# Date 2008-01-16 Time 02:22:26 PST -0800 (1200478946.71 s)
#phil __OFF__

Command line arguments: "../810.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19889
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 810

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01053
Completeness in resolution range: 0.9773
Completeness with d_max=infinity: 0.974189

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   2.0105

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01053
Completeness in resolution range: 0.9773
Completeness with d_max=infinity: 0.974189

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.3013 [2105/2129]  1894   211  10.0%
  bin  2:  4.3013 -  3.4272 [2028/2047]  1826   202  10.0%
  bin  3:  3.4272 -  2.9978 [1994/2013]  1795   199  10.0%
  bin  4:  2.9978 -  2.7255 [1972/2002]  1774   198  10.0%
  bin  5:  2.7255 -  2.5311 [1975/1994]  1779   196   9.9%
  bin  6:  2.5311 -  2.3825 [1947/1972]  1748   199  10.2%
  bin  7:  2.3825 -  2.2636 [1948/1976]  1756   192   9.9%
  bin  8:  2.2636 -  2.1654 [1952/1988]  1757   195  10.0%
  bin  9:  2.1654 -  2.0822 [1905/1947]  1712   193  10.1%
  bin 10:  2.0822 -  2.0105 [1763/1976]  1589   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/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: 12
        2.42 -     3.04: 2161
        3.04 -     3.66: 4602
        3.66 -     4.28: 8896
        4.28 -     4.90: 12263
  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 207 " - " O   HOH Z 341 "  1.972 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.132 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27929 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_810/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/model_refine_001.geo

CPU time processing inputs: 9.79


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4467   r_free= 0.4305   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.241704                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7970 0.99   1375  153 0.3661 0.3351      6.5359      6.4407|
|  2:  4.7970 -  3.8280 0.99   1306  146 0.3423 0.3743      6.6725      6.7733|
|  3:  3.8280 -  3.3501 0.99   1293  143 0.3958 0.3730       6.614      6.5815|
|  4:  3.3501 -  3.0466 0.99   1284  139 0.4263 0.3796      6.4834       6.385|
|  5:  3.0466 -  2.8298 0.99   1268  144 0.4665 0.4422      6.3371      6.3469|
|  6:  2.8298 -  2.6639 0.99   1276  141 0.4714 0.5114      6.2536      6.2006|
|  7:  2.6639 -  2.5311 0.99   1266  140 0.4849 0.4573      6.2179      6.1495|
|  8:  2.5311 -  2.4214 0.98   1250  139 0.4923 0.4224      6.1714      6.1182|
|  9:  2.4214 -  2.3285 0.98   1253  143 0.4954 0.5229      6.1019      6.1328|
| 10:  2.3285 -  2.2485 0.99   1245  136 0.5151 0.4782      6.1225       6.076|
| 11:  2.2485 -  2.1784 0.98   1256  137 0.4941 0.4783      6.0208      6.0359|
| 12:  2.1784 -  2.1163 0.97   1237  142 0.5176 0.4773      5.9845      6.0255|
| 13:  2.1163 -  2.0607 1.00   1250  136 0.5062 0.5027      5.8891      5.8495|
| 14:  2.0607 -  2.0105 0.85   1071  120 0.5154 0.4785      5.8524       5.751|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7970  1375   153  0.74  30.52   0.81     0.76      56682.10|
|  2:  4.7970 -  3.8280  1306   146  0.76  29.57   0.90     0.80      79074.22|
|  3:  3.8280 -  3.3501  1293   143  0.69  36.05   0.85     0.76      83246.28|
|  4:  3.3501 -  3.0466  1284   139  0.63  41.70   0.82     0.68      73129.34|
|  5:  3.0466 -  2.8298  1268   144  0.54  48.60   0.76     0.61      63064.95|
|  6:  2.8298 -  2.6639  1276   141  0.52  50.36   0.74     0.57      57377.63|
|  7:  2.6639 -  2.5311  1266   140  0.50  52.44   0.75     0.55      53299.09|
|  8:  2.5311 -  2.4214  1250   139  0.49  53.31   0.76     0.55      48558.38|
|  9:  2.4214 -  2.3285  1253   143  0.48  53.43   0.73     0.55      44228.77|
| 10:  2.3285 -  2.2485  1245   136  0.48  53.54   0.73     0.55      41274.23|
| 11:  2.2485 -  2.1784  1256   137  0.46  55.67   0.76     0.53      38829.35|
| 12:  2.1784 -  2.1163  1237   142  0.43  57.91   0.76     0.51      37037.14|
| 13:  2.1163 -  2.0607  1250   136  0.42  58.12   0.74     0.49      32012.64|
| 14:  2.0607 -  2.0105  1071   120  0.46  55.36   0.72     0.49      25178.89|
|alpha:            min =        0.49 max =            0.80 mean =         0.60|
|beta:             min =    25178.89 max =        83246.28 mean =     52891.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.03|
|phase err.(test): min =        0.00 max =           89.97 mean =        48.10|
|-----------------------------------------------------------------------------|

