# Date 2008-01-16 Time 03:37:58 PST -0800 (1200483478.32 s)
#phil __OFF__

Command line arguments: "../1312.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8672
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1312

-------------------------------------------------------------------------------
  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: (72.0062, 47.8686, 85.5261, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (72.0062, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.9814
Completeness in resolution range: 0.926939
Completeness with d_max=infinity: 0.924184

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9814

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: (72.0062, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.9814
Completeness in resolution range: 0.926939
Completeness with d_max=infinity: 0.924184

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2409 [2219/2248]  1999   220   9.9%
  bin  2:  4.2409 -  3.3782 [2125/2148]  1913   212  10.0%
  bin  3:  3.3782 -  2.9548 [2099/2124]  1883   216  10.3%
  bin  4:  2.9548 -  2.6862 [2094/2110]  1891   203   9.7%
  bin  5:  2.6862 -  2.4946 [2052/2090]  1845   207  10.1%
  bin  6:  2.4946 -  2.3481 [2068/2101]  1867   201   9.7%
  bin  7:  2.3481 -  2.2308 [2039/2076]  1828   211  10.3%
  bin  8:  2.2308 -  2.1340 [2028/2070]  1826   202  10.0%
  bin  9:  2.1340 -  2.0521 [2055/2091]  1852   203   9.9%
  bin 10:  2.0521 -  1.9814 [ 810/2075]   726    84  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/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:
        1.21 -     1.94: 5
        1.94 -     2.68: 109
        2.68 -     3.42: 4382
        3.42 -     4.16: 9255
        4.16 -     4.90: 14206
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.205 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.618 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.745 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.854 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 27952 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_1312/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 72.00625 47.8686 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5032   r_free= 0.4915   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.303331                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7307 0.99   1435  162 0.4158 0.4156      6.6351      6.6122|
|  2:  4.7307 -  3.7737 0.99   1387  149 0.4328 0.4595      6.8605      6.9314|
|  3:  3.7737 -  3.3022 0.99   1361  155 0.4842 0.4261      6.7122      6.6402|
|  4:  3.3022 -  3.0028 0.99   1347  148 0.4984 0.4688      6.5392      6.5283|
|  5:  3.0028 -  2.7890 0.98   1333  148 0.5351 0.5555       6.384      6.3776|
|  6:  2.7890 -  2.6255 0.99   1342  151 0.5318 0.4989      6.2903      6.2287|
|  7:  2.6255 -  2.4946 0.99   1326  145 0.5292 0.5026      6.2566      6.1924|
|  8:  2.4946 -  2.3864 0.99   1326  148 0.5424 0.5638      6.1668       6.201|
|  9:  2.3864 -  2.2949 0.99   1317  149 0.5504 0.5111      6.1362      6.1291|
| 10:  2.2949 -  2.2159 0.98   1326  147 0.5204 0.5295      6.0912      6.0999|
| 11:  2.2159 -  2.1468 0.98   1311  138 0.5332 0.5465      6.0353      6.0313|
| 12:  2.1468 -  2.0856 1.00   1310  148 0.5451 0.5050      5.9515      5.9787|
| 13:  2.0856 -  2.0308 0.88   1179  140 0.5566 0.5321      5.8804      5.8399|
| 14:  2.0308 -  1.9814 0.24    330   31 0.5770 0.4781       5.825      5.7845|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7307  1435   162  0.67  37.28   0.78     0.70      83792.85|
|  2:  4.7307 -  3.7737  1387   149  0.66  38.98   0.86     0.71     121344.04|
|  3:  3.7737 -  3.3022  1361   155  0.53  49.73   0.79     0.64     134022.71|
|  4:  3.3022 -  3.0028  1347   148  0.41  58.81   0.77     0.51     120322.92|
|  5:  3.0028 -  2.7890  1333   148  0.32  66.14   0.70     0.40      98301.77|
|  6:  2.7890 -  2.6255  1342   151  0.31  66.95   0.71     0.37      79373.02|
|  7:  2.6255 -  2.4946  1326   145  0.32  66.08   0.72     0.35      68740.60|
|  8:  2.4946 -  2.3864  1326   148  0.27  70.07   0.68     0.32      66014.50|
|  9:  2.3864 -  2.2949  1317   149  0.22  73.97   0.71     0.26      62902.13|
| 10:  2.2949 -  2.2159  1326   147  0.21  74.46   0.73     0.25      59394.42|
| 11:  2.2159 -  2.1468  1311   138  0.22  73.36   0.74     0.27      51797.94|
| 12:  2.1468 -  2.0856  1310   148  0.25  71.42   0.72     0.33      46286.68|
| 13:  2.0856 -  2.0308  1179   140  0.27  69.71   0.70     0.35      38469.44|
| 14:  2.0308 -  1.9814   330    31  0.28  69.20   0.68     0.34      31480.61|
|alpha:            min =        0.25 max =            0.71 mean =         0.42|
|beta:             min =    31480.61 max =       134022.71 mean =     79135.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.61|
|phase err.(test): min =        0.00 max =           89.98 mean =        62.55|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.933585             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.821   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.933164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.846   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1490 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2580 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3878 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4977 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6469 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7660 |
|-----------------------------------------------------------------------------|
|-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 |       54.331 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.926 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    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 = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5071   r_free= 0.4980   ksol= 0.00   Bsol= 0.00   scale= 0.739    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.303843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4965   r_free= 0.4817   ksol= 0.30   Bsol= 20.00   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.46,10.21,6.35,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.300629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.265059             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.465   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.534117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.276   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4965      final r-factor (work) = 0.4339          |
| start r-factor (free) = 0.4817      final r-factor (free) = 0.4511          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.8604 = 18.27 * 0.50 * 6.2994 + 1.00 * 54.3305                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.1429 = 18.27 * 0.50 * 6.2388 + 1.00 * 0.1668                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4339      final r-factor (work) = 0.3970          |
| start r-factor (free) = 0.4511      final r-factor (free) = 0.4413          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5858 = 1.53 * 1.00 * 6.2388 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5228 = 1.53 * 1.00 * 6.1930 + 1.00 * 0.0221                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.92  14.28    None  None   None       |
|    all(noH): 2823   0      0.00    121.92  14.28    None  None   None       |
|    Sol.    : 438    0      0.00    83.17   22.82    None  None   None       |
|    Mac.    : 2385   0      0.00    121.92  12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.192: 1411   |   5:    60.961 -  73.153:    4        |
|      1:    12.192 -  24.385:  936   |   6:    73.153 -  85.346:    2        |
|      2:    24.385 -  36.577:  350   |   7:    85.346 -  97.538:    0        |
|      3:    36.577 -  48.769:   88   |   8:    97.538 - 109.730:    0        |
|      4:    48.769 -  60.961:   31   |   9:   109.730 - 121.922:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3970 r_free = 0.4413             target_work(ml) = 6.180         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3963 r_free = 0.4423             target_work(ml) = 6.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3963   r_free= 0.4423   ksol= 0.30   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.46,10.21,6.35,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.179086                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3952   r_free= 0.4384   ksol= 0.29   Bsol= 33.59   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.41,6.66,4.35,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.181274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.749973              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.544  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.820583              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.285  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3952      final r-factor (work) = 0.3300          |
