2.0512 [1978/2016]  1782   196   9.9%
  bin 10:  2.0512 -  1.9806 [1343/2005]  1206   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2203
        3.04 -     3.66: 4681
        3.66 -     4.28: 8990
        4.28 -     4.90: 12386
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.856 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.887 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.985 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.027 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28281 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_466/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/model_refine_001.geo

CPU time processing inputs: 9.36


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.8686 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4831   r_free= 0.4667   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.284594                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7265 0.99   1398  158 0.3946 0.3987       6.589      6.6279|
|  2:  4.7265 -  3.7713 0.99   1349  148 0.4092 0.4095      6.7974      6.8244|
|  3:  3.7713 -  3.3005 0.99   1319  149 0.4416 0.4191      6.6914      6.6655|
|  4:  3.3005 -  3.0014 0.99   1320  136 0.4675 0.4039      6.5235      6.4487|
|  5:  3.0014 -  2.7877 0.98   1297  147 0.5255 0.5154      6.3902      6.4137|
|  6:  2.7877 -  2.6243 0.99   1292  144 0.5032 0.4963      6.2763      6.1895|
|  7:  2.6243 -  2.4935 0.99   1290  154 0.5029 0.4593        6.26      6.1728|
|  8:  2.4935 -  2.3854 0.99   1310  132 0.5235 0.4915      6.1749      6.1563|
|  9:  2.3854 -  2.2939 0.99   1273  149 0.5312 0.5496      6.1178       6.173|
| 10:  2.2939 -  2.2150 0.98   1271  139 0.5365 0.5353      6.1254      6.1054|
| 11:  2.2150 -  2.1459 0.98   1271  145 0.5319 0.5012      6.0331      6.0596|
| 12:  2.1459 -  2.0848 1.00   1284  143 0.5352 0.5060      5.9722       6.001|
| 13:  2.0848 -  2.0300 0.96   1274  130 0.5255 0.5111      5.8931      5.8656|
| 14:  2.0300 -  1.9806 0.55    682   85 0.5593 0.5275      5.8654       5.744|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7265  1398   158  0.66  37.37   0.80     0.68      80827.21|
|  2:  4.7265 -  3.7713  1349   148  0.69  36.46   0.88     0.74     108695.62|
|  3:  3.7713 -  3.3005  1319   149  0.60  43.49   0.84     0.71     111933.28|
|  4:  3.3005 -  3.0014  1320   136  0.54  49.01   0.80     0.62      92828.34|
|  5:  3.0014 -  2.7877  1297   147  0.44  56.81   0.72     0.52      79433.89|
|  6:  2.7877 -  2.6243  1292   144  0.42  58.09   0.73     0.48      67667.79|
|  7:  2.6243 -  2.4935  1290   154  0.41  59.39   0.75     0.45      62581.91|
|  8:  2.4935 -  2.3854  1310   132  0.40  60.32   0.72     0.46      56028.00|
|  9:  2.3854 -  2.2939  1273   149  0.36  63.40   0.71     0.43      53838.14|
| 10:  2.2939 -  2.2150  1271   139  0.35  63.76   0.74     0.41      50139.51|
| 11:  2.2150 -  2.1459  1271   145  0.31  66.49   0.74     0.38      47943.54|
| 12:  2.1459 -  2.0848  1284   143  0.31  67.16   0.75     0.40      44881.78|
| 13:  2.0848 -  2.0300  1274   130  0.31  66.79   0.74     0.38      37927.06|
| 14:  2.0300 -  1.9806   682    85  0.34  64.70   0.71     0.38      28506.69|
|alpha:            min =        0.38 max =            0.74 mean =         0.51|
|beta:             min =    28506.69 max =       111933.28 mean =     67666.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.13|
|phase err.(test): min =        0.00 max =           89.81 mean =        56.08|
|-----------------------------------------------------------------------------|

============================== 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 = 13.593391             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.929   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.199093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.574   (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 |  1.127 -  1.504:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.504 -  1.882:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.882 -  2.259:      143 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.259 -  2.636:      619 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.636 -  3.013:     1444 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.013 -  3.391:     2538 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.391 -  3.768:     3923 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.768 -  4.145:     5123 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.145 -  4.523:     6644 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.523 -  4.900:     7792 |
|-----------------------------------------------------------------------------|
|-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 |       53.856 |
| 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  1.127 |       1.944 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    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 = 11.903)------------------------------------------|
|    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: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4888   r_free= 0.4755   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.286039                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4754   r_free= 0.4625   ksol= 0.32   Bsol= 8.30   scale= 0.991    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,12.03,7.49,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277219                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.312363             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.378   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.198574              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.457   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4754      final r-factor (work) = 0.3937          |
| start r-factor (free) = 0.4625      final r-factor (free) = 0.4093          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.6977 = 13.31 * 0.50 * 6.2861 + 1.00 * 53.8561                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.3936 = 13.31 * 0.50 * 6.1970 + 1.00 * 0.1452                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3937      final r-factor (work) = 0.3474          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.3915          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4423 = 1.20 * 1.00 * 6.1970 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3469 = 1.20 * 1.00 * 6.1145 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.62   13.73    None  None   None       |
|    all(noH): 2823   0      0.00    92.62   13.73    None  None   None       |
|    Sol.    : 438    0      0.00    92.62   26.28    None  None   None       |
|    Mac.    : 2385   0      0.00    70.60   11.42    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 -   9.262: 1304   |   5:    46.309 -  55.571:   49        |
|      1:     9.262 -  18.524:  756   |   6:    55.571 -  64.832:   13        |
|      2:    18.524 -  27.785:  398   |   7:    64.832 -  74.094:   10        |
|      3:    27.785 -  37.047:  202   |   8:    74.094 -  83.356:    2        |
|      4:    37.047 -  46.309:   86   |   9:    83.356 -  92.618:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3474 r_free = 0.3915             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3468 r_free = 0.3903             target_work(ml) = 6.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3468   r_free= 0.3903   ksol= 0.32   Bsol= 8.30   scale= 1.103    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,12.03,7.49,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.092890                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3446   r_free= 0.3837   ksol= 0.31   Bsol= 32.28   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,7.60,4.37,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.093267                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.927431              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.556   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.492008              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3446      final r-factor (work) = 0.2781          |