============================== 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 = 8.555859              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.542   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.757709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.041   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1481 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3866 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5003 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6514 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7639 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.291 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.643 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.4311   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.247062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4387   r_free= 0.4169   ksol= 0.30   Bsol= 20.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.91,9.20,9.28,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.235664                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.931923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.080   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.697054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.479   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4387      final r-factor (work) = 0.3286          |
| start r-factor (free) = 0.4169      final r-factor (free) = 0.3496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.0864 = 7.93 * 0.50 * 6.2521 + 1.00 * 54.2910                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2638 = 7.93 * 0.50 * 6.0862 + 1.00 * 0.1263                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3286      final r-factor (work) = 0.2715          |
| start r-factor (free) = 0.3496      final r-factor (free) = 0.3094          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2568 = 0.70 * 1.00 * 6.0862 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1462 = 0.70 * 1.00 * 5.9297 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.96   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    92.96   11.01    None  None   None       |
|    Sol.    : 438    0      0.00    92.96   27.68    None  None   None       |
|    Mac.    : 2385   0      0.00    62.30   7.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.296: 1713   |   5:    46.481 -  55.777:   41        |
|      1:     9.296 -  18.592:  610   |   6:    55.777 -  65.073:   14        |
|      2:    18.592 -  27.889:  221   |   7:    65.073 -  74.370:    1        |
|      3:    27.889 -  37.185:  136   |   8:    74.370 -  83.666:    0        |
|      4:    37.185 -  46.481:   86   |   9:    83.666 -  92.962:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2715 r_free = 0.3094             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2707 r_free = 0.3099             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2707   r_free= 0.3099   ksol= 0.30   Bsol= 20.00   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.91,9.20,9.28,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.878298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2662   r_free= 0.3040   ksol= 0.33   Bsol= 55.73   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,5.67,5.75,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.878505                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.717599              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.048   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.318477              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.051  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2662      final r-factor (work) = 0.1829          |
| start r-factor (free) = 0.3040      final r-factor (free) = 0.2190          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1542 = 3.72 * 0.50 * 5.9328 + 1.00 * 0.1263                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6716 = 3.72 * 0.50 * 5.7054 + 1.00 * 0.0665                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1829      final r-factor (work) = 0.1657          |
| start r-factor (free) = 0.2190      final r-factor (free) = 0.2041          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9017 = 0.32 * 1.00 * 5.7054 + 1.00 * 0.0847                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9868 = 0.32 * 1.00 * 5.4894 + 1.00 * 0.2385                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.10   11.35    None  None   None       |
|    all(noH): 2823   0      0.00    86.10   11.35    None  None   None       |
|    Sol.    : 438    0      0.00    86.10   32.49    None  None   None       |
|    Mac.    : 2385   0      0.00    65.67   7.47     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 -   8.610: 1750   |   5:    43.051 -  51.661:   82        |
|      1:     8.610 -  17.220:  526   |   6:    51.661 -  60.271:   44        |
|      2:    17.220 -  25.830:  171   |   7:    60.271 -  68.881:    8        |
|      3:    25.830 -  34.441:  119   |   8:    68.881 -  77.491:    0        |
|      4:    34.441 -  43.051:  122   |   9:    77.491 -  86.101:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1657 r_free = 0.2041             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1655 r_free = 0.2044             target_work(ml) = 5.459         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1655   r_free= 0.2044   ksol= 0.33   Bsol= 55.73   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,5.67,5.75,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.459197                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2039   ksol= 0.32   Bsol= 55.73   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.04,4.65,0.00,0.00,0.00); trace/3= 3.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459812                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.442091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 9.096512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.867   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1649      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.2039      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7753 = 2.44 * 0.50 * 5.4942 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6075 = 2.44 * 0.50 * 5.3582 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 48.7624 = 9.10 * 1.00 * 5.3582 + 1.00 * 0.0213                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 47.6544 = 9.10 * 1.00 * 5.2369 + 1.00 * 0.0168                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.62   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    85.62   12.33    None  None   None       |
|    Sol.    : 438    0      0.00    79.69   37.47    None  None   None       |
|    Mac.    : 2385   0      0.00    85.62   7.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.562: 1736   |   5:    42.812 -  51.375:   92        |
|      1:     8.562 -  17.125:  522   |   6:    51.375 -  59.937:   75        |
|      2:    17.125 -  25.687:  146   |   7:    59.937 -  68.499:   41        |
|      3:    25.687 -  34.250:  109   |   8:    68.499 -  77.062:   13        |
|      4:    34.250 -  42.812:   81   |   9:    77.062 -  85.624:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1258 r_free = 0.1690             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1257 r_free = 0.1690             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1690   ksol= 0.32   Bsol= 55.73   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.04,4.65,0.00,0.00,0.00); trace/3= 3.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.233921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1696   ksol= 0.33   Bsol= 64.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.64,4.51,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.445263              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.639  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.852  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4678 = 2.45 * 0.50 * 5.2370 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4324 = 2.45 * 0.50 * 5.2028 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0570 = 0.39 * 1.00 * 5.2028 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1265 = 0.39 * 1.00 * 5.1858 + 1.00 * 0.0978                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.10   11.86    None  None   None       |
|    all(noH): 2823   0      0.00    86.10   11.86    None  None   None       |
|    Sol.    : 438    0      0.57    80.07   35.62    None  None   None       |
|    Mac.    : 2385   0      0.00    86.10   7.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.610: 1774   |   5:    43.050 -  51.660:   80        |
|      1:     8.610 -  17.220:  502   |   6:    51.660 -  60.270:   67        |
|      2:    17.220 -  25.830:  156   |   7:    60.270 -  68.880:   28        |
|      3:    25.830 -  34.440:  100   |   8:    68.880 -  77.490:   12        |
|      4:    34.440 -  43.050:  100   |   9:    77.490 -  86.100:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1614             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1614             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1614   ksol= 0.33   Bsol= 64.18   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.64,4.51,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1614   ksol= 0.33   Bsol= 64.18   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.64,4.51,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.603255              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.598  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625798              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.297   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2277 = 1.60 * 0.50 * 5.1850 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2130 = 1.60 * 0.50 * 5.1830 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2615 = 0.63 * 1.00 * 5.1830 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2571 = 0.63 * 1.00 * 5.1830 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.33   11.74    None  None   None       |
|    all(noH): 2823   0      0.00    87.33   11.74    None  None   None       |
|    Sol.    : 438    0      0.78    80.89   35.19    None  None   None       |
|    Mac.    : 2385   0      0.00    87.33   7.43     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 -   8.733: 1797   |   5:    43.667 -  52.400:   88        |
|      1:     8.733 -  17.467:  478   |   6:    52.400 -  61.134:   53        |
|      2:    17.467 -  26.200:  163   |   7:    61.134 -  69.867:   24        |
|      3:    26.200 -  34.934:  110   |   8:    69.867 -  78.601:   10        |
|      4:    34.934 -  43.667:   96   |   9:    78.601 -  87.334:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1613             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1613             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1613   ksol= 0.33   Bsol= 64.18   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.64,4.51,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184678                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7970 0.99   1375  153 0.1042 0.1328      5.4235       5.538|
|  2:  4.7970 -  3.8280 0.99   1306  146 0.0884 0.1108      5.4636      5.6349|
|  3:  3.8280 -  3.3501 0.99   1293  143 0.1083 0.1494      5.4993      5.8706|
|  4:  3.3501 -  3.0466 0.99   1284  139 0.1245 0.1548      5.4731      5.6115|
|  5:  3.0466 -  2.8298 0.99   1268  144 0.1381 0.1723       5.377      5.5465|
|  6:  2.8298 -  2.6639 0.99   1276  141 0.1296 0.2043      5.2649      5.5556|
|  7:  2.6639 -  2.5311 0.99   1266  140 0.1339 0.1714      5.2198      5.3885|
|  8:  2.5311 -  2.4214 0.98   1250  139 0.1256 0.1776      5.1432      5.4068|
|  9:  2.4214 -  2.3285 0.98   1253  143 0.1234 0.1889      5.0867      5.3279|
| 10:  2.3285 -  2.2485 0.99   1245  136 0.1238 0.1783      5.0411      5.2769|
| 11:  2.2485 -  2.1784 0.98   1256  137 0.1217 0.1745      4.9815      5.2381|
| 12:  2.1784 -  2.1163 0.97   1237  142 0.1197 0.1742      4.9332      5.2585|
| 13:  2.1163 -  2.0607 1.00   1250  136 0.1201 0.1775      4.8354      5.0929|
| 14:  2.0607 -  2.0105 0.85   1071  120 0.1111 0.1822       4.714      4.9902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7970  1375   153  0.94   9.58   0.97     0.94       7824.60|
|  2:  4.7970 -  3.8280  1306   146  0.95   8.08   1.00     0.98       9259.52|
|  3:  3.8280 -  3.3501  1293   143  0.93  11.16   1.01     1.01      10598.91|
|  4:  3.3501 -  3.0466  1284   139  0.92  13.34   1.00     0.98      10230.07|
|  5:  3.0466 -  2.8298  1268   144  0.90  16.25   0.99     0.97       8955.10|
|  6:  2.8298 -  2.6639  1276   141  0.90  16.54   0.98     0.95       7693.99|
|  7:  2.6639 -  2.5311  1266   140  0.90  16.27   0.98     0.96       6770.52|
|  8:  2.5311 -  2.4214  1250   139  0.90  15.74   0.98     0.95       5979.76|
|  9:  2.4214 -  2.3285  1253   143  0.90  16.42   1.00     0.97       5617.24|
| 10:  2.3285 -  2.2485  1245   136  0.89  16.85   0.99     0.94       4975.63|
| 11:  2.2485 -  2.1784  1256   137  0.90  16.20   0.98     0.94       4554.24|
| 12:  2.1784 -  2.1163  1237   142  0.91  15.78   1.00     0.99       4252.48|
| 13:  2.1163 -  2.0607  1250   136  0.90  15.94   0.98     0.96       3533.01|
| 14:  2.0607 -  2.0105  1071   120  0.91  15.40   0.96     0.91       2717.59|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2717.59 max =        10598.91 mean =      6718.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.42 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1613   ksol= 0.32   Bsol= 60.30   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.05,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1613   ksol= 0.32   Bsol= 60.30   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.05,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184551                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7970 0.99   1375  153 0.1038 0.1329      5.4191      5.5348|
|  2:  4.7970 -  3.8280 0.99   1306  146 0.0879 0.1100      5.4594      5.6289|
|  3:  3.8280 -  3.3501 0.99   1293  143 0.1081 0.1492      5.4974      5.8707|
|  4:  3.3501 -  3.0466 0.99   1284  139 0.1247 0.1550      5.4744      5.6124|
|  5:  3.0466 -  2.8298 0.99   1268  144 0.1384 0.1727      5.3795      5.5488|
|  6:  2.8298 -  2.6639 0.99   1276  141 0.1298 0.2047      5.2668      5.5576|
|  7:  2.6639 -  2.5311 0.99   1266  140 0.1341 0.1716      5.2213      5.3901|
|  8:  2.5311 -  2.4214 0.98   1250  139 0.1257 0.1777      5.1439      5.4071|
|  9:  2.4214 -  2.3285 0.98   1253  143 0.1234 0.1888      5.0871      5.3279|
| 10:  2.3285 -  2.2485 0.99   1245  136 0.1238 0.1783      5.0413      5.2775|
| 11:  2.2485 -  2.1784 0.98   1256  137 0.1218 0.1744      4.9818      5.2379|
| 12:  2.1784 -  2.1163 0.97   1237  142 0.1197 0.1742      4.9333      5.2585|
| 13:  2.1163 -  2.0607 1.00   1250  136 0.1201 0.1775      4.8355       5.093|
| 14:  2.0607 -  2.0105 0.85   1071  120 0.1112 0.1822      4.7143      4.9904|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7970  1375   153  0.94   9.55   0.97     0.94       7764.95|
|  2:  4.7970 -  3.8280  1306   146  0.95   8.02   1.00     0.99       9188.23|
|  3:  3.8280 -  3.3501  1293   143  0.93  11.12   1.02     1.01      10542.33|
|  4:  3.3501 -  3.0466  1284   139  0.92  13.36   1.00     0.98      10254.92|
|  5:  3.0466 -  2.8298  1268   144  0.90  16.29   0.99     0.97       8999.88|
|  6:  2.8298 -  2.6639  1276   141  0.90  16.60   0.98     0.95       7729.27|
|  7:  2.6639 -  2.5311  1266   140  0.90  16.30   0.98     0.96       6792.28|
|  8:  2.5311 -  2.4214  1250   139  0.90  15.76   0.98     0.95       5988.97|
|  9:  2.4214 -  2.3285  1253   143  0.90  16.43   1.00     0.97       5621.50|
| 10:  2.3285 -  2.2485  1245   136  0.89  16.85   0.99     0.94       4977.50|
| 11:  2.2485 -  2.1784  1256   137  0.90  16.20   0.98     0.94       4555.52|
| 12:  2.1784 -  2.1163  1237   142  0.91  15.78   1.00     0.99       4253.62|
| 13:  2.1163 -  2.0607  1250   136  0.90  15.94   0.98     0.96       3533.99|
| 14:  2.0607 -  2.0105  1071   120  0.91  15.41   0.96     0.91       2718.98|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2718.98 max =        10542.33 mean =      6715.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.40 mean =        13.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.197)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.69    91.02   15.43    None  None   None       |
|    all(noH): 2823   0      3.69    91.02   15.43    None  None   None       |
|    Sol.    : 438    0      4.47    84.58   38.88    None  None   None       |
|    Mac.    : 2385   0      3.69    91.02   11.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.690 -  12.423: 1797   |   5:    47.357 -  56.090:   88        |
|      1:    12.423 -  21.157:  478   |   6:    56.090 -  64.824:   53        |
|      2:    21.157 -  29.890:  163   |   7:    64.824 -  73.557:   24        |
|      3:    29.890 -  38.624:  110   |   8:    73.557 -  82.291:   10        |
|      4:    38.624 -  47.357:   96   |   9:    82.291 -  91.024:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.284 - 4.567
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 337
   mapped sites are within: 0.708 - 4.567

