# Date 2008-01-16 Time 03:02:44 PST -0800 (1200481364.33 s)
#phil __OFF__

Command line arguments: "../1080.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20828
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1080

-------------------------------------------------------------------------------
  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: (71.3037, 48.1033, 85.0941, 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: 3.46, per 1000 atoms: 1.23


================================== 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: (71.3037, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97152
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.91924

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9715

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: (71.3037, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97152
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.91924

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2195 [2234/2263]  2011   223  10.0%
  bin  2:  4.2195 -  3.3613 [2130/2153]  1917   213  10.0%
  bin  3:  3.3613 -  2.9400 [2109/2134]  1896   213  10.1%
  bin  4:  2.9400 -  2.6728 [2089/2105]  1887   202   9.7%
  bin  5:  2.6728 -  2.4821 [2089/2133]  1877   212  10.1%
  bin  6:  2.4821 -  2.3363 [2062/2090]  1860   202   9.8%
  bin  7:  2.3363 -  2.2197 [2052/2088]  1844   208  10.1%
  bin  8:  2.2197 -  2.1234 [2058/2100]  1852   206  10.0%
  bin  9:  2.1234 -  2.0418 [2014/2074]  1811   203  10.1%
  bin 10:  2.0418 -  1.9715 [ 752/2107]   675    77  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/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:
        1.35 -     2.06: 11
        2.06 -     2.77: 491
        2.77 -     3.48: 4489
        3.48 -     4.19: 9279
        4.19 -     4.90: 13769
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.348 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.409 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.539 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.626 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.650 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28034 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_1080/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/model_refine_001.geo

CPU time processing inputs: 9.40


============================ 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 = 71.30375 48.10325 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5060   r_free= 0.4939   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.308240                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.4227 0.4328      6.6539      6.6503|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.4399 0.4625      6.8697      6.8875|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.4908 0.4227      6.7227      6.6928|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.5027 0.4736      6.5476      6.5184|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.5412 0.5590       6.385      6.3799|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.5320 0.4712      6.2936      6.1961|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.5305 0.4807      6.2673      6.1974|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.5367 0.5596      6.1511      6.1955|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.5524 0.5432      6.1447      6.1287|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.5249 0.5502      6.0858      6.1317|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.5319 0.5180      6.0348      5.9936|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.5414 0.5200      5.9387      5.9845|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.5529 0.5560      5.8817      5.8299|
| 14:  2.0207 -  1.9715 0.22    305   32 0.5907 0.5054      5.8203      5.7652|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.64  39.66   0.77     0.67      92578.09|
|  2:  4.7066 -  3.7547  1386   147  0.64  40.28   0.85     0.70     127560.35|
|  3:  3.7547 -  3.2857  1372   155  0.53  49.43   0.78     0.65     133462.12|
|  4:  3.2857 -  2.9878  1349   151  0.44  56.43   0.77     0.55     114635.71|
|  5:  2.9878 -  2.7751  1340   148  0.37  62.32   0.70     0.46      90339.59|
|  6:  2.7751 -  2.6123  1351   151  0.37  62.34   0.71     0.43      74084.23|
|  7:  2.6123 -  2.4821  1341   147  0.35  63.47   0.72     0.40      66187.60|
|  8:  2.4821 -  2.3745  1316   144  0.27  69.57   0.69     0.33      65160.28|
|  9:  2.3745 -  2.2834  1331   149  0.19  75.96   0.71     0.23      63463.66|
| 10:  2.2834 -  2.2049  1323   147  0.17  77.67   0.73     0.20      60460.29|
| 11:  2.2049 -  2.1361  1311   144  0.19  75.79   0.76     0.24      53141.46|
| 12:  2.1361 -  2.0752  1316   148  0.23  72.79   0.72     0.30      47184.34|
| 13:  2.0752 -  2.0207  1140   132  0.22  73.89   0.71     0.28      40345.72|
| 14:  2.0207 -  1.9715   305    32  0.14  79.57   0.66     0.18      37304.56|
|alpha:            min =        0.18 max =            0.70 mean =         0.42|
|beta:             min =    37304.56 max =       133462.12 mean =     79293.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.91|
|phase err.(test): min =        0.00 max =           89.98 mean =        62.97|
|-----------------------------------------------------------------------------|

