# Date 2008-01-16 Time 03:02:38 PST -0800 (1200481358.32 s)
#phil __OFF__

Command line arguments: "../1079.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 = 20459
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1079

-------------------------------------------------------------------------------
  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, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96158
Completeness in resolution range: 0.913538
Completeness with d_max=infinity: 0.910862

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9616

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, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96158
Completeness in resolution range: 0.913538
Completeness with d_max=infinity: 0.910862

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1985 [2252/2281]  2029   223   9.9%
  bin  2:  4.1985 -  3.3445 [2157/2180]  1941   216  10.0%
  bin  3:  3.3445 -  2.9252 [2124/2149]  1910   214  10.1%
  bin  4:  2.9252 -  2.6593 [2117/2143]  1910   207   9.8%
  bin  5:  2.6593 -  2.4696 [2092/2126]  1880   212  10.1%
  bin  6:  2.4696 -  2.3246 [2100/2128]  1894   206   9.8%
  bin  7:  2.3246 -  2.2085 [2073/2109]  1861   212  10.2%
  bin  8:  2.2085 -  2.1127 [2071/2113]  1865   206   9.9%
  bin  9:  2.1127 -  2.0315 [1996/2103]  1794   202  10.1%
  bin 10:  2.0315 -  1.9616 [ 607/2111]   546    61  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/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: 0.13 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:
        1.31 -     2.03: 13
        2.03 -     2.75: 320
        2.75 -     3.47: 4563
        3.47 -     4.18: 9346
        4.18 -     4.90: 13900
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.315 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.330 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.453 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.485 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.651 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28137 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_1079/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/model_refine_001.geo

CPU time processing inputs: 9.09


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


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5127   r_free= 0.5025   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.312729                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6834 0.99   1464  165 0.4289 0.4389      6.6702      6.6627|
|  2:  4.6834 -  3.7360 0.99   1399  153 0.4515 0.4771      6.8738      6.9463|
|  3:  3.7360 -  3.2692 0.99   1380  150 0.4974 0.4168      6.7241      6.6634|
|  4:  3.2692 -  2.9728 0.98   1359  157 0.5142 0.4792      6.5492       6.515|
|  5:  2.9728 -  2.7611 0.99   1376  151 0.5474 0.5598      6.3885      6.3709|
|  6:  2.7611 -  2.5992 0.99   1345  158 0.5349 0.4763      6.2949      6.1855|
|  7:  2.5992 -  2.4696 0.98   1347  138 0.5409 0.5012      6.2549      6.2046|
|  8:  2.4696 -  2.3625 0.98   1340  144 0.5450 0.5776      6.1522      6.2155|
|  9:  2.3625 -  2.2719 0.99   1342  155 0.5600 0.5704      6.1501      6.1215|
| 10:  2.2719 -  2.1938 0.99   1340  158 0.5348 0.5376      6.0874      6.1278|
| 11:  2.1938 -  2.1254 0.97   1338  137 0.5310 0.5391      6.0257      5.9799|
| 12:  2.1254 -  2.0648 0.98   1315  143 0.5440 0.5458      5.9363      5.9827|
| 13:  2.0648 -  2.0105 0.77   1020  126 0.5619 0.5542      5.8726      5.8483|
| 14:  2.0105 -  1.9616 0.19    265   24 0.5743 0.5443      5.7977      5.6977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6834  1464   165  0.63  40.52   0.77     0.66      96232.60|
|  2:  4.6834 -  3.7360  1399   153  0.62  42.03   0.84     0.69     135912.50|
|  3:  3.7360 -  3.2692  1380   150  0.50  51.54   0.78     0.63     142401.83|
|  4:  3.2692 -  2.9728  1359   157  0.41  58.88   0.76     0.52     121550.86|
|  5:  2.9728 -  2.7611  1376   151  0.34  64.24   0.69     0.44      94117.89|
|  6:  2.7611 -  2.5992  1345   158  0.35  63.95   0.71     0.41      76075.59|
|  7:  2.5992 -  2.4696  1347   138  0.33  65.34   0.71     0.38      67615.19|
|  8:  2.4696 -  2.3625  1340   144  0.27  69.74   0.69     0.33      65768.69|
|  9:  2.3625 -  2.2719  1342   155  0.18  76.54   0.71     0.22      64042.18|
| 10:  2.2719 -  2.1938  1340   158  0.13  80.61   0.73     0.15      61225.90|
| 11:  2.1938 -  2.1254  1338   137  0.12  81.16   0.76     0.15      55151.86|
| 12:  2.1254 -  2.0648  1315   143  0.15  78.83   0.72     0.20      50297.27|
| 13:  2.0648 -  2.0105  1020   126  0.14  79.65   0.71     0.19      42804.69|
| 14:  2.0105 -  1.9616   265    24  0.07  85.11   0.66     0.09      38171.12|
|alpha:            min =        0.09 max =            0.69 mean =         0.39|
|beta:             min =    38171.12 max =       142401.83 mean =     83123.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.34|
|phase err.(test): min =        0.00 max =           89.98 mean =        65.42|
|-----------------------------------------------------------------------------|