peak=   10.265 closest distance to " CG2 VAL A 230 " =    1.460
peak=    5.990 closest distance to " CG  LEU A   5 " =    1.222
peak=    5.950 closest distance to " NH2 ARG A  56 " =    2.299
peak=    5.883 closest distance to " CB  GLN A 223 " =    1.444
peak=    5.606 closest distance to " CG2 VAL A 296 " =    1.045
peak=    5.470 closest distance to " CG  PRO A  54 " =    1.346
peak=    5.398 closest distance to " CG  LEU A 228 " =    1.233
peak=    5.215 closest distance to " CB  VAL A 296 " =    1.100
peak=    5.201 closest distance to " CD2 LEU A   5 " =    1.151
peak=    5.188 closest distance to " CG  PRO A 198 " =    1.282
peak=    5.187 closest distance to " CB  PRO A  54 " =    0.997
peak=    5.107 closest distance to " CG1 VAL A 296 " =    1.152
peak=    4.776 closest distance to " CZ  PHE A 218 " =    1.107
peak=    4.705 closest distance to " CB  GLN A 183 " =    1.281
peak=    4.680 closest distance to " O   HOH Z 232 " =    2.303
peak=    4.612 closest distance to " CB  VAL A 230 " =    1.251
peak=    4.523 closest distance to " O   HOH Z 265 " =    2.233
peak=    4.501 closest distance to " CB  SER A  63 " =    1.265
peak=    4.485 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.467 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.413 closest distance to " CB  ARG A 190 " =    1.600
peak=    4.355 closest distance to " CG  PRO A 243 " =    1.154
peak=    4.341 closest distance to " NE2 GLN A  11 " =    1.086
peak=    4.322 closest distance to " C   PRO A 198 " =    1.556
peak=    4.308 closest distance to " O   HOH Z 298 " =    1.883
peak=    4.287 closest distance to " CB  GLU A 128 " =    1.040
peak=    4.249 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.244 closest distance to " CB  TYR A 169 " =    0.723
peak=    4.229 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.191 closest distance to " O   HOH Z 234 " =    3.746
peak=    4.175 closest distance to " O   HOH Z 189 " =    2.998
peak=    4.150 closest distance to " O   SER A  87 " =    2.305
peak=    4.146 closest distance to " CB  ASN A 148 " =    1.352
peak=    4.145 closest distance to " O   HOH Z 402 " =    1.497
peak=    4.125 closest distance to " O   HOH Z 272 " =    1.930
peak=    4.113 closest distance to " CB  TRP A 266 " =    0.996
peak=    4.112 closest distance to " O   HOH Z  43 " =    2.027
peak=    4.108 closest distance to " CB  ASP A 140 " =    1.008
peak=    4.099 closest distance to " O   HOH Z 236 " =    1.948
peak=    4.095 closest distance to " O   HOH Z 248 " =    1.512
peak=    4.078 closest distance to " CD2 LEU A 228 " =    1.319
peak=    4.059 closest distance to " CB  ARG A  79 " =    1.405
peak=    4.057 closest distance to " CA  ALA A  51 " =    0.966
peak=    4.054 closest distance to " O   HOH Z 142 " =    1.641
peak=    4.040 closest distance to " CD  LYS A 166 " =    1.317
peak=    4.039 closest distance to " CB  ASN A  39 " =    0.881
peak=    4.034 closest distance to " ND2 ASN A 187 " =    1.529
peak=    4.033 closest distance to " O   HOH Z 126 " =    1.905
peak=    4.006 closest distance to " O   HOH Z  63 " =    1.915
peak=    4.002 closest distance to " O   HOH Z 368 " =    2.346
peak=    3.986 closest distance to " CA  ARG A 195 " =    1.207
peak=    3.976 closest distance to " N   ASN A  39 " =    1.224
peak=    3.973 closest distance to " O   HOH Z  78 " =    1.623
peak=    3.967 closest distance to " O   HOH Z 427 " =    3.053
peak=    3.964 closest distance to " CD1 LEU A  96 " =    0.742
peak=    3.964 closest distance to " OG BSER A 164 " =    2.246
peak=    3.960 closest distance to " O   HOH Z 423 " =    1.777
peak=    3.952 closest distance to " CB  GLU A 277 " =    3.713
peak=    3.947 closest distance to " O   HOH Z 346 " =    1.570
peak=    3.939 closest distance to " O   HOH Z 126 " =    1.611
peak=    3.938 closest distance to " CB  VAL A 265 " =    1.276
peak=    3.937 closest distance to " CB  ASP A 124 " =    0.739
peak=    3.927 closest distance to " O   HOH Z  61 " =    1.679
peak=    3.922 closest distance to " CG1 VAL A 153 " =    0.996
peak=    3.921 closest distance to " O   HOH Z 303 " =    2.179
peak=    3.916 closest distance to " ND2 ASN A 249 " =    1.920
peak=    3.910 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.909 closest distance to " CB  GLU A  46 " =    0.996
peak=    3.896 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.887 closest distance to " O   HOH Z 411 " =    3.756
peak=    3.870 closest distance to " O   HOH Z 403 " =    1.671
peak=    3.860 closest distance to " O   HOH Z  48 " =    1.735
peak=    3.856 closest distance to " CB  GLU A 152 " =    1.159
peak=    3.844 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.842 closest distance to " O   HOH Z 316 " =    3.093
peak=    3.841 closest distance to " O   HOH Z 280 " =    2.922
peak=    3.839 closest distance to " CB  ASN A 142 " =    1.098
peak=    3.837 closest distance to " O   HOH Z  80 " =    1.803
peak=    3.832 closest distance to " OD1 ASN A  69 " =    2.610
peak=    3.816 closest distance to " O   HOH Z 158 " =    3.133
peak=    3.792 closest distance to " O   HOH Z 102 " =    1.344
peak=    3.792 closest distance to " CG2 VAL A 257 " =    0.894
peak=    3.786 closest distance to " O   HOH Z  44 " =    2.148
peak=    3.782 closest distance to " CB BVAL A  41 " =    1.022
peak=    3.780 closest distance to " O   HOH Z 130 " =    2.720
peak=    3.762 closest distance to " NH1AARG A 145 " =    1.255
peak=    3.750 closest distance to " CG  MET A 185 " =    1.212
peak=    3.749 closest distance to " O   HOH Z 214 " =    2.386
peak=    3.744 closest distance to " O   HOH Z 425 " =    1.376
peak=    3.743 closest distance to " O   HOH Z  40 " =    1.806
peak=    3.730 closest distance to " O   HOH Z 313 " =    1.759
peak=    3.722 closest distance to " CB  LEU A 143 " =    1.211
peak=    3.721 closest distance to " O   HOH Z 285 " =    2.740
peak=    3.717 closest distance to " O   HOH Z 261 " =    1.727
peak=    3.716 closest distance to " CZ  PHE A 192 " =    0.974
peak=    3.711 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.707 closest distance to " O   HOH Z  97 " =    2.044
peak=    3.707 closest distance to " CA  ALA A 295 " =    1.086
peak=    3.700 closest distance to " CA  ARG A  36 " =    1.086
peak=    3.694 closest distance to " NH2 ARG A 156 " =    1.124
peak=    3.685 closest distance to " O   HOH Z 251 " =    1.475
peak=    3.668 closest distance to " O   HOH Z 246 " =    1.508
peak=    3.668 closest distance to " NE2 GLN A  77 " =    3.345
peak=    3.662 closest distance to " O   HOH Z 172 " =    3.878
peak=    3.638 closest distance to " CB  ASN A 187 " =    1.259
peak=    3.636 closest distance to " CE1 TYR A 186 " =    1.307
peak=    3.625 closest distance to " CA  VAL A  41 " =    0.772
peak=    3.623 closest distance to " CD  ARG A 159 " =    0.751
peak=    3.620 closest distance to " CD BLYS A 290 " =    1.034
peak=    3.619 closest distance to " CE  LYS A  76 " =    0.840