============================== 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 = 20.661496             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.754   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.806700              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.370   (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 |  1.072 -  1.455:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.455 -  1.837:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.837 -  2.220:      115 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.220 -  2.603:      575 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.603 -  2.986:     1336 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.986 -  3.369:     2477 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.369 -  3.752:     3912 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.752 -  4.134:     5083 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.134 -  4.517:     6630 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.517 -  4.900:     7937 |
|-----------------------------------------------------------------------------|
|-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 |       54.115 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.072 |       2.162 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    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 = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5100   r_free= 0.5003   ksol= 0.00   Bsol= 0.00   scale= 0.738    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.308501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4990   r_free= 0.4865   ksol= 0.30   Bsol= 20.00   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,11.02,6.58,0.00,0.00,0.00); trace/3= 8.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.304759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.107724             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.535761              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.732   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4990      final r-factor (work) = 0.4439          |
| start r-factor (free) = 0.4865      final r-factor (free) = 0.4620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.1867 = 18.11 * 0.50 * 6.3035 + 1.00 * 54.1154                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.7535 = 18.11 * 0.50 * 6.2509 + 1.00 * 0.1588                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4439      final r-factor (work) = 0.4069          |
| start r-factor (free) = 0.4620      final r-factor (free) = 0.4549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6147 = 1.54 * 1.00 * 6.2509 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5536 = 1.54 * 1.00 * 6.2080 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.05  16.07    None  None   None       |
|    all(noH): 2823   0      0.00    124.05  16.07    None  None   None       |
|    Sol.    : 438    0      0.00    124.05  26.62    None  None   None       |
|    Mac.    : 2385   0      0.00    72.61   14.14    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 -  12.405: 1387   |   5:    62.025 -  74.430:   22        |
|      1:    12.405 -  24.810:  880   |   6:    74.430 -  86.835:    7        |
|      2:    24.810 -  37.215:  353   |   7:    86.835 -  99.240:    3        |
|      3:    37.215 -  49.620:  123   |   8:    99.240 - 111.646:    1        |
|      4:    49.620 -  62.025:   46   |   9:   111.646 - 124.051:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4069 r_free = 0.4549             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4067 r_free = 0.4547             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4067   r_free= 0.4547   ksol= 0.30   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,11.02,6.58,0.00,0.00,0.00); trace/3= 8.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.198898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4047   r_free= 0.4491   ksol= 0.30   Bsol= 33.43   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,6.31,3.97,0.00,0.00,0.00); trace/3= 4.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.200549                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.053186             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.839  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.487  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4047      final r-factor (work) = 0.3465          |
| start r-factor (free) = 0.4491      final r-factor (free) = 0.4229          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.6567 = 13.05 * 0.50 * 6.2051 + 1.00 * 0.1582                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.1508 = 13.05 * 0.50 * 6.1347 + 1.00 * 0.1120                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3465      final r-factor (work) = 0.3369          |
| start r-factor (free) = 0.4229      final r-factor (free) = 0.4113          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0807 = 0.66 * 1.00 * 6.1347 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0482 = 0.66 * 1.00 * 6.1000 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.28  14.52    None  None   None       |
|    all(noH): 2823   0      0.00    118.28  14.52    None  None   None       |
|    Sol.    : 438    0      0.00    118.28  26.33    None  None   None       |
|    Mac.    : 2385   0      0.00    75.53   12.35    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 -  11.828: 1476   |   5:    59.141 -  70.969:   13        |
|      1:    11.828 -  23.656:  858   |   6:    70.969 -  82.797:    3        |
|      2:    23.656 -  35.485:  305   |   7:    82.797 -  94.626:    0        |
|      3:    35.485 -  47.313:  131   |   8:    94.626 - 106.454:    2        |
|      4:    47.313 -  59.141:   34   |   9:   106.454 - 118.282:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3369 r_free = 0.4113             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3366 r_free = 0.4119             target_work(ml) = 6.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3366   r_free= 0.4119   ksol= 0.30   Bsol= 33.43   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,6.31,3.97,0.00,0.00,0.00); trace/3= 4.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.090178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3370   r_free= 0.4108   ksol= 0.32   Bsol= 57.63   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,4.72,2.94,0.00,0.00,0.00); trace/3= 3.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.090817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.568377             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.570  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3370      final r-factor (work) = 0.2758          |
| start r-factor (free) = 0.4108      final r-factor (free) = 0.3370          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.3503 = 10.57 * 0.50 * 6.1009 + 1.00 * 0.1120                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.9214 = 10.57 * 0.50 * 6.0216 + 1.00 * 0.1019                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2758      final r-factor (work) = 0.2539          |
| start r-factor (free) = 0.3370      final r-factor (free) = 0.3209          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0517 = 0.67 * 1.00 * 6.0216 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9626 = 0.67 * 1.00 * 5.8831 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.40  15.09    None  None   None       |
|    all(noH): 2823   0      0.00    108.40  15.09    None  None   None       |
|    Sol.    : 438    0      0.00    108.40  33.36    None  None   None       |
|    Mac.    : 2385   0      0.00    73.78   11.74    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 -  10.840: 1455   |   5:    54.201 -  65.042:   38        |
|      1:    10.840 -  21.681:  712   |   6:    65.042 -  75.882:   21        |
|      2:    21.681 -  32.521:  326   |   7:    75.882 -  86.722:    3        |
|      3:    32.521 -  43.361:  184   |   8:    86.722 -  97.562:    1        |
|      4:    43.361 -  54.201:   82   |   9:    97.562 - 108.403:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2539 r_free = 0.3209             target_work(ml) = 5.862         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2537 r_free = 0.3200             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2537   r_free= 0.3200   ksol= 0.32   Bsol= 57.63   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,4.72,2.94,0.00,0.00,0.00); trace/3= 3.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.860618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2531   r_free= 0.3188   ksol= 0.32   Bsol= 57.63   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,3.42,1.70,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.859159                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.631257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.110  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354746              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.436  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2531      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.3188      final r-factor (free) = 0.2579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6644 = 5.63 * 0.50 * 5.8823 + 1.00 * 0.1019                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3308 = 5.63 * 0.50 * 5.7704 + 1.00 * 0.0835                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2017      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.2579      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0608 = 0.35 * 1.00 * 5.7704 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0051 = 0.35 * 1.00 * 5.6196 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.95   14.89    None  None   None       |
|    all(noH): 2823   0      0.00    99.95   14.89    None  None   None       |
|    Sol.    : 438    0      2.94    99.95   37.78    None  None   None       |
|    Mac.    : 2385   0      0.00    89.19   10.69    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 -   9.995: 1494   |   5:    49.977 -  59.972:   71        |
|      1:     9.995 -  19.991:  719   |   6:    59.972 -  69.967:   38        |
|      2:    19.991 -  29.986:  211   |   7:    69.967 -  79.963:   12        |
|      3:    29.986 -  39.981:  154   |   8:    79.963 -  89.958:    7        |
|      4:    39.981 -  49.977:  116   |   9:    89.958 -  99.953:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1858 r_free = 0.2380             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1856 r_free = 0.2378             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1856   r_free= 0.2378   ksol= 0.32   Bsol= 57.63   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,3.42,1.70,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.585010                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1857   r_free= 0.2377   ksol= 0.32   Bsol= 57.69   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,2.20,1.37,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.585928                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.340531              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.920  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268430              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.735  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1857      final r-factor (work) = 0.1594          |
| start r-factor (free) = 0.2377      final r-factor (free) = 0.2064          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6619 = 2.34 * 0.50 * 5.6213 + 1.00 * 0.0835                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5197 = 2.34 * 0.50 * 5.5184 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1532          |
| start r-factor (free) = 0.2064      final r-factor (free) = 0.2015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4939 = 0.27 * 1.00 * 5.5184 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5221 = 0.27 * 1.00 * 5.4283 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.63   14.72    None  None   None       |
|    all(noH): 2823   0      0.00    96.63   14.72    None  None   None       |
|    Sol.    : 438    0      2.49    96.63   38.76    None  None   None       |
|    Mac.    : 2385   0      0.00    96.24   10.31    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 -   9.664: 1514   |   5:    48.318 -  57.981:   79        |
|      1:     9.664 -  19.327:  724   |   6:    57.981 -  67.644:   46        |
|      2:    19.327 -  28.991:  170   |   7:    67.644 -  77.308:   15        |
|      3:    28.991 -  38.654:  142   |   8:    77.308 -  86.971:    7        |
|      4:    38.654 -  48.318:  122   |   9:    86.971 -  96.635:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1532 r_free = 0.2015             target_work(ml) = 5.418         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1529 r_free = 0.2010             target_work(ml) = 5.417         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1529   r_free= 0.2010   ksol= 0.32   Bsol= 57.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.91,2.20,1.37,0.00,0.00,0.00); trace/3= 1.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.417180                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.1078 0.1405      5.4731      5.6452|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.1046 0.1254      5.6038      5.8041|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.1409 0.1966       5.722       6.017|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.1769 0.2049      5.7311        5.88|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.1894 0.2164      5.6108      5.7336|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.1751 0.2514      5.4923      5.6882|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.1731 0.2171      5.4442      5.5902|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.1740 0.2110      5.3631      5.5422|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.1709 0.2547      5.3154      5.5497|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.1670 0.2373      5.2754      5.5161|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.1622 0.2184      5.1972      5.4122|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.1608 0.2279       5.139       5.361|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.1641 0.2371      5.0711      5.3065|
| 14:  2.0207 -  1.9715 0.22    305   32 0.1541 0.2244      4.9742      5.2411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.93  10.38   0.96     0.93       8695.91|
|  2:  4.7066 -  3.7547  1386   147  0.94  10.44   1.01     0.99      12063.21|
|  3:  3.7547 -  3.2857  1372   155  0.90  15.58   1.02     1.02      16392.12|
|  4:  3.2857 -  2.9878  1349   151  0.87  19.16   1.01     0.97      16740.94|
|  5:  2.9878 -  2.7751  1340   148  0.84  22.27   1.00     0.98      14546.19|
|  6:  2.7751 -  2.6123  1351   151  0.85  21.69   0.99     0.95      12010.43|
|  7:  2.6123 -  2.4821  1341   147  0.86  21.02   0.99     0.96      10579.63|
|  8:  2.4821 -  2.3745  1316   144  0.84  22.48   1.00     0.96       9683.48|
|  9:  2.3745 -  2.2834  1331   149  0.85  21.64   1.00     0.95       8632.75|
| 10:  2.2834 -  2.2049  1323   147  0.85  21.59   1.00     0.94       8062.67|
| 11:  2.2049 -  2.1361  1311   144  0.85  21.58   1.00     0.94       7150.21|
| 12:  2.1361 -  2.0752  1316   148  0.85  22.09   1.00     0.96       6782.84|
| 13:  2.0752 -  2.0207  1140   132  0.83  23.63   1.00     0.97       6067.42|
| 14:  2.0207 -  1.9715   305    32  0.82  24.36   0.99     0.95       5369.89|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     5369.89 max =        16740.94 mean =     10553.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.94 mean =        19.44|
|phase err.(test): min =        0.00 max =           89.88 mean =        18.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.2013   ksol= 0.32   Bsol= 59.96   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,0.54,-0.01,0.00,-0.00,-0.00); trace/3= -0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.419418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.2013   ksol= 0.32   Bsol= 59.96   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,0.54,-0.01,0.00,-0.00,-0.00); trace/3= -0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.419418                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.1102 0.1423      5.4893      5.6579|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.1050 0.1262      5.6103      5.8135|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.1413 0.1969      5.7264      6.0157|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.1771 0.2055      5.7326      5.8797|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.1896 0.2167       5.612      5.7352|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.1752 0.2504      5.4929      5.6862|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.1728 0.2176       5.444      5.5912|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.1736 0.2111      5.3628       5.542|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.1705 0.2550      5.3143      5.5496|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.1669 0.2375      5.2749       5.517|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.1620 0.2186      5.1965      5.4119|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.1608 0.2284      5.1396      5.3622|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.1640 0.2367      5.0708      5.3065|
| 14:  2.0207 -  1.9715 0.22    305   32 0.1541 0.2239      4.9729      5.2374|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.93  10.62   0.96     0.93       8837.51|
|  2:  4.7066 -  3.7547  1386   147  0.93  10.51   1.01     0.98      12239.25|
|  3:  3.7547 -  3.2857  1372   155  0.90  15.64   1.01     1.02      16563.48|
|  4:  3.2857 -  2.9878  1349   151  0.87  19.15   1.00     0.96      16735.99|
|  5:  2.9878 -  2.7751  1340   148  0.84  22.29   0.99     0.97      14577.15|
|  6:  2.7751 -  2.6123  1351   151  0.85  21.70   0.98     0.94      12032.13|
|  7:  2.6123 -  2.4821  1341   147  0.86  21.01   0.98     0.95      10592.80|
|  8:  2.4821 -  2.3745  1316   144  0.84  22.48   0.99     0.94       9685.86|
|  9:  2.3745 -  2.2834  1331   149  0.85  21.63   0.99     0.94       8636.27|
| 10:  2.2834 -  2.2049  1323   147  0.85  21.58   0.98     0.93       8063.97|
| 11:  2.2049 -  2.1361  1311   144  0.85  21.57   0.98     0.93       7147.59|
| 12:  2.1361 -  2.0752  1316   148  0.85  22.10   0.98     0.94       6798.37|
| 13:  2.0752 -  2.0207  1140   132  0.83  23.62   0.98     0.95       6064.27|
| 14:  2.0207 -  1.9715   305    32  0.82  24.32   0.97     0.93       5344.40|
|alpha:            min =        0.93 max =            1.02 mean =         0.95|
|beta:             min =     5344.40 max =        16735.99 mean =     10597.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.95 mean =        19.47|
|phase err.(test): min =        0.00 max =           89.93 mean =        18.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    97.77   15.85    None  None   None       |
|    all(noH): 2823   0      1.13    97.77   15.85    None  None   None       |
|    Sol.    : 438    0      3.63    97.77   39.89    None  None   None       |
|    Mac.    : 2385   0      1.13    97.37   11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.131 -  10.794: 1514   |   5:    49.448 -  59.111:   79        |
|      1:    10.794 -  20.457:  724   |   6:    59.111 -  68.775:   46        |
|      2:    20.457 -  30.121:  170   |   7:    68.775 -  78.438:   15        |
|      3:    30.121 -  39.784:  142   |   8:    78.438 -  88.102:    7        |
|      4:    39.784 -  49.448:  122   |   9:    88.102 -  97.765:    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)= 352         
Filter by distance & map next to the model:
   mapped sites are within: 0.709 - 5.365
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 352 from: 352
   mapped sites are within: 0.709 - 5.365