| start r-factor (free) = 0.3837      final r-factor (free) = 0.3298          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2527 = 5.93 * 0.50 * 6.1100 + 1.00 * 0.1443                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8277 = 5.93 * 0.50 * 5.9866 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2781      final r-factor (work) = 0.2613          |
| start r-factor (free) = 0.3298      final r-factor (free) = 0.3190          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9635 = 0.49 * 1.00 * 5.9866 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9126 = 0.49 * 1.00 * 5.8962 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.57   13.34    None  None   None       |
|    all(noH): 2823   0      0.00    88.57   13.34    None  None   None       |
|    Sol.    : 438    0      0.00    88.57   29.53    None  None   None       |
|    Mac.    : 2385   0      0.00    78.52   10.37    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 -   8.857: 1368   |   5:    44.285 -  53.142:   59        |
|      1:     8.857 -  17.714:  738   |   6:    53.142 -  61.999:   19        |
|      2:    17.714 -  26.571:  337   |   7:    61.999 -  70.856:   11        |
|      3:    26.571 -  35.428:  172   |   8:    70.856 -  79.713:    6        |
|      4:    35.428 -  44.285:  111   |   9:    79.713 -  88.570:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2613 r_free = 0.3190             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2611 r_free = 0.3192             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2611   r_free= 0.3192   ksol= 0.31   Bsol= 32.28   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,7.60,4.37,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.883471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2597   r_free= 0.3194   ksol= 0.30   Bsol= 41.84   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,4.96,3.12,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.883281                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.739863              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.225  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262374              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.810  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2597      final r-factor (work) = 0.2009          |
| start r-factor (free) = 0.3194      final r-factor (free) = 0.2489          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1132 = 3.74 * 0.50 * 5.8975 + 1.00 * 0.0852                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8731 = 3.74 * 0.50 * 5.7785 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2009      final r-factor (work) = 0.1884          |
| start r-factor (free) = 0.2489      final r-factor (free) = 0.2310          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5276 = 0.26 * 1.00 * 5.7785 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4818 = 0.26 * 1.00 * 5.6113 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.31   13.17    None  None   None       |
|    all(noH): 2823   0      0.00    83.31   13.17    None  None   None       |
|    Sol.    : 438    0      2.16    83.31   32.51    None  None   None       |
|    Mac.    : 2385   0      0.00    77.70   9.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.331: 1408   |   5:    41.653 -  49.983:   97        |
|      1:     8.331 -  16.661:  739   |   6:    49.983 -  58.314:   28        |
|      2:    16.661 -  24.992:  242   |   7:    58.314 -  66.644:   16        |
|      3:    24.992 -  33.322:  167   |   8:    66.644 -  74.975:    8        |
|      4:    33.322 -  41.653:  115   |   9:    74.975 -  83.306:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1884 r_free = 0.2310             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1883 r_free = 0.2312             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1883   r_free= 0.2312   ksol= 0.30   Bsol= 41.84   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,4.96,3.12,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.584885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1877   r_free= 0.2305   ksol= 0.31   Bsol= 41.84   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,3.31,2.51,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.585020                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.957684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.175  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392041              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.012  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1877      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.2305      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3697 = 2.96 * 0.50 * 5.6138 + 1.00 * 0.0677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1530 = 2.96 * 0.50 * 5.4689 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.1863      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1535 = 0.39 * 1.00 * 5.4689 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0973 = 0.39 * 1.00 * 5.3182 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.76   13.67    None  None   None       |
|    all(noH): 2823   0      0.00    84.76   13.67    None  None   None       |
|    Sol.    : 438    0      1.71    76.62   37.03    None  None   None       |
|    Mac.    : 2385   0      0.00    84.76   9.38     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 -   8.476: 1458   |   5:    42.381 -  50.857:   94        |
|      1:     8.476 -  16.952:  747   |   6:    50.857 -  59.333:   65        |
|      2:    16.952 -  25.429:  183   |   7:    59.333 -  67.809:   34        |
|      3:    25.429 -  33.905:  111   |   8:    67.809 -  76.285:   14        |
|      4:    33.905 -  42.381:  112   |   9:    76.285 -  84.762:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1359 r_free = 0.1767             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1358 r_free = 0.1765             target_work(ml) = 5.296         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1765   ksol= 0.31   Bsol= 41.84   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,3.31,2.51,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.296159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1775   ksol= 0.31   Bsol= 51.24   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,2.41,2.32,0.00,0.00,0.00); trace/3= 1.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.298893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.211402              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.414870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.531  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6087 = 3.21 * 0.50 * 5.3206 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4955 = 3.21 * 0.50 * 5.2456 + 1.00 * 0.0726                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1896 = 0.41 * 1.00 * 5.2456 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1667 = 0.41 * 1.00 * 5.1956 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.13   13.50    None  None   None       |
|    all(noH): 2823   0      0.00    86.13   13.50    None  None   None       |
|    Sol.    : 438    0      1.87    77.45   37.08    None  None   None       |
|    Mac.    : 2385   0      0.00    86.13   9.17     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 -   8.613: 1525   |   5:    43.065 -  51.678:   93        |
|      1:     8.613 -  17.226:  716   |   6:    51.678 -  60.291:   60        |
|      2:    17.226 -  25.839:  160   |   7:    60.291 -  68.904:   38        |
|      3:    25.839 -  34.452:  113   |   8:    68.904 -  77.517:    9        |
|      4:    34.452 -  43.065:  104   |   9:    77.517 -  86.130:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1634             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1635             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1635   ksol= 0.31   Bsol= 51.24   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,2.41,2.32,0.00,0.00,0.00); trace/3= 1.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188183                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7265 0.99   1398  158 0.0985 0.1309      5.3847      5.5602|
|  2:  4.7265 -  3.7713 0.99   1349  148 0.0883 0.1091      5.4658      5.6619|
|  3:  3.7713 -  3.3005 0.99   1319  149 0.1112 0.1603      5.5204      5.8946|
|  4:  3.3005 -  3.0014 0.99   1320  136 0.1289 0.1670      5.4887      5.6872|