peak=    3.617 closest distance to " CA  SER A  87 " =    1.063
peak=    3.611 closest distance to " CG1BVAL A  72 " =    1.818
peak=    3.609 closest distance to " O   HOH Z 238 " =    2.313
peak=    3.597 closest distance to " C   ILE A 106 " =    1.897
peak=    3.593 closest distance to " O   HOH Z 273 " =    2.886
peak=    3.591 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.591 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.588 closest distance to " CZ  PHE A  38 " =    1.171
peak=    3.580 closest distance to " CG1 ILE A  49 " =    1.600
peak=    3.579 closest distance to " CB  GLN A  89 " =    1.203
peak=    3.578 closest distance to " CB  SER A   3 " =    1.260
peak=    3.567 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.566 closest distance to " CB  TRP A 179 " =    1.475
peak=    3.564 closest distance to " CB  MET A  40 " =    0.755
peak=    3.560 closest distance to " O   HOH Z 203 " =    1.799
peak=    3.556 closest distance to " O   ASP A 124 " =    1.117
peak=    3.551 closest distance to " O   HOH Z 359 " =    1.421
peak=    3.548 closest distance to " O   HOH Z 187 " =    2.379
peak=    3.547 closest distance to " NZ  LYS A 117 " =    3.185
peak=    3.547 closest distance to " CG2 THR A 221 " =    1.091
peak=    3.545 closest distance to " C   TYR A 214 " =    1.587
peak=    3.543 closest distance to " CB  ALA A 104 " =    0.713
peak=    3.533 closest distance to " CD2 LEU A 297 " =    0.895
peak=    3.533 closest distance to " CA  THR A 264 " =    0.727
peak=    3.532 closest distance to " O   HOH Z 437 " =    1.794
peak=    3.524 closest distance to " O   HOH Z  68 " =    2.026
peak=    3.523 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.521 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.521 closest distance to " O   HOH Z 371 " =    2.954
peak=    3.520 closest distance to " CA  ASN A 215 " =    1.182
peak=    3.520 closest distance to " CB  ALA A 291 " =    1.273
peak=    3.519 closest distance to " CA  VAL A 125 " =    1.294
peak=    3.519 closest distance to " CG  LEU A 167 " =    1.135
peak=    3.517 closest distance to " CA  ASP A 191 " =    1.134
peak=    3.513 closest distance to " O   HOH Z  19 " =    2.017
peak=    3.509 closest distance to " CG  PHE A 204 " =    0.948
peak=    3.504 closest distance to " CD1 LEU A   5 " =    1.385
peak=    3.494 closest distance to " O   HOH Z  63 " =    1.361
peak=    3.492 closest distance to " O   HOH Z   9 " =    2.166
peak=    3.490 closest distance to " CB  MET A  47 " =    1.041
peak=    3.476 closest distance to " O   HOH Z 383 " =    2.058
peak=    3.475 closest distance to " O   HOH Z 368 " =    3.515
peak=    3.473 closest distance to " O   HOH Z 227 " =    1.650
peak=    3.469 closest distance to " CA  LYS A 117 " =    1.284
peak=    3.467 closest distance to " O   HOH Z 261 " =    1.768
peak=    3.456 closest distance to " CB  SER A 273 " =    0.912
peak=    3.447 closest distance to " O   HOH Z 128 " =    2.338
peak=    3.446 closest distance to " O   HOH Z  59 " =    2.268
peak=    3.444 closest distance to " CG1 ILE A  33 " =    1.302
peak=    3.444 closest distance to " CG  MET A 185 " =    1.008
peak=    3.443 closest distance to " CA  ILE A 106 " =    0.754
peak=    3.442 closest distance to " CB  ALA A 242 " =    0.834
peak=    3.441 closest distance to " O   HOH Z 171 " =    3.886
peak=    3.441 closest distance to " CB  ALA A 248 " =    1.412
peak=    3.438 closest distance to " CB  LEU A 228 " =    1.240
peak=    3.438 closest distance to " O   HOH Z 258 " =    2.121
peak=    3.438 closest distance to " CA  THR A 221 " =    0.842
peak=    3.436 closest distance to " O   HOH Z 193 " =    1.733
peak=    3.431 closest distance to " CA  ALA A 291 " =    0.849
peak=    3.430 closest distance to " O   HOH Z 193 " =    2.136
peak=    3.427 closest distance to " CZ3 TRP A 274 " =    4.567
peak=    3.426 closest distance to " N   SER A 135 " =    1.475
peak=    3.425 closest distance to " O   HOH Z 353 " =    2.630
peak=    3.425 closest distance to " O   TRP A 274 " =    1.837
peak=    3.422 closest distance to " CG AARG A 275 " =    1.189
peak=    3.421 closest distance to " CB  PRO A 243 " =    1.403
peak=    3.416 closest distance to " O   HOH Z 294 " =    1.596
peak=    3.410 closest distance to " O   GLN A 278 " =    1.309
peak=    3.410 closest distance to " CB  THR A  31 " =    1.605
peak=    3.405 closest distance to " O   HOH Z 128 " =    1.500
peak=    3.401 closest distance to " CB  TRP A 150 " =    1.412
peak=    3.398 closest distance to " O   ASN A  74 " =    1.600
peak=    3.394 closest distance to " O   ALA A 165 " =    1.425
peak=    3.393 closest distance to " CD2 LEU A   5 " =    0.708
peak=    3.392 closest distance to " O   THR A 220 " =    1.216
peak=    3.390 closest distance to " CA  LYS A 181 " =    1.042
peak=    3.387 closest distance to " CA  LEU A 282 " =    1.055
peak=    3.382 closest distance to " CB  LEU A  83 " =    0.722
peak=    3.377 closest distance to " CA  ASP A 191 " =    0.758
peak=    3.377 closest distance to " O   HOH Z  88 " =    3.059
peak=    3.373 closest distance to " CG2 ILE A  49 " =    1.473
peak=    3.372 closest distance to " O   HOH Z 133 " =    2.434
peak=    3.370 closest distance to " O   HOH Z 403 " =    1.434
peak=    3.367 closest distance to " O   HOH Z 147 " =    1.819
peak=    3.367 closest distance to " CA  MET A 105 " =    0.988
peak=    3.366 closest distance to " O   HOH Z 406 " =    1.537
peak=    3.359 closest distance to " O   HOH Z  97 " =    2.379
peak=    3.358 closest distance to " CA  ALA A 160 " =    0.917
peak=    3.357 closest distance to " CZ3 TRP A  85 " =    1.023
peak=    3.352 closest distance to " O   HOH Z 325 " =    2.246
peak=    3.351 closest distance to " O   GLN A  88 " =    1.646
peak=    3.350 closest distance to " CB  ASN A 110 " =    1.187
peak=    3.349 closest distance to " CB  SER A  26 " =    1.784
peak=    3.346 closest distance to " CA  ASP A 162 " =    1.060
peak=    3.346 closest distance to " CA  ALA A 158 " =    1.256
peak=    3.344 closest distance to " CB  TYR A 247 " =    1.042
peak=    3.343 closest distance to " O   HOH Z 344 " =    2.974
peak=    3.339 closest distance to " CB  HIS A 108 " =    0.762
peak=    3.333 closest distance to " O   HOH Z 245 " =    1.362
peak=    3.331 closest distance to " CA  GLY A 211 " =    1.362
peak=    3.329 closest distance to " CB  SER A  28 " =    1.218
peak=    3.327 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.326 closest distance to " O   HOH Z 145 " =    2.165
peak=    3.326 closest distance to " O   HOH Z 180 " =    2.154
peak=    3.322 closest distance to " O   HOH Z 134 " =    1.329
peak=    3.321 closest distance to " CA  TYR A 116 " =    1.500
peak=    3.321 closest distance to " CA  ALA A 154 " =    0.989
peak=    3.318 closest distance to " CG  LEU A 281 " =    1.095
peak=    3.318 closest distance to " O   HOH Z 435 " =    2.070