peak=    7.841 closest distance to " O   HOH Z 120 " =    2.094
peak=    7.500 closest distance to " O   HOH Z 426 " =    1.452
peak=    6.512 closest distance to " CG2 VAL A 296 " =    1.350
peak=    6.003 closest distance to " CG  GLN A  77 " =    1.052
peak=    5.809 closest distance to " CG  LEU A   5 " =    1.479
peak=    5.672 closest distance to " CD1AILE A 234 " =    1.438
peak=    5.621 closest distance to " O   HOH Z  37 " =    1.477
peak=    5.513 closest distance to " CG  ARG A 138 " =    1.202
peak=    5.273 closest distance to " NH1 ARG A 138 " =    0.979
peak=    5.148 closest distance to " O   HOH Z  57 " =    1.114
peak=    5.125 closest distance to " O   HOH Z 117 " =    1.510
peak=    5.051 closest distance to " NH1BARG A 275 " =    1.179
peak=    5.031 closest distance to " O   HOH Z 126 " =    1.975
peak=    5.018 closest distance to " O   ARG A 275 " =    0.811
peak=    5.011 closest distance to " O   HOH Z 422 " =    1.364
peak=    4.882 closest distance to " O   HOH Z  47 " =    1.996
peak=    4.856 closest distance to " CG  PRO A 280 " =    1.009
peak=    4.852 closest distance to " O   HOH Z 272 " =    1.450
peak=    4.826 closest distance to " OD1 ASN A 301 " =    1.134
peak=    4.810 closest distance to " O   HOH Z 246 " =    1.663
peak=    4.793 closest distance to " O   HOH Z  69 " =    1.522
peak=    4.786 closest distance to " O   HOH Z  54 " =    1.347
peak=    4.725 closest distance to " O   HOH Z 404 " =    1.376
peak=    4.644 closest distance to " CA  GLY A 196 " =    0.929
peak=    4.613 closest distance to " N   VAL A 121 " =    0.900
peak=    4.600 closest distance to " NH2BARG A 102 " =    1.068
peak=    4.548 closest distance to " O   HOH Z 111 " =    1.926
peak=    4.533 closest distance to " O   HOH Z 159 " =    1.234
peak=    4.505 closest distance to " CG  PRO A  54 " =    1.257
peak=    4.501 closest distance to " O   HOH Z 279 " =    1.167
peak=    4.500 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.449 closest distance to " CB  GLN A  73 " =    1.113
peak=    4.424 closest distance to " O   HOH Z 431 " =    1.921
peak=    4.422 closest distance to " CB  ASN A 285 " =    1.011
peak=    4.422 closest distance to " N   ASP A 298 " =    0.970
peak=    4.409 closest distance to " CG1 VAL A 230 " =    1.158
peak=    4.402 closest distance to " O   HOH Z 210 " =    1.768
peak=    4.380 closest distance to " CB  ARG A 275 " =    0.959
peak=    4.371 closest distance to " CA  GLU A 277 " =    1.060
peak=    4.355 closest distance to " CG1 ILE A 120 " =    1.147
peak=    4.313 closest distance to " O   HOH Z 137 " =    2.087
peak=    4.290 closest distance to " NE2 HIS A 115 " =    0.990
peak=    4.260 closest distance to " O   VAL A 121 " =    1.051
peak=    4.255 closest distance to " C   SER A  32 " =    1.129
peak=    4.251 closest distance to " OG ASER A 134 " =    1.467
peak=    4.220 closest distance to " CD  ARG A 138 " =    1.189
peak=    4.190 closest distance to " CB  TRP A 179 " =    1.460
peak=    4.182 closest distance to " O   HOH Z 411 " =    2.956
peak=    4.154 closest distance to " O   HOH Z  63 " =    1.960
peak=    4.138 closest distance to " CB  VAL A 230 " =    1.376
peak=    4.120 closest distance to " O   HOH Z 324 " =    1.884
peak=    4.113 closest distance to " CB  SER A  62 " =    1.013
peak=    4.112 closest distance to " CB  MET A  47 " =    1.044
peak=    4.110 closest distance to " CB  SER A  63 " =    1.317
peak=    4.104 closest distance to " OD1 ASP A 238 " =    0.944
peak=    4.102 closest distance to " O   HOH Z  57 " =    2.283
peak=    4.092 closest distance to " CA  GLU A 152 " =    0.955
peak=    4.089 closest distance to " O   HOH Z  15 " =    2.122
peak=    4.086 closest distance to " CD  ARG A 269 " =    0.863
peak=    4.086 closest distance to " CG AARG A 275 " =    1.057
peak=    4.074 closest distance to " O   HOH Z 374 " =    1.167
peak=    4.072 closest distance to " O   HOH Z 133 " =    1.844
peak=    4.071 closest distance to " N   SER A 164 " =    0.949
peak=    4.063 closest distance to " CB  GLN A 223 " =    1.446
peak=    4.047 closest distance to " CB  PRO A 198 " =    1.121
peak=    4.037 closest distance to " CE  LYS A 119 " =    1.516
peak=    4.034 closest distance to " CA  TYR A  30 " =    1.065
peak=    4.026 closest distance to " NE2 GLN A  89 " =    1.078
peak=    4.023 closest distance to " O   HOH Z  44 " =    1.964
peak=    4.019 closest distance to " O   HOH Z 387 " =    2.566
peak=    4.010 closest distance to " O   HOH Z 128 " =    1.957
peak=    4.009 closest distance to " O   ASP A 298 " =    0.832
peak=    3.994 closest distance to " OE1 GLN A  11 " =    1.970
peak=    3.993 closest distance to " CG1 VAL A 153 " =    1.244
peak=    3.990 closest distance to " CD2 LEU A 228 " =    1.244
peak=    3.988 closest distance to " CD  LYS A 166 " =    1.781
peak=    3.987 closest distance to " CB  GLN A  58 " =    1.072
peak=    3.985 closest distance to " O   HOH Z 416 " =    1.753
peak=    3.983 closest distance to " CB  VAL A 296 " =    1.219
peak=    3.982 closest distance to " O   HOH Z  49 " =    1.423
peak=    3.978 closest distance to " O   HOH Z 128 " =    1.472
peak=    3.975 closest distance to " NH1 ARG A 269 " =    1.010
peak=    3.960 closest distance to " O   HOH Z  88 " =    3.280
peak=    3.949 closest distance to " CG2 THR A 221 " =    1.125
peak=    3.946 closest distance to " CB  SER A  26 " =    0.952
peak=    3.934 closest distance to " O   HOH Z 174 " =    1.695
peak=    3.926 closest distance to " CG1BVAL A 121 " =    1.602
peak=    3.925 closest distance to " CB  ALA A   1 " =    1.436
peak=    3.916 closest distance to " O   HOH Z 149 " =    1.490
peak=    3.899 closest distance to " CG2 VAL A 230 " =    1.151
peak=    3.880 closest distance to " O   HOH Z 182 " =    1.212
peak=    3.868 closest distance to " N   ARG A 275 " =    0.860
peak=    3.863 closest distance to " O   HOH Z 418 " =    1.699
peak=    3.859 closest distance to " O   HOH Z 395 " =    1.471
peak=    3.843 closest distance to " CB  GLU A 277 " =    1.026
peak=    3.840 closest distance to " O   HOH Z 368 " =    1.285
peak=    3.838 closest distance to " O   HOH Z  68 " =    2.004
peak=    3.830 closest distance to " O   HOH Z 394 " =    1.919
peak=    3.827 closest distance to " O   HOH Z 155 " =    1.865
peak=    3.818 closest distance to " O   HOH Z 272 " =    2.055
peak=    3.817 closest distance to " CG  PRO A 198 " =    1.375
peak=    3.816 closest distance to " O   HOH Z 137 " =    1.998
peak=    3.812 closest distance to " CB  GLN A  88 " =    1.223
peak=    3.810 closest distance to " O   HOH Z 234 " =    3.563
peak=    3.809 closest distance to " C   ALA A 299 " =    0.870
peak=    3.807 closest distance to " O   HOH Z 102 " =    1.506
peak=    3.807 closest distance to " CD1 TRP A 274 " =    1.108
peak=    3.797 closest distance to " CB  TRP A 266 " =    0.947
peak=    3.796 closest distance to " O   HOH Z 434 " =    2.241
peak=    3.795 closest distance to " O   HOH Z 134 " =    2.408
peak=    3.795 closest distance to " O   HOH Z 363 " =    1.261
peak=    3.795 closest distance to " NH2 ARG A 156 " =    1.249
peak=    3.793 closest distance to " CD  GLN A  73 " =    1.085
peak=    3.788 closest distance to " CA  ILE A  33 " =    1.544
peak=    3.782 closest distance to " O   HOH Z 276 " =    1.569
peak=    3.775 closest distance to " CZ  PHE A 218 " =    0.994
peak=    3.773 closest distance to " N   ALA A 256 " =    1.166