|  5:  3.0014 -  2.7877 0.98   1297  147 0.1399 0.1617      5.3777      5.4887|
|  6:  2.7877 -  2.6243 0.99   1292  144 0.1358 0.2165      5.2862      5.5654|
|  7:  2.6243 -  2.4935 0.99   1290  154 0.1273 0.1724       5.198      5.4152|
|  8:  2.4935 -  2.3854 0.99   1310  132 0.1261 0.1801      5.1275      5.3696|
|  9:  2.3854 -  2.2939 0.99   1273  149 0.1251 0.1883      5.0618      5.3586|
| 10:  2.2939 -  2.2150 0.98   1271  139 0.1223 0.1814      5.0319      5.2308|
| 11:  2.2150 -  2.1459 0.98   1271  145 0.1239 0.1814      4.9753      5.2704|
| 12:  2.1459 -  2.0848 1.00   1284  143 0.1166 0.1708      4.8928      5.1581|
| 13:  2.0848 -  2.0300 0.96   1274  130 0.1215 0.1792      4.8272      5.0844|
| 14:  2.0300 -  1.9806 0.55    682   85 0.1135 0.1693      4.7183      4.9262|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7265  1398   158  0.94   9.35   0.97     0.95       7503.55|
|  2:  4.7265 -  3.7713  1349   148  0.95   8.60   1.01     1.00       9737.51|
|  3:  3.7713 -  3.3005  1319   149  0.93  12.01   1.02     1.01      11462.78|
|  4:  3.3005 -  3.0014  1320   136  0.91  14.58   1.01     0.99      10963.42|
|  5:  3.0014 -  2.7877  1297   147  0.89  17.15   1.00     0.97       9168.90|
|  6:  2.7877 -  2.6243  1292   144  0.89  17.30   0.98     0.94       7992.12|
|  7:  2.6243 -  2.4935  1290   154  0.90  15.98   0.98     0.95       6581.52|
|  8:  2.4935 -  2.3854  1310   132  0.90  16.21   0.99     0.96       5989.67|
|  9:  2.3854 -  2.2939  1273   149  0.89  16.83   1.00     0.97       5376.82|
| 10:  2.2939 -  2.2150  1271   139  0.89  16.84   0.99     0.96       5095.11|
| 11:  2.2150 -  2.1459  1271   145  0.90  16.45   0.99     0.96       4546.09|
| 12:  2.1459 -  2.0848  1284   143  0.91  15.83   1.00     0.98       4018.55|
| 13:  2.0848 -  2.0300  1274   130  0.89  16.82   0.99     0.99       3519.68|
| 14:  2.0300 -  1.9806   682    85  0.90  15.80   0.96     0.93       2840.07|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2840.07 max =        11462.78 mean =      6945.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.30 mean =        14.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1634   ksol= 0.32   Bsol= 53.13   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,0.41,0.55,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1634   ksol= 0.32   Bsol= 53.13   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,0.41,0.55,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.7265 0.99   1398  158 0.0987 0.1312      5.3872       5.562|
|  2:  4.7265 -  3.7713 0.99   1349  148 0.0881 0.1089      5.4651      5.6603|
|  3:  3.7713 -  3.3005 0.99   1319  149 0.1112 0.1604      5.5202      5.8959|
|  4:  3.3005 -  3.0014 0.99   1320  136 0.1289 0.1670      5.4888      5.6868|
|  5:  3.0014 -  2.7877 0.98   1297  147 0.1400 0.1616      5.3775      5.4881|
|  6:  2.7877 -  2.6243 0.99   1292  144 0.1357 0.2160      5.2856       5.564|
|  7:  2.6243 -  2.4935 0.99   1290  154 0.1273 0.1727      5.1977      5.4156|
|  8:  2.4935 -  2.3854 0.99   1310  132 0.1259 0.1798      5.1278      5.3693|
|  9:  2.3854 -  2.2939 0.99   1273  149 0.1249 0.1883      5.0616      5.3597|
| 10:  2.2939 -  2.2150 0.98   1271  139 0.1222 0.1817      5.0321      5.2316|
| 11:  2.2150 -  2.1459 0.98   1271  145 0.1239 0.1811      4.9752      5.2703|
| 12:  2.1459 -  2.0848 1.00   1284  143 0.1166 0.1712      4.8928      5.1592|
| 13:  2.0848 -  2.0300 0.96   1274  130 0.1217 0.1790      4.8276      5.0839|
| 14:  2.0300 -  1.9806 0.55    682   85 0.1134 0.1690      4.7181       4.925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9590 -  4.7265  1398   158  0.94   9.39   0.97     0.95       7563.74|
|  2:  4.7265 -  3.7713  1349   148  0.95   8.60   1.01     1.00       9744.52|
|  3:  3.7713 -  3.3005  1319   149  0.93  12.00   1.02     1.01      11443.63|
|  4:  3.3005 -  3.0014  1320   136  0.91  14.58   1.01     0.99      10968.32|
|  5:  3.0014 -  2.7877  1297   147  0.89  17.13   1.00     0.97       9152.48|
|  6:  2.7877 -  2.6243  1292   144  0.89  17.28   0.98     0.95       7981.37|
|  7:  2.6243 -  2.4935  1290   154  0.90  15.97   0.99     0.96       6577.11|
|  8:  2.4935 -  2.3854  1310   132  0.90  16.21   1.00     0.96       5995.47|
|  9:  2.3854 -  2.2939  1273   149  0.89  16.84   1.00     0.97       5384.75|
| 10:  2.2939 -  2.2150  1271   139  0.89  16.83   1.00     0.96       5095.42|
| 11:  2.2150 -  2.1459  1271   145  0.90  16.46   1.00     0.96       4548.86|
| 12:  2.1459 -  2.0848  1284   143  0.91  15.82   1.01     0.99       4021.79|
| 13:  2.0848 -  2.0300  1274   130  0.89  16.81   1.00     0.99       3517.79|
| 14:  2.0300 -  1.9806   682    85  0.90  15.78   0.97     0.93       2830.00|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2830.00 max =        11443.63 mean =      6948.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.32 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.903)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.89    88.02   15.40    None  None   None       |
|    all(noH): 2823   0      1.89    88.02   15.40    None  None   None       |
|    Sol.    : 438    0      3.77    79.34   38.97    None  None   None       |
|    Mac.    : 2385   0      1.89    88.02   11.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.895 -  10.508: 1525   |   5:    44.959 -  53.572:   93        |
|      1:    10.508 -  19.121:  716   |   6:    53.572 -  62.185:   60        |
|      2:    19.121 -  27.734:  160   |   7:    62.185 -  70.798:   38        |
|      3:    27.734 -  36.347:  113   |   8:    70.798 -  79.411:    9        |
|      4:    36.347 -  44.959:  104   |   9:    79.411 -  88.024:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.321 - 5.156
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 323
   mapped sites are within: 0.721 - 5.156

peak=    9.873 closest distance to " CB  VAL A 230 " =    1.419
peak=    6.793 closest distance to " CD1AILE A 234 " =    1.394
peak=    6.209 closest distance to " CG2 VAL A 296 " =    1.087
peak=    6.087 closest distance to " CG  LEU A   5 " =    1.238
peak=    5.823 closest distance to " O   HOH Z 210 " =    1.213
peak=    5.528 closest distance to " O   HOH Z 120 " =    1.106
peak=    5.504 closest distance to " O   HOH Z 402 " =    1.643
peak=    5.400 closest distance to " CB  VAL A 296 " =    1.085
peak=    5.356 closest distance to " NH2 ARG A  56 " =    2.329
peak=    5.254 closest distance to " O   HOH Z 124 " =    1.568
peak=    5.120 closest distance to " CB  SER A  63 " =    1.188
peak=    5.051 closest distance to " O   HOH Z 403 " =    1.881
peak=    4.931 closest distance to " O   HOH Z 209 " =    2.359
peak=    4.787 closest distance to " C   PRO A 198 " =    1.487
peak=    4.719 closest distance to " CG  LEU A 228 " =    1.190
peak=    4.704 closest distance to " O   HOH Z 433 " =    1.631
peak=    4.695 closest distance to " CB  GLN A 223 " =    1.378
peak=    4.688 closest distance to " O   HOH Z 247 " =    1.436
peak=    4.682 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.674 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.618 closest distance to " CB  PRO A  54 " =    0.885
peak=    4.586 closest distance to " CB  VAL A 230 " =    1.205
peak=    4.571 closest distance to " O   HOH Z 154 " =    1.652
peak=    4.554 closest distance to " CG1 VAL A 296 " =    1.795
peak=    4.537 closest distance to " O   HOH Z 232 " =    2.362
peak=    4.500 closest distance to " CG  PRO A  54 " =    1.233
peak=    4.500 closest distance to " O   HOH Z 128 " =    1.574
peak=    4.488 closest distance to " O   HOH Z  49 " =    1.214
peak=    4.472 closest distance to " O   HOH Z 263 " =    1.572
peak=    4.433 closest distance to " O   HOH Z 193 " =    1.734
peak=    4.426 closest distance to " CB  ARG A 275 " =    0.887
peak=    4.392 closest distance to " O   HOH Z  80 " =    1.997
peak=    4.391 closest distance to " CB  GLN A 183 " =    1.308
peak=    4.389 closest distance to " NE2 GLN A  11 " =    1.056
peak=    4.381 closest distance to " O   HOH Z  48 " =    1.818
peak=    4.340 closest distance to " O   HOH Z 102 " =    1.378
peak=    4.275 closest distance to " O   HOH Z 130 " =    1.156
peak=    4.273 closest distance to " CD2 LEU A 228 " =    1.204
peak=    4.264 closest distance to " O   HOH Z 234 " =    3.660