peak=    3.317 closest distance to " CG2 ILE A 263 " =    0.927
peak=    3.315 closest distance to " CG2 THR A 220 " =    0.867
peak=    3.309 closest distance to " CB  ALA A 100 " =    1.281
peak=    3.306 closest distance to " CB  THR A  52 " =    0.953
peak=    3.302 closest distance to " O   HOH Z 112 " =    1.641
peak=    3.301 closest distance to " CB  GLN A  88 " =    1.210
peak=    3.301 closest distance to " O  BHOH Z  74 " =    1.270
peak=    3.300 closest distance to " O   HOH Z 417 " =    2.759
peak=    3.293 closest distance to " CB  SER A 212 " =    1.279
peak=    3.288 closest distance to " OG1 THR A 294 " =    2.404
peak=    3.283 closest distance to " CG1 ILE A 151 " =    1.076
peak=    3.283 closest distance to " O   HOH Z 291 " =    1.544
peak=    3.282 closest distance to " NH1 ARG A  14 " =    1.000
peak=    3.278 closest distance to " O   HOH Z 163 " =    1.591
peak=    3.272 closest distance to " CE1 HIS A 108 " =    1.190
peak=    3.270 closest distance to " CA  ASP A 140 " =    1.299
peak=    3.267 closest distance to " N   VAL A 126 " =    1.341
peak=    3.267 closest distance to " NZ  LYS A  48 " =    1.298
peak=    3.266 closest distance to " O   HOH Z 290 " =    1.103
peak=    3.265 closest distance to " O   HOH Z 130 " =    2.252
peak=    3.265 closest distance to " CG  GLU A  37 " =    0.842
peak=    3.264 closest distance to " O   HOH Z 126 " =    1.797
peak=    3.262 closest distance to " CB  GLN A 103 " =    1.020
peak=    3.260 closest distance to " CB  ILE A 120 " =    1.287
peak=    3.258 closest distance to " CG BARG A 102 " =    1.834
peak=    3.257 closest distance to " O   HOH Z 295 " =    1.489
peak=    3.256 closest distance to " O   HOH Z 271 " =    2.453
peak=    3.255 closest distance to " CA  ASN A 217 " =    1.233
peak=    3.252 closest distance to " OG  SER A 245 " =    1.610
peak=    3.251 closest distance to " C   ALA A 299 " =    0.925
peak=    3.250 closest distance to " CD1 LEU A 222 " =    0.723
peak=    3.246 closest distance to " CB  SER A 210 " =    0.889
peak=    3.244 closest distance to " CB  PRO A 198 " =    1.022
peak=    3.242 closest distance to " CA  PHE A 283 " =    1.082
peak=    3.241 closest distance to " OG1 THR A 157 " =    1.189
peak=    3.239 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.238 closest distance to " ND1 HIS A  81 " =    1.623
peak=    3.237 closest distance to " CB  GLN A 205 " =    1.061
peak=    3.236 closest distance to " O   HOH Z 201 " =    2.998
peak=    3.236 closest distance to " CB  ASN A 173 " =    1.076
peak=    3.235 closest distance to " O   HOH Z 407 " =    2.534
peak=    3.234 closest distance to " CD1 ILE A 199 " =    0.833
peak=    3.229 closest distance to " O   HOH Z 329 " =    4.018
peak=    3.227 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.223 closest distance to " O   HOH Z 197 " =    2.892
peak=    3.222 closest distance to " N   ARG A 190 " =    1.046
peak=    3.221 closest distance to " O   HOH Z 357 " =    2.046
peak=    3.219 closest distance to " O   HOH Z 327 " =    2.478
peak=    3.218 closest distance to " O   HOH Z 250 " =    1.336
peak=    3.217 closest distance to " O  BHOH Z 338 " =    2.433
peak=    3.216 closest distance to " O   HOH Z 250 " =    1.378
peak=    3.213 closest distance to " N   PHE A 130 " =    1.242
peak=    3.206 closest distance to " CE2 TYR A  30 " =    0.708
peak=    3.205 closest distance to " CB  ARG A 139 " =    0.838
peak=    3.200 closest distance to " O   ALA A 158 " =    1.356
peak=    3.197 closest distance to " CG2 ILE A  20 " =    1.435
peak=    3.194 closest distance to " NE2 HIS A 207 " =    1.205
peak=    3.191 closest distance to " CA  GLU A 128 " =    1.314
peak=    3.190 closest distance to " O   HOH Z 130 " =    1.039
peak=    3.189 closest distance to " O   HOH Z 365 " =    2.922
peak=    3.180 closest distance to " CG  ARG A 138 " =    1.215
peak=    3.179 closest distance to " O   HOH Z 141 " =    1.629
peak=    3.179 closest distance to " O   ASN A  74 " =    2.108
peak=    3.178 closest distance to " O   PHE A  61 " =    1.328
peak=    3.178 closest distance to " CB  ASN A 215 " =    1.185
peak=    3.175 closest distance to " CB  ALA A 137 " =    1.064
peak=    3.173 closest distance to " CG2 VAL A 197 " =    1.110
peak=    3.173 closest distance to " O   HOH Z 234 " =    1.825
peak=    3.172 closest distance to " CB  ALA A 114 " =    1.063
peak=    3.168 closest distance to " CD  ARG A  66 " =    2.465
peak=    3.168 closest distance to " CG  GLN A 205 " =    0.841
peak=    3.167 closest distance to " OD1 ASN A 217 " =    1.595
peak=    3.166 closest distance to " OG BSER A 134 " =    2.736
peak=    3.163 closest distance to " CG  GLN A  58 " =    2.868
peak=    3.162 closest distance to " O   HOH Z 305 " =    3.796
peak=    3.160 closest distance to " CB  LEU A  96 " =    1.263
peak=    3.159 closest distance to " N   ASP A 162 " =    1.285
peak=    3.153 closest distance to " CB  SER A 216 " =    0.800
peak=    3.153 closest distance to " CB  SER A  62 " =    0.836
peak=    3.151 closest distance to " O   HOH Z 313 " =    1.656
peak=    3.151 closest distance to " O   HOH Z 109 " =    2.664
peak=    3.150 closest distance to " O   ASP A 200 " =    1.664
peak=    3.147 closest distance to " O   HOH Z 148 " =    3.246
peak=    3.147 closest distance to " OG  SER A  22 " =    2.810
peak=    3.145 closest distance to " O   HOH Z 124 " =    1.998
peak=    3.138 closest distance to " OH  TYR A  30 " =    1.163
peak=    3.122 closest distance to " O   HOH Z 302 " =    1.951
peak=    3.122 closest distance to " CA  ALA A 233 " =    1.553
peak=    3.121 closest distance to " O   HOH Z 391 " =    2.951
peak=    3.120 closest distance to " O   HOH Z 216 " =    3.137
peak=    3.120 closest distance to " CB  VAL A 268 " =    0.820
peak=    3.119 closest distance to " O   HOH Z 380 " =    1.816
peak=    3.116 closest distance to " O   HOH Z 172 " =    3.335
peak=    3.113 closest distance to " O   HOH Z 293 " =    1.847
peak=    3.100 closest distance to " O   ALA A 292 " =    1.601
peak=    3.098 closest distance to " O   HOH Z 426 " =    1.495
peak=    3.096 closest distance to " CA  GLN A  88 " =    1.304
peak=    3.089 closest distance to " O   HOH Z 256 " =    2.323
peak=    3.070 closest distance to " O   HOH Z 263 " =    1.651
peak=    3.062 closest distance to " O   THR A  31 " =    1.618
peak=    3.059 closest distance to " CB  ALA A 227 " =    1.041
peak=    3.058 closest distance to " CA  LYS A 290 " =    1.111
peak=    3.058 closest distance to " CB  TYR A 116 " =    0.840
peak=    3.051 closest distance to " CB  PHE A 204 " =    0.948
peak=    3.049 closest distance to " CG2 ILE A 234 " =    0.817
peak=    3.034 closest distance to " CB  ALA A  43 " =    0.875
peak=    3.025 closest distance to " CA  ASN A 176 " =    1.130
peak=    3.014 closest distance to " N   ILE A  20 " =    2.211
peak=    3.004 closest distance to " N   GLY A 133 " =    3.729