============================== 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 = 22.425944             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.362   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.200181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.941   (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 |  0.981 -  1.373:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.373 -  1.765:       13 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.765 -  2.157:       84 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.157 -  2.549:      478 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.549 -  2.941:     1265 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.941 -  3.332:     2402 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.332 -  3.724:     3912 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.724 -  4.116:     5121 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.116 -  4.508:     6801 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.508 -  4.900:     8083 |
|-----------------------------------------------------------------------------|
|-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 |       54.004 |
| 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  0.981 |       2.351 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    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 = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5155   r_free= 0.5076   ksol= 0.00   Bsol= 0.00   scale= 0.735    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.312946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5051   r_free= 0.4946   ksol= 0.30   Bsol= 20.00   scale= 0.936   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,10.50,6.88,0.00,0.00,0.00); trace/3= 7.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.223385                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.713563             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.025   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.748487              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.973   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5051      final r-factor (work) = 0.4568          |
| start r-factor (free) = 0.4946      final r-factor (free) = 0.4756          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 113.0261 = 18.71 * 0.50 * 6.3080 + 1.00 * 54.0036                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.9490 = 18.71 * 0.50 * 6.1765 + 1.00 * 0.1573                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4568      final r-factor (work) = 0.4224          |
| start r-factor (free) = 0.4756      final r-factor (free) = 0.4722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8142 = 1.75 * 1.00 * 6.1765 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9121 = 1.75 * 1.00 * 6.2279 + 1.00 * 0.0227                              |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.30  16.85    None  None   None       |
|    all(noH): 2823   0      0.00    101.30  16.85    None  None   None       |
|    Sol.    : 438    0      0.00    101.30  25.13    None  None   None       |
|    Mac.    : 2385   0      0.00    74.39   15.33    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 -  10.130:  957   |   5:    50.648 -  60.778:   39        |
|      1:    10.130 -  20.259:  980   |   6:    60.778 -  70.908:   17        |
|      2:    20.259 -  30.389:  519   |   7:    70.908 -  81.037:    8        |
|      3:    30.389 -  40.519:  218   |   8:    81.037 -  91.167:    2        |
|      4:    40.519 -  50.648:   82   |   9:    91.167 - 101.297:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4224 r_free = 0.4722             target_work(ml) = 6.222         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4225 r_free = 0.4719             target_work(ml) = 6.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4225   r_free= 0.4719   ksol= 0.30   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.39,10.50,6.88,0.00,0.00,0.00); trace/3= 7.93                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.220786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4206   r_free= 0.4655   ksol= 0.31   Bsol= 30.64   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.04,4.00,0.00,0.00,0.00); trace/3= 4.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.222109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.681038             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.633  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.776659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.013  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4206      final r-factor (work) = 0.3685          |
| start r-factor (free) = 0.4655      final r-factor (free) = 0.4420          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.9674 = 15.68 * 0.50 * 6.2254 + 1.00 * 0.1568                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.4574 = 15.68 * 0.50 * 6.1649 + 1.00 * 0.1217                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3685      final r-factor (work) = 0.3580          |
| start r-factor (free) = 0.4420      final r-factor (free) = 0.4386          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8100 = 0.78 * 1.00 * 6.1649 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7752 = 0.78 * 1.00 * 6.1355 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.99  15.56    None  None   None       |
|    all(noH): 2823   0      0.00    100.99  15.56    None  None   None       |
|    Sol.    : 438    0      0.00    100.99  25.49    None  None   None       |
|    Mac.    : 2385   0      0.00    72.34   13.73    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 -  10.099: 1112   |   5:    50.494 -  60.593:   28        |
|      1:    10.099 -  20.198:  956   |   6:    60.593 -  70.691:    8        |
|      2:    20.198 -  30.296:  456   |   7:    70.691 -  80.790:    6        |
|      3:    30.296 -  40.395:  201   |   8:    80.790 -  90.889:    1        |
|      4:    40.395 -  50.494:   54   |   9:    90.889 - 100.988:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3580 r_free = 0.4386             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3579 r_free = 0.4395             target_work(ml) = 6.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3579   r_free= 0.4395   ksol= 0.31   Bsol= 30.64   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.14,6.04,4.00,0.00,0.00,0.00); trace/3= 4.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.129543                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3582   r_free= 0.4382   ksol= 0.30   Bsol= 51.37   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,3.86,2.53,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.130736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.214791              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.016  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.062098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3582      final r-factor (work) = 0.3128          |
| start r-factor (free) = 0.4382      final r-factor (free) = 0.3878          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3968 = 9.21 * 0.50 * 6.1369 + 1.00 * 0.1217                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1426 = 9.21 * 0.50 * 6.0888 + 1.00 * 0.0893                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3128      final r-factor (work) = 0.2951          |
| start r-factor (free) = 0.3878      final r-factor (free) = 0.3805          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4769 = 1.06 * 1.00 * 6.0888 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3995 = 1.06 * 1.00 * 6.0103 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.26   16.58    None  None   None       |
|    all(noH): 2823   0      0.00    96.26   16.58    None  None   None       |
|    Sol.    : 438    0      0.00    96.26   31.71    None  None   None       |
|    Mac.    : 2385   0      0.00    81.33   13.80    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 -   9.626: 1087   |   5:    48.128 -  57.754:   65        |
|      1:     9.626 -  19.251:  835   |   6:    57.754 -  67.380:   16        |
|      2:    19.251 -  28.877:  436   |   7:    67.380 -  77.005:   16        |
|      3:    28.877 -  38.503:  237   |   8:    77.005 -  86.631:    8        |
|      4:    38.503 -  48.128:  121   |   9:    86.631 -  96.257:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2951 r_free = 0.3805             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2951 r_free = 0.3798             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2951   r_free= 0.3798   ksol= 0.30   Bsol= 51.37   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,3.86,2.53,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 5.997754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2949   r_free= 0.3787   ksol= 0.32   Bsol= 61.05   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,3.14,1.47,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 5.997264                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.965192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.971  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.497425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.912  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2949      final r-factor (work) = 0.2414          |
| start r-factor (free) = 0.3787      final r-factor (free) = 0.3103          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0263 = 8.97 * 0.50 * 6.0092 + 1.00 * 0.0893                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6588 = 8.97 * 0.50 * 5.9250 + 1.00 * 0.0995                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2414      final r-factor (work) = 0.2198          |
| start r-factor (free) = 0.3103      final r-factor (free) = 0.2859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9633 = 0.50 * 1.00 * 5.9250 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8846 = 0.50 * 1.00 * 5.7750 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.75   16.09    None  None   None       |