| start r-factor (free) = 0.4384      final r-factor (free) = 0.4040          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3451 = 9.75 * 0.50 * 6.1905 + 1.00 * 0.1663                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8761 = 9.75 * 0.50 * 6.1079 + 1.00 * 0.1002                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3300      final r-factor (work) = 0.3147          |
| start r-factor (free) = 0.4040      final r-factor (free) = 0.3865          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0314 = 0.82 * 1.00 * 6.1079 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9757 = 0.82 * 1.00 * 6.0486 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.90   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    95.90   13.93    None  None   None       |
|    Sol.    : 438    0      0.00    95.90   28.28    None  None   None       |
|    Mac.    : 2385   0      0.00    66.67   11.30    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 -   9.590: 1308   |   5:    47.950 -  57.540:   41        |
|      1:     9.590 -  19.180:  833   |   6:    57.540 -  67.130:   22        |
|      2:    19.180 -  28.770:  373   |   7:    67.130 -  76.720:    2        |
|      3:    28.770 -  38.360:  162   |   8:    76.720 -  86.310:    4        |
|      4:    38.360 -  47.950:   77   |   9:    86.310 -  95.900:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3147 r_free = 0.3865             target_work(ml) = 6.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3146 r_free = 0.3864             target_work(ml) = 6.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3146   r_free= 0.3864   ksol= 0.29   Bsol= 33.59   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.41,6.66,4.35,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.030896                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3143   r_free= 0.3846   ksol= 0.30   Bsol= 61.82   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,4.62,3.13,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.031551                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.461849             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.724  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.646693              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.168  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3143      final r-factor (work) = 0.2379          |
| start r-factor (free) = 0.3846      final r-factor (free) = 0.3002          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.7393 = 10.46 * 0.50 * 6.0484 + 1.00 * 0.1007                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.1702 = 10.46 * 0.50 * 5.9393 + 1.00 * 0.1019                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2379      final r-factor (work) = 0.2117          |
| start r-factor (free) = 0.3002      final r-factor (free) = 0.2734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8532 = 0.65 * 1.00 * 5.9393 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7251 = 0.65 * 1.00 * 5.7390 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.37   14.68    None  None   None       |
|    all(noH): 2823   0      0.00    99.37   14.68    None  None   None       |
|    Sol.    : 438    0      0.00    99.37   37.95    None  None   None       |
|    Mac.    : 2385   0      0.00    79.13   10.40    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 -   9.937: 1519   |   5:    49.684 -  59.621:   80        |
|      1:     9.937 -  19.874:  673   |   6:    59.621 -  69.558:   43        |
|      2:    19.874 -  29.811:  237   |   7:    69.558 -  79.495:   17        |
|      3:    29.811 -  39.748:  143   |   8:    79.495 -  89.432:    4        |
|      4:    39.748 -  49.684:  105   |   9:    89.432 -  99.369:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2117 r_free = 0.2734             target_work(ml) = 5.693         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2113 r_free = 0.2732             target_work(ml) = 5.692         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2113   r_free= 0.2732   ksol= 0.30   Bsol= 61.82   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,4.62,3.13,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.692205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2101   r_free= 0.2711   ksol= 0.32   Bsol= 64.98   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.19,2.84,1.97,0.00,0.00,0.00); trace/3= 2.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.689489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.629296              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.546  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.282562              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.623  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2101      final r-factor (work) = 0.1709          |
| start r-factor (free) = 0.2711      final r-factor (free) = 0.2242          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5212 = 3.63 * 0.50 * 5.7417 + 1.00 * 0.1019                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2427 = 3.63 * 0.50 * 5.6069 + 1.00 * 0.0681                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1709      final r-factor (work) = 0.1623          |
| start r-factor (free) = 0.2242      final r-factor (free) = 0.2138          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5980 = 0.28 * 1.00 * 5.6069 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5607 = 0.28 * 1.00 * 5.4836 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.62   14.35    None  None   None       |
|    all(noH): 2823   0      0.00    95.62   14.35    None  None   None       |
|    Sol.    : 438    0      1.56    95.62   38.65    None  None   None       |
|    Mac.    : 2385   0      0.00    83.67   9.89     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 -   9.562: 1554   |   5:    47.810 -  57.372:   85        |
|      1:     9.562 -  19.124:  692   |   6:    57.372 -  66.934:   50        |
|      2:    19.124 -  28.686:  169   |   7:    66.934 -  76.496:   14        |
|      3:    28.686 -  38.248:  132   |   8:    76.496 -  86.058:    9        |
|      4:    38.248 -  47.810:  115   |   9:    86.058 -  95.620:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1623 r_free = 0.2138             target_work(ml) = 5.460         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1621 r_free = 0.2136             target_work(ml) = 5.460         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1621   r_free= 0.2136   ksol= 0.32   Bsol= 64.98   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.19,2.84,1.97,0.00,0.00,0.00); trace/3= 2.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459556                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1622   r_free= 0.2138   ksol= 0.33   Bsol= 64.56   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,2.02,1.71,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.461666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.166723              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.990  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707801              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.518  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1622      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2138      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0110 = 2.17 * 0.50 * 5.4856 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9256 = 2.17 * 0.50 * 5.4079 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1371          |
| start r-factor (free) = 0.1896      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8388 = 0.71 * 1.00 * 5.4079 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7884 = 0.71 * 1.00 * 5.3328 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.26   14.75    None  None   None       |
|    all(noH): 2823   0      0.00    94.26   14.75    None  None   None       |
|    Sol.    : 438    0      1.55    94.26   41.48    None  None   None       |
|    Mac.    : 2385   0      0.00    93.08   9.84     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 -   9.426: 1534   |   5:    47.129 -  56.555:   78        |
|      1:     9.426 -  18.852:  693   |   6:    56.555 -  65.980:   68        |
|      2:    18.852 -  28.277:  179   |   7:    65.980 -  75.406:   35        |
|      3:    28.277 -  37.703:  112   |   8:    75.406 -  84.832:   12        |
|      4:    37.703 -  47.129:  102   |   9:    84.832 -  94.258:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1371 r_free = 0.1884             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1370 r_free = 0.1883             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1883   ksol= 0.33   Bsol= 64.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.42,2.02,1.71,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7307 0.99   1435  162 0.1044 0.1338        5.43      5.6006|
|  2:  4.7307 -  3.7737 0.99   1387  149 0.0943 0.1179      5.5125      5.7405|
|  3:  3.7737 -  3.3022 0.99   1361  155 0.1283 0.1895      5.6367       5.979|