peak=    4.242 closest distance to " O   SER A  87 " =    2.341
peak=    4.231 closest distance to " O   GLY A  23 " =    2.366
peak=    4.224 closest distance to " O   HOH Z 357 " =    2.035
peak=    4.200 closest distance to " O   HOH Z 134 " =    1.988
peak=    4.192 closest distance to " CG1 ILE A  33 " =    1.234
peak=    4.186 closest distance to " O   HOH Z 412 " =    3.521
peak=    4.184 closest distance to " O   HOH Z 346 " =    1.577
peak=    4.167 closest distance to " O   HOH Z  85 " =    1.433
peak=    4.165 closest distance to " O   HOH Z 142 " =    1.508
peak=    4.158 closest distance to " O   HOH Z 327 " =    1.681
peak=    4.155 closest distance to " O   HOH Z 126 " =    1.621
peak=    4.154 closest distance to " O   HOH Z 126 " =    2.553
peak=    4.147 closest distance to " O   HOH Z 130 " =    2.738
peak=    4.122 closest distance to " O   HOH Z 414 " =    1.984
peak=    4.121 closest distance to " O   HOH Z  68 " =    2.021
peak=    4.112 closest distance to " O   HOH Z  59 " =    2.348
peak=    4.094 closest distance to " CB  TRP A 179 " =    1.221
peak=    4.054 closest distance to " CG  PRO A 198 " =    1.179
peak=    3.998 closest distance to " CG2 THR A 221 " =    1.252
peak=    3.998 closest distance to " O   ASP A 124 " =    1.553
peak=    3.996 closest distance to " CB  GLU A 277 " =    3.655
peak=    3.976 closest distance to " O   HOH Z  40 " =    1.980
peak=    3.974 closest distance to " O   HOH Z 272 " =    1.975
peak=    3.971 closest distance to " O   HOH Z 395 " =    1.419
peak=    3.970 closest distance to " O   HOH Z 189 " =    2.650
peak=    3.968 closest distance to " CB  SER A   3 " =    1.309
peak=    3.968 closest distance to " O   HOH Z 423 " =    1.804
peak=    3.941 closest distance to " CA  VAL A  41 " =    0.851
peak=    3.935 closest distance to " CD2 TRP A 179 " =    1.401
peak=    3.929 closest distance to " O   HOH Z 261 " =    2.103
peak=    3.924 closest distance to " O   HOH Z 431 " =    1.314
peak=    3.920 closest distance to " O   HOH Z 303 " =    2.305
peak=    3.919 closest distance to " O   HOH Z 404 " =    1.467
peak=    3.918 closest distance to " O   HOH Z 345 " =    2.790
peak=    3.910 closest distance to " O   HOH Z 389 " =    2.012
peak=    3.898 closest distance to " NH2BARG A 145 " =    2.118
peak=    3.885 closest distance to " O   HOH Z 394 " =    1.645
peak=    3.884 closest distance to " CG  ARG A  66 " =    0.977
peak=    3.872 closest distance to " O   HOH Z  44 " =    1.854
peak=    3.871 closest distance to " O   HOH Z 248 " =    1.699
peak=    3.869 closest distance to " O   HOH Z  54 " =    2.234
peak=    3.867 closest distance to " CB  GLU A 152 " =    1.097
peak=    3.859 closest distance to " O   HOH Z 408 " =    1.678
peak=    3.840 closest distance to " CA  ALA A  51 " =    1.113
peak=    3.837 closest distance to " O   HOH Z 316 " =    2.674
peak=    3.833 closest distance to " CD  LYS A 166 " =    1.462
peak=    3.822 closest distance to " O   HOH Z  97 " =    1.976
peak=    3.821 closest distance to " O   HOH Z 132 " =    2.609
peak=    3.814 closest distance to " CB BVAL A  41 " =    1.072
peak=    3.811 closest distance to " O   HOH Z 369 " =    2.068
peak=    3.806 closest distance to " CB  ASN A 148 " =    1.317
peak=    3.806 closest distance to " CE  LYS A 119 " =    1.137
peak=    3.805 closest distance to " O   GLY A  91 " =    1.298
peak=    3.803 closest distance to " O   HOH Z  47 " =    1.439
peak=    3.795 closest distance to " CE1 HIS A 108 " =    1.124
peak=    3.791 closest distance to " OG1 THR A 294 " =    2.294
peak=    3.788 closest distance to " O   HOH Z 126 " =    1.714
peak=    3.787 closest distance to " O   HOH Z 156 " =    3.252
peak=    3.786 closest distance to " CG  PRO A 243 " =    1.162
peak=    3.782 closest distance to " CB  ALA A 100 " =    1.299
peak=    3.780 closest distance to " O   HOH Z 245 " =    1.412
peak=    3.772 closest distance to " O   HOH Z 193 " =    2.016
peak=    3.770 closest distance to " OE1 GLU A   2 " =    2.098
peak=    3.764 closest distance to " O   HOH Z  48 " =    1.587
peak=    3.754 closest distance to " O   ALA A 165 " =    1.249
peak=    3.749 closest distance to " CB  GLU A 128 " =    1.204
peak=    3.744 closest distance to " O   HOH Z  63 " =    2.262
peak=    3.721 closest distance to " O   HOH Z 257 " =    2.215
peak=    3.718 closest distance to " O   HOH Z 403 " =    1.469
peak=    3.715 closest distance to " O   HOH Z 383 " =    2.102
peak=    3.703 closest distance to " OG BSER A 164 " =    2.114
peak=    3.699 closest distance to " CB  PRO A  54 " =    1.315
peak=    3.698 closest distance to " O   HOH Z 425 " =    1.395
peak=    3.692 closest distance to " O   HOH Z 214 " =    2.764
peak=    3.692 closest distance to " NZ  LYS A 117 " =    2.873
peak=    3.691 closest distance to " CB  SER A  26 " =    1.702
peak=    3.678 closest distance to " CD  ARG A 269 " =    1.111
peak=    3.674 closest distance to " O   HOH Z 417 " =    3.157
peak=    3.672 closest distance to " N   ASN A  39 " =    1.274
peak=    3.672 closest distance to " CB  TYR A 169 " =    0.721
peak=    3.669 closest distance to " CA  ASN A 176 " =    1.134
peak=    3.669 closest distance to " O   HOH Z 412 " =    4.058
peak=    3.659 closest distance to " O   HOH Z 298 " =    2.008
peak=    3.656 closest distance to " O   HOH Z  15 " =    2.167
peak=    3.640 closest distance to " CA  ALA A  21 " =    1.211
peak=    3.632 closest distance to " O   HOH Z 146 " =    1.455
peak=    3.630 closest distance to " CD  PRO A  54 " =    1.028
peak=    3.629 closest distance to " O   HOH Z  48 " =    2.342
peak=    3.623 closest distance to " O   HOH Z 123 " =    2.100
peak=    3.619 closest distance to " O   HOH Z  11 " =    1.256
peak=    3.619 closest distance to " O   HOH Z 126 " =    1.947
peak=    3.617 closest distance to " NH2 ARG A 156 " =    1.144
peak=    3.612 closest distance to " CD2 LEU A   5 " =    1.135
peak=    3.605 closest distance to " O   HOH Z 332 " =    1.542
peak=    3.603 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.601 closest distance to " O   HOH Z 146 " =    1.320
peak=    3.596 closest distance to " CD1 LEU A 101 " =    1.263
peak=    3.594 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.591 closest distance to " O   HOH Z 423 " =    3.010
peak=    3.589 closest distance to " O   ALA A 158 " =    1.211
peak=    3.586 closest distance to " O   HOH Z  54 " =    1.420
peak=    3.585 closest distance to " CE1 TYR A 186 " =    1.270
peak=    3.578 closest distance to " OE1 GLN A  11 " =    1.920
peak=    3.576 closest distance to " O   HOH Z 197 " =    2.091
peak=    3.568 closest distance to " CB  VAL A 202 " =    1.414
peak=    3.566 closest distance to " O   HOH Z 280 " =    3.080
peak=    3.564 closest distance to " CB  ARG A 190 " =    1.769
peak=    3.557 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.555 closest distance to " CA  ALA A 295 " =    1.023
peak=    3.550 closest distance to " O   HOH Z 162 " =    1.630
peak=    3.549 closest distance to " CD  ARG A 159 " =    0.806
peak=    3.547 closest distance to " O   HOH Z  43 " =    1.904
peak=    3.541 closest distance to " O   HOH Z  88 " =    3.286
peak=    3.538 closest distance to " O   HOH Z 334 " =    1.443
peak=    3.537 closest distance to " O   HOH Z 155 " =    3.013
peak=    3.537 closest distance to " O   HOH Z 203 " =    1.699
peak=    3.536 closest distance to " CA  ASP A 191 " =    0.937
peak=    3.525 closest distance to " CZ  PHE A 218 " =    1.141
peak=    3.519 closest distance to " O   HOH Z 155 " =    1.516
peak=    3.515 closest distance to " OG  SER A  62 " =    2.904
peak=    3.515 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.508 closest distance to " NH1 ARG A  14 " =    1.190
peak=    3.507 closest distance to " O   HOH Z 435 " =    1.938
peak=    3.506 closest distance to " CB  SER A 141 " =    1.051
peak=    3.502 closest distance to " O   HOH Z 162 " =    1.923
peak=    3.493 closest distance to " OH  TYR A 116 " =    1.199
peak=    3.488 closest distance to " CB  PRO A 198 " =    1.053
peak=    3.486 closest distance to " CG1BVAL A  72 " =    1.817
peak=    3.483 closest distance to " O   HOH Z  28 " =    1.472
peak=    3.479 closest distance to " CB  ALA A   9 " =    1.642
peak=    3.477 closest distance to " CD1 LEU A   5 " =    1.442