|    all(noH): 2823   0      0.00    91.75   16.09    None  None   None       |
|    Sol.    : 438    0      2.30    91.75   37.71    None  None   None       |
|    Mac.    : 2385   0      0.00    83.15   12.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.176: 1197   |   5:    45.877 -  55.053:   84        |
|      1:     9.176 -  18.351:  801   |   6:    55.053 -  64.228:   43        |
|      2:    18.351 -  27.526:  342   |   7:    64.228 -  73.404:   24        |
|      3:    27.526 -  36.702:  187   |   8:    73.404 -  82.579:    8        |
|      4:    36.702 -  45.877:  132   |   9:    82.579 -  91.755:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2198 r_free = 0.2859             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2194 r_free = 0.2854             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2194   r_free= 0.2854   ksol= 0.32   Bsol= 61.05   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,3.14,1.47,0.00,0.00,0.00); trace/3= 1.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.739973                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2189   r_free= 0.2843   ksol= 0.33   Bsol= 61.05   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.46,1.77,0.60,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.738103                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.120922              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.444  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.570  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2189      final r-factor (work) = 0.1804          |
| start r-factor (free) = 0.2843      final r-factor (free) = 0.2334          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0010 = 4.12 * 0.50 * 5.7761 + 1.00 * 0.0995                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7409 = 4.12 * 0.50 * 5.6635 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1804      final r-factor (work) = 0.1700          |
| start r-factor (free) = 0.2334      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5254 = 0.27 * 1.00 * 5.6635 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4890 = 0.27 * 1.00 * 5.5352 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.92   15.55    None  None   None       |
|    all(noH): 2823   0      0.00    86.92   15.55    None  None   None       |
|    Sol.    : 438    0      3.67    86.64   39.12    None  None   None       |
|    Mac.    : 2385   0      0.00    86.92   11.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.692: 1189   |   5:    43.460 -  52.152:  105        |
|      1:     8.692 -  17.384:  901   |   6:    52.152 -  60.844:   56        |
|      2:    17.384 -  26.076:  264   |   7:    60.844 -  69.535:   31        |
|      3:    26.076 -  34.768:  125   |   8:    69.535 -  78.227:   16        |
|      4:    34.768 -  43.460:  129   |   9:    78.227 -  86.919:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1700 r_free = 0.2197             target_work(ml) = 5.508         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1698 r_free = 0.2196             target_work(ml) = 5.507         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1698   r_free= 0.2196   ksol= 0.33   Bsol= 61.05   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.46,1.77,0.60,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.507356                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6834 0.99   1464  165 0.1146 0.1513      5.5331      5.7195|
|  2:  4.6834 -  3.7360 0.99   1399  153 0.1142 0.1466      5.6862      5.9639|
|  3:  3.7360 -  3.2692 0.99   1380  150 0.1556 0.2084      5.8063      6.0535|
|  4:  3.2692 -  2.9728 0.98   1359  157 0.1952 0.2308      5.8181       5.979|
|  5:  2.9728 -  2.7611 0.99   1376  151 0.2030 0.2398      5.6882      5.8017|
|  6:  2.7611 -  2.5992 0.99   1345  158 0.1876 0.2832      5.5682      5.7671|
|  7:  2.5992 -  2.4696 0.98   1347  138 0.1934 0.2315      5.5375      5.6691|
|  8:  2.4696 -  2.3625 0.98   1340  144 0.2048 0.2503      5.4793      5.6962|
|  9:  2.3625 -  2.2719 0.99   1342  155 0.1945 0.2800      5.4227       5.605|
| 10:  2.2719 -  2.1938 0.99   1340  158 0.1938 0.2398      5.3825      5.5577|
| 11:  2.1938 -  2.1254 0.97   1338  137 0.1804 0.2399      5.2765      5.4848|
| 12:  2.1254 -  2.0648 0.98   1315  143 0.1849 0.2621      5.2255      5.4702|
| 13:  2.0648 -  2.0105 0.77   1020  126 0.1831 0.2388      5.1422      5.3592|
| 14:  2.0105 -  1.9616 0.19    265   24 0.1759 0.1870      5.0412      5.1745|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6834  1464   165  0.92  11.46   0.96     0.94       9971.44|
|  2:  4.6834 -  3.7360  1399   153  0.92  12.00   1.02     0.99      14389.76|
|  3:  3.7360 -  3.2692  1380   150  0.88  17.70   1.03     1.03      20263.01|
|  4:  3.2692 -  2.9728  1359   157  0.84  22.02   1.01     0.96      20741.14|
|  5:  2.9728 -  2.7611  1376   151  0.81  24.92   1.01     0.99      17814.48|
|  6:  2.7611 -  2.5992  1345   158  0.82  24.32   1.00     0.95      15027.81|
|  7:  2.5992 -  2.4696  1347   138  0.83  23.93   1.00     0.94      13042.81|
|  8:  2.4696 -  2.3625  1340   144  0.81  25.94   1.02     0.97      12384.59|
|  9:  2.3625 -  2.2719  1342   155  0.81  25.25   1.02     0.96      10880.08|
| 10:  2.2719 -  2.1938  1340   158  0.83  24.17   1.00     0.93       9600.59|
| 11:  2.1938 -  2.1254  1338   137  0.84  23.28   1.01     0.95       8384.40|
| 12:  2.1254 -  2.0648  1315   143  0.82  24.63   1.01     0.96       7972.62|
| 13:  2.0648 -  2.0105  1020   126  0.81  25.45   1.01     0.98       6935.96|
| 14:  2.0105 -  1.9616   265    24  0.81  25.50   1.00     0.96       5784.03|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     5784.03 max =        20741.14 mean =     12906.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.99 mean =        21.80|
|phase err.(test): min =        0.00 max =           89.67 mean =        20.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2199   ksol= 0.33   Bsol= 56.65   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.61,-0.14,0.00,-0.00,-0.00); trace/3= -0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.509765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2199   ksol= 0.33   Bsol= 56.65   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,0.61,-0.14,0.00,-0.00,-0.00); trace/3= -0.00                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.509765                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6834 0.99   1464  165 0.1163 0.1544      5.5548      5.7411|
|  2:  4.6834 -  3.7360 0.99   1399  153 0.1157 0.1474      5.6938      5.9686|
|  3:  3.7360 -  3.2692 0.99   1380  150 0.1556 0.2080      5.8075      6.0498|
|  4:  3.2692 -  2.9728 0.98   1359  157 0.1947 0.2302      5.8177      5.9772|
|  5:  2.9728 -  2.7611 0.99   1376  151 0.2035 0.2386      5.6895      5.8018|
|  6:  2.7611 -  2.5992 0.99   1345  158 0.1876 0.2823      5.5671      5.7657|
|  7:  2.5992 -  2.4696 0.98   1347  138 0.1932 0.2321      5.5367      5.6699|
|  8:  2.4696 -  2.3625 0.98   1340  144 0.2049 0.2510      5.4793      5.6979|
|  9:  2.3625 -  2.2719 0.99   1342  155 0.1944 0.2806      5.4227      5.6038|
| 10:  2.2719 -  2.1938 0.99   1340  158 0.1937 0.2400      5.3823      5.5589|
| 11:  2.1938 -  2.1254 0.97   1338  137 0.1799 0.2400      5.2761      5.4843|
| 12:  2.1254 -  2.0648 0.98   1315  143 0.1851 0.2631      5.2267      5.4741|
| 13:  2.0648 -  2.0105 0.77   1020  126 0.1828 0.2385      5.1414      5.3575|
| 14:  2.0105 -  1.9616 0.19    265   24 0.1763 0.1860      5.0402      5.1707|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6834  1464   165  0.92  11.83   0.96     0.92      10390.02|
|  2:  4.6834 -  3.7360  1399   153  0.92  12.23   1.01     0.98      14791.07|
|  3:  3.7360 -  3.2692  1380   150  0.88  17.71   1.02     1.02      20342.35|
|  4:  3.2692 -  2.9728  1359   157  0.85  21.94   0.99     0.95      20679.12|
|  5:  2.9728 -  2.7611  1376   151  0.81  24.87   0.99     0.97      17772.30|
|  6:  2.7611 -  2.5992  1345   158  0.82  24.24   0.98     0.94      14963.70|
|  7:  2.5992 -  2.4696  1347   138  0.83  23.89   0.98     0.92      13026.60|
|  8:  2.4696 -  2.3625  1340   144  0.81  25.93   1.00     0.94      12372.04|
|  9:  2.3625 -  2.2719  1342   155  0.81  25.25   1.00     0.94      10904.79|
| 10:  2.2719 -  2.1938  1340   158  0.83  24.15   0.98     0.91       9605.46|
| 11:  2.1938 -  2.1254  1338   137  0.84  23.27   0.98     0.93       8389.89|
| 12:  2.1254 -  2.0648  1315   143  0.82  24.65   0.98     0.94       7997.16|
| 13:  2.0648 -  2.0105  1020   126  0.81  25.44   0.98     0.95       6927.25|
| 14:  2.0105 -  1.9616   265    24  0.81  25.47   0.98     0.94       5753.65|
|alpha:            min =        0.91 max =            1.02 mean =         0.95|
|beta:             min =     5753.65 max =        20679.12 mean =     12967.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.96 mean =        21.83|
|phase err.(test): min =        0.00 max =           89.45 mean =        20.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.088)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    87.34   15.97    None  None   None       |
|    all(noH): 2823   0      0.43    87.34   15.97    None  None   None       |
|    Sol.    : 438    0      4.10    87.06   39.55    None  None   None       |
|    Mac.    : 2385   0      0.43    87.34   11.65    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:     0.425 -   9.117: 1189   |   5:    43.885 -  52.577:  105        |
|      1:     9.117 -  17.809:  901   |   6:    52.577 -  61.269:   56        |
|      2:    17.809 -  26.501:  264   |   7:    61.269 -  69.961:   31        |
|      3:    26.501 -  35.193:  125   |   8:    69.961 -  78.652:   16        |
|      4:    35.193 -  43.885:  129   |   9:    78.652 -  87.344:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 356         
Filter by distance & map next to the model:
   mapped sites are within: 0.685 - 5.465
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 353 from: 356
   mapped sites are within: 0.700 - 5.465