|  4:  3.3022 -  3.0028 0.99   1347  148 0.1562 0.1877      5.6394      5.8046|
|  5:  3.0028 -  2.7890 0.98   1333  148 0.1695 0.2051      5.5404      5.6996|
|  6:  2.7890 -  2.6255 0.99   1342  151 0.1578 0.2336      5.4194      5.6483|
|  7:  2.6255 -  2.4946 0.99   1326  145 0.1541 0.2094      5.3493      5.5443|
|  8:  2.4946 -  2.3864 0.99   1326  148 0.1476 0.2018      5.2427      5.4501|
|  9:  2.3864 -  2.2949 0.99   1317  149 0.1523 0.2416      5.2275      5.5137|
| 10:  2.2949 -  2.2159 0.98   1326  147 0.1444 0.2062       5.188      5.3828|
| 11:  2.2159 -  2.1468 0.98   1311  138 0.1474 0.2263      5.1425      5.4664|
| 12:  2.1468 -  2.0856 1.00   1310  148 0.1416 0.2006      5.0601      5.2407|
| 13:  2.0856 -  2.0308 0.88   1179  140 0.1439 0.2129      4.9695      5.2193|
| 14:  2.0308 -  1.9814 0.24    330   31 0.1305 0.2022      4.8386      5.1185|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7307  1435   162  0.93   9.93   0.96     0.94       8157.31|
|  2:  4.7307 -  3.7737  1387   149  0.94   9.17   1.00     0.99      10458.01|
|  3:  3.7737 -  3.3022  1361   155  0.92  13.87   1.02     1.03      13866.65|
|  4:  3.3022 -  3.0028  1347   148  0.89  17.77   1.01     0.98      14859.65|
|  5:  3.0028 -  2.7890  1333   148  0.85  21.00   0.99     0.98      13283.60|
|  6:  2.7890 -  2.6255  1342   151  0.87  20.08   0.98     0.95      10522.75|
|  7:  2.6255 -  2.4946  1326   145  0.87  19.36   0.99     0.95       9096.98|
|  8:  2.4946 -  2.3864  1326   148  0.87  19.40   0.99     0.94       7582.09|
|  9:  2.3864 -  2.2949  1317   149  0.86  20.23   1.00     0.95       7393.18|
| 10:  2.2949 -  2.2159  1326   147  0.87  19.70   0.99     0.93       6993.26|
| 11:  2.2159 -  2.1468  1311   138  0.86  20.99   0.98     0.93       6724.83|
| 12:  2.1468 -  2.0856  1310   148  0.87  20.18   0.98     0.96       5943.39|
| 13:  2.0856 -  2.0308  1179   140  0.86  20.79   0.98     0.96       4966.38|
| 14:  2.0308 -  1.9814   330    31  0.86  20.59   0.97     0.93       3986.50|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     3986.50 max =        14859.65 mean =      9179.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.85 mean =        17.82|
|phase err.(test): min =        0.00 max =           89.16 mean =        17.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1883   ksol= 0.33   Bsol= 64.88   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,0.18,0.07,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1883   ksol= 0.33   Bsol= 64.88   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,0.18,0.07,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331601                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7307 0.99   1435  162 0.1042 0.1334      5.4282      5.5994|
|  2:  4.7307 -  3.7737 0.99   1387  149 0.0943 0.1178      5.5124      5.7402|
|  3:  3.7737 -  3.3022 0.99   1361  155 0.1283 0.1895       5.637      5.9795|
|  4:  3.3022 -  3.0028 0.99   1347  148 0.1562 0.1877      5.6394      5.8042|
|  5:  3.0028 -  2.7890 0.98   1333  148 0.1694 0.2050      5.5405      5.6997|
|  6:  2.7890 -  2.6255 0.99   1342  151 0.1578 0.2331      5.4192      5.6476|
|  7:  2.6255 -  2.4946 0.99   1326  145 0.1541 0.2096      5.3491      5.5443|
|  8:  2.4946 -  2.3864 0.99   1326  148 0.1475 0.2018      5.2426      5.4501|
|  9:  2.3864 -  2.2949 0.99   1317  149 0.1523 0.2417      5.2274      5.5136|
| 10:  2.2949 -  2.2159 0.98   1326  147 0.1444 0.2065       5.188      5.3835|
| 11:  2.2159 -  2.1468 0.98   1311  138 0.1474 0.2262      5.1424       5.466|
| 12:  2.1468 -  2.0856 1.00   1310  148 0.1416 0.2010      5.0604      5.2417|
| 13:  2.0856 -  2.0308 0.88   1179  140 0.1439 0.2129      4.9695       5.219|
| 14:  2.0308 -  1.9814 0.24    330   31 0.1306 0.2016      4.8382      5.1159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7307  1435   162  0.93   9.92   0.96     0.94       8132.73|
|  2:  4.7307 -  3.7737  1387   149  0.94   9.16   1.00     0.99      10443.51|
|  3:  3.7737 -  3.3022  1361   155  0.92  13.86   1.02     1.03      13865.53|
|  4:  3.3022 -  3.0028  1347   148  0.89  17.76   1.00     0.98      14853.50|
|  5:  3.0028 -  2.7890  1333   148  0.85  20.99   0.99     0.97      13277.64|
|  6:  2.7890 -  2.6255  1342   151  0.87  20.06   0.98     0.94      10514.51|
|  7:  2.6255 -  2.4946  1326   145  0.87  19.36   0.99     0.95       9093.92|
|  8:  2.4946 -  2.3864  1326   148  0.87  19.40   0.98     0.94       7583.14|
|  9:  2.3864 -  2.2949  1317   149  0.86  20.22   0.99     0.95       7395.57|
| 10:  2.2949 -  2.2159  1326   147  0.87  19.70   0.98     0.93       6996.01|
| 11:  2.2159 -  2.1468  1311   138  0.86  20.99   0.98     0.92       6727.39|
| 12:  2.1468 -  2.0856  1310   148  0.87  20.19   0.98     0.96       5949.25|
| 13:  2.0856 -  2.0308  1179   140  0.86  20.78   0.97     0.95       4963.30|
| 14:  2.0308 -  1.9814   330    31  0.86  20.56   0.96     0.92       3977.41|
|alpha:            min =        0.92 max =            1.03 mean =         0.96|
|beta:             min =     3977.41 max =        14853.50 mean =      9174.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.80 mean =        17.81|
|phase err.(test): min =        0.00 max =           89.18 mean =        17.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    95.88   16.37    None  None   None       |
|    all(noH): 2823   0      1.62    95.88   16.37    None  None   None       |
|    Sol.    : 438    0      3.18    95.88   43.10    None  None   None       |
|    Mac.    : 2385   0      1.62    94.70   11.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.621 -  11.047: 1534   |   5:    48.750 -  58.176:   78        |
|      1:    11.047 -  20.473:  693   |   6:    58.176 -  67.602:   68        |
|      2:    20.473 -  29.898:  179   |   7:    67.602 -  77.027:   35        |
|      3:    29.898 -  39.324:  112   |   8:    77.027 -  86.453:   12        |
|      4:    39.324 -  48.750:  102   |   9:    86.453 -  95.879:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 364         
Filter by distance & map next to the model:
   mapped sites are within: 0.728 - 5.920
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 362 from: 364
   mapped sites are within: 0.728 - 5.920

peak=    7.687 closest distance to " CG2 VAL A 296 " =    1.324
peak=    7.310 closest distance to " O   HOH Z 120 " =    1.380
peak=    6.643 closest distance to " CG  ARG A 138 " =    1.275
peak=    6.596 closest distance to " O   HOH Z 400 " =    1.094
peak=    6.393 closest distance to " O   HOH Z  37 " =    1.575
peak=    5.924 closest distance to " O   HOH Z  84 " =    1.026
peak=    5.766 closest distance to " CD1AILE A 234 " =    1.164
peak=    5.731 closest distance to " NH1 ARG A 138 " =    1.040
peak=    5.711 closest distance to " O   HOH Z 117 " =    1.515
peak=    5.440 closest distance to " NH1BARG A 275 " =    1.174
peak=    5.384 closest distance to " CG  PRO A  54 " =    1.232
peak=    5.381 closest distance to " CG  LEU A   5 " =    1.323
peak=    5.164 closest distance to " CB  SER A  63 " =    1.396
peak=    5.127 closest distance to " O   HOH Z 111 " =    1.991
peak=    5.081 closest distance to " CB  VAL A 230 " =    1.271
peak=    5.007 closest distance to " O   HOH Z 102 " =    1.399
peak=    4.997 closest distance to " CB  GLN A 223 " =    1.488
peak=    4.958 closest distance to " CA  TYR A  30 " =    1.134
peak=    4.884 closest distance to " O   HOH Z 210 " =    1.337
peak=    4.694 closest distance to " CG1 VAL A 230 " =    1.122
peak=    4.689 closest distance to " CG2 VAL A 230 " =    1.131
peak=    4.652 closest distance to " O   HOH Z 182 " =    1.271
peak=    4.637 closest distance to " O   HOH Z 426 " =    1.289
peak=    4.542 closest distance to " O   HOH Z 411 " =    2.947
peak=    4.511 closest distance to " CD2 LEU A 228 " =    1.262
peak=    4.490 closest distance to " O   HOH Z 404 " =    1.432
peak=    4.476 closest distance to " O   HOH Z  69 " =    1.286
peak=    4.472 closest distance to " O   HOH Z 395 " =    1.386
peak=    4.470 closest distance to " CG2 THR A 221 " =    1.062
peak=    4.441 closest distance to " O   HOH Z 126 " =    1.818
peak=    4.433 closest distance to " O   HOH Z  68 " =    1.930
peak=    4.413 closest distance to " O   HOH Z 394 " =    1.869
peak=    4.392 closest distance to " N   ILE A  33 " =    1.127
peak=    4.389 closest distance to " NH2AARG A 102 " =    1.105
peak=    4.375 closest distance to " CD2 LEU A   5 " =    1.192
peak=    4.350 closest distance to " O   HOH Z  47 " =    1.668
peak=    4.319 closest distance to " O   HOH Z 425 " =    1.746
peak=    4.314 closest distance to " CB  PRO A  54 " =    0.896
peak=    4.277 closest distance to " CB  ARG A 275 " =    0.941
peak=    4.272 closest distance to " CB  PRO A 198 " =    1.077
peak=    4.271 closest distance to " O   HOH Z 433 " =    2.070
peak=    4.269 closest distance to " CA  GLU A 152 " =    0.937
peak=    4.267 closest distance to " O   HOH Z 402 " =    1.776
peak=    4.266 closest distance to " O   HOH Z 178 " =    1.197