peak=    3.768 closest distance to " O   HOH Z 389 " =    2.058
peak=    3.764 closest distance to " CE BMET A  47 " =    1.419
peak=    3.763 closest distance to " O   HOH Z 144 " =    1.770
peak=    3.755 closest distance to " CB  ILE A 199 " =    1.043
peak=    3.750 closest distance to " O   LYS A 289 " =    1.009
peak=    3.744 closest distance to " O   HOH Z 335 " =    1.062
peak=    3.736 closest distance to " CA  SER A  87 " =    0.735
peak=    3.731 closest distance to " CA  ALA A  21 " =    1.599
peak=    3.720 closest distance to " CD1 LEU A 222 " =    0.956
peak=    3.718 closest distance to " O   HOH Z 277 " =    2.205
peak=    3.716 closest distance to " O   HOH Z  48 " =    1.756
peak=    3.715 closest distance to " O   HOH Z   1 " =    2.666
peak=    3.712 closest distance to " O   HOH Z 124 " =    1.764
peak=    3.711 closest distance to " ND1 HIS A  81 " =    1.458
peak=    3.696 closest distance to " O   HOH Z 209 " =    2.124
peak=    3.691 closest distance to " O   HOH Z 139 " =    4.701
peak=    3.690 closest distance to " O   HOH Z 368 " =    2.873
peak=    3.690 closest distance to " CB  SER A  28 " =    1.030
peak=    3.689 closest distance to " ND2 ASN A  45 " =    1.313
peak=    3.684 closest distance to " CD  LYS A 289 " =    1.141
peak=    3.679 closest distance to " O   HOH Z 119 " =    2.026
peak=    3.676 closest distance to " NZ  LYS A 117 " =    3.075
peak=    3.672 closest distance to " N   TYR A  15 " =    0.949
peak=    3.669 closest distance to " O   HOH Z  80 " =    2.191
peak=    3.664 closest distance to " OG1 THR A 157 " =    0.903
peak=    3.663 closest distance to " NH1AARG A 145 " =    1.078
peak=    3.663 closest distance to " CA  THR A 246 " =    1.326
peak=    3.662 closest distance to " CB  ASN A 187 " =    1.198
peak=    3.660 closest distance to " NZ  LYS A  76 " =    1.238
peak=    3.655 closest distance to " CD2 LEU A 255 " =    1.434
peak=    3.654 closest distance to " CB  ALA A 129 " =    0.936
peak=    3.639 closest distance to " O   HOH Z 427 " =    3.578
peak=    3.635 closest distance to " CB  LYS A  76 " =    0.944
peak=    3.632 closest distance to " O   HOH Z 350 " =    1.244
peak=    3.632 closest distance to " N   LYS A 166 " =    0.818
peak=    3.624 closest distance to " O   PHE A  16 " =    1.293
peak=    3.622 closest distance to " CD BLYS A 290 " =    1.050
peak=    3.618 closest distance to " O   HOH Z   4 " =    1.187
peak=    3.616 closest distance to " O   HOH Z  52 " =    1.521
peak=    3.599 closest distance to " CA  VAL A  41 " =    0.737
peak=    3.598 closest distance to " O   HOH Z 424 " =    3.404
peak=    3.596 closest distance to " O   HOH Z 236 " =    1.951
peak=    3.591 closest distance to " CB  GLU A 175 " =    1.319
peak=    3.588 closest distance to " O   HOH Z 295 " =    1.204
peak=    3.581 closest distance to " O   HOH Z 124 " =    1.869
peak=    3.575 closest distance to " O   HOH Z 410 " =    1.215
peak=    3.575 closest distance to " OG1 THR A 294 " =    3.958
peak=    3.572 closest distance to " CB  SER A 141 " =    1.003
peak=    3.567 closest distance to " O   HOH Z 156 " =    3.257
peak=    3.563 closest distance to " CB  ALA A 100 " =    1.641
peak=    3.557 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.537 closest distance to " O   GLY A  91 " =    1.161
peak=    3.535 closest distance to " CG1 ILE A  33 " =    1.472
peak=    3.530 closest distance to " CA  ALA A 248 " =    1.219
peak=    3.529 closest distance to " OG  SER A 276 " =    0.927
peak=    3.525 closest distance to " O   HOH Z  43 " =    2.051
peak=    3.525 closest distance to " O   HOH Z 303 " =    2.423
peak=    3.521 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.519 closest distance to " O   HOH Z 234 " =    2.134
peak=    3.519 closest distance to " CG2 THR A 220 " =    0.771
peak=    3.519 closest distance to " O   HOH Z  61 " =    1.349
peak=    3.516 closest distance to " O   HOH Z 193 " =    1.841
peak=    3.515 closest distance to " O   HOH Z 136 " =    1.579
peak=    3.506 closest distance to " N   ASN A 110 " =    1.315
peak=    3.502 closest distance to " OE1 GLN A  88 " =    0.927
peak=    3.495 closest distance to " O   HOH Z 108 " =    1.217
peak=    3.495 closest distance to " O   HOH Z 222 " =    2.851
peak=    3.491 closest distance to " CB  GLN A 183 " =    1.266
peak=    3.490 closest distance to " CA  ARG A  66 " =    1.112
peak=    3.485 closest distance to " CB BVAL A  41 " =    1.540
peak=    3.483 closest distance to " CA  GLY A 267 " =    1.256
peak=    3.481 closest distance to " CB  TYR A  30 " =    1.156
peak=    3.479 closest distance to " CA  ILE A 106 " =    0.815
peak=    3.474 closest distance to " OD1 ASN A  60 " =    0.858
peak=    3.472 closest distance to " O   HOH Z 185 " =    1.773
peak=    3.472 closest distance to " CD2 LEU A   5 " =    1.187
peak=    3.468 closest distance to " OG  SER A  62 " =    3.912
peak=    3.465 closest distance to " O   HOH Z 418 " =    3.341
peak=    3.461 closest distance to " CD1 TRP A 266 " =    1.348
peak=    3.460 closest distance to " C   PRO A  54 " =    0.787
peak=    3.459 closest distance to " CB  TRP A 150 " =    1.079
peak=    3.453 closest distance to " CA  GLN A 223 " =    0.797
peak=    3.453 closest distance to " ND2 ASN A 301 " =    0.978
peak=    3.453 closest distance to " CB  ALA A 137 " =    1.340
peak=    3.452 closest distance to " CB  ARG A 275 " =    1.458
peak=    3.449 closest distance to " CG  GLN A  11 " =    1.351
peak=    3.448 closest distance to " CG2 VAL A  78 " =    1.055
peak=    3.448 closest distance to " O   HOH Z 411 " =    1.523
peak=    3.448 closest distance to " O   HOH Z   5 " =    1.859
peak=    3.443 closest distance to " CB  GLN A 194 " =    0.847
peak=    3.443 closest distance to " O   SER A  62 " =    1.007
peak=    3.435 closest distance to " CZ  PHE A 192 " =    1.000
peak=    3.433 closest distance to " O   HOH Z 420 " =    5.365
peak=    3.433 closest distance to " ND2 ASN A 285 " =    1.177
peak=    3.433 closest distance to " CB  MET A 105 " =    1.333
peak=    3.431 closest distance to " O   HOH Z 132 " =    2.508
peak=    3.430 closest distance to " O   GLU A 277 " =    1.488
peak=    3.428 closest distance to " O   HOH Z 261 " =    1.876
peak=    3.422 closest distance to " O   HOH Z 425 " =    1.583
peak=    3.421 closest distance to " O   HOH Z 154 " =    1.347
peak=    3.417 closest distance to " O   HOH Z  39 " =    2.094
peak=    3.413 closest distance to " N   ASN A  39 " =    1.229
peak=    3.409 closest distance to " CA  LEU A 282 " =    1.090
peak=    3.406 closest distance to " CB  TYR A 247 " =    1.077
peak=    3.404 closest distance to " CG2 THR A  42 " =    0.976
peak=    3.403 closest distance to " O   HOH Z 389 " =    1.698
peak=    3.400 closest distance to " CG  GLU A 277 " =    3.220
peak=    3.400 closest distance to " O   HOH Z  85 " =    2.229
peak=    3.398 closest distance to " O   HOH Z 192 " =    1.653
peak=    3.396 closest distance to " OE1 GLN A  77 " =    0.901
peak=    3.395 closest distance to " OE1 GLU A   2 " =    2.006
peak=    3.394 closest distance to " CA  ARG A 195 " =    1.112
peak=    3.390 closest distance to " O   PHE A  61 " =    1.015
peak=    3.389 closest distance to " O   GLN A  11 " =    0.888
peak=    3.385 closest distance to " O   HOH Z 214 " =    1.411
peak=    3.385 closest distance to " O   GLY A  98 " =    1.533
peak=    3.380 closest distance to " O   HOH Z  30 " =    1.781
peak=    3.378 closest distance to " NH1 ARG A  14 " =    1.144
