# Date 2008-01-16 Time 02:38:36 PST -0800 (1200479916.17 s)
#phil __OFF__

Command line arguments: "../915.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 415
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 915

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97124
Completeness in resolution range: 0.945598
Completeness with d_max=infinity: 0.942731

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9712

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97124
Completeness in resolution range: 0.945598
Completeness with d_max=infinity: 0.942731

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2186 [2180/2209]  1965   215   9.9%
  bin  2:  4.2186 -  3.3607 [2085/2104]  1874   211  10.1%
  bin  3:  3.3607 -  2.9395 [2056/2076]  1850   206  10.0%
  bin  4:  2.9395 -  2.6724 [2051/2076]  1852   199   9.7%
  bin  5:  2.6724 -  2.4817 [2046/2065]  1834   212  10.4%
  bin  6:  2.4817 -  2.3360 [2020/2066]  1822   198   9.8%
  bin  7:  2.3360 -  2.2194 [1998/2031]  1795   203  10.2%
  bin  8:  2.2194 -  2.1231 [1999/2035]  1799   200  10.0%
  bin  9:  2.1231 -  2.0415 [2000/2029]  1801   199   9.9%
  bin 10:  2.0415 -  1.9712 [1154/2025]  1038   116  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 24
        2.42 -     3.04: 2198
        3.04 -     3.66: 4678
        3.66 -     4.28: 9004
        4.28 -     4.90: 12401
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.916 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.943 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.048 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.180 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28300 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_915/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4446   r_free= 0.4361   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.241859                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7055 0.99   1410  157 0.3708 0.3595      6.5405      6.5171|
|  2:  4.7055 -  3.7540 0.99   1362  146 0.3459 0.3548      6.6853       6.688|
|  3:  3.7540 -  3.2851 0.99   1328  156 0.3936 0.3642      6.5835      6.6095|
|  4:  3.2851 -  2.9873 0.99   1340  147 0.4206 0.4109      6.4584      6.4254|
|  5:  2.9873 -  2.7746 0.99   1315  146 0.4620 0.4883      6.3294      6.3693|
|  6:  2.7746 -  2.6119 0.98   1307  142 0.4671 0.4764      6.2311      6.1686|
|  7:  2.6119 -  2.4817 0.99   1313  149 0.4926 0.4365      6.2428      6.1507|
|  8:  2.4817 -  2.3741 0.98   1288  142 0.4956 0.5003       6.137      6.1695|
|  9:  2.3741 -  2.2831 0.98   1304  149 0.4959 0.4861      6.1084       6.094|
| 10:  2.2831 -  2.2045 0.98   1279  137 0.4943 0.5117      6.0762      6.0981|
| 11:  2.2045 -  2.1358 0.99   1292  145 0.4955 0.4551      6.0198      6.0011|
| 12:  2.1358 -  2.0749 0.98   1273  138 0.5067 0.5375      5.9515      6.0052|
| 13:  2.0749 -  2.0204 0.97   1277  143 0.5211 0.5030      5.8706      5.8159|
| 14:  2.0204 -  1.9712 0.42    542   62 0.5254 0.5095      5.8365      5.7695|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7055  1410   157  0.73  31.22   0.81     0.76      59323.14|
|  2:  4.7055 -  3.7540  1362   146  0.75  30.47   0.91     0.81      81188.20|
|  3:  3.7540 -  3.2851  1328   156  0.66  38.38   0.86     0.78      88289.77|
|  4:  3.2851 -  2.9873  1340   147  0.59  44.54   0.83     0.68      81573.51|
|  5:  2.9873 -  2.7746  1315   146  0.50  52.18   0.76     0.59      70874.12|
|  6:  2.7746 -  2.6119  1307   142  0.49  52.96   0.77     0.56      60203.75|
|  7:  2.6119 -  2.4817  1313   149  0.51  51.34   0.75     0.56      51908.13|
|  8:  2.4817 -  2.3741  1288   142  0.49  52.72   0.73     0.57      47232.63|
|  9:  2.3741 -  2.2831  1304   149  0.47  54.58   0.75     0.54      44127.22|
| 10:  2.2831 -  2.2045  1279   137  0.44  56.95   0.78     0.51      43652.68|
| 11:  2.2045 -  2.1358  1292   145  0.39  60.66   0.79     0.47      42239.15|
| 12:  2.1358 -  2.0749  1273   138  0.35  63.91   0.75     0.43      41992.52|
| 13:  2.0749 -  2.0204  1277   143  0.33  65.31   0.74     0.41      36078.49|
| 14:  2.0204 -  1.9712   542    62  0.39  60.96   0.72     0.44      27969.57|
|alpha:            min =        0.41 max =            0.81 mean =         0.59|