                           ----------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: 0.789 - 5.542
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.789 - 5.542

peak=   -5.206 closest distance to " CG2 VAL A 230 " =    0.794
peak=   -4.594 closest distance to " CD  GLN A  58 " =    1.067
peak=   -4.514 closest distance to " CG1 VAL A 296 " =    1.129
peak=   -4.304 closest distance to " CD  ARG A 156 " =    2.037
peak=   -4.268 closest distance to " CD  ARG A  14 " =    3.377
peak=   -4.256 closest distance to " CB  PRO A 243 " =    2.692
peak=   -4.222 closest distance to " O   HOH Z 266 " =    5.385
peak=   -4.186 closest distance to " O   HOH Z 166 " =    1.748
peak=   -4.131 closest distance to " O   HOH Z 196 " =    2.293
peak=   -4.100 closest distance to " O   HOH Z 351 " =    1.534
peak=   -4.090 closest distance to " C   HIS A 108 " =    1.116
peak=   -4.087 closest distance to " CE2 TYR A  30 " =    2.731
peak=   -4.081 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.998 closest distance to " O   VAL A  67 " =    2.689
peak=   -3.968 closest distance to " OG  SER A  97 " =    2.334
peak=   -3.950 closest distance to " CB  PHE A 192 " =    1.989
peak=   -3.938 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.928 closest distance to " O   ILE A 109 " =    2.614
peak=   -3.894 closest distance to " CG1 VAL A 112 " =    2.662
peak=   -3.869 closest distance to " O   HOH Z 114 " =    3.110
peak=   -3.863 closest distance to " OXT GLY A 302 " =    2.932
peak=   -3.860 closest distance to " CE3 TRP A 150 " =    2.230
peak=   -3.856 closest distance to " OE1 GLN A 223 " =    2.217
peak=   -3.853 closest distance to " O   HOH Z 231 " =    2.187
peak=   -3.840 closest distance to " CG1 VAL A 250 " =    2.773
peak=   -3.833 closest distance to " O   HOH Z  52 " =    1.736
peak=   -3.829 closest distance to " O   HOH Z 394 " =    1.540
peak=   -3.793 closest distance to " O   HOH Z 128 " =    2.664
peak=   -3.785 closest distance to " O   HOH Z  37 " =    1.903
peak=   -3.765 closest distance to " CG1 VAL A 112 " =    2.817
peak=   -3.761 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -3.749 closest distance to " O   HOH Z 290 " =    1.192
peak=   -3.748 closest distance to " O   SER A 271 " =    2.168
peak=   -3.737 closest distance to " C   ALA A 158 " =    1.313
peak=   -3.733 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.732 closest distance to " N   ALA A 226 " =    2.083
peak=   -3.723 closest distance to " N   ALA A  43 " =    2.585
peak=   -3.696 closest distance to " CG  ARG A 269 " =    2.452
peak=   -3.694 closest distance to " CG2 ILE A  49 " =    2.832
peak=   -3.686 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.685 closest distance to " O   HOH Z 283 " =    2.275
peak=   -3.681 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.678 closest distance to " CA  VAL A  67 " =    2.879
peak=   -3.666 closest distance to " NH2AARG A 275 " =    5.124
peak=   -3.665 closest distance to " OG BSER A 134 " =    1.215
peak=   -3.661 closest distance to " OD1 ASN A 148 " =    1.403
peak=   -3.638 closest distance to " CD1 LEU A 101 " =    2.432
peak=   -3.638 closest distance to " CG  GLU A 277 " =    1.109
peak=   -3.634 closest distance to " O   PRO A 163 " =    2.202
peak=   -3.620 closest distance to " CB  ALA A 248 " =    2.359
peak=   -3.609 closest distance to " O   HOH Z  10 " =    1.525
peak=   -3.605 closest distance to " O   HOH Z 222 " =    1.539
peak=   -3.595 closest distance to " CA  GLY A 241 " =    3.145
peak=   -3.593 closest distance to " CB  ALA A 248 " =    2.102
peak=   -3.589 closest distance to " NE2 GLN A 103 " =    1.859
peak=   -3.562 closest distance to " C   LEU A 143 " =    1.089
peak=   -3.543 closest distance to " CE BMET A  47 " =    1.968
peak=   -3.539 closest distance to " CD2 PHE A  61 " =    2.563
peak=   -3.533 closest distance to " NE2 GLN A  88 " =    2.058
peak=   -3.522 closest distance to " O   HOH Z  44 " =    2.247
peak=   -3.518 closest distance to " N   THR A  18 " =    1.314
peak=   -3.512 closest distance to " O   VAL A 189 " =    2.571
peak=   -3.511 closest distance to " O   HOH Z 177 " =    1.793
peak=   -3.508 closest distance to " CA  GLY A 241 " =    2.375
peak=   -3.507 closest distance to " O   HOH Z 113 " =    2.370
peak=   -3.486 closest distance to " O   HOH Z 102 " =    1.649
peak=   -3.481 closest distance to " CD2 LEU A 167 " =    1.813
peak=   -3.477 closest distance to " CG1 VAL A 265 " =    2.441
peak=   -3.473 closest distance to " O   HOH Z 292 " =    4.600
peak=   -3.466 closest distance to " O   HOH Z  11 " =    1.910
peak=   -3.462 closest distance to " CZ  TYR A 169 " =    1.735
peak=   -3.459 closest distance to " ND2 ASN A  45 " =    1.749
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.218
peak=   -3.450 closest distance to " O   HOH Z 435 " =    2.679
peak=   -3.447 closest distance to " O   HOH Z 252 " =    4.003
peak=   -3.446 closest distance to " CG  TRP A 266 " =    1.882
peak=   -3.440 closest distance to " NE2 GLN A  88 " =    1.015
peak=   -3.432 closest distance to " ND2 ASN A 187 " =    1.702
peak=   -3.431 closest distance to " CB  ALA A 114 " =    2.561
peak=   -3.429 closest distance to " O   HOH Z 211 " =    1.461
peak=   -3.428 closest distance to " N   ASP A 171 " =    2.404
peak=   -3.421 closest distance to " CD2 LEU A 300 " =    2.742
peak=   -3.419 closest distance to " O   HOH Z 136 " =    2.466
peak=   -3.417 closest distance to " CE2 PHE A 218 " =    2.621
peak=   -3.417 closest distance to " NE2 GLN A 194 " =    1.874
peak=   -3.414 closest distance to " O   HOH Z 165 " =    1.873
peak=   -3.411 closest distance to " C   MET A 188 " =    1.424
peak=   -3.411 closest distance to " CD1 PHE A  59 " =    1.999
peak=   -3.408 closest distance to " N   SER A 212 " =    1.939
peak=   -3.405 closest distance to " C   ASN A 285 " =    2.387
peak=   -3.397 closest distance to " CG2 VAL A 296 " =    1.156
peak=   -3.396 closest distance to " O   HOH Z  19 " =    2.275
peak=   -3.389 closest distance to " O   HOH Z 241 " =    1.278
peak=   -3.382 closest distance to " O   HOH Z  38 " =    1.577
peak=   -3.378 closest distance to " O   HOH Z 377 " =    2.059
peak=   -3.378 closest distance to " O   HOH Z 407 " =    3.153
peak=   -3.375 closest distance to " CB  ALA A  10 " =    2.259
peak=   -3.373 closest distance to " CG  ASP A 132 " =    2.370
peak=   -3.358 closest distance to " CE  MET A 105 " =    2.157
peak=   -3.357 closest distance to " N   ASN A  60 " =    1.300
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    1.578
peak=   -3.336 closest distance to " O   HOH Z 251 " =    4.926
peak=   -3.331 closest distance to " O   HOH Z 411 " =    1.663