peak=    3.475 closest distance to " O   HOH Z  90 " =    3.523
peak=    3.471 closest distance to " CA  ILE A 106 " =    0.722
peak=    3.465 closest distance to " CB  ALA A  71 " =    1.280
peak=    3.465 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.464 closest distance to " O   HOH Z 136 " =    1.365
peak=    3.456 closest distance to " O   HOH Z 128 " =    2.298
peak=    3.454 closest distance to " O   HOH Z 368 " =    2.210
peak=    3.452 closest distance to " O   HOH Z 163 " =    1.426
peak=    3.452 closest distance to " CG2 VAL A 197 " =    1.148
peak=    3.443 closest distance to " O   HOH Z 438 " =    2.207
peak=    3.441 closest distance to " O   HOH Z 380 " =    1.837
peak=    3.439 closest distance to " O   HOH Z 250 " =    1.394
peak=    3.428 closest distance to " O  BHOH Z  74 " =    1.427
peak=    3.424 closest distance to " O   HOH Z 362 " =    3.347
peak=    3.424 closest distance to " O   HOH Z 227 " =    1.647
peak=    3.420 closest distance to " O   HOH Z 427 " =    3.026
peak=    3.419 closest distance to " CG2 ILE A  20 " =    1.435
peak=    3.417 closest distance to " O   HOH Z 271 " =    2.357
peak=    3.416 closest distance to " O   HOH Z 236 " =    1.580
peak=    3.414 closest distance to " O   HOH Z 366 " =    2.785
peak=    3.413 closest distance to " O   HOH Z 298 " =    5.156
peak=    3.410 closest distance to " O   HOH Z 128 " =    1.803
peak=    3.408 closest distance to " O   HOH Z 336 " =    1.725
peak=    3.401 closest distance to " O   HOH Z 339 " =    1.250
peak=    3.399 closest distance to " CB  ARG A  79 " =    1.028
peak=    3.398 closest distance to " O   HOH Z 250 " =    1.593
peak=    3.396 closest distance to " O   HOH Z 345 " =    1.711
peak=    3.394 closest distance to " CZ  PHE A  38 " =    1.216
peak=    3.393 closest distance to " O   HOH Z 273 " =    2.842
peak=    3.385 closest distance to " NH2AARG A 275 " =    3.632
peak=    3.382 closest distance to " NH1BARG A 190 " =    2.226
peak=    3.380 closest distance to " CG  MET A 185 " =    1.154
peak=    3.377 closest distance to " O   HOH Z 421 " =    1.837
peak=    3.375 closest distance to " O   HOH Z 358 " =    2.169
peak=    3.374 closest distance to " CB  ASN A  39 " =    0.786
peak=    3.368 closest distance to " CB  ARG A 139 " =    0.944
peak=    3.367 closest distance to " NH2 ARG A  79 " =    1.285
peak=    3.366 closest distance to " O   HOH Z  35 " =    2.127
peak=    3.366 closest distance to " O   HOH Z  21 " =    1.857
peak=    3.363 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.361 closest distance to " CG2 THR A 220 " =    0.760
peak=    3.355 closest distance to " OD1 ASN A  69 " =    2.435
peak=    3.347 closest distance to " NZ  LYS A 117 " =    1.409
peak=    3.347 closest distance to " O   HOH Z 344 " =    3.027
peak=    3.346 closest distance to " O   HOH Z 361 " =    2.853
peak=    3.346 closest distance to " OD2 ASP A 298 " =    3.809
peak=    3.343 closest distance to " OG  SER A 245 " =    1.452
peak=    3.342 closest distance to " CB  SER A  62 " =    0.765
peak=    3.334 closest distance to " O   HOH Z 185 " =    1.651
peak=    3.329 closest distance to " CA  ASP A 162 " =    1.059
peak=    3.325 closest distance to " ND2 ASN A 187 " =    1.613
peak=    3.324 closest distance to " CB  LEU A   5 " =    1.286
peak=    3.320 closest distance to " O   HOH Z 355 " =    1.871
peak=    3.319 closest distance to " CG1 VAL A 296 " =    1.124
peak=    3.308 closest distance to " CD  LYS A 119 " =    1.902
peak=    3.306 closest distance to " CA  SER A  12 " =    1.576
peak=    3.306 closest distance to " N   SER A 164 " =    1.009
peak=    3.299 closest distance to " CB  ALA A 295 " =    1.268
peak=    3.297 closest distance to " O   HOH Z 374 " =    2.671
peak=    3.296 closest distance to " O   HOH Z   9 " =    2.448
peak=    3.295 closest distance to " O   HOH Z 313 " =    1.668
peak=    3.294 closest distance to " C   SER A  32 " =    1.106
peak=    3.293 closest distance to " CZ3 TRP A  85 " =    1.012
peak=    3.292 closest distance to " O   HOH Z 387 " =    2.638
peak=    3.287 closest distance to " O   HOH Z  66 " =    2.137
peak=    3.283 closest distance to " O   HOH Z 166 " =    1.602
peak=    3.282 closest distance to " O   HOH Z 420 " =    1.897
peak=    3.277 closest distance to " O   HOH Z 329 " =    3.802
peak=    3.276 closest distance to " CG2 ILE A 234 " =    1.002
peak=    3.272 closest distance to " O   HOH Z  47 " =    2.260
peak=    3.271 closest distance to " O   HOH Z 359 " =    1.890
peak=    3.268 closest distance to " O   HOH Z 280 " =    2.546
peak=    3.266 closest distance to " O   ASN A  74 " =    1.856
peak=    3.262 closest distance to " CB  ARG A 219 " =    1.571
peak=    3.262 closest distance to " CG1 ILE A  49 " =    1.628
peak=    3.259 closest distance to " O   HOH Z   4 " =    1.599
peak=    3.259 closest distance to " CG2 ILE A 120 " =    1.284
peak=    3.259 closest distance to " O   HOH Z 236 " =    1.890
peak=    3.258 closest distance to " CD2 LEU A 297 " =    0.894
peak=    3.258 closest distance to " O   HOH Z 189 " =    2.587
peak=    3.258 closest distance to " NZ  LYS A 166 " =    2.888
peak=    3.255 closest distance to " OD1 ASP A 286 " =    1.820
peak=    3.254 closest distance to " ND1 HIS A  81 " =    1.532
peak=    3.253 closest distance to " O   HOH Z 422 " =    2.561
peak=    3.252 closest distance to " CD  ARG A 195 " =    0.952
peak=    3.251 closest distance to " O   HOH Z 137 " =    2.302
peak=    3.250 closest distance to " O   HOH Z 279 " =    2.044
peak=    3.241 closest distance to " O   HOH Z 112 " =    1.703
peak=    3.239 closest distance to " O   HOH Z  54 " =    1.232
peak=    3.238 closest distance to " CD  GLN A 194 " =    1.559
peak=    3.234 closest distance to " CB  PHE A 283 " =    0.780
peak=    3.232 closest distance to " CA  TYR A 116 " =    1.397
peak=    3.232 closest distance to " CB  ASN A 285 " =    0.931
peak=    3.227 closest distance to " O   HOH Z 214 " =    1.483
peak=    3.226 closest distance to " CG2 THR A 294 " =    1.421
peak=    3.221 closest distance to " O   HOH Z 419 " =    2.377
peak=    3.214 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.212 closest distance to " O   HOH Z 402 " =    2.723
peak=    3.203 closest distance to " CB  LEU A 228 " =    1.412
peak=    3.201 closest distance to " CB  ASP A 140 " =    0.776
peak=    3.200 closest distance to " O   HOH Z 281 " =    4.507
peak=    3.195 closest distance to " CB  PHE A 204 " =    1.070
peak=    3.195 closest distance to " O   HOH Z 109 " =    1.970
peak=    3.192 closest distance to " CB  LYS A 289 " =    1.013
peak=    3.184 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.182 closest distance to " CB  ALA A 256 " =    0.991
peak=    3.178 closest distance to " CA  LYS A 117 " =    1.340
peak=    3.175 closest distance to " O   HOH Z 145 " =    2.645
peak=    3.174 closest distance to " CA  THR A 264 " =    0.810
peak=    3.174 closest distance to " CA  CYS A 260 " =    1.649
peak=    3.174 closest distance to " CD1 LEU A  96 " =    0.800
peak=    3.172 closest distance to " CB  TYR A 247 " =    1.037
peak=    3.172 closest distance to " CB  THR A  31 " =    1.506
peak=    3.167 closest distance to " CA  ARG A  66 " =    0.934
peak=    3.162 closest distance to " N   ASP A 231 " =    1.696
peak=    3.162 closest distance to " O   HOH Z 151 " =    1.933
peak=    3.162 closest distance to " CD1 ILE A  33 " =    1.588
peak=    3.160 closest distance to " O   HOH Z 196 " =    1.058
peak=    3.152 closest distance to " C   VAL A 265 " =    1.230
peak=    3.150 closest distance to " CG2AVAL A 121 " =    1.976
peak=    3.148 closest distance to " CA  GLY A  80 " =    0.744
peak=    3.145 closest distance to " OD2 ASP A 298 " =    3.553
peak=    3.145 closest distance to " O   HOH Z  78 " =    1.574
peak=    3.137 closest distance to " CA  ARG A 275 " =    1.869
peak=    3.128 closest distance to " CG  GLN A  58 " =    2.638
peak=    3.118 closest distance to " CD1 LEU A 228 " =    1.556
peak=    3.116 closest distance to " O   HOH Z 427 " =    2.707
peak=    3.114 closest distance to " O   HOH Z 404 " =    2.022
peak=    3.111 closest distance to " OD1 ASN A  60 " =    1.687
peak=    3.106 closest distance to " O   HOH Z 227 " =    1.636
peak=    3.106 closest distance to " O   HOH Z 420 " =    4.820