|beta:             min =    27969.57 max =        88289.77 mean =     56965.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.45|
|phase err.(test): min =        0.00 max =           89.96 mean =        50.47|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.982453              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.564   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.725   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1510 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3911 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5067 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6566 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7751 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.722 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.720 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4521   r_free= 0.4437   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.245831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4361   r_free= 0.4260   ksol= 0.34   Bsol= 14.28   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.87,8.38,8.76,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.240705                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.702503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.907   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4361      final r-factor (work) = 0.3353          |
| start r-factor (free) = 0.4260      final r-factor (free) = 0.3700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.9049 = 8.70 * 0.50 * 6.2472 + 1.00 * 53.7216                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6949 = 8.70 * 0.50 * 6.1054 + 1.00 * 0.1287                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3353      final r-factor (work) = 0.2808          |
| start r-factor (free) = 0.3700      final r-factor (free) = 0.3336          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6779 = 0.76 * 1.00 * 6.1054 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5679 = 0.76 * 1.00 * 5.9641 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.33   11.15    None  None   None       |
|    all(noH): 2823   0      0.00    72.33   11.15    None  None   None       |
|    Sol.    : 438    0      0.00    72.33   27.68    None  None   None       |
|    Mac.    : 2385   0      0.00    68.46   8.11     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 -   7.233: 1418   |   5:    36.166 -  43.399:   84        |
|      1:     7.233 -  14.466:  713   |   6:    43.399 -  50.632:   41        |
|      2:    14.466 -  21.700:  266   |   7:    50.632 -  57.865:   20        |
|      3:    21.700 -  28.933:  167   |   8:    57.865 -  65.099:    7        |
|      4:    28.933 -  36.166:  105   |   9:    65.099 -  72.332:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2808 r_free = 0.3336             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2804 r_free = 0.3342             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2804   r_free= 0.3342   ksol= 0.34   Bsol= 14.28   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.87,8.38,8.76,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.921092                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2761   r_free= 0.3283   ksol= 0.33   Bsol= 40.87   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.28,4.51,5.57,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.919204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.737267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.176   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358752              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.288  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2761      final r-factor (work) = 0.1865          |
| start r-factor (free) = 0.3283      final r-factor (free) = 0.2409          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2620 = 4.74 * 0.50 * 5.9669 + 1.00 * 0.1287                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7163 = 4.74 * 0.50 * 5.7634 + 1.00 * 0.0648                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1865      final r-factor (work) = 0.1689          |