peak=    4.250 closest distance to " O   HOH Z 184 " =    1.739
peak=    4.240 closest distance to " CG  GLN A  77 " =    0.875
peak=    4.230 closest distance to " CD  ARG A 138 " =    1.178
peak=    4.224 closest distance to " O   HOH Z 124 " =    1.358
peak=    4.222 closest distance to " O   HOH Z 410 " =    1.238
peak=    4.217 closest distance to " O   HOH Z  80 " =    2.303
peak=    4.192 closest distance to " CG  PRO A 198 " =    1.353
peak=    4.153 closest distance to " CG1 VAL A 153 " =    1.166
peak=    4.118 closest distance to " O   HOH Z 174 " =    1.799
peak=    4.116 closest distance to " O   HOH Z 134 " =    2.156
peak=    4.105 closest distance to " CA  GLY A 196 " =    0.972
peak=    4.092 closest distance to " CE  LYS A 119 " =    1.238
peak=    4.082 closest distance to " NH1 ARG A  56 " =    1.198
peak=    4.067 closest distance to " CB  ALA A 100 " =    1.624
peak=    4.054 closest distance to " O   HOH Z 246 " =    1.684
peak=    4.033 closest distance to " O   HOH Z 133 " =    2.080
peak=    4.026 closest distance to " CA  ALA A  21 " =    1.451
peak=    4.023 closest distance to " CA  ALA A 160 " =    1.028
peak=    4.017 closest distance to " O   HOH Z 234 " =    3.673
peak=    4.008 closest distance to " CB  TRP A 179 " =    1.468
peak=    3.995 closest distance to " CD1 LEU A   5 " =    1.355
peak=    3.988 closest distance to " O   HOH Z  54 " =    1.275
peak=    3.986 closest distance to " CD ALYS A 290 " =    1.068
peak=    3.975 closest distance to " O   HOH Z  47 " =    1.681
peak=    3.973 closest distance to " N   TYR A  15 " =    0.845
peak=    3.972 closest distance to " OE1 GLN A  11 " =    1.949
peak=    3.966 closest distance to " CA  ALA A 295 " =    1.117
peak=    3.965 closest distance to " CB  ASN A 187 " =    1.211
peak=    3.963 closest distance to " O   HOH Z 418 " =    1.583
peak=    3.961 closest distance to " O   HOH Z  19 " =    2.277
peak=    3.951 closest distance to " CB  ALA A 137 " =    1.166
peak=    3.940 closest distance to " O   HOH Z 431 " =    1.467
peak=    3.911 closest distance to " CG  PRO A 213 " =    1.344
peak=    3.909 closest distance to " O   HOH Z 153 " =    1.928
peak=    3.905 closest distance to " CG1BVAL A 121 " =    1.278
peak=    3.903 closest distance to " CD1 TRP A 266 " =    1.219
peak=    3.891 closest distance to " O   HOH Z  63 " =    1.565
peak=    3.890 closest distance to " CB  ALA A 256 " =    1.298
peak=    3.885 closest distance to " CD2 LEU A 255 " =    1.446
peak=    3.875 closest distance to " CB  GLN A 183 " =    1.230
peak=    3.870 closest distance to " OG ASER A 134 " =    1.323
peak=    3.862 closest distance to " OD1 ASN A 217 " =    1.674
peak=    3.861 closest distance to " CD  ARG A 159 " =    0.836
peak=    3.861 closest distance to " O   HOH Z 387 " =    2.771
peak=    3.858 closest distance to " CB  ASN A 148 " =    1.286
peak=    3.856 closest distance to " O   HOH Z 411 " =    1.549
peak=    3.850 closest distance to " CD  ARG A 269 " =    0.834
peak=    3.826 closest distance to " O   HOH Z 192 " =    1.588
peak=    3.824 closest distance to " O   HOH Z  15 " =    2.197
peak=    3.823 closest distance to " O   HOH Z 137 " =    2.019
peak=    3.821 closest distance to " O   PRO A 198 " =    1.583
peak=    3.821 closest distance to " CG2 THR A  42 " =    1.015
peak=    3.812 closest distance to " O   HOH Z 339 " =    1.216
peak=    3.810 closest distance to " O   HOH Z 272 " =    1.981
peak=    3.808 closest distance to " CG1 ILE A  49 " =    1.696
peak=    3.808 closest distance to " CA  SER A  87 " =    0.838
peak=    3.808 closest distance to " O   HOH Z  13 " =    1.799
peak=    3.807 closest distance to " O   HOH Z  49 " =    1.180
peak=    3.806 closest distance to " O   HOH Z 196 " =    1.965
peak=    3.799 closest distance to " CB  GLN A  58 " =    1.050
peak=    3.788 closest distance to " CG AARG A 275 " =    1.200
peak=    3.787 closest distance to " O   HOH Z  88 " =    2.996
peak=    3.785 closest distance to " CB  ASP A 124 " =    0.900
peak=    3.777 closest distance to " O   HOH Z 389 " =    1.920
peak=    3.777 closest distance to " O   HOH Z 163 " =    1.924
peak=    3.753 closest distance to " O   HOH Z 112 " =    1.539
peak=    3.744 closest distance to " CA  ASN A 127 " =    1.160
peak=    3.743 closest distance to " CZ  PHE A 218 " =    1.163
peak=    3.735 closest distance to " O   HOH Z  78 " =    1.293
peak=    3.721 closest distance to " CB  TRP A 266 " =    1.017
peak=    3.713 closest distance to " CZ  PHE A 192 " =    1.108
peak=    3.700 closest distance to " O   HOH Z 420 " =    5.920
peak=    3.686 closest distance to " CA  ILE A  33 " =    1.693
peak=    3.685 closest distance to " CB  GLU A 152 " =    1.186
peak=    3.681 closest distance to " CG1 ILE A  33 " =    1.384
peak=    3.669 closest distance to " O   HOH Z 132 " =    2.238
peak=    3.660 closest distance to " O   HOH Z  40 " =    1.919
peak=    3.659 closest distance to " O   HOH Z 128 " =    2.299
peak=    3.657 closest distance to " O   HOH Z 236 " =    1.827
peak=    3.656 closest distance to " O   HOH Z 301 " =    1.446
peak=    3.655 closest distance to " O   HOH Z 437 " =    2.432
peak=    3.652 closest distance to " O   HOH Z 227 " =    1.674
peak=    3.648 closest distance to " N   ALA A 256 " =    1.103
peak=    3.648 closest distance to " O   HOH Z 186 " =    1.626
peak=    3.647 closest distance to " O   HOH Z  57 " =    2.082
peak=    3.643 closest distance to " O   HOH Z  54 " =    1.314
peak=    3.641 closest distance to " CB  GLU A 128 " =    1.221
peak=    3.640 closest distance to " O   HOH Z 344 " =    2.937
peak=    3.633 closest distance to " N   ASP A 231 " =    0.769
peak=    3.633 closest distance to " CD  LYS A 166 " =    1.551
peak=    3.617 closest distance to " CB  TYR A 169 " =    0.881
peak=    3.608 closest distance to " O   HOH Z 284 " =    3.059
peak=    3.605 closest distance to " NZ  LYS A 117 " =    3.224
peak=    3.602 closest distance to " CD1 LEU A 222 " =    0.849
peak=    3.601 closest distance to " CA  MET A  40 " =    1.158
peak=    3.601 closest distance to " O   HOH Z   4 " =    1.665
peak=    3.596 closest distance to " CB  ASN A 285 " =    0.850
peak=    3.591 closest distance to " O   HOH Z 245 " =    1.402
peak=    3.590 closest distance to " O   HOH Z 277 " =    2.491
peak=    3.581 closest distance to " O   HOH Z 393 " =    3.853
peak=    3.573 closest distance to " CB  GLU A 236 " =    1.271
peak=    3.569 closest distance to " CG2BVAL A  41 " =    1.180
peak=    3.567 closest distance to " O   HOH Z 368 " =    2.883
peak=    3.567 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.567 closest distance to " O   HOH Z  11 " =    1.298
peak=    3.566 closest distance to " CD1 LEU A 300 " =    1.166
peak=    3.563 closest distance to " CB  ALA A 242 " =    1.090
peak=    3.561 closest distance to " CD1 LEU A 101 " =    1.144
peak=    3.559 closest distance to " O   HOH Z  99 " =    2.369
peak=    3.559 closest distance to " O   HOH Z 416 " =    1.290
peak=    3.558 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.556 closest distance to " CB  MET A  47 " =    1.053
peak=    3.554 closest distance to " CD  ARG A  66 " =    2.891
peak=    3.551 closest distance to " CB  TRP A 123 " =    1.074
peak=    3.550 closest distance to " NH1AARG A 145 " =    1.132
peak=    3.550 closest distance to " O   HOH Z 303 " =    2.360
peak=    3.544 closest distance to " CB  LEU A 143 " =    1.184
peak=    3.539 closest distance to " OG  SER A  97 " =    3.405
peak=    3.528 closest distance to " O   HOH Z 104 " =    3.030
peak=    3.527 closest distance to " CB  LEU A 228 " =    1.219
peak=    3.524 closest distance to " C   GLY A  80 " =    1.253
peak=    3.523 closest distance to " NE2 GLN A  11 " =    1.089
peak=    3.522 closest distance to " CG2 ILE A 234 " =    0.971
peak=    3.522 closest distance to " N   HIS A 108 " =    1.890
peak=    3.521 closest distance to " NE2 HIS A 115 " =    1.012
peak=    3.518 closest distance to " CE3 TRP A  85 " =    1.342
peak=    3.515 closest distance to " CG2 THR A 220 " =    0.919
peak=    3.513 closest distance to " CB  ASP A 140 " =    0.737
peak=    3.504 closest distance to " CD  LYS A 289 " =    1.273
peak=    3.502 closest distance to " CB  GLN A 194 " =    0.884
peak=    3.500 closest distance to " O   HOH Z  89 " =    3.739
peak=    3.490 closest distance to " CD  PRO A 280 " =    0.918
peak=    3.490 closest distance to " CA  ILE A 106 " =    0.878
peak=    3.489 closest distance to " O   HOH Z 327 " =    2.673
peak=    3.484 closest distance to " OD2 ASP A 286 " =    3.202
peak=    3.484 closest distance to " CB  SER A 141 " =    1.028
peak=    3.483 closest distance to " CG  LEU A 228 " =    1.293
peak=    3.482 closest distance to " OE1 GLN A  58 " =    1.218
peak=    3.479 closest distance to " CB  ALA A 248 " =    1.340
peak=    3.476 closest distance to " O   HOH Z 118 " =    1.649
peak=    3.474 closest distance to " O   HOH Z 369 " =    1.838
peak=    3.471 closest distance to " O   HOH Z   5 " =    1.694