peak=   -3.330 closest distance to " O   HOH Z 113 " =    2.022
peak=   -3.323 closest distance to " O   HOH Z  60 " =    1.936
peak=   -3.323 closest distance to " CG1 VAL A 125 " =    1.985
peak=   -3.319 closest distance to " CB  ASP A 171 " =    2.322
peak=   -3.316 closest distance to " CA  ASN A 127 " =    1.072
peak=   -3.315 closest distance to " CG1 VAL A 112 " =    2.904
peak=   -3.313 closest distance to " O   HOH Z 353 " =    2.095
peak=   -3.312 closest distance to " NH2 ARG A 159 " =    2.306
peak=   -3.309 closest distance to " CG  LEU A   5 " =    1.637
peak=   -3.297 closest distance to " O   HOH Z 377 " =    1.425
peak=   -3.296 closest distance to " O   HOH Z 150 " =    2.322
peak=   -3.296 closest distance to " OD1 ASN A 249 " =    2.352
peak=   -3.293 closest distance to " O   HOH Z 231 " =    1.851
peak=   -3.292 closest distance to " O   HOH Z 389 " =    1.934
peak=   -3.291 closest distance to " N   SER A   3 " =    2.093
peak=   -3.291 closest distance to " O   ARG A  24 " =    2.110
peak=   -3.289 closest distance to " CG  HIS A  86 " =    1.119
peak=   -3.284 closest distance to " ND2 ASN A  69 " =    1.851
peak=   -3.280 closest distance to " CD1 LEU A   5 " =    2.518
peak=   -3.276 closest distance to " CG  MET A 105 " =    0.924
peak=   -3.275 closest distance to " CB  GLN A  11 " =    1.678
peak=   -3.275 closest distance to " O   HOH Z  13 " =    1.567
peak=   -3.269 closest distance to " NH2 ARG A  66 " =    1.787
peak=   -3.269 closest distance to " CD1 LEU A 101 " =    2.871
peak=   -3.266 closest distance to " CD  GLN A 223 " =    1.382
peak=   -3.264 closest distance to " O   HOH Z 133 " =    1.349
peak=   -3.264 closest distance to " CE3 TRP A  70 " =    1.766
peak=   -3.264 closest distance to " CB  ALA A  43 " =    2.656
peak=   -3.263 closest distance to " CZ  PHE A 155 " =    1.144
peak=   -3.260 closest distance to " O   ILE A 234 " =    1.228
peak=   -3.257 closest distance to " O   HOH Z 234 " =    4.346
peak=   -3.246 closest distance to " CB  ALA A 291 " =    2.280
peak=   -3.245 closest distance to " N   THR A  52 " =    1.602
peak=   -3.244 closest distance to " O   HOH Z   6 " =    1.700
peak=   -3.238 closest distance to " O   HOH Z 431 " =    1.948
peak=   -3.237 closest distance to " O   HOH Z 216 " =    1.550
peak=   -3.235 closest distance to " O   HOH Z 106 " =    1.941
peak=   -3.233 closest distance to " OE1 GLN A  88 " =    0.873
peak=   -3.232 closest distance to " O   HOH Z 166 " =    1.836
peak=   -3.232 closest distance to " O   HOH Z 238 " =    1.013
peak=   -3.231 closest distance to " CD1 ILE A 199 " =    2.570
peak=   -3.230 closest distance to " O   HOH Z  49 " =    1.185
peak=   -3.229 closest distance to " OG1 THR A  82 " =    1.333
peak=   -3.229 closest distance to " CG  GLU A  53 " =    1.595
peak=   -3.223 closest distance to " CA  GLY A 133 " =    2.347
peak=   -3.222 closest distance to " CE2 TRP A  70 " =    2.116
peak=   -3.216 closest distance to " O   GLY A  80 " =    2.573
peak=   -3.215 closest distance to " OG  SER A  63 " =    1.231
peak=   -3.214 closest distance to " CA  GLY A  98 " =    2.083
peak=   -3.212 closest distance to " CB  VAL A 230 " =    1.075
peak=   -3.211 closest distance to " N   THR A 157 " =    1.546
peak=   -3.210 closest distance to " O   HOH Z 191 " =    5.542
peak=   -3.209 closest distance to " CG  ARG A 259 " =    2.514
peak=   -3.204 closest distance to " O   GLY A  75 " =    2.018
peak=   -3.200 closest distance to " O   HOH Z 275 " =    1.484
peak=   -3.199 closest distance to " CD  PRO A 243 " =    1.999
peak=   -3.198 closest distance to " OE2 GLU A 277 " =    3.008
peak=   -3.183 closest distance to " CB  PRO A 163 " =    2.581
peak=   -3.180 closest distance to " O   HOH Z 392 " =    1.875
peak=   -3.179 closest distance to " O   HOH Z 193 " =    1.866
peak=   -3.178 closest distance to " OG1 THR A  82 " =    1.383
peak=   -3.175 closest distance to " CD  PRO A 213 " =    2.119
peak=   -3.173 closest distance to " O   HOH Z 368 " =    1.781
peak=   -3.170 closest distance to " O   HOH Z 175 " =    4.080
peak=   -3.167 closest distance to " CA  SER A  62 " =    2.500
peak=   -3.163 closest distance to " CD1 LEU A 228 " =    2.317
peak=   -3.162 closest distance to " CA  VAL A 197 " =    1.036
peak=   -3.161 closest distance to " CG1 VAL A  67 " =    2.979
peak=   -3.160 closest distance to " O   LEU A 167 " =    1.525
peak=   -3.160 closest distance to " O   HOH Z 423 " =    2.182
peak=   -3.158 closest distance to " O   GLY A 211 " =    1.340
peak=   -3.158 closest distance to " O   HOH Z 426 " =    1.714
peak=   -3.156 closest distance to " OG  SER A 206 " =    1.736
peak=   -3.154 closest distance to " O   HOH Z 262 " =    2.837
peak=   -3.150 closest distance to " O   HOH Z  17 " =    1.327
peak=   -3.148 closest distance to " O   ALA A  34 " =    2.587
peak=   -3.145 closest distance to " O   ALA A  10 " =    1.712
peak=   -3.144 closest distance to " OD2 ASP A  50 " =    2.366
peak=   -3.142 closest distance to " CB  ALA A 291 " =    2.204
peak=   -3.133 closest distance to " O   SER A  95 " =    1.824
peak=   -3.132 closest distance to " NH2 ARG A  79 " =    2.133
peak=   -3.129 closest distance to " CA  GLY A 203 " =    2.472
peak=   -3.128 closest distance to " CD1 ILE A 151 " =    2.401
peak=   -3.124 closest distance to " O   HOH Z 348 " =    2.297
peak=   -3.121 closest distance to " O   HOH Z 313 " =    1.232
peak=   -3.120 closest distance to " O   TYR A 247 " =    2.898
peak=   -3.115 closest distance to " O   HOH Z 298 " =    2.764
peak=   -3.110 closest distance to " CG2 VAL A 189 " =    2.088
peak=   -3.106 closest distance to " CG  PRO A 243 " =    1.644
peak=   -3.104 closest distance to " N   ALA A 248 " =    2.505
peak=   -3.103 closest distance to " OG  SER A  62 " =    1.795
peak=   -3.095 closest distance to " O   HOH Z 139 " =    3.158
peak=   -3.084 closest distance to " O   HOH Z  90 " =    1.636
peak=   -3.083 closest distance to " CG1 VAL A  78 " =    2.690
peak=   -3.079 closest distance to " O   HOH Z 429 " =    2.077
peak=   -3.076 closest distance to " NE2 GLN A 194 " =    1.989
peak=   -3.073 closest distance to " N   ALA A 248 " =    1.906
peak=   -3.073 closest distance to " CB  TRP A  85 " =    2.498
peak=   -3.069 closest distance to " O   LEU A 282 " =    2.147
peak=   -3.067 closest distance to " OG BSER A 134 " =    1.956
peak=   -3.065 closest distance to " O   HOH Z 236 " =    1.426
peak=   -3.055 closest distance to " OD1 ASN A 173 " =    1.380
peak=   -3.049 closest distance to " OE1 GLN A  77 " =    1.979
peak=   -3.041 closest distance to " O   HOH Z 326 " =    5.057
peak=   -3.025 closest distance to " C   ASP A 270 " =    1.163