peak=    3.104 closest distance to " CG BARG A 275 " =    1.450
peak=    3.103 closest distance to " O   HOH Z 173 " =    2.429
peak=    3.102 closest distance to " NE1 TRP A 274 " =    0.915
peak=    3.089 closest distance to " CB  GLN A  58 " =    1.067
peak=    3.083 closest distance to " CA  ARG A  36 " =    1.032
peak=    3.081 closest distance to " CB  ALA A 242 " =    0.980
peak=    3.079 closest distance to " CB  ASN A 215 " =    1.120
peak=    3.075 closest distance to " CA  ALA A 160 " =    0.913
peak=    3.062 closest distance to " CB  ARG A 259 " =    1.887
peak=    3.055 closest distance to " CB  ALA A  34 " =    0.827
peak=    3.049 closest distance to " CG  ARG A  66 " =    2.937
peak=    3.043 closest distance to " CB  TRP A 179 " =    1.916
peak=    3.040 closest distance to " N   TYR A 247 " =    1.249
peak=    3.037 closest distance to " CB  ALA A 291 " =    1.329
peak=    3.028 closest distance to " OG BSER A 210 " =    1.124
peak=    3.026 closest distance to " O   HOH Z  88 " =    2.950
peak=    3.025 closest distance to " CA  GLU A  46 " =    0.795
peak=    3.022 closest distance to " O   HOH Z  55 " =    2.096
peak=    3.008 closest distance to " O   HOH Z 280 " =    2.971

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.702 - 5.732
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.702 - 5.732

peak=   -5.117 closest distance to " CG2 VAL A 230 " =    0.766
peak=   -4.552 closest distance to " O   PRO A 163 " =    2.073
peak=   -4.512 closest distance to " CG2BVAL A  41 " =    2.668
peak=   -4.469 closest distance to " O   HOH Z 266 " =    4.787
peak=   -4.392 closest distance to " O   HOH Z  13 " =    1.732
peak=   -4.327 closest distance to " O   HOH Z 166 " =    1.699
peak=   -4.238 closest distance to " OXT GLY A 302 " =    2.883
peak=   -4.168 closest distance to " CD  ARG A 156 " =    2.047
peak=   -4.119 closest distance to " O   HOH Z 290 " =    0.900
peak=   -4.113 closest distance to " SG  CYS A 254 " =    3.212
peak=   -4.047 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -4.042 closest distance to " O   HOH Z 210 " =    0.702
peak=   -4.018 closest distance to " CG  MET A  93 " =    2.507
peak=   -4.011 closest distance to " C   THR A 279 " =    1.152
peak=   -3.973 closest distance to " CD  GLN A  58 " =    1.189
peak=   -3.965 closest distance to " O   HOH Z 426 " =    1.725
peak=   -3.949 closest distance to " CD1 PHE A  59 " =    1.973
peak=   -3.931 closest distance to " O   HOH Z 151 " =    1.067
peak=   -3.926 closest distance to " O   HOH Z 196 " =    2.385
peak=   -3.921 closest distance to " O   HOH Z 351 " =    1.564
peak=   -3.919 closest distance to " CG1 VAL A 250 " =    2.698
peak=   -3.918 closest distance to " O   VAL A  67 " =    2.677
peak=   -3.874 closest distance to " O   HOH Z 423 " =    2.244
peak=   -3.867 closest distance to " N   ALA A 226 " =    2.003
peak=   -3.850 closest distance to " CG2 THR A 182 " =    2.285
peak=   -3.849 closest distance to " O   ALA A   1 " =    1.914
peak=   -3.832 closest distance to " O   HOH Z 165 " =    1.943
peak=   -3.832 closest distance to " CG1 VAL A 112 " =    2.491
peak=   -3.817 closest distance to " O   HOH Z 136 " =    2.431
peak=   -3.804 closest distance to " C   HIS A 108 " =    1.230
peak=   -3.800 closest distance to " O   HOH Z 103 " =    1.893
peak=   -3.785 closest distance to " NH2 ARG A  66 " =    1.311
peak=   -3.770 closest distance to " OG  SER A  97 " =    2.330
peak=   -3.758 closest distance to " OG BSER A 210 " =    1.238
peak=   -3.750 closest distance to " OG BSER A 134 " =    1.329
peak=   -3.749 closest distance to " CB  ALA A 161 " =    2.508
peak=   -3.746 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.738 closest distance to " O   HOH Z 174 " =    1.945
peak=   -3.737 closest distance to " CB  ALA A 248 " =    2.138
peak=   -3.692 closest distance to " O   TRP A  92 " =    2.017
peak=   -3.677 closest distance to " CG  ASP A 231 " =    0.861
peak=   -3.675 closest distance to " SG  CYS A 260 " =    2.596
peak=   -3.664 closest distance to " OD1 ASN A 148 " =    1.556
peak=   -3.652 closest distance to " CB  PHE A 208 " =    2.355
peak=   -3.647 closest distance to " CA  SER A 276 " =    1.477
peak=   -3.642 closest distance to " CH2 TRP A 179 " =    1.258
peak=   -3.607 closest distance to " CD1 LEU A  25 " =    2.517
peak=   -3.605 closest distance to " CB  ALA A 248 " =    2.031
peak=   -3.598 closest distance to " CA  ASP A 298 " =    1.023
peak=   -3.594 closest distance to " N   THR A 235 " =    1.307
peak=   -3.591 closest distance to " CA  GLY A 203 " =    2.242
peak=   -3.584 closest distance to " ND2 ASN A  39 " =    1.160
peak=   -3.581 closest distance to " C   SER A 206 " =    1.554
peak=   -3.575 closest distance to " O   HOH Z 407 " =    1.428
peak=   -3.573 closest distance to " O   HOH Z 166 " =    1.374
peak=   -3.566 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.564 closest distance to " OG1 THR A  82 " =    1.341
peak=   -3.562 closest distance to " O   HOH Z   6 " =    2.052
peak=   -3.550 closest distance to " CE3 TRP A 150 " =    2.370
peak=   -3.537 closest distance to " OG  SER A  26 " =    1.250
peak=   -3.535 closest distance to " O   HOH Z  10 " =    1.642
peak=   -3.531 closest distance to " O   HOH Z  20 " =    1.135
peak=   -3.528 closest distance to " O   HOH Z 422 " =    1.475
peak=   -3.527 closest distance to " O   HOH Z 196 " =    2.094
peak=   -3.523 closest distance to " O   HOH Z  15 " =    1.485
peak=   -3.521 closest distance to " OD1 ASN A  39 " =    2.203
peak=   -3.518 closest distance to " O   HOH Z 234 " =    4.137
peak=   -3.518 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.518 closest distance to " O   HOH Z 252 " =    3.937
peak=   -3.506 closest distance to " OG  SER A   3 " =    1.509
peak=   -3.502 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.498 closest distance to " O   HOH Z  52 " =    2.073
peak=   -3.493 closest distance to " CG  ARG A 219 " =    2.434
peak=   -3.488 closest distance to " CD2 LEU A 300 " =    2.744
peak=   -3.485 closest distance to " CG  ASP A  50 " =    2.113
peak=   -3.483 closest distance to " O   ASN A  45 " =    1.853
peak=   -3.478 closest distance to " O   HOH Z 126 " =    1.809
peak=   -3.477 closest distance to " O   HOH Z 171 " =    2.306
peak=   -3.475 closest distance to " O   HOH Z 150 " =    1.797
peak=   -3.474 closest distance to " O   HOH Z 120 " =    1.366
peak=   -3.474 closest distance to " O   HOH Z 377 " =    1.205
peak=   -3.474 closest distance to " CB  SER A 210 " =    1.283
peak=   -3.464 closest distance to " O   HOH Z  60 " =    2.180
peak=   -3.460 closest distance to " O   HOH Z 407 " =    3.097
peak=   -3.449 closest distance to " O   HOH Z  49 " =    0.883
peak=   -3.444 closest distance to " OG1 THR A   4 " =    1.876
peak=   -3.433 closest distance to " O   HOH Z 387 " =    2.780
peak=   -3.431 closest distance to " O   ASN A 187 " =    1.586
peak=   -3.424 closest distance to " O   HOH Z 275 " =    1.451
peak=   -3.422 closest distance to " O   HOH Z 120 " =    0.889
peak=   -3.421 closest distance to " ND2 ASN A  69 " =    1.710
peak=   -3.421 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.415 closest distance to " O   HOH Z  71 " =    1.569
peak=   -3.414 closest distance to " CG2 VAL A 296 " =    0.970
peak=   -3.409 closest distance to " O   ALA A 256 " =    1.630
peak=   -3.405 closest distance to " NH1 ARG A 195 " =    2.505
peak=   -3.403 closest distance to " CG  ARG A 269 " =    2.238
peak=   -3.400 closest distance to " N   LEU A 281 " =    1.879
peak=   -3.389 closest distance to " O   HOH Z 231 " =    2.173
peak=   -3.387 closest distance to " CD  GLN A  88 " =    1.115
peak=   -3.378 closest distance to " CG2 ILE A  49 " =    2.699
peak=   -3.378 closest distance to " OD2 ASP A 171 " =    2.370
peak=   -3.373 closest distance to " NE1 TRP A 266 " =    2.425
peak=   -3.361 closest distance to " O  BHOH Z 338 " =    1.398
peak=   -3.357 closest distance to " O   HOH Z 353 " =    2.156
peak=   -3.353 closest distance to " OD1 ASP A 298 " =    1.886
peak=   -3.353 closest distance to " CD1 LEU A 167 " =    2.094
peak=   -3.352 closest distance to " CD1 LEU A 228 " =    2.218
peak=   -3.351 closest distance to " OD1 ASN A 173 " =    1.720
peak=   -3.351 closest distance to " NH2 ARG A  79 " =    2.026