| start r-factor (free) = 0.2409      final r-factor (free) = 0.2183          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0801 = 0.36 * 1.00 * 5.7634 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9968 = 0.36 * 1.00 * 5.5385 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.00   11.57    None  None   None       |
|    all(noH): 2823   0      0.00    72.00   11.57    None  None   None       |
|    Sol.    : 438    0      1.46    72.00   31.76    None  None   None       |
|    Mac.    : 2385   0      0.00    69.30   7.87     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 -   7.200: 1476   |   5:    36.000 -  43.200:  119        |
|      1:     7.200 -  14.400:  688   |   6:    43.200 -  50.400:   69        |
|      2:    14.400 -  21.600:  204   |   7:    50.400 -  57.600:   26        |
|      3:    21.600 -  28.800:  114   |   8:    57.600 -  64.800:    4        |
|      4:    28.800 -  36.000:  119   |   9:    64.800 -  72.000:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1689 r_free = 0.2183             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1687 r_free = 0.2182             target_work(ml) = 5.488         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1687   r_free= 0.2182   ksol= 0.33   Bsol= 40.87   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.28,4.51,5.57,0.00,0.00,0.00); trace/3= 4.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.488035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2160   ksol= 0.33   Bsol= 42.35   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.18,3.80,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.486929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.871240              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.623  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.950428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.413  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1675      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.2160      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8043 = 3.87 * 0.50 * 5.5483 + 1.00 * 0.0649                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4909 = 3.87 * 0.50 * 5.3835 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1263 = 0.95 * 1.00 * 5.3835 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9796 = 0.95 * 1.00 * 5.2261 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.90   12.31    None  None   None       |
|    all(noH): 2823   0      0.00    84.90   12.31    None  None   None       |
|    Sol.    : 438    0      1.14    73.57   35.72    None  None   None       |
|    Mac.    : 2385   0      0.00    84.90   8.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.490: 1690   |   5:    42.449 -  50.939:   99        |
|      1:     8.490 -  16.980:  569   |   6:    50.939 -  59.429:   59        |
|      2:    16.980 -  25.470:  156   |   7:    59.429 -  67.919:   23        |
|      3:    25.470 -  33.960:  105   |   8:    67.919 -  76.409:   10        |
|      4:    33.960 -  42.449:  109   |   9:    76.409 -  84.899:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1655             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1654             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1654   ksol= 0.33   Bsol= 42.35   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.18,3.80,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.207926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1658   ksol= 0.32   Bsol= 42.35   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.66,2.87,3.35,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210263                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.405204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.003  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.192323              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.059  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1209      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9709 = 3.41 * 0.50 * 5.2275 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8963 = 3.41 * 0.50 * 5.1809 + 1.00 * 0.0753                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0089 = 0.19 * 1.00 * 5.1809 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0032 = 0.19 * 1.00 * 5.1645 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.44   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    81.44   11.67    None  None   None       |