================= 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    :  0.4467 0.4305   6.241704e+00   6.214451e+00
   1_bss:  0.4387 0.4169   6.235664e+00   6.201896e+00
   1_xyz:  0.3286 0.3496   6.038950e+00   6.074518e+00
   1_adp:  0.2715 0.3094   5.879446e+00   5.978382e+00
   1_occ:  0.2707 0.3099   5.878298e+00   5.979582e+00
   2_bss:  0.2662 0.3040   5.878505e+00   5.975444e+00
   2_xyz:  0.1829 0.2190   5.540923e+00   5.700631e+00
   2_adp:  0.1657 0.2041   5.459275e+00   5.631855e+00
   2_occ:  0.1655 0.2044   5.459197e+00   5.632791e+00
   3_bss:  0.1649 0.2039   5.459812e+00   5.632422e+00
   3_xyz:  0.1322 0.1695   5.262194e+00   5.466316e+00
   3_adp:  0.1258 0.1690   5.234083e+00   5.457090e+00
   3_occ:  0.1257 0.1690   5.233921e+00   5.456899e+00
   4_bss:  0.1259 0.1696   5.234934e+00   5.457433e+00
   4_xyz:  0.1169 0.1642   5.186044e+00   5.426375e+00
   4_adp:  0.1166 0.1614   5.177606e+00   5.412590e+00
   4_occ:  0.1163 0.1614   5.176589e+00   5.412039e+00
   5_bss:  0.1163 0.1614   5.176593e+00   5.412024e+00
   5_xyz:  0.1178 0.1616   5.185081e+00   5.415866e+00
   5_adp:  0.1176 0.1613   5.184673e+00   5.417207e+00
   5_occ:  0.1175 0.1613   5.184678e+00   5.417447e+00
   5_bss:  0.1175 0.1613   5.184551e+00   5.417327e+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:  0.300  20.000   6.910   9.197   9.284   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.910   9.197   9.284   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.910   9.197   9.284   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.910   9.197   9.284   0.000   0.000   0.000
   2_bss:  0.329  55.733   3.716   5.673   5.750   0.000   0.000   0.000
   2_xyz:  0.329  55.733   3.716   5.673   5.750   0.000   0.000   0.000
   2_adp:  0.329  55.733   3.716   5.673   5.750   0.000   0.000   0.000
   2_occ:  0.329  55.733   3.716   5.673   5.750   0.000   0.000   0.000
   3_bss:  0.323  55.733   2.963   4.040   4.649   0.000   0.000   0.000
   3_xyz:  0.323  55.733   2.963   4.040   4.649   0.000   0.000   0.000
   3_adp:  0.323  55.733   2.963   4.040   4.649   0.000   0.000   0.000
   3_occ:  0.323  55.733   2.963   4.040   4.649   0.000   0.000   0.000
   4_bss:  0.331  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   4_xyz:  0.331  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   4_adp:  0.331  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   4_occ:  0.331  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   5_bss:  0.333  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   5_xyz:  0.333  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   5_adp:  0.333  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   5_occ:  0.333  64.176   2.922   3.642   4.506   0.000   0.000   0.000
   5_bss:  0.323  60.302  -0.768  -0.048   0.816   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.034 0.5466  0.6037    52888.499
   1_bss:  47.056 0.5577  0.7943    50658.959
   1_xyz:  37.968 0.6659  0.9167    33409.297
   1_adp:  31.479 0.7419  1.0044    24853.083
   1_occ:  31.521 0.7414  1.0036    24923.591
   2_bss:  31.291 0.7439  0.8912    24610.784
   2_xyz:  21.626 0.8455  0.9830    12404.712
   2_adp:  19.583 0.8660  0.9969    10712.804
   2_occ:  19.603 0.8658  0.9966    10734.992
   3_bss:  19.562 0.8663  0.9559    10729.680
   3_xyz:  15.615 0.9015  0.9754     7393.420
   3_adp:  15.353 0.9041  0.9727     7245.101
   3_occ:  15.349 0.9041  0.9727     7243.525
   4_bss:  15.362 0.9040  0.9658     7273.849
   4_xyz:  14.695 0.9097  0.9683     6843.350
   4_adp:  14.371 0.9125  0.9662     6678.624
   4_occ:  14.359 0.9126  0.9661     6672.557
   5_bss:  14.358 0.9126  0.9661     6671.994
   5_xyz:  14.387 0.9125  0.9656     6700.363
   5_adp:  14.418 0.9123  0.9622     6715.654
   5_occ:  14.422 0.9122  0.9620     6718.316
   5_bss:  14.425 0.9122  0.9619     6714.793
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4291e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4291e+01
   1_xyz:   1.588  0.012  0.105 17.843  0.006  4.113   1.2628e-01
   1_adp:   1.588  0.012  0.105 17.843  0.006  4.113   1.2628e-01
   1_occ:   1.588  0.012  0.105 17.843  0.006  4.113   1.2628e-01
   2_bss:   1.588  0.012  0.105 17.843  0.006  4.113   1.2628e-01
   2_xyz:   1.049  0.008  0.072 16.175  0.004  4.130   6.6490e-02
   2_adp:   1.049  0.008  0.072 16.175  0.004  4.130   6.6490e-02
   2_occ:   1.049  0.008  0.072 16.175  0.004  4.130   6.6490e-02
   3_bss:   1.049  0.008  0.072 16.175  0.004  4.130   6.6490e-02
   3_xyz:   1.020  0.008  0.080 15.721  0.004  4.114   6.4854e-02
   3_adp:   1.020  0.008  0.080 15.721  0.004  4.114   6.4854e-02
   3_occ:   1.020  0.008  0.080 15.721  0.004  4.114   6.4854e-02
   4_bss:   1.020  0.008  0.080 15.721  0.004  4.114   6.4854e-02
   4_xyz:   1.078  0.009  0.085 15.561  0.004  4.119   7.1326e-02
   4_adp:   1.078  0.009  0.085 15.561  0.004  4.119   7.1326e-02
   4_occ:   1.078  0.009  0.085 15.561  0.004  4.119   7.1326e-02
   5_bss:   1.078  0.009  0.085 15.561  0.004  4.119   7.1326e-02
   5_xyz:   0.960  0.007  0.077 15.229  0.003  4.119   5.8159e-02
   5_adp:   0.960  0.007  0.077 15.229  0.003  4.119   5.8159e-02
   5_occ:   0.960  0.007  0.077 15.229  0.003  4.119   5.8159e-02
   5_bss:   0.960  0.007  0.077 15.229  0.003  4.119   5.8159e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0396e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0396e+00
   1_xyz:  13.922  0.149  0.450 88.678  0.038  2.295   9.6164e-02
   1_adp:  13.922  0.149  0.450 88.678  0.038  2.295   9.6164e-02
   1_occ:  13.922  0.149  0.450 88.678  0.038  2.295   9.6164e-02
   2_bss:  13.922  0.149  0.450 88.678  0.038  2.295   9.6164e-02
   2_xyz:   7.503  0.059  0.231 83.547  0.023  2.174   4.9407e-02
   2_adp:   7.503  0.059  0.231 83.547  0.023  2.174   4.9407e-02
   2_occ:   7.503  0.059  0.231 83.547  0.023  2.174   4.9407e-02
   3_bss:   7.503  0.059  0.231 83.547  0.023  2.174   4.9407e-02
   3_xyz:   6.677  0.047  0.397 82.732  0.042  2.350   6.9859e-02
   3_adp:   6.677  0.047  0.397 82.732  0.042  2.350   6.9859e-02
   3_occ:   6.677  0.047  0.397 82.732  0.042  2.350   6.9859e-02
   4_bss:   6.677  0.047  0.397 82.732  0.042  2.350   6.9859e-02
   4_xyz:   7.376  0.048  0.499 82.609  0.042  2.339   7.5561e-02
   4_adp:   7.376  0.048  0.499 82.609  0.042  2.339   7.5561e-02
   4_occ:   7.376  0.048  0.499 82.609  0.042  2.339   7.5561e-02
   5_bss:   7.376  0.048  0.499 82.609  0.042  2.339   7.5561e-02
   5_xyz:   7.195  0.045  0.365 81.125  0.039  2.397   3.3056e-02
   5_adp:   7.195  0.045  0.365 81.125  0.039  2.397   3.3056e-02
   5_occ:   7.195  0.045  0.365 81.125  0.039  2.397   3.3056e-02
   5_bss:   7.195  0.045  0.365 81.125  0.039  2.397   3.3056e-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:  92.96   0.00  11.01  62.30   0.00   7.95  92.96   0.00  27.68
   1_occ:  92.96   0.00  11.01  62.30   0.00   7.95  92.96   0.00  27.68
   2_bss:  92.96   0.00  11.01  62.30   0.00   7.95  92.96   0.00  27.68
   2_xyz:  92.96   0.00  11.01  62.30   0.00   7.95  92.96   0.00  27.68
   2_adp:  86.10   0.00  11.35  65.67   0.00   7.47  86.10   0.00  32.49
   2_occ:  86.10   0.00  11.35  65.67   0.00   7.47  86.10   0.00  32.49
   3_bss:  86.10   0.00  11.35  65.67   0.00   7.47  86.10   0.00  32.49
   3_xyz:  86.10   0.00  11.35  65.67   0.00   7.47  86.10   0.00  32.49
   3_adp:  85.62   0.00  12.33  85.62   0.00   7.71  79.69   0.00  37.47
   3_occ:  85.62   0.00  12.33  85.62   0.00   7.71  79.69   0.00  37.47
   4_bss:  85.62   0.00  12.33  85.62   0.00   7.71  79.69   0.00  37.47
   4_xyz:  85.62   0.00  12.33  85.62   0.00   7.71  79.69   0.00  37.47
   4_adp:  86.10   0.00  11.86  86.10   0.00   7.50  80.07   0.57  35.62
   4_occ:  86.10   0.00  11.86  86.10   0.00   7.50  80.07   0.57  35.62
   5_bss:  86.10   0.00  11.86  86.10   0.00   7.50  80.07   0.57  35.62
   5_xyz:  86.10   0.00  11.86  86.10   0.00   7.50  80.07   0.57  35.62
   5_adp:  87.33   0.00  11.74  87.33   0.00   7.43  80.89   0.78  35.19
   5_occ:  87.33   0.00  11.74  87.33   0.00   7.43  80.89   0.78  35.19
   5_bss:  91.02   3.69  15.43  91.02   3.69  11.12  84.58   4.47  38.88
------------------------------------------------------------------------
 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:    1.224    0.022    0.407
   1_adp:    1.224    0.022    0.407
   1_occ:    1.224    0.022    0.407
   2_bss:    1.224    0.022    0.407
   2_xyz:    1.609    0.027    0.528
   2_adp:    1.609    0.027    0.528
   2_occ:    1.609    0.027    0.528
   3_bss:    1.609    0.027    0.528
   3_xyz:    1.571    0.054    0.564
   3_adp:    1.571    0.054    0.564
   3_occ:    1.571    0.054    0.564
   4_bss:    1.571    0.054    0.564
   4_xyz:    1.668    0.041    0.591
   4_adp:    1.668    0.041    0.591
   4_occ:    1.668    0.041    0.591
   5_bss:    1.668    0.041    0.591
   5_xyz:    1.767    0.017    0.596
   5_adp:    1.767    0.017    0.596
   5_occ:    1.767    0.017    0.596
   5_bss:    1.767    0.017    0.596
------------------------------------------------------------------------

CPU time actual refinement: 327.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/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_810/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_810/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.90 
  Macro-tasks:
    bulk solvent and scale       = 42.11  
    individual site refinement   = 132.69 
    weights calculation          = 32.20  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.74 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 98.87  
    alpha_beta                      = 8.32   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 109.28 
    fmodel                         = 7.21   
    r_factors                      = 0.28   
    phase_errors                   = 10.70  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 237.97 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.629 micro seconds
Total CPU time: 5.68 minutes
from_scatterers_fft:    634 calls, 98.56 s
gradients_fft:          578 calls, 96.10 s

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

# Date 2008-01-16 Time 02:28:07 PST -0800 (1200479287.77 s)
Start R-work = 0.4467, R-free = 0.4305 (no bulk solvent and anisotropic scale)
Final R-work = 0.1338, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.4387, R-free = 0.4169
Final R-work = 0.1175, R-free = 0.1613