peak=    7.294 closest distance to " O   HOH Z 426 " =    1.574
peak=    7.206 closest distance to " NH2 ARG A  66 " =    2.262
peak=    6.948 closest distance to " O   HOH Z  41 " =    1.165
peak=    6.399 closest distance to " O   HOH Z 400 " =    1.491
peak=    6.053 closest distance to " CG  GLN A  77 " =    1.224
peak=    5.696 closest distance to " O   HOH Z 335 " =    1.210
peak=    5.515 closest distance to " CG  LEU A   5 " =    1.650
peak=    5.291 closest distance to " CD1AILE A 234 " =    1.507
peak=    5.269 closest distance to " O   HOH Z 342 " =    0.978
peak=    5.219 closest distance to " CD  ARG A 269 " =    0.933
peak=    5.092 closest distance to " CG2 VAL A 230 " =    1.107
peak=    5.053 closest distance to " CB  GLN A  73 " =    1.208
peak=    5.039 closest distance to " O   PHE A  61 " =    0.933
peak=    5.021 closest distance to " O   HOH Z 279 " =    1.312
peak=    5.015 closest distance to " CG2 VAL A 296 " =    1.207
peak=    5.004 closest distance to " O   ARG A 275 " =    0.846
peak=    4.991 closest distance to " O   HOH Z 159 " =    1.292
peak=    4.955 closest distance to " N   ASP A 298 " =    1.001
peak=    4.953 closest distance to " O   HOH Z 117 " =    1.649
peak=    4.880 closest distance to " O   HOH Z  37 " =    1.832
peak=    4.846 closest distance to " O   HOH Z 422 " =    1.381
peak=    4.844 closest distance to " CB  ASN A 285 " =    1.069
peak=    4.813 closest distance to " O   HOH Z  69 " =    1.559
peak=    4.788 closest distance to " CG1BVAL A 121 " =    1.689
peak=    4.787 closest distance to " O   HOH Z   4 " =    1.512
peak=    4.773 closest distance to " O   THR A  29 " =    0.894
peak=    4.732 closest distance to " O   ASP A 298 " =    0.915
peak=    4.718 closest distance to " CB  GLN A  88 " =    1.351
peak=    4.714 closest distance to " N   ARG A 275 " =    0.847
peak=    4.671 closest distance to " CG  ARG A 138 " =    1.186
peak=    4.662 closest distance to " CG  PRO A 280 " =    1.074
peak=    4.656 closest distance to " CB  PRO A 198 " =    1.136
peak=    4.646 closest distance to " O   HOH Z 246 " =    1.685
peak=    4.632 closest distance to " C   TYR A  30 " =    0.891
peak=    4.606 closest distance to " O   HOH Z  48 " =    2.134
peak=    4.598 closest distance to " NE2 GLN A  89 " =    1.189
peak=    4.571 closest distance to " O   HOH Z 404 " =    1.599
peak=    4.547 closest distance to " CD  LYS A 289 " =    1.116
peak=    4.528 closest distance to " OD1 ASN A 301 " =    1.027
peak=    4.527 closest distance to " O   HOH Z 103 " =    0.902
peak=    4.508 closest distance to " OD2 ASP A  65 " =    1.135
peak=    4.491 closest distance to " C   VAL A 121 " =    1.042
peak=    4.490 closest distance to " N   VAL A 121 " =    0.962
peak=    4.488 closest distance to " CB  ASP A  65 " =    1.075
peak=    4.481 closest distance to " CB  SER A  62 " =    1.112
peak=    4.458 closest distance to " NE2 HIS A 115 " =    0.837
peak=    4.456 closest distance to " O   HOH Z 277 " =    1.922
peak=    4.436 closest distance to " CD  GLN A  73 " =    1.323
peak=    4.431 closest distance to " C   ALA A 299 " =    0.821
peak=    4.400 closest distance to " CG1 ILE A 120 " =    1.284
peak=    4.329 closest distance to " CG2 VAL A  67 " =    1.048
peak=    4.323 closest distance to " O   HOH Z  46 " =    1.269
peak=    4.319 closest distance to " O   HOH Z 131 " =    1.120
peak=    4.315 closest distance to " CB  ARG A 275 " =    0.950
peak=    4.308 closest distance to " NH2AARG A 102 " =    1.012
peak=    4.273 closest distance to " N   PHE A  61 " =    0.712
peak=    4.273 closest distance to " O   SER A  62 " =    1.039
peak=    4.271 closest distance to " N   ILE A  33 " =    1.183
peak=    4.260 closest distance to " CA  GLU A 277 " =    1.151
peak=    4.234 closest distance to " O   HOH Z  84 " =    1.118
peak=    4.206 closest distance to " CG1 VAL A 153 " =    1.304
peak=    4.199 closest distance to " N   VAL A  67 " =    1.014
peak=    4.194 closest distance to " O   HOH Z 192 " =    2.475
peak=    4.193 closest distance to " O   HOH Z   1 " =    2.580
peak=    4.191 closest distance to " O   GLN A  55 " =    0.973
peak=    4.188 closest distance to " O   HOH Z  61 " =    1.489
peak=    4.179 closest distance to " CB  VAL A 230 " =    1.313
peak=    4.179 closest distance to " CB  GLN A  58 " =    1.281
peak=    4.170 closest distance to " O   HOH Z  54 " =    1.369
peak=    4.155 closest distance to " CA  GLY A 196 " =    1.018
peak=    4.152 closest distance to " O   HOH Z 206 " =    1.221
peak=    4.152 closest distance to " O   HOH Z 149 " =    1.372
peak=    4.142 closest distance to " CA  VAL A 296 " =    1.237
peak=    4.135 closest distance to " O   HOH Z 138 " =    1.057
peak=    4.129 closest distance to " OG ASER A 164 " =    1.172
peak=    4.113 closest distance to " CA  GLU A 152 " =    1.067
peak=    4.112 closest distance to " OG ASER A 134 " =    1.346
peak=    4.112 closest distance to " O   GLU A   2 " =    1.000
peak=    4.104 closest distance to " O   HOH Z 182 " =    1.575
peak=    4.103 closest distance to " O   LYS A 289 " =    1.043
peak=    4.103 closest distance to " O   HOH Z 324 " =    1.893
peak=    4.085 closest distance to " CB  TRP A 266 " =    1.030
peak=    4.083 closest distance to " O   HOH Z 221 " =    1.671
peak=    4.078 closest distance to " CA  THR A 246 " =    1.089
peak=    4.069 closest distance to " O   HOH Z   9 " =    2.248
peak=    4.062 closest distance to " CA  ILE A 120 " =    1.513
peak=    4.058 closest distance to " NH1 ARG A 269 " =    1.110
peak=    4.058 closest distance to " CB  PHE A  61 " =    0.987
peak=    4.054 closest distance to " O   HOH Z 390 " =    0.990
peak=    4.053 closest distance to " CD  LYS A 166 " =    1.810
peak=    4.051 closest distance to " O   HOH Z 217 " =    1.867
peak=    4.041 closest distance to " O   HOH Z 427 " =    3.857
peak=    4.022 closest distance to " CG AARG A 275 " =    1.205
peak=    4.008 closest distance to " CG  PRO A  54 " =    1.292
peak=    4.000 closest distance to " OG  SER A  32 " =    1.076
peak=    3.999 closest distance to " O   HOH Z 126 " =    2.163
peak=    3.990 closest distance to " O   HOH Z 256 " =    1.104
peak=    3.990 closest distance to " CB  ALA A  34 " =    1.028
peak=    3.973 closest distance to " CB  SER A  63 " =    1.336
peak=    3.960 closest distance to " CD1 TRP A 274 " =    1.186
peak=    3.957 closest distance to " O   HOH Z  57 " =    1.814
peak=    3.943 closest distance to " O   HOH Z  62 " =    2.118
peak=    3.933 closest distance to " OG1 THR A  31 " =    0.943
peak=    3.933 closest distance to " OD1 ASN A  60 " =    0.933
peak=    3.927 closest distance to " CA  ARG A  66 " =    1.311
peak=    3.914 closest distance to " O   HOH Z 277 " =    1.626
peak=    3.913 closest distance to " CB  LYS A  76 " =    1.156
peak=    3.912 closest distance to " O  BHOH Z  74 " =    1.073
peak=    3.899 closest distance to " C   PRO A  54 " =    0.924
peak=    3.886 closest distance to " O   HOH Z 278 " =    1.324
peak=    3.882 closest distance to " CB  ARG A 138 " =    1.252
peak=    3.878 closest distance to " O   HOH Z  20 " =    2.074
peak=    3.869 closest distance to " O   HOH Z 374 " =    1.093
peak=    3.852 closest distance to " O   HOH Z 119 " =    2.004
peak=    3.851 closest distance to " NH1BARG A 275 " =    1.264
peak=    3.850 closest distance to " NZ  LYS A  76 " =    1.118
peak=    3.840 closest distance to " CA  ALA A 295 " =    0.918
peak=    3.839 closest distance to " O   HOH Z 144 " =    1.854
peak=    3.829 closest distance to " CB  SER A  26 " =    1.036
peak=    3.820 closest distance to " CD2 LEU A 228 " =    1.519
peak=    3.817 closest distance to " O   HOH Z 174 " =    1.729
peak=    3.802 closest distance to " CB  TRP A 179 " =    1.693
peak=    3.790 closest distance to " CA  ALA A  21 " =    1.794
peak=    3.781 closest distance to " O   HOH Z  44 " =    2.056
peak=    3.779 closest distance to " O   HOH Z 124 " =    1.941
peak=    3.774 closest distance to " CG  GLU A 236 " =    0.819
peak=    3.770 closest distance to " O   HOH Z 295 " =    1.313
peak=    3.768 closest distance to " O   HOH Z 111 " =    2.008
peak=    3.765 closest distance to " CB  MET A  47 " =    1.077
peak=    3.755 closest distance to " CA  GLY A 147 " =    0.854
peak=    3.754 closest distance to " CB BVAL A  41 " =    1.415
peak=    3.744 closest distance to " CG2 VAL A 268 " =    1.194
peak=    3.743 closest distance to " NH1 ARG A 138 " =    0.970
peak=    3.737 closest distance to " ND1 HIS A  81 " =    1.401
peak=    3.722 closest distance to " CA  GLY A  23 " =    1.160
peak=    3.709 closest distance to " N   SER A   3 " =    0.871
peak=    3.708 closest distance to " CD BLYS A 290 " =    1.170
peak=    3.702 closest distance to " O   HOH Z 139 " =    4.530
peak=    3.689 closest distance to " O   HOH Z 272 " =    2.059
peak=    3.673 closest distance to " CB  PRO A  90 " =    1.446
peak=    3.671 closest distance to " N   ALA A 256 " =    1.218
peak=    3.667 closest distance to " CB  TYR A  30 " =    1.305
peak=    3.637 closest distance to " O   HOH Z 368 " =    2.747
peak=    3.621 closest distance to " OD1 ASP A 238 " =    0.977
peak=    3.618 closest distance to " O   HOH Z 258 " =    3.176
peak=    3.613 closest distance to " ND2 ASN A  69 " =    2.577
peak=    3.610 closest distance to " O   HOH Z  52 " =    1.468
peak=    3.606 closest distance to " NE  ARG A 138 " =    1.353
peak=    3.606 closest distance to " CA  HIS A 115 " =    0.993
peak=    3.603 closest distance to " O   HOH Z 261 " =    1.973
peak=    3.595 closest distance to " O   HOH Z 203 " =    1.884
peak=    3.588 closest distance to " NH2AARG A 145 " =    0.998
peak=    3.581 closest distance to " CB  ALA A 244 " =    1.133
peak=    3.580 closest distance to " O   HOH Z  49 " =    1.500
peak=    3.576 closest distance to " CA  THR A  18 " =    1.114
peak=    3.567 closest distance to " N   SER A 271 " =    1.198
peak=    3.564 closest distance to " O   HOH Z 394 " =    1.951
peak=    3.561 closest distance to " O   GLY A  91 " =    1.316
peak=    3.557 closest distance to " O   HOH Z 272 " =    1.825
peak=    3.556 closest distance to " O   HOH Z 257 " =    2.189
peak=    3.553 closest distance to " O   HOH Z 352 " =    1.538
peak=    3.550 closest distance to " O   HOH Z 133 " =    2.230
peak=    3.547 closest distance to " CG  PRO A 163 " =    4.746
peak=    3.544 closest distance to " O   HOH Z 156 " =    3.317
peak=    3.534 closest distance to " O   HOH Z 108 " =    1.481
peak=    3.527 closest distance to " N   THR A  29 " =    0.911
peak=    3.527 closest distance to " OG  SER A  62 " =    3.801
peak=    3.520 closest distance to " CE  LYS A 119 " =    1.699
peak=    3.518 closest distance to " N   TYR A  15 " =    1.002
peak=    3.513 closest distance to " O   HOH Z 128 " =    1.880
peak=    3.513 closest distance to " O   HOH Z 124 " =    1.964
peak=    3.511 closest distance to " O   ILE A 151 " =    1.342
peak=    3.508 closest distance to " O   HOH Z   6 " =    2.291
peak=    3.506 closest distance to " O   HOH Z 391 " =    1.218
peak=    3.505 closest distance to " CZ3 TRP A 274 " =    4.775
peak=    3.498 closest distance to " CA  ARG A 102 " =    1.562