|    Sol.    : 438    0      1.24    69.21   32.75    None  None   None       |
|    Mac.    : 2385   0      0.00    81.44   7.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.144: 1667   |   5:    40.721 -  48.865:   89        |
|      1:     8.144 -  16.288:  600   |   6:    48.865 -  57.009:   51        |
|      2:    16.288 -  24.432:  152   |   7:    57.009 -  65.153:   14        |
|      3:    24.432 -  32.577:  129   |   8:    65.153 -  73.297:    5        |
|      4:    32.577 -  40.721:  112   |   9:    73.297 -  81.441:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1579             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1577             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1577   ksol= 0.32   Bsol= 42.35   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.66,2.87,3.35,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156915                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1577   ksol= 0.32   Bsol= 42.26   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.82,3.27,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.483343              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.251120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.427   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4875 = 2.48 * 0.50 * 5.1641 + 1.00 * 0.0754                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4685 = 2.48 * 0.50 * 5.1554 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3061 = 0.25 * 1.00 * 5.1554 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3182 = 0.25 * 1.00 * 5.1513 + 1.00 * 0.0246                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.84   11.60    None  None   None       |
|    all(noH): 2823   0      0.00    81.84   11.60    None  None   None       |
|    Sol.    : 438    0      1.45    65.87   32.40    None  None   None       |
|    Mac.    : 2385   0      0.00    81.84   7.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.184: 1683   |   5:    40.918 -  49.102:   87        |
|      1:     8.184 -  16.367:  585   |   6:    49.102 -  57.286:   47        |
|      2:    16.367 -  24.551:  156   |   7:    57.286 -  65.469:   11        |
|      3:    24.551 -  32.735:  124   |   8:    65.469 -  73.653:    4        |
|      4:    32.735 -  40.918:  122   |   9:    73.653 -  81.837:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1574             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1575             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1575   ksol= 0.32   Bsol= 42.26   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.82,3.27,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152743                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7055 0.99   1410  157 0.1003 0.1283      5.3826      5.5371|
|  2:  4.7055 -  3.7540 0.99   1362  146 0.0863 0.1122      5.4379      5.6435|
|  3:  3.7540 -  3.2851 0.99   1328  156 0.1063 0.1589      5.4745      5.8688|
|  4:  3.2851 -  2.9873 0.99   1340  147 0.1209 0.1484      5.4524      5.5798|
|  5:  2.9873 -  2.7746 0.99   1315  146 0.1304 0.1724      5.3272      5.5158|
|  6:  2.7746 -  2.6119 0.98   1307  142 0.1231 0.1926      5.2188      5.4825|
|  7:  2.6119 -  2.4817 0.99   1313  149 0.1251 0.1669      5.1787      5.4083|
|  8:  2.4817 -  2.3741 0.98   1288  142 0.1169 0.1697      5.0626      5.2932|
|  9:  2.3741 -  2.2831 0.98   1304  149 0.1171 0.1772      5.0289      5.3143|
| 10:  2.2831 -  2.2045 0.98   1279  137 0.1134 0.1722      4.9682      5.2254|
| 11:  2.2045 -  2.1358 0.99   1292  145 0.1137 0.1796      4.9416       5.292|
| 12:  2.1358 -  2.0749 0.98   1273  138 0.1082 0.1567       4.869      5.0613|
| 13:  2.0749 -  2.0204 0.97   1277  143 0.1178 0.1817      4.7893      5.0636|
| 14:  2.0204 -  1.9712 0.42    542   62 0.0997 0.1690       4.637      4.9098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7055  1410   157  0.94   8.69   0.98     0.96       6900.98|
|  2:  4.7055 -  3.7540  1362   146  0.95   8.00   1.01     1.00       8935.02|
|  3:  3.7540 -  3.2851  1328   156  0.93  11.58   1.02     1.01      10598.54|
|  4:  3.2851 -  2.9873  1340   147  0.92  13.84   1.00     0.98      10404.53|
|  5:  2.9873 -  2.7746  1315   146  0.90  16.33   0.99     0.95       8411.84|