peak=    3.466 closest distance to " CB  LYS A  76 " =    0.987
peak=    3.466 closest distance to " O   HOH Z 232 " =    2.116
peak=    3.465 closest distance to " CA  ARG A  66 " =    0.993
peak=    3.458 closest distance to " CA  ASP A 191 " =    0.852
peak=    3.454 closest distance to " O   HOH Z 183 " =    1.621
peak=    3.446 closest distance to " O   HOH Z 243 " =    1.104
peak=    3.445 closest distance to " CB  ALA A  34 " =    0.872
peak=    3.443 closest distance to " NH1 ARG A  14 " =    1.198
peak=    3.440 closest distance to " O   HOH Z 374 " =    2.748
peak=    3.440 closest distance to " O   HOH Z 108 " =    2.492
peak=    3.438 closest distance to " CG  PRO A 243 " =    1.185
peak=    3.437 closest distance to " CB  SER A  28 " =    1.139
peak=    3.436 closest distance to " OD1 ASN A 301 " =    1.352
peak=    3.432 closest distance to " O   HOH Z 386 " =    2.219
peak=    3.431 closest distance to " O   HOH Z 126 " =    2.051
peak=    3.430 closest distance to " CA  ASP A 140 " =    1.344
peak=    3.423 closest distance to " CB  VAL A 202 " =    1.430
peak=    3.422 closest distance to " N   SER A 164 " =    1.057
peak=    3.422 closest distance to " CA  THR A 246 " =    1.251
peak=    3.419 closest distance to " CB  TYR A  30 " =    1.068
peak=    3.414 closest distance to " O   HOH Z 155 " =    1.746
peak=    3.410 closest distance to " O   HOH Z  22 " =    2.624
peak=    3.408 closest distance to " CA  MET A 105 " =    1.379
peak=    3.404 closest distance to " O   HOH Z   1 " =    2.697
peak=    3.404 closest distance to " O   PHE A  61 " =    1.124
peak=    3.402 closest distance to " OE1 GLN A  58 " =    5.911
peak=    3.402 closest distance to " O   HOH Z 368 " =    1.179
peak=    3.401 closest distance to " O   HOH Z 359 " =    1.481
peak=    3.400 closest distance to " CB  LEU A 261 " =    1.103
peak=    3.394 closest distance to " O   HOH Z 279 " =    2.326
peak=    3.391 closest distance to " O   HOH Z 222 " =    2.876
peak=    3.387 closest distance to " C   VAL A 265 " =    1.215
peak=    3.387 closest distance to " CB  LEU A 237 " =    0.904
peak=    3.383 closest distance to " N   GLN A  55 " =    0.873
peak=    3.381 closest distance to " O   HOH Z 185 " =    1.733
peak=    3.373 closest distance to " O   HOH Z 244 " =    1.767
peak=    3.373 closest distance to " O   TYR A 116 " =    1.184
peak=    3.368 closest distance to " O   HOH Z 433 " =    1.838
peak=    3.363 closest distance to " O   HOH Z  97 " =    1.911
peak=    3.360 closest distance to " O   HOH Z 215 " =    1.449
peak=    3.360 closest distance to " CE BMET A  47 " =    1.468
peak=    3.358 closest distance to " O   HOH Z 406 " =    1.747
peak=    3.356 closest distance to " CB  ILE A 199 " =    1.059
peak=    3.356 closest distance to " N   ASN A  39 " =    1.229
peak=    3.351 closest distance to " CB  MET A  40 " =    0.736
peak=    3.350 closest distance to " O   HOH Z 119 " =    2.048
peak=    3.348 closest distance to " O   GLU A  53 " =    0.902
peak=    3.348 closest distance to " OE1 GLU A   2 " =    2.153
peak=    3.345 closest distance to " O   HOH Z  21 " =    1.889
peak=    3.342 closest distance to " O   HOH Z 377 " =    1.598
peak=    3.340 closest distance to " O   HOH Z 281 " =    4.118
peak=    3.340 closest distance to " O   HOH Z  78 " =    2.085
peak=    3.336 closest distance to " CA  LEU A 282 " =    1.070
peak=    3.336 closest distance to " O   HOH Z 363 " =    1.079
peak=    3.336 closest distance to " CA  LEU A 101 " =    1.536
peak=    3.333 closest distance to " CB  LEU A 255 " =    1.153
peak=    3.332 closest distance to " CB  GLU A 277 " =    0.945
peak=    3.329 closest distance to " O   HOH Z 124 " =    1.375
peak=    3.327 closest distance to " O   HOH Z 332 " =    1.698
peak=    3.327 closest distance to " NH1 ARG A 269 " =    0.954
peak=    3.325 closest distance to " CA  GLN A 223 " =    0.994
peak=    3.325 closest distance to " O   HOH Z  43 " =    1.954
peak=    3.322 closest distance to " CA  GLY A 267 " =    1.176
peak=    3.322 closest distance to " O   HOH Z 118 " =    1.627
peak=    3.319 closest distance to " O   ALA A  71 " =    0.834
peak=    3.317 closest distance to " CA  GLN A 183 " =    1.807
peak=    3.309 closest distance to " O   HOH Z  94 " =    2.308
peak=    3.308 closest distance to " ND2 ASN A  45 " =    1.417
peak=    3.306 closest distance to " O   HOH Z 403 " =    2.016
peak=    3.302 closest distance to " O   GLY A  91 " =    1.175
peak=    3.300 closest distance to " CA  LYS A 117 " =    1.249
peak=    3.299 closest distance to " O   HOH Z 313 " =    1.999
peak=    3.299 closest distance to " O   HOH Z  63 " =    1.946
peak=    3.298 closest distance to " CB  SER A 216 " =    0.892
peak=    3.296 closest distance to " O   HOH Z 174 " =    1.625
peak=    3.290 closest distance to " CA  ARG A 102 " =    1.437
peak=    3.290 closest distance to " ND1 HIS A  81 " =    1.591
peak=    3.287 closest distance to " O   HOH Z  66 " =    1.857
peak=    3.287 closest distance to " CG  GLN A  88 " =    1.085
peak=    3.286 closest distance to " CA  LYS A  48 " =    1.352
peak=    3.281 closest distance to " NH2 ARG A 156 " =    1.127
peak=    3.281 closest distance to " CD  ARG A 195 " =    1.057
peak=    3.277 closest distance to " O   HOH Z 253 " =    1.353
peak=    3.275 closest distance to " O   HOH Z 298 " =    2.594
peak=    3.275 closest distance to " O   ASP A 124 " =    1.187
peak=    3.274 closest distance to " CG1 ILE A 120 " =    1.115
peak=    3.272 closest distance to " O   HOH Z 214 " =    1.449
peak=    3.267 closest distance to " O   HOH Z 109 " =    2.535
peak=    3.266 closest distance to " CB  SER A   3 " =    1.533
peak=    3.265 closest distance to " CD  ARG A  56 " =    1.229
peak=    3.265 closest distance to " CA  ALA A 100 " =    1.223
peak=    3.263 closest distance to " CB  SER A  62 " =    0.869
peak=    3.262 closest distance to " N   PHE A 130 " =    1.192
peak=    3.261 closest distance to " O   HOH Z 344 " =    1.779
peak=    3.257 closest distance to " O   GLY A  23 " =    2.467
peak=    3.256 closest distance to " N   LYS A 166 " =    0.949
peak=    3.256 closest distance to " O   HOH Z 327 " =    1.849
peak=    3.254 closest distance to " OG  SER A  22 " =    2.816
peak=    3.250 closest distance to " CE1 PHE A 208 " =    1.154
peak=    3.249 closest distance to " CG2 ILE A 106 " =    1.023
peak=    3.249 closest distance to " O   HOH Z 225 " =    1.890
peak=    3.247 closest distance to " O   HOH Z 261 " =    1.713
peak=    3.246 closest distance to " O   HOH Z 149 " =    2.051
peak=    3.246 closest distance to " O   SER A  87 " =    2.461
peak=    3.245 closest distance to " OD2 ASP A 200 " =    1.308
peak=    3.239 closest distance to " CB  SER A 212 " =    1.164
peak=    3.238 closest distance to " O   HOH Z 240 " =    2.252
peak=    3.237 closest distance to " N   ALA A 100 " =    0.961
peak=    3.237 closest distance to " CA  GLU A 277 " =    0.945
peak=    3.234 closest distance to " O   HOH Z 316 " =    3.038
peak=    3.232 closest distance to " CB  GLU A 175 " =    1.290
peak=    3.231 closest distance to " CB  GLN A  89 " =    1.102
peak=    3.230 closest distance to " CG  MET A 188 " =    0.784
peak=    3.226 closest distance to " N   TYR A 247 " =    1.432
peak=    3.226 closest distance to " O   HOH Z 146 " =    1.573
peak=    3.219 closest distance to " NH1BARG A 145 " =    1.545
peak=    3.214 closest distance to " CZ3 TRP A  92 " =    1.396
peak=    3.212 closest distance to " N   GLU A  53 " =    1.706
peak=    3.211 closest distance to " CB  TYR A 247 " =    1.002
peak=    3.210 closest distance to " O   HOH Z 214 " =    2.245
peak=    3.206 closest distance to " O   THR A 251 " =    1.286
peak=    3.204 closest distance to " CB  ALA A   1 " =    1.241
peak=    3.202 closest distance to " CB  ALA A  71 " =    1.316
peak=    3.200 closest distance to " CA  ARG A  36 " =    1.160
peak=    3.200 closest distance to " OG BSER A 164 " =    2.013
peak=    3.199 closest distance to " O   HOH Z 157 " =    1.330
peak=    3.197 closest distance to " CB  ASN A 217 " =    1.101
peak=    3.194 closest distance to " CB  ASN A 142 " =    0.987
peak=    3.191 closest distance to " O   HOH Z  85 " =    2.222
peak=    3.191 closest distance to " CB  PHE A  61 " =    0.952
peak=    3.190 closest distance to " O   HOH Z 135 " =    2.179
peak=    3.187 closest distance to " O   HOH Z 365 " =    3.090
peak=    3.186 closest distance to " O   HOH Z 207 " =    2.686
peak=    3.182 closest distance to " CB  MET A 105 " =    1.357
peak=    3.176 closest distance to " N   SER A 271 " =    1.136
peak=    3.174 closest distance to " O   HOH Z 290 " =    1.253
peak=    3.173 closest distance to " CA  ASP A 132 " =    1.121
peak=    3.171 closest distance to " O   HOH Z  50 " =    3.781
peak=    3.170 closest distance to " CG  GLN A 278 " =    1.070
peak=    3.169 closest distance to " O   HOH Z 189 " =    3.038
peak=    3.168 closest distance to " O   HOH Z 368 " =    3.848
peak=    3.163 closest distance to " O   HOH Z 371 " =    3.514