peak=    3.498 closest distance to " CB  MET A  40 " =    0.750
peak=    3.496 closest distance to " O   HOH Z 395 " =    1.508
peak=    3.494 closest distance to " N   GLY A 111 " =    1.460
peak=    3.485 closest distance to " CG  GLU A 277 " =    3.235
peak=    3.484 closest distance to " O   HOH Z 417 " =    1.505
peak=    3.474 closest distance to " N   ALA A 100 " =    0.783
peak=    3.471 closest distance to " O   HOH Z 214 " =    1.575
peak=    3.469 closest distance to " CD2 TYR A  68 " =    1.100
peak=    3.468 closest distance to " CB  SER A 141 " =    1.027
peak=    3.460 closest distance to " CB  ALA A   1 " =    1.711
peak=    3.459 closest distance to " O   HOH Z  19 " =    1.660
peak=    3.458 closest distance to " O   HOH Z 178 " =    1.240
peak=    3.457 closest distance to " O   HOH Z  89 " =    3.570
peak=    3.455 closest distance to " CA  GLY A 267 " =    1.498
peak=    3.451 closest distance to " O   HOH Z  39 " =    1.830
peak=    3.445 closest distance to " NH1AARG A 145 " =    1.104
peak=    3.441 closest distance to " O   HOH Z 102 " =    1.464
peak=    3.440 closest distance to " O   HOH Z 155 " =    2.142
peak=    3.437 closest distance to " O   HOH Z 327 " =    2.767
peak=    3.435 closest distance to " CB  ILE A 263 " =    0.917
peak=    3.431 closest distance to " N   ASN A  39 " =    1.253
peak=    3.427 closest distance to " CA  THR A 235 " =    0.931
peak=    3.424 closest distance to " O   HOH Z 416 " =    1.733
peak=    3.420 closest distance to " OE1 GLN A  11 " =    1.972
peak=    3.417 closest distance to " O   HOH Z  48 " =    1.943
peak=    3.415 closest distance to " O   HOH Z  85 " =    2.137
peak=    3.414 closest distance to " N   SER A 164 " =    0.824
peak=    3.411 closest distance to " O   HOH Z 377 " =    1.898
peak=    3.406 closest distance to " O   LEU A  25 " =    0.923
peak=    3.405 closest distance to " N   ASN A  74 " =    1.140
peak=    3.403 closest distance to " CB  ASN A 148 " =    1.930
peak=    3.402 closest distance to " O   HOH Z 368 " =    1.442
peak=    3.400 closest distance to " N   ASN A 224 " =    1.324
peak=    3.396 closest distance to " CB  ALA A 137 " =    1.452
peak=    3.390 closest distance to " CA  GLY A   6 " =    1.038
peak=    3.390 closest distance to " N   ASP A 286 " =    1.063
peak=    3.387 closest distance to " OD2 ASP A  50 " =    1.185
peak=    3.387 closest distance to " CB  GLN A 194 " =    0.880
peak=    3.384 closest distance to " CB  GLU A 277 " =    1.037
peak=    3.384 closest distance to " N   ALA A 299 " =    1.010
peak=    3.382 closest distance to " CG  TRP A 150 " =    1.132
peak=    3.380 closest distance to " O   HOH Z 431 " =    2.137
peak=    3.375 closest distance to " NE2 GLN A 240 " =    1.086
peak=    3.373 closest distance to " O   VAL A  72 " =    0.870
peak=    3.369 closest distance to " O   HOH Z 358 " =    1.717
peak=    3.365 closest distance to " CB  GLN A  89 " =    0.988
peak=    3.365 closest distance to " NH2BARG A 145 " =    1.830
peak=    3.364 closest distance to " CD1 LEU A 297 " =    1.007
peak=    3.361 closest distance to " O   HOH Z 323 " =    3.158
peak=    3.357 closest distance to " CB  PRO A  54 " =    0.830
peak=    3.355 closest distance to " ND2 ASN A 301 " =    0.889
peak=    3.354 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.353 closest distance to " CB  ASN A 187 " =    1.310
peak=    3.350 closest distance to " N   PHE A  59 " =    1.237
peak=    3.347 closest distance to " CA  PRO A 243 " =    0.921
peak=    3.345 closest distance to " O   HOH Z 133 " =    1.597
peak=    3.345 closest distance to " CD1 LEU A 255 " =    1.344
peak=    3.342 closest distance to " CG  MET A 185 " =    0.923
peak=    3.340 closest distance to " CB  PHE A 283 " =    0.957
peak=    3.339 closest distance to " CA  GLY A  80 " =    1.091
peak=    3.339 closest distance to " CG  GLN A  11 " =    1.592
peak=    3.339 closest distance to " CA  LEU A   5 " =    1.058
peak=    3.339 closest distance to " CD1 TRP A 266 " =    1.170
peak=    3.338 closest distance to " O   ARG A  56 " =    1.343
peak=    3.335 closest distance to " O   HOH Z 258 " =    1.877
peak=    3.335 closest distance to " OH  TYR A 247 " =    1.001
peak=    3.334 closest distance to " OG  SER A  97 " =    3.527
peak=    3.332 closest distance to " O   HOH Z  11 " =    1.376
peak=    3.330 closest distance to " CB  ALA A 299 " =    0.951
peak=    3.325 closest distance to " O   HOH Z 136 " =    1.715
peak=    3.325 closest distance to " O   HOH Z 427 " =    1.247
peak=    3.324 closest distance to " CA  SER A  63 " =    1.285
peak=    3.324 closest distance to " O   HOH Z 364 " =    1.560
peak=    3.322 closest distance to " O   HOH Z 407 " =    2.705
peak=    3.318 closest distance to " OG  SER A   3 " =    1.027
peak=    3.315 closest distance to " CA  TYR A  30 " =    1.092
peak=    3.313 closest distance to " O   HOH Z  80 " =    2.502
peak=    3.311 closest distance to " CG2 THR A  31 " =    1.081
peak=    3.310 closest distance to " CB  GLU A   2 " =    1.351
peak=    3.310 closest distance to " O   SER A 273 " =    1.095
peak=    3.309 closest distance to " O   HOH Z 272 " =    1.474
peak=    3.309 closest distance to " O   GLU A 277 " =    1.495
peak=    3.308 closest distance to " O   HOH Z 329 " =    2.524
peak=    3.307 closest distance to " CA  ILE A  33 " =    1.606
peak=    3.305 closest distance to " C   PHE A  16 " =    1.271
peak=    3.300 closest distance to " O   HOH Z  63 " =    2.012
peak=    3.300 closest distance to " O   HOH Z 209 " =    1.957
peak=    3.299 closest distance to " O   HOH Z 191 " =    1.359
peak=    3.297 closest distance to " CA  ASN A 110 " =    1.087
peak=    3.294 closest distance to " O   HOH Z 363 " =    1.506
peak=    3.290 closest distance to " O   HOH Z 215 " =    1.577
peak=    3.290 closest distance to " NE2 HIS A  86 " =    1.522
peak=    3.290 closest distance to " CG2 THR A  18 " =    1.605
peak=    3.284 closest distance to " O   SER A  26 " =    1.199
peak=    3.281 closest distance to " CA  LEU A 282 " =    1.150
peak=    3.277 closest distance to " CA  ARG A  36 " =    1.129
peak=    3.275 closest distance to " N   THR A  31 " =    0.700
peak=    3.272 closest distance to " O   HOH Z 362 " =    4.792
peak=    3.272 closest distance to " O   HOH Z 118 " =    2.073
peak=    3.268 closest distance to " OE1 GLN A  77 " =    1.034
peak=    3.262 closest distance to " O   ASN A 301 " =    2.647
peak=    3.262 closest distance to " O   HOH Z 116 " =    3.998
peak=    3.258 closest distance to " CD  ARG A  36 " =    1.363
peak=    3.257 closest distance to " CE1 TYR A 116 " =    1.040
peak=    3.254 closest distance to " OD2 ASP A 162 " =    1.127
peak=    3.254 closest distance to " N   VAL A 265 " =    0.879
peak=    3.252 closest distance to " O   HOH Z 418 " =    1.757
peak=    3.250 closest distance to " O   HOH Z 411 " =    2.913
peak=    3.248 closest distance to " O   GLY A  57 " =    1.123
peak=    3.248 closest distance to " CG2 VAL A 112 " =    1.256
peak=    3.242 closest distance to " O   HOH Z 420 " =    5.465
peak=    3.240 closest distance to " O   HOH Z 271 " =    2.145
peak=    3.239 closest distance to " O   HOH Z 128 " =    1.366
peak=    3.236 closest distance to " CG2 VAL A 197 " =    1.272
peak=    3.233 closest distance to " CZ  PHE A 192 " =    0.993
peak=    3.231 closest distance to " CG  GLN A  55 " =    1.685
peak=    3.220 closest distance to " NH2 ARG A 156 " =    1.242
peak=    3.218 closest distance to " O   HOH Z 152 " =    2.316
peak=    3.218 closest distance to " CB  GLN A 183 " =    1.201
peak=    3.215 closest distance to " O   HOH Z 137 " =    1.561
peak=    3.213 closest distance to " O   HOH Z 425 " =    1.584
peak=    3.213 closest distance to " OE1 GLU A  37 " =    0.855
peak=    3.207 closest distance to " NH2AARG A 190 " =    1.166
peak=    3.207 closest distance to " CB  ALA A 100 " =    1.702
peak=    3.204 closest distance to " O   HOH Z 263 " =    2.006
peak=    3.203 closest distance to " CA  ALA A 100 " =    1.110
peak=    3.203 closest distance to " CA  ALA A 158 " =    1.224
peak=    3.203 closest distance to " NZ  LYS A 117 " =    3.165
peak=    3.200 closest distance to " O   HOH Z 174 " =    1.809
peak=    3.200 closest distance to " CZ  PHE A 218 " =    1.002
peak=    3.192 closest distance to " CE BMET A  47 " =    1.478
peak=    3.183 closest distance to " CE  MET A 188 " =    1.546
peak=    3.178 closest distance to " O   HOH Z 402 " =    1.714
peak=    3.175 closest distance to " O   HOH Z 351 " =    1.237
peak=    3.174 closest distance to " CB  ARG A 219 " =    0.917
peak=    3.172 closest distance to " CE3 TRP A 274 " =    2.507
peak=    3.171 closest distance to " O   HOH Z 142 " =    1.882
peak=    3.171 closest distance to " N   TRP A 177 " =    1.666
peak=    3.170 closest distance to " CD  LYS A 119 " =    1.108
peak=    3.169 closest distance to " CB  SER A  28 " =    1.066
peak=    3.168 closest distance to " ND2 ASN A  45 " =    1.272
peak=    3.166 closest distance to " CA  ALA A 248 " =    1.205
peak=    3.161 closest distance to " N   HIS A 108 " =    1.869
peak=    3.160 closest distance to " CB  ARG A 139 " =    0.734
peak=    3.159 closest distance to " O   HOH Z 189 " =    2.502
peak=    3.157 closest distance to " N   THR A  31 " =    0.925
peak=    3.149 closest distance to " CB  ALA A 114 " =    1.777
peak=    3.147 closest distance to " N   LEU A   5 " =    1.021
peak=    3.144 closest distance to " O   HOH Z 426 " =    1.708
peak=    3.143 closest distance to " O   HOH Z  68 " =    1.991
peak=    3.142 closest distance to " CA  ALA A 160 " =    1.018
peak=    3.140 closest distance to " CA  GLY A  75 " =    0.863
peak=    3.137 closest distance to " CB  PHE A  59 " =    1.051
peak=    3.131 closest distance to " N   GLY A 302 " =    1.178
peak=    3.129 closest distance to " CB  ASP A 140 " =    0.855
peak=    3.129 closest distance to " CD2 LEU A   5 " =    1.704
peak=    3.128 closest distance to " C   VAL A 296 " =    0.852
peak=    3.122 closest distance to " OG1 THR A 157 " =    0.914
peak=    3.110 closest distance to " NH2 ARG A 195 " =    1.094
peak=    3.103 closest distance to " CZ  PHE A  38 " =    0.911
peak=    3.101 closest distance to " CA  LEU A 101 " =    1.459
peak=    3.097 closest distance to " O   HOH Z 411 " =    1.659
peak=    3.094 closest distance to " N   THR A 264 " =    1.464
peak=    3.093 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.083 closest distance to " O   HOH Z  24 " =    1.907
peak=    3.083 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.071 closest distance to " O   HOH Z 172 " =    2.171
peak=    3.066 closest distance to " OE1 GLU A   2 " =    1.403
peak=    3.054 closest distance to " OG  SER A 276 " =    0.893
peak=    3.052 closest distance to " O   HOH Z  87 " =    2.410
peak=    3.051 closest distance to " CD1 ILE A  49 " =    1.174
peak=    3.051 closest distance to " OH  TYR A  30 " =    1.347
peak=    3.048 closest distance to " CG2 THR A 220 " =    0.867
peak=    3.039 closest distance to " CD2 LEU A 297 " =    0.813
peak=    3.030 closest distance to " CG2 VAL A  78 " =    0.988
peak=    3.011 closest distance to " CB  VAL A 296 " =    1.316
peak=    3.005 closest distance to " C   TRP A 274 " =    0.839