peak=   -3.346 closest distance to " O   HOH Z 388 " =    1.989
peak=   -3.335 closest distance to " O   HOH Z 377 " =    2.151
peak=   -3.326 closest distance to " CB  PRO A 163 " =    2.702
peak=   -3.315 closest distance to " O   GLY A  80 " =    2.425
peak=   -3.312 closest distance to " ND2 ASN A  45 " =    1.108
peak=   -3.311 closest distance to " N   GLN A  58 " =    1.662
peak=   -3.310 closest distance to " CD1 TRP A 179 " =    1.169
peak=   -3.299 closest distance to " CG  PRO A 243 " =    1.669
peak=   -3.297 closest distance to " CD2 TYR A 293 " =    1.939
peak=   -3.296 closest distance to " O   TYR A  15 " =    1.722
peak=   -3.296 closest distance to " C   ASN A 285 " =    2.263
peak=   -3.294 closest distance to " O   HOH Z 385 " =    3.765
peak=   -3.293 closest distance to " ND2BASN A 224 " =    1.881
peak=   -3.292 closest distance to " O   VAL A 174 " =    2.160
peak=   -3.292 closest distance to " ND2 ASN A 187 " =    1.690
peak=   -3.290 closest distance to " O   HOH Z 139 " =    3.307
peak=   -3.288 closest distance to " O   HOH Z  56 " =    1.448
peak=   -3.287 closest distance to " O   HOH Z  78 " =    1.688
peak=   -3.287 closest distance to " O   HOH Z 297 " =    2.756
peak=   -3.286 closest distance to " CE BMET A  47 " =    1.491
peak=   -3.286 closest distance to " N   MET A 188 " =    1.795
peak=   -3.283 closest distance to " CD2 PHE A 192 " =    2.098
peak=   -3.280 closest distance to " O   HOH Z 200 " =    1.375
peak=   -3.277 closest distance to " CD  GLN A 223 " =    1.660
peak=   -3.276 closest distance to " CG  MET A 105 " =    0.835
peak=   -3.274 closest distance to " O   HOH Z 283 " =    1.835
peak=   -3.265 closest distance to " CB  ASP A 162 " =    2.553
peak=   -3.265 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.265 closest distance to " O   HOH Z 340 " =    1.075
peak=   -3.260 closest distance to " OG ASER A 134 " =    1.280
peak=   -3.260 closest distance to " O   HOH Z 285 " =    1.490
peak=   -3.257 closest distance to " O   SER A 273 " =    1.209
peak=   -3.257 closest distance to " CD2 LEU A 237 " =    2.767
peak=   -3.256 closest distance to " O   ALA A 161 " =    1.713
peak=   -3.253 closest distance to " CD1 TYR A 247 " =    2.279
peak=   -3.253 closest distance to " O   GLY A  80 " =    2.559
peak=   -3.252 closest distance to " CD2 LEU A 167 " =    1.699
peak=   -3.251 closest distance to " CD  ARG A  36 " =    1.893
peak=   -3.251 closest distance to " NH1 ARG A 195 " =    2.292
peak=   -3.249 closest distance to " CA  GLY A 241 " =    2.380
peak=   -3.249 closest distance to " OD1 ASN A 249 " =    2.311
peak=   -3.243 closest distance to " O   SER A 271 " =    2.037
peak=   -3.240 closest distance to " O   HOH Z  92 " =    1.636
peak=   -3.230 closest distance to " CG1 VAL A 296 " =    1.243
peak=   -3.229 closest distance to " CG1 VAL A  78 " =    2.623
peak=   -3.227 closest distance to " O   HOH Z 119 " =    2.068
peak=   -3.226 closest distance to " CD  GLN A 223 " =    0.821
peak=   -3.225 closest distance to " CA  VAL A 197 " =    0.951
peak=   -3.224 closest distance to " O   HOH Z  17 " =    1.139
peak=   -3.220 closest distance to " O   HOH Z 124 " =    1.638
peak=   -3.215 closest distance to " CE  LYS A 166 " =    3.016
peak=   -3.215 closest distance to " CH2 TRP A 150 " =    1.069
peak=   -3.206 closest distance to " NE2 GLN A 194 " =    1.755
peak=   -3.203 closest distance to " CD2 PHE A  59 " =    2.556
peak=   -3.202 closest distance to " O   HOH Z 193 " =    1.551
peak=   -3.198 closest distance to " O   ALA A  34 " =    2.377
peak=   -3.192 closest distance to " O   HOH Z  39 " =    1.843
peak=   -3.185 closest distance to " O   HOH Z 426 " =    2.283
peak=   -3.182 closest distance to " NE2 GLN A 103 " =    1.629
peak=   -3.180 closest distance to " CB  ALA A  43 " =    2.459
peak=   -3.178 closest distance to " OH  TYR A 169 " =    0.944
peak=   -3.178 closest distance to " CD  ARG A 195 " =    5.072
peak=   -3.177 closest distance to " O   HOH Z  56 " =    2.460
peak=   -3.174 closest distance to " CG  GLU A  53 " =    1.477
peak=   -3.166 closest distance to " N   ALA A 242 " =    1.935
peak=   -3.160 closest distance to " O   SER A 210 " =    1.976
peak=   -3.160 closest distance to " O   HOH Z 397 " =    1.176
peak=   -3.160 closest distance to " CE2 PHE A  38 " =    1.966
peak=   -3.154 closest distance to " O   HOH Z 424 " =    2.725
peak=   -3.152 closest distance to " CG1 VAL A 197 " =    2.243
peak=   -3.152 closest distance to " O   HOH Z 151 " =    1.803
peak=   -3.149 closest distance to " O   HOH Z 292 " =    4.345
peak=   -3.148 closest distance to " N   THR A 157 " =    1.617
peak=   -3.147 closest distance to " CG  GLU A 277 " =    1.129
peak=   -3.144 closest distance to " CG  GLN A  58 " =    1.261
peak=   -3.143 closest distance to " O   ASP A 171 " =    1.887
peak=   -3.141 closest distance to " O   HOH Z 372 " =    2.509
peak=   -3.140 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -3.131 closest distance to " NH2 ARG A  66 " =    5.402
peak=   -3.129 closest distance to " ND2 ASN A  60 " =    1.553
peak=   -3.129 closest distance to " O   HOH Z 123 " =    2.320
peak=   -3.128 closest distance to " O   HOH Z 191 " =    5.732
peak=   -3.120 closest distance to " CB  ALA A  10 " =    2.196
peak=   -3.117 closest distance to " O   GLY A 196 " =    1.015
peak=   -3.112 closest distance to " OG  SER A  62 " =    1.419
peak=   -3.103 closest distance to " O   HOH Z 222 " =    1.454
peak=   -3.100 closest distance to " CA  ASN A 110 " =    1.055
peak=   -3.088 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.076 closest distance to " N   ALA A 248 " =    1.664
peak=   -3.068 closest distance to " ND2 ASN A  45 " =    1.980
peak=   -3.062 closest distance to " CG  ASP A 132 " =    2.373
peak=   -3.054 closest distance to " O   HOH Z 150 " =    2.041
peak=   -3.048 closest distance to " O   HOH Z 221 " =    1.274
peak=   -3.048 closest distance to " CZ3 TRP A 266 " =    1.565
peak=   -3.043 closest distance to " O   ASP A  27 " =    2.120
peak=   -3.036 closest distance to " N   SER A   3 " =    2.341
peak=   -3.026 closest distance to " CG2 VAL A 189 " =    1.993
peak=   -3.024 closest distance to " O   HOH Z 185 " =    2.353

================= 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    :  0.4831 0.4667   6.284594e+00   6.268868e+00
   1_bss:  0.4754 0.4625   6.277219e+00   6.263071e+00
   1_xyz:  0.3937 0.4093   6.175346e+00   6.196500e+00
   1_adp:  0.3474 0.3915   6.094120e+00   6.169494e+00
   1_occ:  0.3468 0.3903   6.092890e+00   6.169250e+00
   2_bss:  0.3446 0.3837   6.093267e+00   6.167646e+00
   2_xyz:  0.2781 0.3298   5.920384e+00   6.052890e+00
   2_adp:  0.2613 0.3190   5.883671e+00   6.023622e+00
   2_occ:  0.2611 0.3192   5.883471e+00   6.024076e+00
   3_bss:  0.2597 0.3194   5.883281e+00   6.022986e+00
   3_xyz:  0.2009 0.2489   5.642991e+00   5.807374e+00
   3_adp:  0.1884 0.2310   5.585236e+00   5.748019e+00
   3_occ:  0.1883 0.2312   5.584885e+00   5.748521e+00
   4_bss:  0.1877 0.2305   5.585020e+00   5.746589e+00
   4_xyz:  0.1464 0.1863   5.354466e+00   5.550640e+00
   4_adp:  0.1359 0.1767   5.296803e+00   5.505652e+00
   4_occ:  0.1358 0.1765   5.296159e+00   5.505288e+00
   5_bss:  0.1360 0.1775   5.298893e+00   5.508735e+00
   5_xyz:  0.1203 0.1652   5.204325e+00   5.437006e+00
   5_adp:  0.1180 0.1634   5.188478e+00   5.424446e+00
   5_occ:  0.1180 0.1635   5.188183e+00   5.424310e+00
   5_bss:  0.1179 0.1634   5.188275e+00   5.424395e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.320   8.298   6.839  12.031   7.493   0.000   0.000   0.000
   1_xyz:  0.320   8.298   6.839  12.031   7.493   0.000   0.000   0.000
   1_adp:  0.320   8.298   6.839  12.031   7.493   0.000   0.000   0.000
   1_occ:  0.320   8.298   6.839  12.031   7.493   0.000   0.000   0.000
   2_bss:  0.308  32.279   3.325   7.600   4.375   0.000   0.000   0.000
   2_xyz:  0.308  32.279   3.325   7.600   4.375   0.000   0.000   0.000
   2_adp:  0.308  32.279   3.325   7.600   4.375   0.000   0.000   0.000
   2_occ:  0.308  32.279   3.325   7.600   4.375   0.000   0.000   0.000
   3_bss:  0.298  41.840   1.787   4.956   3.118   0.000   0.000   0.000
   3_xyz:  0.298  41.840   1.787   4.956   3.118   0.000   0.000   0.000
   3_adp:  0.298  41.840   1.787   4.956   3.118   0.000   0.000   0.000