|  6:  2.7746 -  2.6119  1307   142  0.90  16.32   0.98     0.95       7255.63|
|  7:  2.6119 -  2.4817  1313   149  0.91  15.43   0.99     0.95       6315.58|
|  8:  2.4817 -  2.3741  1288   142  0.90  15.77   0.99     0.96       5425.96|
|  9:  2.3741 -  2.2831  1304   149  0.90  15.83   1.00     0.97       5042.21|
| 10:  2.2831 -  2.2045  1279   137  0.90  15.54   1.00     0.97       4501.54|
| 11:  2.2045 -  2.1358  1292   145  0.90  16.29   1.00     0.96       4353.66|
| 12:  2.1358 -  2.0749  1273   138  0.91  15.25   1.00     0.99       3993.78|
| 13:  2.0749 -  2.0204  1277   143  0.90  16.44   1.00     0.99       3343.82|
| 14:  2.0204 -  1.9712   542    62  0.91  15.06   0.99     0.96       2497.84|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2497.84 max =        10598.54 mean =      6489.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.21|
|phase err.(test): min =        0.00 max =           88.39 mean =        13.68|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1575   ksol= 0.32   Bsol= 45.17   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.07,0.37,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1575   ksol= 0.32   Bsol= 45.17   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.07,0.37,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152751                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7055 0.99   1410  157 0.1003 0.1283      5.3827      5.5372|
|  2:  4.7055 -  3.7540 0.99   1362  146 0.0863 0.1122       5.438      5.6435|
|  3:  3.7540 -  3.2851 0.99   1328  156 0.1063 0.1589      5.4745      5.8688|
|  4:  3.2851 -  2.9873 0.99   1340  147 0.1209 0.1484      5.4524      5.5798|
|  5:  2.9873 -  2.7746 0.99   1315  146 0.1303 0.1723      5.3272      5.5157|
|  6:  2.7746 -  2.6119 0.98   1307  142 0.1231 0.1926      5.2188      5.4825|
|  7:  2.6119 -  2.4817 0.99   1313  149 0.1252 0.1669      5.1787      5.4084|
|  8:  2.4817 -  2.3741 0.98   1288  142 0.1169 0.1697      5.0626      5.2932|
|  9:  2.3741 -  2.2831 0.98   1304  149 0.1171 0.1772      5.0289      5.3143|
| 10:  2.2831 -  2.2045 0.98   1279  137 0.1134 0.1722      4.9682      5.2254|
| 11:  2.2045 -  2.1358 0.99   1292  145 0.1137 0.1796      4.9416       5.292|
| 12:  2.1358 -  2.0749 0.98   1273  138 0.1082 0.1567       4.869      5.0613|
| 13:  2.0749 -  2.0204 0.97   1277  143 0.1178 0.1817      4.7893      5.0636|
| 14:  2.0204 -  1.9712 0.42    542   62 0.0997 0.1689       4.637      4.9097|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7055  1410   157  0.94   8.69   0.98     0.96       6902.50|
|  2:  4.7055 -  3.7540  1362   146  0.95   8.00   1.01     1.00       8936.08|
|  3:  3.7540 -  3.2851  1328   156  0.93  11.58   1.02     1.01      10598.80|
|  4:  3.2851 -  2.9873  1340   147  0.92  13.84   1.00     0.98      10404.28|
|  5:  2.9873 -  2.7746  1315   146  0.90  16.33   0.99     0.96       8411.44|
|  6:  2.7746 -  2.6119  1307   142  0.90  16.32   0.98     0.95       7255.36|
|  7:  2.6119 -  2.4817  1313   149  0.91  15.43   0.99     0.95       6315.50|
|  8:  2.4817 -  2.3741  1288   142  0.90  15.78   0.99     0.96       5425.95|
|  9:  2.3741 -  2.2831  1304   149  0.90  15.83   1.00     0.98       5042.24|
| 10:  2.2831 -  2.2045  1279   137  0.90  15.54   1.00     0.97       4501.55|
| 11:  2.2045 -  2.1358  1292   145  0.90  16.29   1.00     0.96       4353.64|
| 12:  2.1358 -  2.0749  1273   138  0.91  15.25   1.01     0.99       3993.67|
| 13:  2.0749 -  2.0204  1277   143  0.90  16.44   1.00     1.00       3343.62|
| 14:  2.0204 -  1.9712   542    62  0.91  15.06   0.99     0.96       2497.63|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2497.63 max =        10598.80 mean =      6489.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.21|
|phase err.(test): min =        0.00 max =           88.39 mean =        13.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.933)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.92    84.75   14.52    None  None   None       |
|    all(noH): 2823   0      2.92    84.75   14.52    None  None   None       |
|    Sol.    : 438    0      4.37    68.78   35.31    None  None   None       |
|    Mac.    : 2385   0      2.92    84.75   10.70    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:     2.915 -  11.099: 1683   |   5:    43.833 -  52.017:   87        |