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 243         
Filter by distance & map next to the model:
   mapped sites are within: 0.503 - 5.153
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 234 from: 243
   mapped sites are within: 0.710 - 5.153

peak=   -5.057 closest distance to " N   ARG A 275 " =    0.857
peak=   -5.000 closest distance to " O   VAL A 121 " =    0.965
peak=   -4.787 closest distance to " C   TYR A  30 " =    0.838
peak=   -4.719 closest distance to " C   ASN A 285 " =    2.504
peak=   -4.691 closest distance to " NH2 ARG A  66 " =    1.114
peak=   -4.666 closest distance to " O   HOH Z 422 " =    2.355
peak=   -4.593 closest distance to " OG ASER A 134 " =    0.997
peak=   -4.560 closest distance to " CA  ALA A 114 " =    1.025
peak=   -4.531 closest distance to " O   HOH Z  52 " =    2.305
peak=   -4.435 closest distance to " O   HOH Z 335 " =    0.837
peak=   -4.371 closest distance to " CG2 VAL A 230 " =    1.056
peak=   -4.354 closest distance to " O   HOH Z 231 " =    0.933
peak=   -4.320 closest distance to " CA  SER A 164 " =    1.373
peak=   -4.256 closest distance to " CD  GLN A  77 " =    0.715
peak=   -4.249 closest distance to " N   ARG A 275 " =    1.248
peak=   -4.239 closest distance to " CG  LEU A   5 " =    0.889
peak=   -4.211 closest distance to " N   ASP A 272 " =    1.219
peak=   -4.203 closest distance to " CG2BVAL A  41 " =    2.387
peak=   -4.198 closest distance to " O   ARG A 275 " =    0.884
peak=   -4.194 closest distance to " O   HOH Z 151 " =    1.117
peak=   -4.167 closest distance to " O   HOH Z 166 " =    1.363
peak=   -4.135 closest distance to " O   HOH Z 292 " =    4.477
peak=   -4.133 closest distance to " N   GLN A  55 " =    1.757
peak=   -4.082 closest distance to " CB  ALA A 291 " =    2.436
peak=   -4.027 closest distance to " CD2 PHE A  59 " =    2.348
peak=   -4.018 closest distance to " O   THR A  29 " =    0.887
peak=   -4.017 closest distance to " NE2 GLN A  88 " =    0.726
peak=   -4.010 closest distance to " O   HOH Z 221 " =    0.951
peak=   -3.990 closest distance to " O   HOH Z 210 " =    0.710
peak=   -3.978 closest distance to " O   PHE A  61 " =    0.763
peak=   -3.978 closest distance to " C   ALA A 299 " =    0.889
peak=   -3.968 closest distance to " O   GLN A  73 " =    2.720
peak=   -3.958 closest distance to " N   SER A   3 " =    1.157
peak=   -3.941 closest distance to " N   VAL A  67 " =    0.820
peak=   -3.905 closest distance to " OG  SER A  32 " =    1.352
peak=   -3.891 closest distance to " O   HOH Z 198 " =    1.454
peak=   -3.882 closest distance to " OD1 ASN A 301 " =    0.811
peak=   -3.860 closest distance to " O   HOH Z 380 " =    4.116
peak=   -3.855 closest distance to " CA  ALA A 137 " =    2.831
peak=   -3.854 closest distance to " O   ASP A 298 " =    0.938
peak=   -3.852 closest distance to " O   HOH Z 407 " =    1.145
peak=   -3.843 closest distance to " CG  GLU A   2 " =    1.100
peak=   -3.834 closest distance to " N   GLY A  75 " =    1.160
peak=   -3.834 closest distance to " OD2 ASP A 171 " =    1.703
peak=   -3.829 closest distance to " NE2 GLN A  58 " =    3.055
peak=   -3.817 closest distance to " OD2 ASP A  50 " =    2.230
peak=   -3.806 closest distance to " O   HOH Z 426 " =    0.715
peak=   -3.778 closest distance to " CB  TRP A 150 " =    1.584
peak=   -3.762 closest distance to " O   HOH Z  58 " =    0.878
peak=   -3.747 closest distance to " CG  PHE A 130 " =    1.834
peak=   -3.741 closest distance to " O   HOH Z 340 " =    0.993
peak=   -3.722 closest distance to " CB  GLN A  73 " =    0.920
peak=   -3.721 closest distance to " O   HOH Z 342 " =    1.218
peak=   -3.714 closest distance to " CE2 TRP A  85 " =    1.104
peak=   -3.701 closest distance to " N   THR A 264 " =    1.480
peak=   -3.700 closest distance to " O   HOH Z 250 " =    1.109
peak=   -3.699 closest distance to " O   HOH Z  50 " =    1.357
peak=   -3.696 closest distance to " CD  ARG A 138 " =    1.172
peak=   -3.695 closest distance to " OG  SER A  28 " =    2.097
peak=   -3.693 closest distance to " OG  SER A   3 " =    1.796
peak=   -3.684 closest distance to " O   HOH Z 132 " =    1.021
peak=   -3.677 closest distance to " O   GLN A  55 " =    0.927
peak=   -3.676 closest distance to " CD2 LEU A 237 " =    2.401
peak=   -3.672 closest distance to " OG1 THR A  82 " =    2.057
peak=   -3.652 closest distance to " O   ILE A 120 " =    0.854
peak=   -3.647 closest distance to " O   HOH Z 186 " =    1.178
peak=   -3.624 closest distance to " O   THR A  31 " =    1.783
peak=   -3.624 closest distance to " N   GLN A  58 " =    1.658
peak=   -3.614 closest distance to " O   LYS A 289 " =    3.059
peak=   -3.611 closest distance to " O   PRO A 198 " =    1.335
peak=   -3.597 closest distance to " O   HOH Z 414 " =    1.321
peak=   -3.585 closest distance to " N   THR A 235 " =    1.246
peak=   -3.577 closest distance to " O   HOH Z 369 " =    2.329
peak=   -3.571 closest distance to " O   HOH Z 274 " =    2.691
peak=   -3.570 closest distance to " O   HOH Z 263 " =    3.746
peak=   -3.570 closest distance to " CA  VAL A 197 " =    1.036
peak=   -3.567 closest distance to " SG  CYS A 254 " =    2.975
peak=   -3.564 closest distance to " O   HOH Z 138 " =    1.027
peak=   -3.559 closest distance to " O   HOH Z  83 " =    0.867
peak=   -3.559 closest distance to " CD2 HIS A 115 " =    0.947
peak=   -3.559 closest distance to " CD2 TRP A 274 " =    0.791
peak=   -3.557 closest distance to " CA  GLU A  53 " =    1.504
peak=   -3.553 closest distance to " CG1AVAL A 121 " =    0.963
peak=   -3.552 closest distance to " O   HOH Z 423 " =    2.787
peak=   -3.546 closest distance to " N   LEU A  25 " =    1.375
peak=   -3.535 closest distance to " ND2 ASN A 285 " =    2.295
peak=   -3.533 closest distance to " CB  PHE A 130 " =    1.204
peak=   -3.529 closest distance to " SG  CYS A 168 " =    1.275
peak=   -3.525 closest distance to " O   HOH Z 401 " =    1.376
peak=   -3.515 closest distance to " CG  ARG A 138 " =    0.976
peak=   -3.512 closest distance to " O   LEU A 300 " =    2.601
peak=   -3.509 closest distance to " N   PHE A  61 " =    0.909
peak=   -3.505 closest distance to " O   HOH Z  92 " =    1.084
peak=   -3.499 closest distance to " CB  SER A 276 " =    0.955
peak=   -3.491 closest distance to " O   HOH Z  13 " =    0.790
peak=   -3.490 closest distance to " CA  SER A 276 " =    1.345
peak=   -3.490 closest distance to " NH1 ARG A  36 " =    1.080
peak=   -3.487 closest distance to " O   ALA A   1 " =    2.277
peak=   -3.483 closest distance to " O   HOH Z  30 " =    0.960
peak=   -3.481 closest distance to " CD  ARG A 269 " =    2.599
peak=   -3.479 closest distance to " O   HOH Z 222 " =    1.449
peak=   -3.473 closest distance to " O   HOH Z 295 " =    1.084
peak=   -3.473 closest distance to " O   HOH Z 423 " =    0.839
peak=   -3.469 closest distance to " O   HOH Z 275 " =    1.120
peak=   -3.466 closest distance to " O   HOH Z  87 " =    1.797
peak=   -3.462 closest distance to " CA  ASN A 127 " =    1.037
peak=   -3.461 closest distance to " O   HOH Z 396 " =    1.841
peak=   -3.458 closest distance to " CA  VAL A 121 " =    1.174
peak=   -3.458 closest distance to " O   HOH Z 174 " =    2.420
peak=   -3.446 closest distance to " O   HOH Z 156 " =    1.208
peak=   -3.438 closest distance to " O   PRO A  54 " =    1.381
peak=   -3.436 closest distance to " O   HOH Z  91 " =    2.020
peak=   -3.429 closest distance to " O   HOH Z   7 " =    1.614
peak=   -3.425 closest distance to " CB  ALA A 100 " =    2.178
peak=   -3.423 closest distance to " C   ALA A   1 " =    1.230