peak=    3.376 closest distance to " O   HOH Z 415 " =    1.927
peak=    3.376 closest distance to " O   HOH Z 215 " =    1.402
peak=    3.368 closest distance to " CG2 VAL A 268 " =    1.439
peak=    3.365 closest distance to " O   HOH Z 327 " =    2.937
peak=    3.365 closest distance to " CD2 LEU A 297 " =    0.797
peak=    3.363 closest distance to " O   HOH Z 146 " =    1.849
peak=    3.362 closest distance to " CB  PHE A 283 " =    1.062
peak=    3.360 closest distance to " O   HOH Z  19 " =    1.653
peak=    3.358 closest distance to " CG  GLU A 236 " =    0.791
peak=    3.355 closest distance to " CD  ARG A  36 " =    1.098
peak=    3.354 closest distance to " O   GLU A   2 " =    1.121
peak=    3.348 closest distance to " CB  VAL A 202 " =    1.419
peak=    3.345 closest distance to " NH1BARG A 145 " =    1.551
peak=    3.342 closest distance to " CA  GLY A 147 " =    0.827
peak=    3.341 closest distance to " O   HOH Z 344 " =    2.863
peak=    3.341 closest distance to " OE2 GLU A 152 " =    2.082
peak=    3.335 closest distance to " O   HOH Z 389 " =    1.852
peak=    3.331 closest distance to " O   HOH Z 298 " =    1.796
peak=    3.330 closest distance to " O   ILE A 106 " =    1.808
peak=    3.327 closest distance to " CA  PRO A 243 " =    0.977
peak=    3.324 closest distance to " O   HOH Z 369 " =    1.753
peak=    3.323 closest distance to " CB  HIS A 108 " =    0.751
peak=    3.316 closest distance to " O   HOH Z 133 " =    2.201
peak=    3.314 closest distance to " ND2 ASN A 209 " =    1.526
peak=    3.313 closest distance to " OG  SER A  97 " =    3.411
peak=    3.309 closest distance to " CZ3 TRP A 274 " =    4.570
peak=    3.304 closest distance to " CB  ALA A 299 " =    0.984
peak=    3.299 closest distance to " O   HOH Z  62 " =    2.083
peak=    3.298 closest distance to " N   PHE A 130 " =    1.222
peak=    3.297 closest distance to " O   HOH Z 203 " =    1.784
peak=    3.295 closest distance to " O   HOH Z 116 " =    4.110
peak=    3.292 closest distance to " O   HOH Z 184 " =    1.577
peak=    3.292 closest distance to " NH2AARG A 145 " =    0.971
peak=    3.282 closest distance to " O   HOH Z 358 " =    1.608
peak=    3.280 closest distance to " CA  THR A  42 " =    1.041
peak=    3.279 closest distance to " CB  ALA A  34 " =    0.821
peak=    3.275 closest distance to " O   HOH Z 146 " =    1.764
peak=    3.274 closest distance to " O   HOH Z 281 " =    4.127
peak=    3.273 closest distance to " C   GLY A  80 " =    1.257
peak=    3.272 closest distance to " CA  MET A 105 " =    1.632
peak=    3.272 closest distance to " CB  PRO A 243 " =    1.246
peak=    3.266 closest distance to " CG2 ILE A 109 " =    1.146
peak=    3.266 closest distance to " CG  MET A 185 " =    1.336
peak=    3.265 closest distance to " NZ  LYS A 289 " =    0.909
peak=    3.263 closest distance to " CA  ALA A 295 " =    1.015
peak=    3.259 closest distance to " CA  ALA A 160 " =    1.029
peak=    3.253 closest distance to " CB  GLU A 236 " =    1.326
peak=    3.250 closest distance to " O   LEU A  25 " =    1.003
peak=    3.247 closest distance to " CA  ARG A 102 " =    1.500
peak=    3.242 closest distance to " CG  MET A 185 " =    0.933
peak=    3.242 closest distance to " CE3 TRP A 274 " =    2.487
peak=    3.241 closest distance to " O   HOH Z 142 " =    1.927
peak=    3.239 closest distance to " O   HOH Z 258 " =    1.937
peak=    3.237 closest distance to " O   ALA A 292 " =    1.418
peak=    3.233 closest distance to " CA  ILE A 120 " =    1.349
peak=    3.230 closest distance to " O   ASP A 124 " =    1.127
peak=    3.228 closest distance to " O   HOH Z 118 " =    1.774
peak=    3.227 closest distance to " CE1 HIS A 108 " =    1.088
peak=    3.225 closest distance to " CG  GLN A 205 " =    1.406
peak=    3.216 closest distance to " O   HOH Z 269 " =    1.923
peak=    3.213 closest distance to " CG2 VAL A  67 " =    0.979
peak=    3.212 closest distance to " O   HOH Z  91 " =    2.580
peak=    3.211 closest distance to " CB  GLU A   2 " =    1.146
peak=    3.209 closest distance to " O   HOH Z 336 " =    1.679
peak=    3.208 closest distance to " O   HOH Z 130 " =    2.943
peak=    3.205 closest distance to " O   HOH Z  43 " =    2.356
peak=    3.202 closest distance to " O   HOH Z 193 " =    2.314
peak=    3.200 closest distance to " CA  HIS A 115 " =    1.026
peak=    3.200 closest distance to " O   HOH Z  22 " =    2.651
peak=    3.198 closest distance to " CB  GLU A 128 " =    1.108
peak=    3.190 closest distance to " O   HOH Z 417 " =    1.374
peak=    3.190 closest distance to " CG  PRO A 213 " =    1.374
peak=    3.189 closest distance to " N   THR A 178 " =    1.074
peak=    3.187 closest distance to " N   ASP A 231 " =    0.881
peak=    3.181 closest distance to " CB  TRP A 123 " =    1.139
peak=    3.180 closest distance to " N   SER A 271 " =    1.132
peak=    3.175 closest distance to " O   PRO A 198 " =    1.595
peak=    3.175 closest distance to " CG2 VAL A 257 " =    1.015
peak=    3.174 closest distance to " CE3 TRP A  85 " =    1.225
peak=    3.171 closest distance to " CA  VAL A  78 " =    1.071
peak=    3.170 closest distance to " OE1 GLN A 223 " =    2.082
peak=    3.168 closest distance to " O   HOH Z 282 " =    2.398
peak=    3.167 closest distance to " O   HOH Z 245 " =    1.494
peak=    3.166 closest distance to " OG1 THR A 279 " =    1.728
peak=    3.165 closest distance to " OD2 ASP A  50 " =    1.137
peak=    3.162 closest distance to " CB  ALA A  34 " =    0.709
peak=    3.159 closest distance to " O   HOH Z 258 " =    3.138
peak=    3.157 closest distance to " O   HOH Z 294 " =    1.723
peak=    3.155 closest distance to " CG2 THR A 251 " =    1.318
peak=    3.152 closest distance to " O   SER A 164 " =    1.530
peak=    3.145 closest distance to " O   VAL A  72 " =    1.027
peak=    3.143 closest distance to " CG  GLN A  55 " =    1.679
peak=    3.142 closest distance to " CB  ALA A 256 " =    1.198
peak=    3.140 closest distance to " CG2 THR A  18 " =    1.924
peak=    3.138 closest distance to " O   HOH Z 403 " =    2.210
peak=    3.133 closest distance to " O   HOH Z 185 " =    2.188
peak=    3.131 closest distance to " O   ALA A  84 " =    1.392
peak=    3.130 closest distance to " O   HOH Z 280 " =    3.356
peak=    3.127 closest distance to " CA  THR A 294 " =    1.948
peak=    3.125 closest distance to " O   HOH Z 271 " =    2.052
peak=    3.114 closest distance to " CB  ARG A 156 " =    1.003
peak=    3.114 closest distance to " O   HOH Z 342 " =    0.973
peak=    3.114 closest distance to " CG1 ILE A 106 " =    1.105
peak=    3.106 closest distance to " CE1 PHE A 208 " =    1.162
peak=    3.103 closest distance to " O   HOH Z 265 " =    2.180
peak=    3.099 closest distance to " NZ  LYS A 166 " =    3.299
peak=    3.098 closest distance to " CA  LEU A 101 " =    1.453
peak=    3.088 closest distance to " CB  SER A 276 " =    0.996
peak=    3.085 closest distance to " CD  GLN A  73 " =    1.414
peak=    3.084 closest distance to " OG BSER A 258 " =    2.762
peak=    3.070 closest distance to " N   ALA A 100 " =    0.777
peak=    3.060 closest distance to " O   HOH Z 311 " =    4.493
peak=    3.058 closest distance to " CA  ARG A 156 " =    0.963
peak=    3.055 closest distance to " CD2 HIS A  81 " =    1.468
peak=    3.046 closest distance to " O   HOH Z 196 " =    2.644
peak=    3.037 closest distance to " CB  ALA A 248 " =    1.489
peak=    3.030 closest distance to " O   HOH Z  39 " =    2.819