|      1:    11.099 -  19.282:  585   |   6:    52.017 -  60.201:   47        |
|      2:    19.282 -  27.466:  156   |   7:    60.201 -  68.384:   11        |
|      3:    27.466 -  35.650:  124   |   8:    68.384 -  76.568:    4        |
|      4:    35.650 -  43.833:  122   |   9:    76.568 -  84.752:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.394 - 5.838
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 331
   mapped sites are within: 0.707 - 5.838

peak=    9.635 closest distance to " CG2 VAL A 230 " =    1.287
peak=    6.529 closest distance to " CG2 VAL A 296 " =    1.084
peak=    6.464 closest distance to " CG  LEU A   5 " =    1.257
peak=    6.459 closest distance to " NH2 ARG A  56 " =    2.245
peak=    5.679 closest distance to " CG  LEU A 228 " =    1.217
peak=    5.421 closest distance to " CG  PRO A  54 " =    1.232
peak=    5.391 closest distance to " CB  VAL A 296 " =    1.120
peak=    5.329 closest distance to " CB  GLN A 223 " =    1.425
peak=    5.216 closest distance to " CB  VAL A 230 " =    1.244
peak=    5.215 closest distance to " CD2 LEU A   5 " =    1.194
peak=    5.068 closest distance to " CB  PRO A  54 " =    0.911
peak=    4.956 closest distance to " CB  SER A  63 " =    1.297
peak=    4.938 closest distance to " O   HOH Z 126 " =    1.885
peak=    4.781 closest distance to " CB  ARG A 275 " =    0.851
peak=    4.704 closest distance to " C   PRO A 198 " =    1.525
peak=    4.632 closest distance to " CB  GLU A 152 " =    1.144
peak=    4.631 closest distance to " OD1 ASN A  69 " =    2.632
peak=    4.602 closest distance to " NE2 GLN A  11 " =    1.121
peak=    4.601 closest distance to " CG  PRO A 213 " =    1.208
peak=    4.584 closest distance to " CB  GLN A 183 " =    1.316
peak=    4.559 closest distance to " O   HOH Z 232 " =    2.290
peak=    4.544 closest distance to " CG  PRO A 243 " =    1.154
peak=    4.512 closest distance to " O   HOH Z 272 " =    1.914
peak=    4.510 closest distance to " CB  SER A   3 " =    1.333
peak=    4.495 closest distance to " CB  GLU A 128 " =    1.005
peak=    4.458 closest distance to " O   HOH Z 193 " =    1.905
peak=    4.450 closest distance to " O   HOH Z 236 " =    1.890
peak=    4.441 closest distance to " CB  ASN A 148 " =    1.377
peak=    4.358 closest distance to " O   HOH Z 298 " =    1.784
peak=    4.307 closest distance to " O   HOH Z 316 " =    2.988
peak=    4.301 closest distance to " CD2 LEU A 228 " =    1.159
peak=    4.286 closest distance to " CB  TYR A 169 " =    0.768
peak=    4.271 closest distance to " O   HOH Z 427 " =    2.991
peak=    4.250 closest distance to " O   HOH Z 368 " =    2.130
peak=    4.187 closest distance to " O   HOH Z 303 " =    2.011
peak=    4.112 closest distance to " O   TRP A 274 " =    1.863
peak=    4.088 closest distance to " O   HOH Z 344 " =    2.861
peak=    4.088 closest distance to " O   HOH Z 265 " =    2.432
peak=    4.077 closest distance to " O   HOH Z 369 " =    2.004
peak=    4.064 closest distance to " CA  THR A 221 " =    0.896
peak=    4.063 closest distance to " CB  VAL A 265 " =    1.256
peak=    4.036 closest distance to " O   HOH Z 234 " =    3.675
peak=    4.035 closest distance to " OD2 ASP A 286 " =    2.851
peak=    4.029 closest distance to " O   HOH Z 371 " =    3.258
peak=    4.022 closest distance to " O   SER A  87 " =    2.254
peak=    3.996 closest distance to " CG  PRO A 198 " =    1.313
peak=    3.988 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.984 closest distance to " O   HOH Z 423 " =    1.820
peak=    3.982 closest distance to " O   HOH Z 263 " =    1.696
peak=    3.981 closest distance to " O   HOH Z 142 " =    1.621
peak=    3.981 closest distance to " CA  TYR A  30 " =    0.933
peak=    3.980 closest distance to " CG1BVAL A  72 " =    1.669
peak=    3.977 closest distance to " O   HOH Z 128 " =    2.094
peak=    3.968 closest distance to " CA  ALA A  21 " =    1.178
peak=    3.959 closest distance to " NH2 ARG A 156 " =    1.204
peak=    3.944 closest distance to " CB  ASN A 187 " =    1.333
peak=    3.937 closest distance to " CG  ARG A  66 " =    2.723
peak=    3.928 closest distance to " CB  ARG A  79 " =    1.414
peak=    3.914 closest distance to " CG  PRO A 280 " =    0.765