peak=   -3.414 closest distance to " CB  MET A  93 " =    2.051
peak=   -3.411 closest distance to " O   HOH Z 117 " =    1.364
peak=   -3.410 closest distance to " NH2BARG A 145 " =    1.690
peak=   -3.410 closest distance to " C   PRO A 280 " =    0.932
peak=   -3.409 closest distance to " O   HOH Z 427 " =    1.148
peak=   -3.404 closest distance to " CB  LEU A 167 " =    1.890
peak=   -3.393 closest distance to " CG AARG A 102 " =    2.045
peak=   -3.387 closest distance to " O   HOH Z 351 " =    1.464
peak=   -3.384 closest distance to " O   HOH Z 141 " =    0.865
peak=   -3.382 closest distance to " CA  ALA A  34 " =    2.310
peak=   -3.373 closest distance to " O   HOH Z 425 " =    1.092
peak=   -3.367 closest distance to " O  BHOH Z  74 " =    1.347
peak=   -3.360 closest distance to " CD1 PHE A  59 " =    1.893
peak=   -3.359 closest distance to " OG1 THR A 294 " =    2.738
peak=   -3.355 closest distance to " O   HOH Z  46 " =    1.246
peak=   -3.354 closest distance to " O   ALA A  34 " =    1.883
peak=   -3.353 closest distance to " CG2 ILE A 151 " =    2.423
peak=   -3.353 closest distance to " O  BHOH Z  74 " =    0.884
peak=   -3.352 closest distance to " CB  GLN A  58 " =    1.057
peak=   -3.352 closest distance to " CD2 TYR A 293 " =    1.683
peak=   -3.350 closest distance to " CB  ASP A 132 " =    1.714
peak=   -3.348 closest distance to " CG1 VAL A  78 " =    1.855
peak=   -3.345 closest distance to " O   HOH Z  18 " =    0.828
peak=   -3.343 closest distance to " CG2 ILE A  20 " =    2.961
peak=   -3.336 closest distance to " NH2 ARG A  36 " =    1.223
peak=   -3.332 closest distance to " OD2 ASP A 132 " =    1.772
peak=   -3.325 closest distance to " C   LEU A 101 " =    1.415
peak=   -3.324 closest distance to " CB  ALA A  43 " =    2.646
peak=   -3.324 closest distance to " OG  SER A  97 " =    2.474
peak=   -3.322 closest distance to " O   HOH Z 179 " =    2.275
peak=   -3.310 closest distance to " O   HOH Z 384 " =    1.336
peak=   -3.309 closest distance to " O   HOH Z 309 " =    0.972
peak=   -3.308 closest distance to " O   HOH Z 424 " =    2.180
peak=   -3.307 closest distance to " CD2 LEU A 143 " =    2.204
peak=   -3.306 closest distance to " O   HOH Z  92 " =    1.410
peak=   -3.303 closest distance to " O   HOH Z  99 " =    3.991
peak=   -3.302 closest distance to " O   HOH Z  53 " =    1.847
peak=   -3.301 closest distance to " O   HOH Z 314 " =    2.475
peak=   -3.296 closest distance to " O   HOH Z 120 " =    2.274
peak=   -3.296 closest distance to " OD1 ASP A 107 " =    1.821
peak=   -3.295 closest distance to " CB  ALA A 227 " =    2.512
peak=   -3.295 closest distance to " O   ARG A  56 " =    1.071
peak=   -3.292 closest distance to " O   HOH Z 130 " =    2.379
peak=   -3.292 closest distance to " CA  GLY A 203 " =    2.377
peak=   -3.291 closest distance to " O   HOH Z  50 " =    1.794
peak=   -3.289 closest distance to " O   TRP A  85 " =    2.108
peak=   -3.288 closest distance to " CD  GLU A 236 " =    1.011
peak=   -3.287 closest distance to " O   HOH Z 352 " =    2.410
peak=   -3.280 closest distance to " CG  GLU A   2 " =    1.361
peak=   -3.278 closest distance to " O   HOH Z 119 " =    2.843
peak=   -3.276 closest distance to " OG  SER A  63 " =    1.280
peak=   -3.275 closest distance to " O   HOH Z 377 " =    1.211
peak=   -3.273 closest distance to " N   ASP A 298 " =    1.138
peak=   -3.271 closest distance to " O   LYS A 289 " =    0.813
peak=   -3.266 closest distance to " O   TYR A  15 " =    1.346
peak=   -3.255 closest distance to " NE1 TRP A 150 " =    2.196
peak=   -3.254 closest distance to " O   HOH Z   1 " =    0.930
peak=   -3.252 closest distance to " OH  TYR A 247 " =    2.216
peak=   -3.250 closest distance to " CB  GLU A 277 " =    2.476
peak=   -3.235 closest distance to " CG1 VAL A 296 " =    1.406
peak=   -3.232 closest distance to " O   HOH Z 410 " =    2.341
peak=   -3.228 closest distance to " O   HOH Z 348 " =    2.077
peak=   -3.223 closest distance to " O   HOH Z 185 " =    2.484
peak=   -3.223 closest distance to " CD2 LEU A 237 " =    2.823
peak=   -3.221 closest distance to " CD  LYS A 119 " =    1.018
peak=   -3.216 closest distance to " O   HOH Z 300 " =    1.574
peak=   -3.213 closest distance to " CB  SER A 288 " =    1.907
peak=   -3.212 closest distance to " CA  SER A 288 " =    1.087
peak=   -3.208 closest distance to " O   THR A   4 " =    1.152
peak=   -3.206 closest distance to " O   HOH Z  15 " =    1.354
peak=   -3.206 closest distance to " O   MET A  47 " =    2.623
peak=   -3.206 closest distance to " O   TYR A 186 " =    2.450
peak=   -3.203 closest distance to " CB  ALA A 114 " =    2.480
peak=   -3.201 closest distance to " N   ALA A 184 " =    1.089
peak=   -3.190 closest distance to " CB  SER A  62 " =    2.325
peak=   -3.189 closest distance to " NH1BARG A 190 " =    1.961
peak=   -3.187 closest distance to " O   HOH Z 193 " =    0.878
peak=   -3.186 closest distance to " CB  ALA A  64 " =    1.930
peak=   -3.186 closest distance to " O   ASP A 200 " =    1.057
peak=   -3.181 closest distance to " N   ASP A  65 " =    1.193
peak=   -3.180 closest distance to " N   SER A   3 " =    2.718
peak=   -3.173 closest distance to " O   HOH Z 137 " =    0.896
peak=   -3.172 closest distance to " O   HOH Z 244 " =    1.442
peak=   -3.168 closest distance to " O   HOH Z 124 " =    1.207
peak=   -3.163 closest distance to " C   LEU A   5 " =    1.438
peak=   -3.162 closest distance to " CB  ALA A 161 " =    2.420
peak=   -3.161 closest distance to " CE  MET A 188 " =    2.199
peak=   -3.158 closest distance to " O   HOH Z 137 " =    1.647
peak=   -3.157 closest distance to " O   GLU A  44 " =    1.955
peak=   -3.155 closest distance to " CD2 PHE A  61 " =    2.174
peak=   -3.151 closest distance to " O   HOH Z 277 " =    0.981
peak=   -3.150 closest distance to " O   HOH Z  62 " =    0.817
peak=   -3.142 closest distance to " O   HOH Z 336 " =    5.153
peak=   -3.140 closest distance to " CD1 ILE A 151 " =    2.374
peak=   -3.134 closest distance to " CD  PRO A  54 " =    2.274
peak=   -3.131 closest distance to " O   HOH Z 316 " =    1.176
peak=   -3.129 closest distance to " O   HOH Z 150 " =    2.632
peak=   -3.125 closest distance to " O   HOH Z 411 " =    4.778
peak=   -3.124 closest distance to " O   HOH Z 158 " =    1.746
peak=   -3.122 closest distance to " CD  PRO A 163 " =    1.774
peak=   -3.121 closest distance to " OE2 GLU A 277 " =    2.789
peak=   -3.117 closest distance to " O   HOH Z 435 " =    1.126
peak=   -3.115 closest distance to " O   HOH Z  55 " =    2.601
peak=   -3.114 closest distance to " CD2 LEU A 143 " =    2.698
peak=   -3.112 closest distance to " N   GLY A  17 " =    1.450
peak=   -3.107 closest distance to " OG  SER A 271 " =    2.193
peak=   -3.105 closest distance to " O   HOH Z 171 " =    3.588
peak=   -3.100 closest distance to " CG2 ILE A  49 " =    2.526
peak=   -3.093 closest distance to " O   HOH Z 111 " =    1.103
peak=   -3.088 closest distance to " O   HOH Z 237 " =    1.212
peak=   -3.085 closest distance to " NH1 ARG A  36 " =    1.426
peak=   -3.083 closest distance to " O   HOH Z 184 " =    0.781
peak=   -3.062 closest distance to " O   HOH Z  37 " =    1.595
peak=   -3.062 closest distance to " O   PHE A  16 " =    1.444
peak=   -3.060 closest distance to " CB  SER A 258 " =    2.451
peak=   -3.055 closest distance to " O   HOH Z  60 " =    1.370
peak=   -3.048 closest distance to " O   HOH Z 100 " =    1.126
peak=   -3.027 closest distance to " O   HOH Z  56 " =    2.085
peak=   -3.022 closest distance to " O   HOH Z 331 " =    0.939