   3_occ:  0.298  41.840   1.787   4.956   3.118   0.000   0.000   0.000
   4_bss:  0.310  41.840   1.080   3.313   2.513   0.000   0.000   0.000
   4_xyz:  0.310  41.840   1.080   3.313   2.513   0.000   0.000   0.000
   4_adp:  0.310  41.840   1.080   3.313   2.513   0.000   0.000   0.000
   4_occ:  0.310  41.840   1.080   3.313   2.513   0.000   0.000   0.000
   5_bss:  0.312  51.235   0.778   2.409   2.317   0.000   0.000   0.000
   5_xyz:  0.312  51.235   0.778   2.409   2.317   0.000   0.000   0.000
   5_adp:  0.312  51.235   0.778   2.409   2.317   0.000   0.000   0.000
   5_occ:  0.312  51.235   0.778   2.409   2.317   0.000   0.000   0.000
   5_bss:  0.322  53.130  -0.964   0.410   0.553   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.125 0.4444  0.5096    67655.207
   1_bss:  56.566 0.4370  0.6461    66273.803
   1_xyz:  47.823 0.5461  0.7913    49570.981
   1_adp:  43.413 0.6014  0.9204    43840.542
   1_occ:  43.312 0.6026  0.9208    43649.982
   2_bss:  42.850 0.6083  0.8197    43004.348
   2_xyz:  35.875 0.6905  0.9202    30660.957
   2_adp:  34.275 0.7094  0.9350    28511.973
   2_occ:  34.298 0.7091  0.9345    28538.762
   3_bss:  34.140 0.7110  0.8791    28375.915
   3_xyz:  24.899 0.8124  0.9692    16025.328
   3_adp:  22.750 0.8353  0.9850    14036.367
   3_occ:  22.754 0.8352  0.9852    14050.339
   4_bss:  22.698 0.8358  0.9524    13984.593
   4_xyz:  17.696 0.8829  0.9830     8856.392
   4_adp:  16.601 0.8930  0.9843     8092.529
   4_occ:  16.594 0.8931  0.9843     8091.606
   5_bss:  16.649 0.8927  0.9683     8187.882
   5_xyz:  15.160 0.9054  0.9734     7094.443
   5_adp:  14.830 0.9084  0.9698     6943.328
   5_occ:  14.822 0.9084  0.9697     6943.779
   5_bss:  14.822 0.9084  0.9722     6946.635
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3856e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3856e+01
   1_xyz:   1.711  0.013  0.109 18.086  0.007  4.120   1.4518e-01
   1_adp:   1.711  0.013  0.109 18.086  0.007  4.120   1.4518e-01
   1_occ:   1.711  0.013  0.109 18.086  0.007  4.120   1.4518e-01
   2_bss:   1.711  0.013  0.109 18.086  0.007  4.120   1.4518e-01
   2_xyz:   1.227  0.009  0.081 16.273  0.005  4.108   8.5213e-02
   2_adp:   1.227  0.009  0.081 16.273  0.005  4.108   8.5213e-02
   2_occ:   1.227  0.009  0.081 16.273  0.005  4.108   8.5213e-02
   3_bss:   1.227  0.009  0.081 16.273  0.005  4.108   8.5213e-02
   3_xyz:   1.100  0.008  0.080 15.220  0.004  4.123   6.7661e-02
   3_adp:   1.100  0.008  0.080 15.220  0.004  4.123   6.7661e-02
   3_occ:   1.100  0.008  0.080 15.220  0.004  4.123   6.7661e-02
   4_bss:   1.100  0.008  0.080 15.220  0.004  4.123   6.7661e-02
   4_xyz:   1.053  0.008  0.079 15.259  0.004  4.126   6.5406e-02
   4_adp:   1.053  0.008  0.079 15.259  0.004  4.126   6.5406e-02
   4_occ:   1.053  0.008  0.079 15.259  0.004  4.126   6.5406e-02
   5_bss:   1.053  0.008  0.079 15.259  0.004  4.126   6.5406e-02
   5_xyz:   1.126  0.009  0.089 15.481  0.004  4.113   7.2576e-02
   5_adp:   1.126  0.009  0.089 15.481  0.004  4.113   7.2576e-02
   5_occ:   1.126  0.009  0.089 15.481  0.004  4.113   7.2576e-02
   5_bss:   1.126  0.009  0.089 15.481  0.004  4.113   7.2576e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.127   6.9810e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.127   6.9810e+00
   1_xyz:  15.768  0.164  0.530 87.003  0.045  2.226   1.0464e-01
   1_adp:  15.768  0.164  0.530 87.003  0.045  2.226   1.0464e-01
   1_occ:  15.768  0.164  0.530 87.003  0.045  2.226   1.0464e-01
   2_bss:  15.768  0.164  0.530 87.003  0.045  2.226   1.0464e-01
   2_xyz:   8.300  0.121  0.259 85.010  0.045  2.084   7.4535e-02
   2_adp:   8.300  0.121  0.259 85.010  0.045  2.084   7.4535e-02
   2_occ:   8.300  0.121  0.259 85.010  0.045  2.084   7.4535e-02
   3_bss:   8.300  0.121  0.259 85.010  0.045  2.084   7.4535e-02
   3_xyz:   6.854  0.092  0.267 85.691  0.030  2.205   5.5470e-02
   3_adp:   6.854  0.092  0.267 85.691  0.030  2.205   5.5470e-02
   3_occ:   6.854  0.092  0.267 85.691  0.030  2.205   5.5470e-02
   4_bss:   6.854  0.092  0.267 85.691  0.030  2.205   5.5470e-02
   4_xyz:   7.082  0.058  0.428 80.563  0.026  2.243   4.7994e-02
   4_adp:   7.082  0.058  0.428 80.563  0.026  2.243   4.7994e-02
   4_occ:   7.082  0.058  0.428 80.563  0.026  2.243   4.7994e-02
   5_bss:   7.082  0.058  0.428 80.563  0.026  2.243   4.7994e-02
   5_xyz:   7.555  0.045  0.650 83.227  0.028  2.284   5.1410e-02
   5_adp:   7.555  0.045  0.650 83.227  0.028  2.284   5.1410e-02
   5_occ:   7.555  0.045  0.650 83.227  0.028  2.284   5.1410e-02
   5_bss:   7.555  0.045  0.650 83.227  0.028  2.284   5.1410e-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:  92.62   0.00  13.73  70.60   0.00  11.42  92.62   0.00  26.28
   1_occ:  92.62   0.00  13.73  70.60   0.00  11.42  92.62   0.00  26.28
   2_bss:  92.62   0.00  13.73  70.60   0.00  11.42  92.62   0.00  26.28
   2_xyz:  92.62   0.00  13.73  70.60   0.00  11.42  92.62   0.00  26.28
   2_adp:  88.57   0.00  13.34  78.52   0.00  10.37  88.57   0.00  29.53
   2_occ:  88.57   0.00  13.34  78.52   0.00  10.37  88.57   0.00  29.53
   3_bss:  88.57   0.00  13.34  78.52   0.00  10.37  88.57   0.00  29.53
   3_xyz:  88.57   0.00  13.34  78.52   0.00  10.37  88.57   0.00  29.53
   3_adp:  83.31   0.00  13.17  77.70   0.00   9.61  83.31   2.16  32.51
   3_occ:  83.31   0.00  13.17  77.70   0.00   9.61  83.31   2.16  32.51
   4_bss:  83.31   0.00  13.17  77.70   0.00   9.61  83.31   2.16  32.51
   4_xyz:  83.31   0.00  13.17  77.70   0.00   9.61  83.31   2.16  32.51
   4_adp:  84.76   0.00  13.67  84.76   0.00   9.38  76.62   1.71  37.03
   4_occ:  84.76   0.00  13.67  84.76   0.00   9.38  76.62   1.71  37.03
   5_bss:  84.76   0.00  13.67  84.76   0.00   9.38  76.62   1.71  37.03
   5_xyz:  84.76   0.00  13.67  84.76   0.00   9.38  76.62   1.71  37.03
   5_adp:  86.13   0.00  13.50  86.13   0.00   9.17  77.45   1.87  37.08
   5_occ:  86.13   0.00  13.50  86.13   0.00   9.17  77.45   1.87  37.08
   5_bss:  88.02   1.89  15.40  88.02   1.89  11.07  79.34   3.77  38.97
------------------------------------------------------------------------
 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:    1.135    0.014    0.413
   1_adp:    1.135    0.014    0.413
   1_occ:    1.135    0.014    0.413
   2_bss:    1.135    0.014    0.413
   2_xyz:    1.688    0.018    0.565
   2_adp:    1.688    0.018    0.565
   2_occ:    1.688    0.018    0.565
   3_bss:    1.688    0.018    0.565
   3_xyz:    1.734    0.046    0.650
   3_adp:    1.734    0.046    0.650
   3_occ:    1.734    0.046    0.650
   4_bss:    1.734    0.046    0.650
   4_xyz:    1.939    0.056    0.742
   4_adp:    1.939    0.056    0.742
   4_occ:    1.939    0.056    0.742
   5_bss:    1.939    0.056    0.742
   5_xyz:    1.959    0.052    0.776
   5_adp:    1.959    0.052    0.776
   5_occ:    1.959    0.052    0.776
   5_bss:    1.959    0.052    0.776
------------------------------------------------------------------------

CPU time actual refinement: 349.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/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_466/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_466/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.71 
  Macro-tasks:
    bulk solvent and scale       = 41.71  
    individual site refinement   = 142.07 
    weights calculation          = 33.21  
    collect and process          = 6.51   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.63 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 110.08 
    alpha_beta                      = 8.32   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.27 
    fmodel                         = 7.57   
    r_factors                      = 0.22   
    phase_errors                   = 10.41  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 259.75 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.932 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    655 calls, 109.70 s
gradients_fft:          600 calls, 106.11 s

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

# Date 2008-01-16 Time 01:39:13 PST -0800 (1200476353.30 s)
Start R-work = 0.4831, R-free = 0.4667 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1787 (no bulk solvent and anisotropic scale)

Start R-work = 0.4754, R-free = 0.4625
Final R-work = 0.1179, R-free = 0.1634