peak=    3.891 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.890 closest distance to " O   HOH Z 193 " =    1.955
peak=    3.885 closest distance to " O   HOH Z 261 " =    2.095
peak=    3.880 closest distance to " O   HOH Z 280 " =    2.987
peak=    3.880 closest distance to " CB  TRP A 266 " =    0.928
peak=    3.868 closest distance to " O   HOH Z 403 " =    1.682
peak=    3.864 closest distance to " CA  ALA A  51 " =    1.005
peak=    3.860 closest distance to " O   HOH Z 203 " =    1.745
peak=    3.840 closest distance to " ND2 ASN A 187 " =    1.485
peak=    3.838 closest distance to " O   HOH Z  97 " =    1.963
peak=    3.837 closest distance to " O   HOH Z  15 " =    2.088
peak=    3.836 closest distance to " O   HOH Z 158 " =    3.163
peak=    3.830 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.825 closest distance to " CA  THR A 264 " =    0.778
peak=    3.823 closest distance to " O   HOH Z 126 " =    2.194
peak=    3.806 closest distance to " O   HOH Z 411 " =    3.735
peak=    3.801 closest distance to " O   HOH Z  48 " =    1.504
peak=    3.799 closest distance to " O   HOH Z 197 " =    2.888
peak=    3.798 closest distance to " CA  LYS A 117 " =    1.256
peak=    3.797 closest distance to " O   HOH Z  78 " =    1.734
peak=    3.796 closest distance to " CB  TRP A 179 " =    1.409
peak=    3.794 closest distance to " CB  LEU A 143 " =    1.142
peak=    3.790 closest distance to " O   HOH Z 346 " =    1.624
peak=    3.783 closest distance to " O   HOH Z  21 " =    1.651
peak=    3.778 closest distance to " CB  ALA A 291 " =    1.360
peak=    3.776 closest distance to " CB  ASN A 148 " =    1.927
peak=    3.768 closest distance to " ND2 ASN A 249 " =    1.909
peak=    3.768 closest distance to " O   HOH Z  88 " =    3.219
peak=    3.767 closest distance to " O   MET A 105 " =    1.788
peak=    3.759 closest distance to " O   HOH Z  44 " =    2.302
peak=    3.751 closest distance to " CB  ASN A  39 " =    0.860
peak=    3.742 closest distance to " O   HOH Z 426 " =    1.519
peak=    3.737 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.728 closest distance to " CA  ASN A 215 " =    1.242
peak=    3.719 closest distance to " O   HOH Z 108 " =    2.213
peak=    3.708 closest distance to " O   HOH Z  49 " =    2.421
peak=    3.703 closest distance to " O   HOH Z 402 " =    1.481
peak=    3.698 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.695 closest distance to " CD1 LEU A 300 " =    1.171
peak=    3.683 closest distance to " O   HOH Z 124 " =    1.360
peak=    3.670 closest distance to " CA  ALA A 248 " =    1.394
peak=    3.669 closest distance to " CB  VAL A 202 " =    1.544
peak=    3.668 closest distance to " O   HOH Z 135 " =    1.754
peak=    3.665 closest distance to " OG BSER A 164 " =    2.189
peak=    3.661 closest distance to " O   HOH Z  97 " =    2.636
peak=    3.647 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.646 closest distance to " O   HOH Z 273 " =    2.599
peak=    3.639 closest distance to " O   HOH Z 130 " =    2.246
peak=    3.635 closest distance to " OG  SER A  22 " =    2.832
peak=    3.634 closest distance to " CG2 THR A 221 " =    1.150
peak=    3.630 closest distance to " O   HOH Z  54 " =    1.621
peak=    3.619 closest distance to " O   HOH Z 134 " =    1.473
peak=    3.618 closest distance to " O   HOH Z 329 " =    3.851
peak=    3.608 closest distance to " CG  MET A 185 " =    1.178
peak=    3.607 closest distance to " O   HOH Z 214 " =    2.097
peak=    3.606 closest distance to " CB  SER A 216 " =    0.749
peak=    3.606 closest distance to " CG1 VAL A 296 " =    1.179
peak=    3.603 closest distance to " O   HOH Z 313 " =    1.799
peak=    3.591 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.588 closest distance to " N   ASN A  39 " =    1.181
peak=    3.587 closest distance to " O   HOH Z  43 " =    2.008
peak=    3.581 closest distance to " CD BLYS A 290 " =    1.063
peak=    3.580 closest distance to " O   HOH Z 245 " =    1.408
peak=    3.572 closest distance to " O   HOH Z 132 " =    2.674
peak=    3.571 closest distance to " O   HOH Z 425 " =    1.990
peak=    3.562 closest distance to " O   HOH Z 295 " =    1.505
peak=    3.548 closest distance to " O   HOH Z 248 " =    1.785
peak=    3.538 closest distance to " CB  ASP A 140 " =    0.899