================= 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    :  0.5127 0.5025   6.312729e+00   6.299394e+00
   1_bss:  0.5051 0.4946   6.223385e+00   6.225834e+00
   1_xyz:  0.4568 0.4756   6.259279e+00   6.275449e+00
   1_adp:  0.4224 0.4722   6.221884e+00   6.270019e+00
   1_occ:  0.4225 0.4719   6.220786e+00   6.270336e+00
   2_bss:  0.4206 0.4655   6.222109e+00   6.269620e+00
   2_xyz:  0.3685 0.4420   6.140910e+00   6.240578e+00
   2_adp:  0.3580 0.4386   6.129011e+00   6.232828e+00
   2_occ:  0.3579 0.4395   6.129543e+00   6.233282e+00
   3_bss:  0.3582 0.4382   6.130736e+00   6.233768e+00
   3_xyz:  0.3128 0.3878   6.032710e+00   6.167170e+00
   3_adp:  0.2951 0.3805   5.998226e+00   6.151376e+00
   3_occ:  0.2951 0.3798   5.997754e+00   6.150812e+00
   4_bss:  0.2949 0.3787   5.997264e+00   6.149940e+00
   4_xyz:  0.2414 0.3103   5.811623e+00   5.990546e+00
   4_adp:  0.2198 0.2859   5.740680e+00   5.924114e+00
   4_occ:  0.2194 0.2854   5.739973e+00   5.923570e+00
   5_bss:  0.2189 0.2843   5.738103e+00   5.922058e+00
   5_xyz:  0.1804 0.2334   5.559446e+00   5.755963e+00
   5_adp:  0.1700 0.2197   5.507734e+00   5.703622e+00
   5_occ:  0.1698 0.2196   5.507356e+00   5.703281e+00
   5_bss:  0.1700 0.2199   5.509765e+00   5.705211e+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   6.391  10.504   6.881   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.391  10.504   6.881   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.391  10.504   6.881   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.391  10.504   6.881   0.000   0.000   0.000
   2_bss:  0.306  30.641   3.141   6.042   3.996   0.000   0.000   0.000
   2_xyz:  0.306  30.641   3.141   6.042   3.996   0.000   0.000   0.000
   2_adp:  0.306  30.641   3.141   6.042   3.996   0.000   0.000   0.000
   2_occ:  0.306  30.641   3.141   6.042   3.996   0.000   0.000   0.000
   3_bss:  0.295  51.375   2.053   3.865   2.535   0.000   0.000   0.000
   3_xyz:  0.295  51.375   2.053   3.865   2.535   0.000   0.000   0.000
   3_adp:  0.295  51.375   2.053   3.865   2.535   0.000   0.000   0.000
   3_occ:  0.295  51.375   2.053   3.865   2.535   0.000   0.000   0.000
   4_bss:  0.316  61.052   1.289   3.142   1.468   0.000   0.000   0.000
   4_xyz:  0.316  61.052   1.289   3.142   1.468   0.000   0.000   0.000
   4_adp:  0.316  61.052   1.289   3.142   1.468   0.000   0.000   0.000
   4_occ:  0.316  61.052   1.289   3.142   1.468   0.000   0.000   0.000
   5_bss:  0.333  61.052   0.464   1.767   0.602   0.000   0.000   0.000
   5_xyz:  0.333  61.052   0.464   1.767   0.602   0.000   0.000   0.000
   5_adp:  0.333  61.052   0.464   1.767   0.602   0.000   0.000   0.000
   5_occ:  0.333  61.052   0.464   1.767   0.602   0.000   0.000   0.000
   5_bss:  0.328  56.647  -0.478   0.607  -0.139   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.347 0.3240  0.3860    83121.625
   1_bss:  64.731 0.3307  0.4863    80524.384
   1_xyz:  60.458 0.3853  0.5584    71622.716
   1_adp:  59.645 0.3953  0.6458    69317.558
   1_occ:  59.362 0.3990  0.6528    69221.618
   2_bss:  59.070 0.4026  0.5923    68664.180
   2_xyz:  53.965 0.4679  0.6993    60750.504
   2_adp:  52.211 0.4905  0.7254    58251.964
   2_occ:  52.352 0.4887  0.7224    58449.449
   3_bss:  52.181 0.4908  0.6895    58185.075
   3_xyz:  44.142 0.5912  0.8182    44405.000
   3_adp:  42.455 0.6118  0.8390    41721.993
   3_occ:  42.386 0.6127  0.8400    41621.031
   4_bss:  42.312 0.6135  0.8164    41473.483
   4_xyz:  32.837 0.7247  0.9294    25944.155
   4_adp:  29.693 0.7606  0.9437    22182.076
   4_occ:  29.652 0.7611  0.9436    22118.563
   5_bss:  29.492 0.7626  0.9130    21911.808
   5_xyz:  23.500 0.8261  0.9601    14441.295
   5_adp:  21.711 0.8447  0.9645    12906.211
   5_occ:  21.698 0.8449  0.9646    12907.223
   5_bss:  21.721 0.8449  0.9469    12968.382
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4004e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4004e+01
   1_xyz:   1.780  0.013  0.109 18.405  0.007  4.121   1.5732e-01
   1_adp:   1.780  0.013  0.109 18.405  0.007  4.121   1.5732e-01
   1_occ:   1.780  0.013  0.109 18.405  0.007  4.121   1.5732e-01
   2_bss:   1.780  0.013  0.109 18.405  0.007  4.121   1.5732e-01
   2_xyz:   1.375  0.009  0.089 17.748  0.005  4.109   1.2174e-01
   2_adp:   1.375  0.009  0.089 17.748  0.005  4.109   1.2174e-01
   2_occ:   1.375  0.009  0.089 17.748  0.005  4.109   1.2174e-01
   3_bss:   1.375  0.009  0.089 17.748  0.005  4.109   1.2174e-01
   3_xyz:   1.228  0.009  0.086 16.272  0.004  4.109   8.9286e-02
   3_adp:   1.228  0.009  0.086 16.272  0.004  4.109   8.9286e-02
   3_occ:   1.228  0.009  0.086 16.272  0.004  4.109   8.9286e-02
   4_bss:   1.228  0.009  0.086 16.272  0.004  4.109   8.9286e-02
   4_xyz:   1.292  0.010  0.089 16.181  0.004  4.109   9.9491e-02
   4_adp:   1.292  0.010  0.089 16.181  0.004  4.109   9.9491e-02
   4_occ:   1.292  0.010  0.089 16.181  0.004  4.109   9.9491e-02
   5_bss:   1.292  0.010  0.089 16.181  0.004  4.109   9.9491e-02
   5_xyz:   1.074  0.008  0.079 15.591  0.004  4.123   7.1448e-02
   5_adp:   1.074  0.008  0.079 15.591  0.004  4.123   7.1448e-02
   5_occ:   1.074  0.008  0.079 15.591  0.004  4.123   7.1448e-02
   5_bss:   1.074  0.008  0.079 15.591  0.004  4.123   7.1448e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.981   6.9967e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.981   6.9967e+00
   1_xyz:  15.370  0.127  0.502 87.941  0.049  2.099   1.0399e-01
   1_adp:  15.370  0.127  0.502 87.941  0.049  2.099   1.0399e-01
   1_occ:  15.370  0.127  0.502 87.941  0.049  2.099   1.0399e-01
   2_bss:  15.370  0.127  0.502 87.941  0.049  2.099   1.0399e-01
   2_xyz:   9.408  0.074  0.288 88.904  0.048  1.987   6.2512e-02
   2_adp:   9.408  0.074  0.288 88.904  0.048  1.987   6.2512e-02
   2_occ:   9.408  0.074  0.288 88.904  0.048  1.987   6.2512e-02
   3_bss:   9.408  0.074  0.288 88.904  0.048  1.987   6.2512e-02
   3_xyz:   9.978  0.080  0.271 80.191  0.027  2.256   6.2915e-02
   3_adp:   9.978  0.080  0.271 80.191  0.027  2.256   6.2915e-02
   3_occ:   9.978  0.080  0.271 80.191  0.027  2.256   6.2915e-02
   4_bss:   9.978  0.080  0.271 80.191  0.027  2.256   6.2915e-02
   4_xyz:   9.261  0.077  0.259 81.794  0.026  2.086   1.0639e-01
   4_adp:   9.261  0.077  0.259 81.794  0.026  2.086   1.0639e-01
   4_occ:   9.261  0.077  0.259 81.794  0.026  2.086   1.0639e-01
   5_bss:   9.261  0.077  0.259 81.794  0.026  2.086   1.0639e-01
   5_xyz:   8.059  0.052  0.351 88.046  0.052  2.348   7.7672e-02
   5_adp:   8.059  0.052  0.351 88.046  0.052  2.348   7.7672e-02
   5_occ:   8.059  0.052  0.351 88.046  0.052  2.348   7.7672e-02
   5_bss:   8.059  0.052  0.351 88.046  0.052  2.348   7.7672e-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: 101.30   0.00  16.85  74.39   0.00  15.33 101.30   0.00  25.13
   1_occ: 101.30   0.00  16.85  74.39   0.00  15.33 101.30   0.00  25.13
   2_bss: 101.30   0.00  16.85  74.39   0.00  15.33 101.30   0.00  25.13
   2_xyz: 101.30   0.00  16.85  74.39   0.00  15.33 101.30   0.00  25.13
   2_adp: 100.99   0.00  15.56  72.34   0.00  13.73 100.99   0.00  25.49
   2_occ: 100.99   0.00  15.56  72.34   0.00  13.73 100.99   0.00  25.49
   3_bss: 100.99   0.00  15.56  72.34   0.00  13.73 100.99   0.00  25.49
   3_xyz: 100.99   0.00  15.56  72.34   0.00  13.73 100.99   0.00  25.49
   3_adp:  96.26   0.00  16.58  81.33   0.00  13.80  96.26   0.00  31.71
   3_occ:  96.26   0.00  16.58  81.33   0.00  13.80  96.26   0.00  31.71
   4_bss:  96.26   0.00  16.58  81.33   0.00  13.80  96.26   0.00  31.71
   4_xyz:  96.26   0.00  16.58  81.33   0.00  13.80  96.26   0.00  31.71
   4_adp:  91.75   0.00  16.09  83.15   0.00  12.12  91.75   2.30  37.71
   4_occ:  91.75   0.00  16.09  83.15   0.00  12.12  91.75   2.30  37.71
   5_bss:  91.75   0.00  16.09  83.15   0.00  12.12  91.75   2.30  37.71
   5_xyz:  91.75   0.00  16.09  83.15   0.00  12.12  91.75   2.30  37.71
   5_adp:  86.92   0.00  15.55  86.92   0.00  11.22  86.64   3.67  39.12
   5_occ:  86.92   0.00  15.55  86.92   0.00  11.22  86.64   3.67  39.12
   5_bss:  87.34   0.43  15.97  87.34   0.43  11.65  87.06   4.10  39.55
------------------------------------------------------------------------
 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:    1.091    0.031    0.412
   1_adp:    1.091    0.031    0.412
   1_occ:    1.091    0.031    0.412
   2_bss:    1.091    0.031    0.412
   2_xyz:    1.624    0.034    0.593
   2_adp:    1.624    0.034    0.593
   2_occ:    1.624    0.034    0.593
   3_bss:    1.624    0.034    0.593
   3_xyz:    1.987    0.061    0.699
   3_adp:    1.987    0.061    0.699
   3_occ:    1.987    0.061    0.699
   4_bss:    1.987    0.061    0.699
   4_xyz:    1.948    0.051    0.889
   4_adp:    1.948    0.051    0.889
   4_occ:    1.948    0.051    0.889
   5_bss:    1.948    0.051    0.889
   5_xyz:    2.005    0.048    0.941
   5_adp:    2.005    0.048    0.941
   5_occ:    2.005    0.048    0.941
   5_bss:    2.005    0.048    0.941
------------------------------------------------------------------------

CPU time actual refinement: 372.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/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_1079/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1079/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 372.14 
  Macro-tasks:
    bulk solvent and scale       = 43.03  
    individual site refinement   = 164.79 
    weights calculation          = 32.83  
    collect and process          = 6.21   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 246.97 
  Micro-tasks:
    mask                            = 3.12   
    f_calc                          = 120.89 
    alpha_beta                      = 8.26   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 131.64 
    fmodel                         = 7.09   
    r_factors                      = 0.22   
    phase_errors                   = 9.51   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 282.10 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.171 micro seconds
Total CPU time: 6.43 minutes
from_scatterers_fft:    641 calls, 120.51 s
gradients_fft:          585 calls, 117.87 s

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

# Date 2008-01-16 Time 03:09:04 PST -0800 (1200481744.12 s)
Start R-work = 0.5127, R-free = 0.5025 (no bulk solvent and anisotropic scale)
Final R-work = 0.1848, R-free = 0.2375 (no bulk solvent and anisotropic scale)

Start R-work = 0.5051, R-free = 0.4946
Final R-work = 0.1700, R-free = 0.2199