peak=    3.159 closest distance to " CB  ILE A 120 " =    1.336
peak=    3.156 closest distance to " O   HOH Z   6 " =    2.343
peak=    3.152 closest distance to " O   HOH Z 258 " =    2.251
peak=    3.147 closest distance to " O   HOH Z 350 " =    1.345
peak=    3.145 closest distance to " CD  ARG A  14 " =    1.253
peak=    3.143 closest distance to " NZ  LYS A 181 " =    1.196
peak=    3.138 closest distance to " O   HOH Z 345 " =    3.826
peak=    3.138 closest distance to " O   HOH Z 141 " =    1.697
peak=    3.136 closest distance to " CD1 TRP A 274 " =    1.069
peak=    3.132 closest distance to " ND2 ASN A 209 " =    1.577
peak=    3.131 closest distance to " N   ASN A 110 " =    1.136
peak=    3.126 closest distance to " O   HOH Z 282 " =    2.337
peak=    3.123 closest distance to " O   HOH Z 167 " =    1.531
peak=    3.121 closest distance to " CB  GLN A 103 " =    1.055
peak=    3.120 closest distance to " O   HOH Z 146 " =    1.435
peak=    3.119 closest distance to " CD  GLU A 236 " =    1.142
peak=    3.117 closest distance to " CA  THR A 294 " =    1.744
peak=    3.116 closest distance to " ND1 HIS A  81 " =    1.389
peak=    3.116 closest distance to " O   HOH Z 392 " =    1.409
peak=    3.113 closest distance to " CG2 VAL A  78 " =    1.036
peak=    3.110 closest distance to " O   HOH Z  44 " =    2.454
peak=    3.109 closest distance to " CB  ALA A 291 " =    1.317
peak=    3.105 closest distance to " O   HOH Z 149 " =    1.478
peak=    3.098 closest distance to " O   HOH Z 417 " =    3.496
peak=    3.097 closest distance to " OH  TYR A 186 " =    1.072
peak=    3.085 closest distance to " CG2 VAL A 257 " =    0.947
peak=    3.085 closest distance to " O   HOH Z 292 " =    4.508
peak=    3.080 closest distance to " CD  LYS A 119 " =    1.300
peak=    3.069 closest distance to " O   ALA A 158 " =    1.256
peak=    3.064 closest distance to " C   TYR A 214 " =    1.322
peak=    3.063 closest distance to " NH2AARG A 190 " =    1.254
peak=    3.054 closest distance to " O   HOH Z 402 " =    2.841
peak=    3.046 closest distance to " CD2 LEU A   5 " =    0.728
peak=    3.034 closest distance to " CG  LYS A  76 " =    1.053

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 229         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 5.248
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 229
   mapped sites are within: 0.743 - 5.248

peak=   -5.095 closest distance to " O   HOH Z 166 " =    1.565
peak=   -4.931 closest distance to " CD  ARG A 138 " =    1.190
peak=   -4.783 closest distance to " N   ARG A 275 " =    0.891
peak=   -4.450 closest distance to " NH2 ARG A  66 " =    1.114
peak=   -4.406 closest distance to " O   HOH Z  13 " =    1.440
peak=   -4.388 closest distance to " CA  GLU A 277 " =    1.151
peak=   -4.377 closest distance to " CD2 PHE A  59 " =    2.448
peak=   -4.335 closest distance to " O   HOH Z  52 " =    2.233
peak=   -4.319 closest distance to " O   HOH Z 222 " =    1.296
peak=   -4.213 closest distance to " O   HOH Z 231 " =    1.527
peak=   -4.148 closest distance to " CA  ASN A 127 " =    1.008
peak=   -4.147 closest distance to " NE2 GLN A  55 " =    2.537
peak=   -4.129 closest distance to " O   VAL A 121 " =    0.902
peak=   -4.103 closest distance to " O   HOH Z 103 " =    2.300
peak=   -4.099 closest distance to " CG  GLN A  88 " =    0.890
peak=   -4.087 closest distance to " O   HOH Z 151 " =    1.121
peak=   -4.048 closest distance to " O   HOH Z  19 " =    1.891
peak=   -4.047 closest distance to " CG  ASP A 231 " =    0.778
peak=   -4.018 closest distance to " CG2 ILE A  49 " =    2.691
peak=   -3.981 closest distance to " CG  ARG A 138 " =    0.887
peak=   -3.978 closest distance to " CA  GLY A  23 " =    2.250
peak=   -3.977 closest distance to " CD1 LEU A 167 " =    2.243
peak=   -3.935 closest distance to " OG ASER A 134 " =    1.163
peak=   -3.917 closest distance to " O   HOH Z 231 " =    1.105
peak=   -3.905 closest distance to " CD  LYS A 289 " =    2.416
peak=   -3.899 closest distance to " O   HOH Z 400 " =    1.094
peak=   -3.886 closest distance to " NH2 ARG A  66 " =    0.790
peak=   -3.884 closest distance to " O   HOH Z 246 " =    1.042
peak=   -3.871 closest distance to " O   HOH Z 184 " =    0.812
peak=   -3.871 closest distance to " O   HOH Z  38 " =    0.814
peak=   -3.870 closest distance to " CA  ASP A 298 " =    1.061
peak=   -3.862 closest distance to " OG1 THR A  82 " =    1.750
peak=   -3.846 closest distance to " CD1 PHE A  59 " =    1.965
peak=   -3.840 closest distance to " N   GLN A  58 " =    1.372
peak=   -3.825 closest distance to " O   HOH Z 183 " =    1.349
peak=   -3.824 closest distance to " O   HOH Z 411 " =    4.715
peak=   -3.820 closest distance to " CE  MET A  93 " =    1.096
peak=   -3.810 closest distance to " CA  SER A 164 " =    1.988
peak=   -3.793 closest distance to " O   HOH Z 186 " =    1.281
peak=   -3.781 closest distance to " OH  TYR A 169 " =    1.031
peak=   -3.767 closest distance to " CD2 LEU A 167 " =    1.695
peak=   -3.763 closest distance to " N   ALA A 226 " =    2.250
peak=   -3.761 closest distance to " O   HOH Z 290 " =    1.113
peak=   -3.759 closest distance to " OG  SER A  97 " =    2.181
peak=   -3.758 closest distance to " CB  ALA A 161 " =    2.730
peak=   -3.756 closest distance to " N   SER A 134 " =    1.219
peak=   -3.744 closest distance to " O   HOH Z  60 " =    1.912
peak=   -3.723 closest distance to " C   THR A 279 " =    1.123
peak=   -3.717 closest distance to " O   HOH Z 113 " =    2.166
peak=   -3.715 closest distance to " O   HOH Z  92 " =    1.575
peak=   -3.708 closest distance to " NH1 ARG A 195 " =    0.910
peak=   -3.707 closest distance to " O   GLY A 118 " =    2.346
peak=   -3.690 closest distance to " O   HOH Z 210 " =    0.954
peak=   -3.689 closest distance to " CE2 TRP A  85 " =    1.115
peak=   -3.689 closest distance to " O   HOH Z 124 " =    1.268
peak=   -3.687 closest distance to " O   TYR A  15 " =    1.634
peak=   -3.684 closest distance to " O   HOH Z  69 " =    0.854
peak=   -3.675 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.660 closest distance to " O   HOH Z  17 " =    1.277
peak=   -3.655 closest distance to " OD2 ASP A 171 " =    2.013
peak=   -3.647 closest distance to " NE2 HIS A  86 " =    0.991
peak=   -3.647 closest distance to " CD1 LEU A  25 " =    2.559
peak=   -3.623 closest distance to " O   HOH Z 423 " =    1.043
peak=   -3.621 closest distance to " N   THR A 235 " =    1.203
peak=   -3.604 closest distance to " O   HOH Z 388 " =    1.663
peak=   -3.594 closest distance to " N   ASP A 272 " =    1.237
peak=   -3.588 closest distance to " O   ASN A  60 " =    1.124
peak=   -3.586 closest distance to " OD2 ASP A 298 " =    1.037
peak=   -3.584 closest distance to " O   HOH Z  55 " =    2.446
peak=   -3.580 closest distance to " O   HOH Z 177 " =    1.456
peak=   -3.575 closest distance to " O   HOH Z 120 " =    0.900
peak=   -3.570 closest distance to " CB  ALA A  43 " =    2.703
peak=   -3.566 closest distance to " O   HOH Z 351 " =    1.664
peak=   -3.565 closest distance to " OG  SER A  26 " =    1.446
peak=   -3.547 closest distance to " CA  GLY A 203 " =    2.309
peak=   -3.544 closest distance to " CG  GLU A   2 " =    1.531
peak=   -3.544 closest distance to " CB  ALA A 100 " =    2.087
peak=   -3.539 closest distance to " CG2BVAL A  41 " =    2.448
peak=   -3.537 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.528 closest distance to " O   HOH Z 384 " =    1.782
peak=   -3.526 closest distance to " O   HOH Z 118 " =    4.996
peak=   -3.520 closest distance to " O   HOH Z 430 " =    1.333
peak=   -3.515 closest distance to " O   HOH Z 221 " =    1.396
peak=   -3.512 closest distance to " CE3 TRP A 150 " =    2.221
peak=   -3.508 closest distance to " O   HOH Z 179 " =    2.297
peak=   -3.501 closest distance to " CG  ARG A 269 " =    2.345
peak=   -3.497 closest distance to " O   HOH Z  71 " =    1.043
peak=   -3.489 closest distance to " O   HOH Z  43 " =    1.784
peak=   -3.484 closest distance to " O   HOH Z 396 " =    1.688
peak=   -3.482 closest distance to " OE1 GLN A  88 " =    1.132
peak=   -3.461 closest distance to " O   VAL A  67 " =    2.593
peak=   -3.460 closest distance to " O   MET A  47 " =    2.509
peak=   -3.458 closest distance to " O   HOH Z  37 " =    1.442
peak=   -3.454 closest distance to " CD2 PHE A  61 " =    2.087
peak=   -3.451 closest distance to " O   HOH Z 132 " =    1.291
peak=   -3.450 closest distance to " CE2 PHE A 283 " =    2.651
peak=   -3.446 closest distance to " N   SER A   3 " =    2.411
peak=   -3.440 closest distance to " NZ  LYS A 119 " =    1.450
peak=   -3.437 closest distance to " O   HOH Z  91 " =    1.815
peak=   -3.433 closest distance to " O   LEU A 101 " =    2.886
peak=   -3.426 closest distance to " CB  SER A  63 " =    3.298
peak=   -3.424 closest distance to " CG1 VAL A 296 " =    1.268
peak=   -3.423 closest distance to " O   HOH Z 385 " =    4.058
peak=   -3.422 closest distance to " O   HOH Z 426 " =    0.936
peak=   -3.421 closest distance to " NH2AARG A 275 " =    5.248