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 229         
Filter by distance & map next to the model:
   mapped sites are within: 0.331 - 5.174
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 229
   mapped sites are within: 0.723 - 5.174

peak=   -5.144 closest distance to " O   VAL A 121 " =    0.912
peak=   -5.076 closest distance to " O   HOH Z  52 " =    2.164
peak=   -5.066 closest distance to " N   ARG A 275 " =    0.822
peak=   -4.656 closest distance to " NH2 ARG A  66 " =    1.134
peak=   -4.616 closest distance to " NE  ARG A 138 " =    1.259
peak=   -4.510 closest distance to " OD1 ASN A 301 " =    0.753
peak=   -4.490 closest distance to " O   HOH Z 426 " =    0.865
peak=   -4.406 closest distance to " O   HOH Z 151 " =    0.940
peak=   -4.367 closest distance to " O   HOH Z 166 " =    1.454
peak=   -4.346 closest distance to " O   HOH Z 422 " =    2.443
peak=   -4.313 closest distance to " C   ASN A 285 " =    2.563
peak=   -4.313 closest distance to " CG2BVAL A  41 " =    2.361
peak=   -4.264 closest distance to " CD  GLN A  77 " =    0.725
peak=   -4.249 closest distance to " CA  ALA A 137 " =    2.748
peak=   -4.187 closest distance to " N   ASP A 272 " =    1.177
peak=   -4.149 closest distance to " OG ASER A 134 " =    1.123
peak=   -4.149 closest distance to " O   HOH Z 210 " =    0.857
peak=   -4.104 closest distance to " O   ARG A 275 " =    0.923
peak=   -4.080 closest distance to " CG  ARG A 138 " =    0.979
peak=   -4.072 closest distance to " CB  ALA A 291 " =    2.464
peak=   -4.062 closest distance to " O   HOH Z 272 " =    0.740
peak=   -4.059 closest distance to " CA  GLU A 277 " =    1.104
peak=   -4.051 closest distance to " CA  SER A 164 " =    1.622
peak=   -3.974 closest distance to " O   HOH Z  13 " =    1.204
peak=   -3.962 closest distance to " NE1 TRP A  85 " =    1.181
peak=   -3.954 closest distance to " O   HOH Z 401 " =    1.461
peak=   -3.928 closest distance to " O   HOH Z 132 " =    1.178
peak=   -3.893 closest distance to " CG  GLU A   2 " =    1.566
peak=   -3.887 closest distance to " O   HOH Z  46 " =    0.840
peak=   -3.881 closest distance to " O   HOH Z 189 " =    2.033
peak=   -3.880 closest distance to " CE2 TYR A 293 " =    2.673
peak=   -3.873 closest distance to " O   HOH Z 184 " =    0.856
peak=   -3.863 closest distance to " CA  ASP A 298 " =    1.219
peak=   -3.862 closest distance to " CD1 PHE A  59 " =    1.917
peak=   -3.851 closest distance to " O   HOH Z 369 " =    2.356
peak=   -3.846 closest distance to " SG BCYS A 201 " =    1.122
peak=   -3.840 closest distance to " N   GLN A  58 " =    1.721
peak=   -3.827 closest distance to " OG  SER A  28 " =    2.289
peak=   -3.824 closest distance to " C   ALA A 299 " =    0.881
peak=   -3.815 closest distance to " O   HOH Z 222 " =    1.332
peak=   -3.813 closest distance to " O   HOH Z  58 " =    0.750
peak=   -3.811 closest distance to " CG  LEU A   5 " =    1.047
peak=   -3.807 closest distance to " CD2 PHE A  59 " =    2.355
peak=   -3.800 closest distance to " CD  ARG A  14 " =    3.054
peak=   -3.798 closest distance to " O   HOH Z 407 " =    1.221
peak=   -3.777 closest distance to " CB  PHE A 130 " =    1.212
peak=   -3.770 closest distance to " O   HOH Z 198 " =    1.428
peak=   -3.770 closest distance to " O   HOH Z  37 " =    1.254
peak=   -3.760 closest distance to " O   HOH Z 186 " =    1.558
peak=   -3.754 closest distance to " O   HOH Z 231 " =    1.159
peak=   -3.749 closest distance to " N   THR A 235 " =    1.222
peak=   -3.720 closest distance to " O   VAL A 174 " =    1.890
peak=   -3.716 closest distance to " O   HOH Z  60 " =    1.447
peak=   -3.710 closest distance to " O   HOH Z 411 " =    4.728
peak=   -3.708 closest distance to " CA  ASN A 127 " =    0.982
peak=   -3.695 closest distance to " ND2 ASN A 285 " =    2.524
peak=   -3.691 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.689 closest distance to " CA  ALA A 114 " =    1.111
peak=   -3.688 closest distance to " O   HOH Z 336 " =    5.174
peak=   -3.683 closest distance to " CG  GLU A   2 " =    1.166
peak=   -3.650 closest distance to " O   HOH Z  55 " =    2.612
peak=   -3.648 closest distance to " CA  SER A 276 " =    1.363
peak=   -3.639 closest distance to " O   TYR A  15 " =    1.363
peak=   -3.626 closest distance to " OG  SER A  32 " =    1.393
peak=   -3.622 closest distance to " CE  MET A 105 " =    2.262
peak=   -3.621 closest distance to " OG1 THR A  82 " =    2.142
peak=   -3.619 closest distance to " O   HOH Z 402 " =    1.214
peak=   -3.617 closest distance to " CG  PRO A 243 " =    1.531
peak=   -3.607 closest distance to " O   HOH Z 274 " =    2.908
peak=   -3.601 closest distance to " OE1 GLN A  88 " =    1.065
peak=   -3.597 closest distance to " C   TYR A  30 " =    0.906
peak=   -3.592 closest distance to " O   HOH Z  91 " =    2.204
peak=   -3.586 closest distance to " N   THR A 264 " =    1.322
peak=   -3.581 closest distance to " O   HOH Z 290 " =    0.914
peak=   -3.577 closest distance to " O   HOH Z 295 " =    1.152
peak=   -3.574 closest distance to " CA  VAL A 197 " =    1.062
peak=   -3.573 closest distance to " NH1BARG A 190 " =    2.146
peak=   -3.573 closest distance to " N   GLN A  55 " =    1.669
peak=   -3.570 closest distance to " CG  GLN A  73 " =    0.776
peak=   -3.561 closest distance to " O   HOH Z 117 " =    0.973
peak=   -3.560 closest distance to " O   HOH Z 335 " =    1.046
peak=   -3.560 closest distance to " O   HOH Z   7 " =    1.335
peak=   -3.548 closest distance to " O   HOH Z 166 " =    2.602
peak=   -3.534 closest distance to " N   GLY A  75 " =    1.147
peak=   -3.533 closest distance to " CB  SER A 276 " =    0.984
peak=   -3.528 closest distance to " C   ASP A 132 " =    1.672
peak=   -3.528 closest distance to " NH2BARG A 145 " =    2.025
peak=   -3.523 closest distance to " O   HOH Z  15 " =    1.630
peak=   -3.513 closest distance to " CD2 HIS A 115 " =    0.904
peak=   -3.508 closest distance to " O   HOH Z 246 " =    0.816
peak=   -3.503 closest distance to " O   ALA A  34 " =    1.934
peak=   -3.500 closest distance to " O   ALA A   1 " =    2.249
peak=   -3.488 closest distance to " CD  GLU A 236 " =    1.005
peak=   -3.484 closest distance to " OE2 GLU A 277 " =    2.749
peak=   -3.484 closest distance to " CB  LEU A 167 " =    1.979
peak=   -3.482 closest distance to " OH  TYR A 169 " =    1.105
peak=   -3.476 closest distance to " CG1 VAL A 296 " =    1.312
peak=   -3.475 closest distance to " CD2 LEU A 237 " =    2.402
peak=   -3.475 closest distance to " OG  SER A  26 " =    1.625
peak=   -3.474 closest distance to " O   HOH Z 275 " =    1.553
peak=   -3.473 closest distance to " O   HOH Z 277 " =    0.900
peak=   -3.470 closest distance to " N   SER A   3 " =    1.119
peak=   -3.468 closest distance to " CB  ALA A  43 " =    2.664
peak=   -3.464 closest distance to " O   HOH Z 221 " =    0.998
peak=   -3.458 closest distance to " N   SER A 134 " =    1.159
peak=   -3.455 closest distance to " O   HOH Z 423 " =    0.932