peak=   -3.420 closest distance to " CD  GLN A 223 " =    1.490
peak=   -3.413 closest distance to " CB  ALA A 291 " =    2.543
peak=   -3.406 closest distance to " O   HOH Z 400 " =    0.768
peak=   -3.406 closest distance to " O   HOH Z 117 " =    1.034
peak=   -3.401 closest distance to " O   HOH Z 198 " =    1.544
peak=   -3.395 closest distance to " O   HOH Z 185 " =    2.182
peak=   -3.392 closest distance to " CD  ARG A  14 " =    3.062
peak=   -3.388 closest distance to " O   HOH Z 221 " =    1.301
peak=   -3.382 closest distance to " ND2BASN A 224 " =    1.861
peak=   -3.380 closest distance to " N   LEU A 261 " =    1.371
peak=   -3.379 closest distance to " CB  PRO A 163 " =    2.766
peak=   -3.379 closest distance to " C   GLY A  91 " =    1.678
peak=   -3.378 closest distance to " CD  GLU A 236 " =    1.039
peak=   -3.374 closest distance to " O   HOH Z 156 " =    1.544
peak=   -3.370 closest distance to " O   HOH Z 380 " =    4.324
peak=   -3.370 closest distance to " CG  ARG A 259 " =    2.551
peak=   -3.370 closest distance to " CB  SER A 146 " =    2.169
peak=   -3.367 closest distance to " CD2 LEU A 143 " =    2.526
peak=   -3.362 closest distance to " CB  ALA A 291 " =    2.113
peak=   -3.362 closest distance to " CD  PRO A 213 " =    2.326
peak=   -3.361 closest distance to " CH2 TRP A 177 " =    2.129
peak=   -3.361 closest distance to " OG  SER A  87 " =    1.736
peak=   -3.358 closest distance to " OE2 GLU A  53 " =    1.084
peak=   -3.356 closest distance to " O   HOH Z 326 " =    4.510
peak=   -3.352 closest distance to " CD1 TYR A 247 " =    2.379
peak=   -3.350 closest distance to " CG2 THR A 182 " =    2.363
peak=   -3.347 closest distance to " CG1 VAL A  78 " =    2.398
peak=   -3.337 closest distance to " O   HOH Z 166 " =    2.127
peak=   -3.331 closest distance to " O   HOH Z 275 " =    1.517
peak=   -3.330 closest distance to " CG1 VAL A 112 " =    2.568
peak=   -3.327 closest distance to " O   HOH Z  98 " =    1.835
peak=   -3.324 closest distance to " CD  GLN A  77 " =    0.994
peak=   -3.324 closest distance to " O   HOH Z 189 " =    1.931
peak=   -3.323 closest distance to " CB  ASP A 171 " =    2.348
peak=   -3.322 closest distance to " CB  GLN A  55 " =    1.383
peak=   -3.319 closest distance to " CG  ARG A 219 " =    2.483
peak=   -3.318 closest distance to " CG  TRP A 266 " =    2.081
peak=   -3.318 closest distance to " N   LYS A 166 " =    2.065
peak=   -3.314 closest distance to " O   GLY A 136 " =    2.630
peak=   -3.313 closest distance to " O   HOH Z 417 " =    1.023
peak=   -3.311 closest distance to " CG  GLU A  53 " =    1.502
peak=   -3.311 closest distance to " O   ALA A   7 " =    1.655
peak=   -3.306 closest distance to " CD2 TYR A 293 " =    2.008
peak=   -3.304 closest distance to " O   HOH Z 234 " =    4.311
peak=   -3.304 closest distance to " O   HOH Z  30 " =    0.809
peak=   -3.300 closest distance to " C   ASN A 187 " =    1.826
peak=   -3.296 closest distance to " CB  ALA A 227 " =    2.407
peak=   -3.293 closest distance to " OXT GLY A 302 " =    2.899
peak=   -3.284 closest distance to " O   HOH Z  18 " =    1.039
peak=   -3.283 closest distance to " N   ILE A 120 " =    0.996
peak=   -3.280 closest distance to " OG1 THR A   4 " =    1.702
peak=   -3.277 closest distance to " CD2 LEU A 237 " =    2.469
peak=   -3.277 closest distance to " O   HOH Z  37 " =    1.862
peak=   -3.272 closest distance to " O   HOH Z  49 " =    0.936
peak=   -3.270 closest distance to " OG  SER A 276 " =    1.015
peak=   -3.265 closest distance to " O   HOH Z   5 " =    2.076
peak=   -3.262 closest distance to " O   HOH Z 407 " =    3.702
peak=   -3.261 closest distance to " CD  ARG A 156 " =    1.960
peak=   -3.260 closest distance to " OD1 ASP A 191 " =    1.467
peak=   -3.258 closest distance to " CD2 LEU A 237 " =    2.812
peak=   -3.256 closest distance to " N   ALA A  43 " =    2.609
peak=   -3.251 closest distance to " O   HOH Z   5 " =    1.583
peak=   -3.240 closest distance to " O   HOH Z 252 " =    1.111
peak=   -3.234 closest distance to " O   HOH Z 292 " =    4.374
peak=   -3.230 closest distance to " CG  LYS A 166 " =    1.993
peak=   -3.227 closest distance to " CD1 LEU A   5 " =    2.561
peak=   -3.224 closest distance to " O   HOH Z 118 " =    1.768
peak=   -3.223 closest distance to " O   THR A  18 " =    1.567
peak=   -3.220 closest distance to " OD2 ASP A 132 " =    1.590
peak=   -3.218 closest distance to " O   GLY A 196 " =    1.243
peak=   -3.216 closest distance to " CG  PRO A 243 " =    1.611
peak=   -3.211 closest distance to " O   HOH Z 389 " =    1.286
peak=   -3.210 closest distance to " O   HOH Z  84 " =    0.923
peak=   -3.204 closest distance to " O   HOH Z 407 " =    1.110
peak=   -3.196 closest distance to " O   HOH Z 283 " =    2.285
peak=   -3.193 closest distance to " O   HOH Z 377 " =    1.964
peak=   -3.191 closest distance to " O   HOH Z 348 " =    2.319
peak=   -3.184 closest distance to " CD  GLN A 223 " =    0.743
peak=   -3.184 closest distance to " O   HOH Z 165 " =    1.935
peak=   -3.181 closest distance to " CG2 VAL A 197 " =    2.415
peak=   -3.177 closest distance to " O   HOH Z  94 " =    1.764
peak=   -3.175 closest distance to " O   HOH Z 422 " =    1.707
peak=   -3.174 closest distance to " O   HOH Z 171 " =    2.443
peak=   -3.170 closest distance to " OE2 GLU A 277 " =    2.826
peak=   -3.169 closest distance to " O   HOH Z 369 " =    2.399
peak=   -3.166 closest distance to " C   GLY A  17 " =    1.295
peak=   -3.164 closest distance to " O   HOH Z 157 " =    3.696
peak=   -3.159 closest distance to " O   GLY A  80 " =    2.405
peak=   -3.158 closest distance to " CE  MET A 105 " =    2.061
peak=   -3.158 closest distance to " O   HOH Z   6 " =    2.059
peak=   -3.157 closest distance to " CA  GLY A 241 " =    3.322
peak=   -3.154 closest distance to " CG BMET A  47 " =    0.927
peak=   -3.154 closest distance to " O   HOH Z 418 " =    1.546
peak=   -3.152 closest distance to " O   LEU A 255 " =    1.696
peak=   -3.152 closest distance to " NE1 TRP A 266 " =    2.042
peak=   -3.151 closest distance to " O   HOH Z 198 " =    2.143
peak=   -3.148 closest distance to " O   HOH Z 120 " =    4.312
peak=   -3.147 closest distance to " O   HOH Z 119 " =    2.587
peak=   -3.144 closest distance to " C   ASP A 270 " =    1.192
peak=   -3.140 closest distance to " C   PRO A 213 " =    2.191
peak=   -3.139 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.137 closest distance to " N   ASP A 191 " =    1.264
peak=   -3.136 closest distance to " O   HOH Z 393 " =    5.172
peak=   -3.133 closest distance to " O   HOH Z 402 " =    1.218
peak=   -3.126 closest distance to " CD1 ILE A  33 " =    1.818
peak=   -3.125 closest distance to " OD1 ASN A 148 " =    1.323
peak=   -3.121 closest distance to " CD  ARG A 139 " =    1.329
peak=   -3.120 closest distance to " O   HOH Z  92 " =    1.439
peak=   -3.106 closest distance to " CA  MET A  93 " =    1.011
peak=   -3.101 closest distance to " CZ2 TRP A  70 " =    1.014
peak=   -3.099 closest distance to " CE  LYS A 119 " =    0.915
peak=   -3.097 closest distance to " CD2 LEU A 228 " =    2.519
peak=   -3.091 closest distance to " CB  ARG A 138 " =    1.376
peak=   -3.077 closest distance to " O   HOH Z 414 " =    1.386
peak=   -3.075 closest distance to " OG1 THR A  29 " =    1.777
peak=   -3.073 closest distance to " O   HOH Z  92 " =    1.393
peak=   -3.062 closest distance to " O   HOH Z 154 " =    1.313
peak=   -3.029 closest distance to " O   HOH Z 421 " =    2.989
peak=   -3.027 closest distance to " O   SER A 135 " =    1.878
peak=   -3.023 closest distance to " CA  TYR A  68 " =    2.675

================= 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    :  0.5032 0.4915   6.303331e+00   6.290667e+00
   1_bss:  0.4965 0.4817   6.300629e+00   6.286784e+00
   1_xyz:  0.4339 0.4511   6.227037e+00   6.257198e+00
   1_adp:  0.3970 0.4413   6.179697e+00   6.242381e+00
   1_occ:  0.3963 0.4423   6.179086e+00   6.242700e+00
   2_bss:  0.3952 0.4384   6.181274e+00   6.242732e+00
   2_xyz:  0.3300 0.4040   6.064279e+00   6.186927e+00
   2_adp:  0.3147 0.3865   6.031648e+00   6.163856e+00
   2_occ:  0.3146 0.3864   6.030896e+00   6.163502e+00
   3_bss:  0.3143 0.3846   6.031551e+00   6.163498e+00
   3_xyz:  0.2379 0.3002   5.791119e+00   5.964668e+00
   3_adp:  0.2117 0.2734   5.692896e+00   5.882256e+00
   3_occ:  0.2113 0.2732   5.692205e+00   5.881847e+00
   4_bss:  0.2101 0.2711   5.689489e+00   5.878767e+00
   4_xyz:  0.1709 0.2242   5.502786e+00   5.713933e+00
   4_adp:  0.1623 0.2138   5.460416e+00   5.666536e+00
   4_occ:  0.1621 0.2136   5.459556e+00   5.665507e+00
   5_bss:  0.1622 0.2138   5.461666e+00   5.667108e+00
   5_xyz:  0.1429 0.1896   5.351142e+00   5.561969e+00
   5_adp:  0.1371 0.1884   5.332226e+00   5.558247e+00
   5_occ:  0.1370 0.1883   5.331779e+00   5.557736e+00
   5_bss:  0.1370 0.1883   5.331601e+00   5.557617e+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:  0.299  20.001   8.460  10.210   6.351   0.000   0.000   0.000
   1_xyz:  0.299  20.001   8.460  10.210   6.351   0.000   0.000   0.000
   1_adp:  0.299  20.001   8.460  10.210   6.351   0.000   0.000   0.000
   1_occ:  0.299  20.001   8.460  10.210   6.351   0.000   0.000   0.000
   2_bss:  0.294  33.593   5.413   6.657   4.355   0.000   0.000   0.000
   2_xyz:  0.294  33.593   5.413   6.657   4.355   0.000   0.000   0.000
   2_adp:  0.294  33.593   5.413   6.657   4.355   0.000   0.000   0.000
   2_occ:  0.294  33.593   5.413   6.657   4.355   0.000   0.000   0.000
   3_bss:  0.298  61.824   3.546   4.618   3.130   0.000   0.000   0.000
   3_xyz:  0.298  61.824   3.546   4.618   3.130   0.000   0.000   0.000
   3_adp:  0.298  61.824   3.546   4.618   3.130   0.000   0.000   0.000
   3_occ:  0.298  61.824   3.546   4.618   3.130   0.000   0.000   0.000
   4_bss:  0.322  64.979   2.192   2.838   1.970   0.000   0.000   0.000
   4_xyz:  0.322  64.979   2.192   2.838   1.970   0.000   0.000   0.000
   4_adp:  0.322  64.979   2.192   2.838   1.970   0.000   0.000   0.000
   4_occ:  0.322  64.979   2.192   2.838   1.970   0.000   0.000   0.000
   5_bss:  0.331  64.563   1.419   2.015   1.708   0.000   0.000   0.000
   5_xyz:  0.331  64.563   1.419   2.015   1.708   0.000   0.000   0.000
   5_adp:  0.331  64.563   1.419   2.015   1.708   0.000   0.000   0.000
   5_occ:  0.331  64.563   1.419   2.015   1.708   0.000   0.000   0.000
   5_bss:  0.326  64.880  -0.252   0.184   0.068   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.607 0.3599  0.4217    79132.361
   1_bss:  63.053 0.3522  0.5195    77255.301
   1_xyz:  57.047 0.4288  0.6209    65280.194
   1_adp:  53.580 0.4733  0.7411    59802.757
   1_occ:  53.735 0.4713  0.7372    60037.181
   2_bss:  53.618 0.4727  0.6748    59942.125
   2_xyz:  47.318 0.5513  0.7888    48797.440
   2_adp:  44.251 0.5897  0.8329    44296.065
   2_occ:  44.178 0.5906  0.8340    44193.543
   3_bss:  44.021 0.5925  0.7893    43971.174
   3_xyz:  31.509 0.7397  0.9426    24101.281
   3_adp:  27.748 0.7816  0.9658    19534.765
   3_occ:  27.726 0.7819  0.9657    19520.872
   4_bss:  27.550 0.7834  0.9210    19283.550
   4_xyz:  21.961 0.8414  0.9630    12812.621
   4_adp:  20.503 0.8565  0.9675    11604.637
   4_occ:  20.473 0.8568  0.9675    11584.945
   5_bss:  20.483 0.8568  0.9469    11623.099
   5_xyz:  17.914 0.8812  0.9624     9257.130
   5_adp:  17.752 0.8830  0.9600     9187.483
   5_occ:  17.738 0.8831  0.9600     9179.025
   5_bss:  17.733 0.8831  0.9570     9174.733
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4331e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4331e+01
   1_xyz:   1.850  0.015  0.115 18.272  0.008  4.125   1.6680e-01
   1_adp:   1.850  0.015  0.115 18.272  0.008  4.125   1.6680e-01
   1_occ:   1.850  0.015  0.115 18.272  0.008  4.125   1.6680e-01
   2_bss:   1.850  0.015  0.115 18.272  0.008  4.125   1.6680e-01
   2_xyz:   1.294  0.009  0.087 16.612  0.005  4.133   1.0017e-01
   2_adp:   1.294  0.009  0.087 16.612  0.005  4.133   1.0017e-01
   2_occ:   1.294  0.009  0.087 16.612  0.005  4.133   1.0017e-01
   3_bss:   1.294  0.009  0.087 16.612  0.005  4.133   1.0017e-01
   3_xyz:   1.330  0.010  0.095 16.255  0.005  4.109   1.0192e-01
   3_adp:   1.330  0.010  0.095 16.255  0.005  4.109   1.0192e-01
   3_occ:   1.330  0.010  0.095 16.255  0.005  4.109   1.0192e-01
   4_bss:   1.330  0.010  0.095 16.255  0.005  4.109   1.0192e-01
   4_xyz:   1.036  0.008  0.076 15.755  0.004  4.125   6.8137e-02
   4_adp:   1.036  0.008  0.076 15.755  0.004  4.125   6.8137e-02
   4_occ:   1.036  0.008  0.076 15.755  0.004  4.125   6.8137e-02
   5_bss:   1.036  0.008  0.076 15.755  0.004  4.125   6.8137e-02
   5_xyz:   1.052  0.008  0.080 15.590  0.004  4.135   6.6855e-02
   5_adp:   1.052  0.008  0.080 15.590  0.004  4.135   6.6855e-02
   5_occ:   1.052  0.008  0.080 15.590  0.004  4.135   6.6855e-02
   5_bss:   1.052  0.008  0.080 15.590  0.004  4.135   6.6855e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0424e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0424e+00
   1_xyz:  16.435  0.144  0.540 87.677  0.050  2.159   1.1342e-01
   1_adp:  16.435  0.144  0.540 87.677  0.050  2.159   1.1342e-01
   1_occ:  16.435  0.144  0.540 87.677  0.050  2.159   1.1342e-01
   2_bss:  16.435  0.144  0.540 87.677  0.050  2.159   1.1342e-01
   2_xyz:   8.944  0.078  0.281 82.951  0.037  1.922   6.6536e-02
   2_adp:   8.944  0.078  0.281 82.951  0.037  1.922   6.6536e-02
   2_occ:   8.944  0.078  0.281 82.951  0.037  1.922   6.6536e-02
   3_bss:   8.944  0.078  0.281 82.951  0.037  1.922   6.6536e-02
   3_xyz:   8.764  0.050  0.331 79.779  0.049  2.199   8.8071e-02
   3_adp:   8.764  0.050  0.331 79.779  0.049  2.199   8.8071e-02
   3_occ:   8.764  0.050  0.331 79.779  0.049  2.199   8.8071e-02
   4_bss:   8.764  0.050  0.331 79.779  0.049  2.199   8.8071e-02
   4_xyz:   8.301  0.056  0.303 80.720  0.046  2.315   5.5366e-02
   4_adp:   8.301  0.056  0.303 80.720  0.046  2.315   5.5366e-02
   4_occ:   8.301  0.056  0.303 80.720  0.046  2.315   5.5366e-02
   5_bss:   8.301  0.056  0.303 80.720  0.046  2.315   5.5366e-02
   5_xyz:   7.948  0.051  0.419 84.701  0.038  2.280   5.1691e-02
   5_adp:   7.948  0.051  0.419 84.701  0.038  2.280   5.1691e-02
   5_occ:   7.948  0.051  0.419 84.701  0.038  2.280   5.1691e-02
   5_bss:   7.948  0.051  0.419 84.701  0.038  2.280   5.1691e-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: 121.92   0.00  14.28 121.92   0.00  12.72  83.17   0.00  22.82
   1_occ: 121.92   0.00  14.28 121.92   0.00  12.72  83.17   0.00  22.82
   2_bss: 121.92   0.00  14.28 121.92   0.00  12.72  83.17   0.00  22.82
   2_xyz: 121.92   0.00  14.28 121.92   0.00  12.72  83.17   0.00  22.82
   2_adp:  95.90   0.00  13.93  66.67   0.00  11.30  95.90   0.00  28.28
   2_occ:  95.90   0.00  13.93  66.67   0.00  11.30  95.90   0.00  28.28
   3_bss:  95.90   0.00  13.93  66.67   0.00  11.30  95.90   0.00  28.28
   3_xyz:  95.90   0.00  13.93  66.67   0.00  11.30  95.90   0.00  28.28
   3_adp:  99.37   0.00  14.68  79.13   0.00  10.40  99.37   0.00  37.95
   3_occ:  99.37   0.00  14.68  79.13   0.00  10.40  99.37   0.00  37.95
   4_bss:  99.37   0.00  14.68  79.13   0.00  10.40  99.37   0.00  37.95
   4_xyz:  99.37   0.00  14.68  79.13   0.00  10.40  99.37   0.00  37.95
   4_adp:  95.62   0.00  14.35  83.67   0.00   9.89  95.62   1.56  38.65
   4_occ:  95.62   0.00  14.35  83.67   0.00   9.89  95.62   1.56  38.65
   5_bss:  95.62   0.00  14.35  83.67   0.00   9.89  95.62   1.56  38.65
   5_xyz:  95.62   0.00  14.35  83.67   0.00   9.89  95.62   1.56  38.65
   5_adp:  94.26   0.00  14.75  93.08   0.00   9.84  94.26   1.55  41.48
   5_occ:  94.26   0.00  14.75  93.08   0.00   9.84  94.26   1.55  41.48
   5_bss:  95.88   1.62  16.37  94.70   1.62  11.46  95.88   3.18  43.10
------------------------------------------------------------------------
 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:    1.125    0.020    0.421
   1_adp:    1.125    0.020    0.421
   1_occ:    1.125    0.020    0.421
   2_bss:    1.125    0.020    0.421
   2_xyz:    1.594    0.037    0.593
   2_adp:    1.594    0.037    0.593
   2_occ:    1.594    0.037    0.593
   3_bss:    1.594    0.037    0.593
   3_xyz:    1.780    0.084    0.778
   3_adp:    1.780    0.084    0.778
   3_occ:    1.780    0.084    0.778
   4_bss:    1.780    0.084    0.778
   4_xyz:    1.987    0.067    0.840
   4_adp:    1.987    0.067    0.840
   4_occ:    1.987    0.067    0.840
   5_bss:    1.987    0.067    0.840
   5_xyz:    1.980    0.083    0.885
   5_adp:    1.980    0.083    0.885
   5_occ:    1.980    0.083    0.885
   5_bss:    1.980    0.083    0.885
------------------------------------------------------------------------

CPU time actual refinement: 359.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/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_1312/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1312/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.36 
  Macro-tasks:
    bulk solvent and scale       = 43.41  
    individual site refinement   = 151.49 
    weights calculation          = 33.39  
    collect and process          = 6.37   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 234.77 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 114.82 
    alpha_beta                      = 8.48   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 124.80 
    fmodel                         = 7.35   
    r_factors                      = 0.24   
    phase_errors                   = 10.15  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 269.69 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.034 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    645 calls, 114.47 s
gradients_fft:          589 calls, 111.49 s

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

# Date 2008-01-16 Time 03:44:10 PST -0800 (1200483850.40 s)
Start R-work = 0.5032, R-free = 0.4915 (no bulk solvent and anisotropic scale)
Final R-work = 0.1525, R-free = 0.2038 (no bulk solvent and anisotropic scale)

Start R-work = 0.4965, R-free = 0.4817
Final R-work = 0.1370, R-free = 0.1883