peak=   -3.447 closest distance to " CB  ALA A 100 " =    2.010
peak=   -3.442 closest distance to " O   HOH Z  92 " =    1.090
peak=   -3.441 closest distance to " O   THR A  31 " =    1.828
peak=   -3.435 closest distance to " OD2 ASP A 171 " =    1.706
peak=   -3.427 closest distance to " CG  GLN A  88 " =    0.905
peak=   -3.423 closest distance to " O   ASP A 298 " =    1.152
peak=   -3.419 closest distance to " NE2 GLN A  58 " =    3.450
peak=   -3.416 closest distance to " CA  VAL A 121 " =    1.187
peak=   -3.413 closest distance to " N   VAL A  72 " =    1.061
peak=   -3.409 closest distance to " CA  TYR A  68 " =    2.638
peak=   -3.405 closest distance to " OG  SER A  87 " =    1.353
peak=   -3.403 closest distance to " O   HOH Z 407 " =    1.634
peak=   -3.399 closest distance to " NH2 ARG A  36 " =    1.272
peak=   -3.395 closest distance to " O   HOH Z 124 " =    1.208
peak=   -3.381 closest distance to " CB  TRP A 150 " =    1.625
peak=   -3.381 closest distance to " N   GLU A   2 " =    1.113
peak=   -3.381 closest distance to " NE2 GLN A  88 " =    0.852
peak=   -3.379 closest distance to " SG  CYS A 254 " =    3.022
peak=   -3.376 closest distance to " O   HOH Z 174 " =    1.547
peak=   -3.371 closest distance to " CD1 LEU A 228 " =    2.589
peak=   -3.365 closest distance to " CA  LEU A 143 " =    0.882
peak=   -3.364 closest distance to " CG  ASP A  50 " =    2.284
peak=   -3.364 closest distance to " O   HOH Z 193 " =    1.020
peak=   -3.354 closest distance to " O   GLY A  80 " =    2.489
peak=   -3.353 closest distance to " O   HOH Z 283 " =    2.343
peak=   -3.350 closest distance to " O   MET A  47 " =    2.505
peak=   -3.346 closest distance to " O   HOH Z  49 " =    0.723
peak=   -3.344 closest distance to " CB  ALA A 161 " =    2.606
peak=   -3.342 closest distance to " CD2 TRP A 274 " =    1.201
peak=   -3.341 closest distance to " N   SER A   3 " =    2.562
peak=   -3.337 closest distance to " CB  ALA A 227 " =    2.445
peak=   -3.336 closest distance to " CD  ARG A 269 " =    2.445
peak=   -3.336 closest distance to " O   HOH Z 414 " =    1.482
peak=   -3.335 closest distance to " O   HOH Z 113 " =    2.176
peak=   -3.330 closest distance to " CG  ARG A 219 " =    2.240
peak=   -3.325 closest distance to " SG  CYS A 168 " =    0.922
peak=   -3.324 closest distance to " OG  SER A  97 " =    2.309
peak=   -3.322 closest distance to " CA  GLY A  23 " =    2.173
peak=   -3.316 closest distance to " CD2 LEU A 237 " =    2.625
peak=   -3.309 closest distance to " O   HOH Z 396 " =    1.929
peak=   -3.307 closest distance to " CD1 LEU A  96 " =    2.254
peak=   -3.306 closest distance to " CD1 PHE A  59 " =    1.759
peak=   -3.304 closest distance to " N   GLY A  17 " =    1.618
peak=   -3.304 closest distance to " CB  ALA A 114 " =    2.350
peak=   -3.301 closest distance to " O   ILE A 120 " =    0.825
peak=   -3.292 closest distance to " O   HOH Z 351 " =    1.615
peak=   -3.291 closest distance to " CE  MET A 188 " =    2.323
peak=   -3.288 closest distance to " NH1 ARG A  36 " =    1.071
peak=   -3.280 closest distance to " C   THR A 279 " =    1.005
peak=   -3.276 closest distance to " NE2 GLN A 278 " =    2.643
peak=   -3.265 closest distance to " CG1 VAL A 232 " =    2.307
peak=   -3.264 closest distance to " CG2 ILE A  49 " =    2.578
peak=   -3.261 closest distance to " CA  GLY A 203 " =    2.366
peak=   -3.261 closest distance to " OD1 ASN A 148 " =    1.320
peak=   -3.260 closest distance to " O   HOH Z 130 " =    2.619
peak=   -3.258 closest distance to " O   HOH Z  71 " =    0.820
peak=   -3.256 closest distance to " O   HOH Z 384 " =    1.503
peak=   -3.256 closest distance to " O   ASP A  27 " =    1.509
peak=   -3.254 closest distance to " NH2 ARG A 156 " =    1.112
peak=   -3.253 closest distance to " O   VAL A  67 " =    2.540
peak=   -3.251 closest distance to " O   HOH Z  93 " =    1.214
peak=   -3.249 closest distance to " CD  GLN A 223 " =    1.386
peak=   -3.247 closest distance to " O   HOH Z  50 " =    1.354
peak=   -3.246 closest distance to " O   HOH Z 368 " =    1.047
peak=   -3.245 closest distance to " O   HOH Z 119 " =    2.616
peak=   -3.222 closest distance to " O   HOH Z 109 " =    3.612
peak=   -3.222 closest distance to " O   HOH Z 300 " =    1.587
peak=   -3.220 closest distance to " O   HOH Z 263 " =    3.482
peak=   -3.219 closest distance to " O   GLN A  11 " =    0.872
peak=   -3.218 closest distance to " O   HOH Z 430 " =    1.235
peak=   -3.217 closest distance to " O   HOH Z 156 " =    1.323
peak=   -3.217 closest distance to " O   HOH Z 174 " =    2.110
peak=   -3.212 closest distance to " OD2 ASP A 298 " =    0.932
peak=   -3.202 closest distance to " O   HOH Z  11 " =    1.377
peak=   -3.199 closest distance to " CE  LYS A 119 " =    0.901
peak=   -3.195 closest distance to " O   HOH Z 314 " =    1.939
peak=   -3.187 closest distance to " O   THR A  18 " =    1.713
peak=   -3.184 closest distance to " O   HOH Z 269 " =    3.869
peak=   -3.181 closest distance to " O   HOH Z  48 " =    4.104
peak=   -3.180 closest distance to " O   HOH Z 293 " =    0.973
peak=   -3.178 closest distance to " CB  HIS A  86 " =    2.271
peak=   -3.175 closest distance to " CG  TRP A 266 " =    1.978
peak=   -3.173 closest distance to " O   HOH Z 423 " =    2.586
peak=   -3.167 closest distance to " O   HOH Z  43 " =    1.627
peak=   -3.165 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.163 closest distance to " O   HOH Z 139 " =    4.327
peak=   -3.161 closest distance to " O   SER A 164 " =    2.111
peak=   -3.161 closest distance to " O   HOH Z 348 " =    2.205
peak=   -3.157 closest distance to " CG1 VAL A 112 " =    2.394
peak=   -3.150 closest distance to " O   HOH Z 380 " =    4.145
peak=   -3.149 closest distance to " O   HOH Z 366 " =    1.335
peak=   -3.142 closest distance to " CB  SER A 271 " =    2.243
peak=   -3.140 closest distance to " O   HOH Z 111 " =    1.006
peak=   -3.133 closest distance to " NE  ARG A  24 " =    1.287
peak=   -3.127 closest distance to " O   TRP A  85 " =    2.047
peak=   -3.118 closest distance to " O   HOH Z 422 " =    1.106
peak=   -3.108 closest distance to " O   HOH Z 176 " =    1.095
peak=   -3.098 closest distance to " O   ASN A 301 " =    1.051
peak=   -3.094 closest distance to " CD2 TYR A 293 " =    1.899
peak=   -3.092 closest distance to " O   HOH Z 108 " =    2.363
peak=   -3.075 closest distance to " O   HOH Z  40 " =    3.416
peak=   -3.074 closest distance to " O   HOH Z 244 " =    1.500
peak=   -3.073 closest distance to " O   HOH Z 288 " =    0.834
peak=   -3.069 closest distance to " O   HOH Z  56 " =    1.479
peak=   -3.068 closest distance to " O   HOH Z 154 " =    1.979
peak=   -3.066 closest distance to " O   HOH Z 233 " =    2.232
peak=   -3.058 closest distance to " O   SER A 135 " =    1.780
peak=   -3.036 closest distance to " O   VAL A 174 " =    1.712
peak=   -3.017 closest distance to " O   HOH Z 198 " =    2.052
peak=   -2.952 closest distance to " O   SER A  62 " =    1.600

================= 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    :  0.5060 0.4939   6.308240e+00   6.291554e+00
   1_bss:  0.4990 0.4865   6.304759e+00   6.287247e+00
   1_xyz:  0.4439 0.4620   6.243665e+00   6.261696e+00
   1_adp:  0.4069 0.4549   6.199684e+00   6.254102e+00
   1_occ:  0.4067 0.4547   6.198898e+00   6.254247e+00
   2_bss:  0.4047 0.4491   6.200549e+00   6.253749e+00
   2_xyz:  0.3465 0.4229   6.106454e+00   6.215148e+00
   2_adp:  0.3369 0.4113   6.090278e+00   6.202985e+00
   2_occ:  0.3366 0.4119   6.090178e+00   6.203093e+00
   3_bss:  0.3370 0.4108   6.090817e+00   6.203477e+00
   3_xyz:  0.2758 0.3370   5.918838e+00   6.065534e+00
   3_adp:  0.2539 0.3209   5.862070e+00   6.026599e+00
   3_occ:  0.2537 0.3200   5.860618e+00   6.024476e+00
   4_bss:  0.2531 0.3188   5.859159e+00   6.023097e+00
   4_xyz:  0.2017 0.2579   5.654802e+00   5.841325e+00
   4_adp:  0.1858 0.2380   5.585354e+00   5.770517e+00
   4_occ:  0.1856 0.2378   5.585010e+00   5.770489e+00
   5_bss:  0.1857 0.2377   5.585928e+00   5.770231e+00
   5_xyz:  0.1594 0.2064   5.444874e+00   5.640105e+00
   5_adp:  0.1532 0.2015   5.417864e+00   5.618201e+00
   5_occ:  0.1529 0.2010   5.417180e+00   5.617950e+00
   5_bss:  0.1533 0.2013   5.419418e+00   5.619694e+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   6.583  11.018   6.578   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.583  11.018   6.578   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.583  11.018   6.578   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.583  11.018   6.578   0.000   0.000   0.000
   2_bss:  0.304  33.433   3.290   6.306   3.968   0.000   0.000   0.000
   2_xyz:  0.304  33.433   3.290   6.306   3.968   0.000   0.000   0.000
   2_adp:  0.304  33.433   3.290   6.306   3.968   0.000   0.000   0.000
   2_occ:  0.304  33.433   3.290   6.306   3.968   0.000   0.000   0.000
   3_bss:  0.323  57.628   2.528   4.718   2.942   0.000   0.000   0.000
   3_xyz:  0.323  57.628   2.528   4.718   2.942   0.000   0.000   0.000
   3_adp:  0.323  57.628   2.528   4.718   2.942   0.000   0.000   0.000
   3_occ:  0.323  57.628   2.528   4.718   2.942   0.000   0.000   0.000
   4_bss:  0.319  57.628   1.600   3.415   1.703   0.000   0.000   0.000
   4_xyz:  0.319  57.628   1.600   3.415   1.703   0.000   0.000   0.000
   4_adp:  0.319  57.628   1.600   3.415   1.703   0.000   0.000   0.000
   4_occ:  0.319  57.628   1.600   3.415   1.703   0.000   0.000   0.000
   5_bss:  0.323  57.694   0.906   2.200   1.365   0.000   0.000   0.000
   5_xyz:  0.323  57.694   0.906   2.200   1.365   0.000   0.000   0.000
   5_adp:  0.323  57.694   0.906   2.200   1.365   0.000   0.000   0.000
   5_occ:  0.323  57.694   0.906   2.200   1.365   0.000   0.000   0.000
   5_bss:  0.324  59.955  -0.533   0.539  -0.006   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.918 0.3559  0.4194    79281.363
   1_bss:  62.633 0.3581  0.5253    77017.622
   1_xyz:  56.931 0.4313  0.6259    66640.351
   1_adp:  55.249 0.4525  0.7272    63361.409
   1_occ:  55.202 0.4531  0.7276    63347.058
   2_bss:  54.872 0.4572  0.6566    62844.548
   2_xyz:  50.238 0.5153  0.7426    54494.598
   2_adp:  48.017 0.5436  0.7687    51314.006
   2_occ:  48.027 0.5434  0.7680    51352.589
   3_bss:  47.869 0.5453  0.7432    51054.174
   3_xyz:  36.810 0.6791  0.8939    31968.134
   3_adp:  34.289 0.7088  0.9121    28446.839
   3_occ:  34.161 0.7104  0.9135    28277.379
   4_bss:  34.021 0.7118  0.8788    28017.357
   4_xyz:  26.373 0.7960  0.9533    17697.319
   4_adp:  23.888 0.8226  0.9618    15136.279
   4_occ:  23.884 0.8227  0.9619    15152.291
   5_bss:  23.823 0.8233  0.9379    15110.690
   5_xyz:  20.009 0.8613  0.9640    11001.043
   5_adp:  19.364 0.8678  0.9636    10549.002
   5_occ:  19.353 0.8680  0.9632    10552.656
   5_bss:  19.379 0.8678  0.9512    10596.952
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4115e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4115e+01
   1_xyz:   1.800  0.014  0.110 18.328  0.007  4.123   1.5877e-01
   1_adp:   1.800  0.014  0.110 18.328  0.007  4.123   1.5877e-01
   1_occ:   1.800  0.014  0.110 18.328  0.007  4.123   1.5877e-01
   2_bss:   1.800  0.014  0.110 18.328  0.007  4.123   1.5877e-01
   2_xyz:   1.340  0.009  0.088 17.360  0.005  4.110   1.1202e-01
   2_adp:   1.340  0.009  0.088 17.360  0.005  4.110   1.1202e-01
   2_occ:   1.340  0.009  0.088 17.360  0.005  4.110   1.1202e-01
   3_bss:   1.340  0.009  0.088 17.360  0.005  4.110   1.1202e-01
   3_xyz:   1.311  0.010  0.097 16.164  0.005  4.113   1.0193e-01
   3_adp:   1.311  0.010  0.097 16.164  0.005  4.113   1.0193e-01
   3_occ:   1.311  0.010  0.097 16.164  0.005  4.113   1.0193e-01
   4_bss:   1.311  0.010  0.097 16.164  0.005  4.113   1.0193e-01
   4_xyz:   1.195  0.009  0.082 15.854  0.004  4.112   8.3488e-02
   4_adp:   1.195  0.009  0.082 15.854  0.004  4.112   8.3488e-02
   4_occ:   1.195  0.009  0.082 15.854  0.004  4.112   8.3488e-02
   5_bss:   1.195  0.009  0.082 15.854  0.004  4.112   8.3488e-02
   5_xyz:   0.996  0.007  0.077 15.170  0.003  4.122   6.1624e-02
   5_adp:   0.996  0.007  0.077 15.170  0.003  4.122   6.1624e-02
   5_occ:   0.996  0.007  0.077 15.170  0.003  4.122   6.1624e-02
   5_bss:   0.996  0.007  0.077 15.170  0.003  4.122   6.1624e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.072   7.0127e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.072   7.0127e+00
   1_xyz:  15.776  0.128  0.519 87.759  0.051  2.140   1.0702e-01
   1_adp:  15.776  0.128  0.519 87.759  0.051  2.140   1.0702e-01
   1_occ:  15.776  0.128  0.519 87.759  0.051  2.140   1.0702e-01
   2_bss:  15.776  0.128  0.519 87.759  0.051  2.140   1.0702e-01
   2_xyz:   9.709  0.073  0.284 84.556  0.049  2.047   6.3377e-02
   2_adp:   9.709  0.073  0.284 84.556  0.049  2.047   6.3377e-02
   2_occ:   9.709  0.073  0.284 84.556  0.049  2.047   6.3377e-02
   3_bss:   9.709  0.073  0.284 84.556  0.049  2.047   6.3377e-02
   3_xyz:   9.779  0.055  0.320 79.327  0.047  2.171   9.2003e-02
   3_adp:   9.779  0.055  0.320 79.327  0.047  2.171   9.2003e-02
   3_occ:   9.779  0.055  0.320 79.327  0.047  2.171   9.2003e-02
   4_bss:   9.779  0.055  0.320 79.327  0.047  2.171   9.2003e-02
   4_xyz:   7.678  0.061  0.238 86.726  0.032  2.191   7.6237e-02
   4_adp:   7.678  0.061  0.238 86.726  0.032  2.191   7.6237e-02
   4_occ:   7.678  0.061  0.238 86.726  0.032  2.191   7.6237e-02
   5_bss:   7.678  0.061  0.238 86.726  0.032  2.191   7.6237e-02
   5_xyz:   7.287  0.049  0.368 85.669  0.039  2.292   4.5864e-02
   5_adp:   7.287  0.049  0.368 85.669  0.039  2.292   4.5864e-02
   5_occ:   7.287  0.049  0.368 85.669  0.039  2.292   4.5864e-02
   5_bss:   7.287  0.049  0.368 85.669  0.039  2.292   4.5864e-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: 124.05   0.00  16.07  72.61   0.00  14.14 124.05   0.00  26.62
   1_occ: 124.05   0.00  16.07  72.61   0.00  14.14 124.05   0.00  26.62
   2_bss: 124.05   0.00  16.07  72.61   0.00  14.14 124.05   0.00  26.62
   2_xyz: 124.05   0.00  16.07  72.61   0.00  14.14 124.05   0.00  26.62
   2_adp: 118.28   0.00  14.52  75.53   0.00  12.35 118.28   0.00  26.33
   2_occ: 118.28   0.00  14.52  75.53   0.00  12.35 118.28   0.00  26.33
   3_bss: 118.28   0.00  14.52  75.53   0.00  12.35 118.28   0.00  26.33
   3_xyz: 118.28   0.00  14.52  75.53   0.00  12.35 118.28   0.00  26.33
   3_adp: 108.40   0.00  15.09  73.78   0.00  11.74 108.40   0.00  33.36
   3_occ: 108.40   0.00  15.09  73.78   0.00  11.74 108.40   0.00  33.36
   4_bss: 108.40   0.00  15.09  73.78   0.00  11.74 108.40   0.00  33.36
   4_xyz: 108.40   0.00  15.09  73.78   0.00  11.74 108.40   0.00  33.36
   4_adp:  99.95   0.00  14.89  89.19   0.00  10.69  99.95   2.94  37.78
   4_occ:  99.95   0.00  14.89  89.19   0.00  10.69  99.95   2.94  37.78
   5_bss:  99.95   0.00  14.89  89.19   0.00  10.69  99.95   2.94  37.78
   5_xyz:  99.95   0.00  14.89  89.19   0.00  10.69  99.95   2.94  37.78
   5_adp:  96.63   0.00  14.72  96.24   0.00  10.31  96.63   2.49  38.76
   5_occ:  96.63   0.00  14.72  96.24   0.00  10.31  96.63   2.49  38.76
   5_bss:  97.77   1.13  15.85  97.37   1.13  11.44  97.77   3.63  39.89
------------------------------------------------------------------------
 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:    1.094    0.009    0.415
   1_adp:    1.094    0.009    0.415
   1_occ:    1.094    0.009    0.415
   2_bss:    1.094    0.009    0.415
   2_xyz:    1.807    0.028    0.592
   2_adp:    1.807    0.028    0.592
   2_occ:    1.807    0.028    0.592
   3_bss:    1.807    0.028    0.592
   3_xyz:    1.874    0.008    0.760
   3_adp:    1.874    0.008    0.760
   3_occ:    1.874    0.008    0.760
   4_bss:    1.874    0.008    0.760
   4_xyz:    1.918    0.032    0.880
   4_adp:    1.918    0.032    0.880
   4_occ:    1.918    0.032    0.880
   5_bss:    1.918    0.032    0.880
   5_xyz:    2.011    0.072    0.928
   5_adp:    2.011    0.072    0.928
   5_occ:    2.011    0.072    0.928
   5_bss:    2.011    0.072    0.928
------------------------------------------------------------------------

CPU time actual refinement: 360.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/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_1080/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1080/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 360.12 
  Macro-tasks:
    bulk solvent and scale       = 42.93  
    individual site refinement   = 151.44 
    weights calculation          = 33.42  
    collect and process          = 6.52   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 234.46 
  Micro-tasks:
    mask                            = 3.13   
    f_calc                          = 115.10 
    alpha_beta                      = 8.58   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 124.27 
    fmodel                         = 7.40   
    r_factors                      = 0.24   
    phase_errors                   = 9.86   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 270.00 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.118 micro seconds
Total CPU time: 6.24 minutes
from_scatterers_fft:    627 calls, 114.70 s
gradients_fft:          571 calls, 111.59 s

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

# Date 2008-01-16 Time 03:08:57 PST -0800 (1200481737.62 s)
Start R-work = 0.5060, R-free = 0.4939 (no bulk solvent and anisotropic scale)
Final R-work = 0.1682, R-free = 0.2175 (no bulk solvent and anisotropic scale)

Start R-work = 0.4990, R-free = 0.4865
Final R-work = 0.1533, R-free = 0.2013