peak=    3.535 closest distance to " CA  ASP A 191 " =    0.811
peak=    3.533 closest distance to " CZ  PHE A 218 " =    1.039
peak=    3.532 closest distance to " O   HOH Z  80 " =    1.697
peak=    3.530 closest distance to " CZ  PHE A 192 " =    0.968
peak=    3.529 closest distance to " O   ALA A   1 " =    1.548
peak=    3.527 closest distance to " CB  ARG A 190 " =    1.682
peak=    3.526 closest distance to " O   HOH Z 189 " =    2.688
peak=    3.525 closest distance to " O   HOH Z  40 " =    2.469
peak=    3.525 closest distance to " O   HOH Z 368 " =    3.617
peak=    3.508 closest distance to " O   HOH Z 227 " =    1.647
peak=    3.506 closest distance to " CB  LEU A 228 " =    1.264
peak=    3.506 closest distance to " O   HOH Z 180 " =    2.127
peak=    3.503 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.500 closest distance to " CA  ASP A 140 " =    1.229
peak=    3.496 closest distance to " CG1 ILE A  33 " =    1.307
peak=    3.493 closest distance to " N   VAL A 126 " =    1.318
peak=    3.492 closest distance to " CD2 LEU A 255 " =    1.429
peak=    3.490 closest distance to " CA  ARG A 195 " =    1.203
peak=    3.489 closest distance to " O   HOH Z 411 " =    1.785
peak=    3.487 closest distance to " CD  ARG A 269 " =    0.932
peak=    3.487 closest distance to " CD1 ILE A 106 " =    1.032
peak=    3.480 closest distance to " CA  VAL A  41 " =    0.839
peak=    3.480 closest distance to " O   HOH Z  68 " =    1.594
peak=    3.476 closest distance to " O   HOH Z  61 " =    1.621
peak=    3.475 closest distance to " O   HOH Z  20 " =    1.811
peak=    3.473 closest distance to " O   HOH Z 133 " =    1.657
peak=    3.472 closest distance to " NH1AARG A 145 " =    1.034
peak=    3.472 closest distance to " O   HOH Z  10 " =    1.837
peak=    3.469 closest distance to " CA  MET A  40 " =    1.127
peak=    3.466 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.459 closest distance to " CD1 LEU A   5 " =    1.309
peak=    3.455 closest distance to " CB  GLN A 278 " =    0.924
peak=    3.451 closest distance to " O   HOH Z 345 " =    3.362
peak=    3.444 closest distance to " CA  SER A  87 " =    0.930
peak=    3.443 closest distance to " CB BVAL A  41 " =    1.064
peak=    3.443 closest distance to " N   PHE A 130 " =    1.297
peak=    3.442 closest distance to " CG  GLN A  88 " =    1.020
peak=    3.440 closest distance to " CB  THR A  31 " =    1.723
peak=    3.437 closest distance to " ND2 ASN A 110 " =    1.764
peak=    3.434 closest distance to " CB  ASN A 142 " =    1.000
peak=    3.431 closest distance to " O   HOH Z 171 " =    2.443
peak=    3.424 closest distance to " CG1 ILE A  49 " =    1.434
peak=    3.416 closest distance to " NZ  LYS A 166 " =    3.124
peak=    3.415 closest distance to " CB  PRO A 198 " =    0.953
peak=    3.414 closest distance to " O   HOH Z 420 " =    1.978
peak=    3.412 closest distance to " CE  LYS A  76 " =    0.904
peak=    3.405 closest distance to " O   HOH Z  68 " =    2.149
peak=    3.404 closest distance to " CG  GLN A  77 " =    2.046
peak=    3.401 closest distance to " O   HOH Z 112 " =    1.622
peak=    3.400 closest distance to " O   HOH Z 383 " =    2.011
peak=    3.400 closest distance to " CB  ILE A 120 " =    1.419
peak=    3.399 closest distance to " CB  ALA A   9 " =    1.577
peak=    3.394 closest distance to " CB  ALA A 248 " =    0.972
peak=    3.393 closest distance to " CA  GLY A 267 " =    0.909
peak=    3.393 closest distance to " CD1 LEU A  96 " =    0.724
peak=    3.392 closest distance to " CG BARG A 102 " =    1.821
peak=    3.391 closest distance to " CB  ALA A   1 " =    1.269
peak=    3.391 closest distance to " O   HOH Z 281 " =    4.519
peak=    3.391 closest distance to " O   HOH Z 247 " =    1.289
peak=    3.389 closest distance to " CA  ASP A 162 " =    1.120
peak=    3.385 closest distance to " O   HOH Z 286 " =    2.236
peak=    3.384 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.382 closest distance to " O   HOH Z  48 " =    1.440
peak=    3.378 closest distance to " O   HOH Z  59 " =    2.296
peak=    3.376 closest distance to " O   HOH Z 425 " =    1.341
peak=    3.368 closest distance to " CA  LEU A 282 " =    1.075
peak=    3.368 closest distance to " O   HOH Z 422 " =    2.751
peak=    3.367 closest distance to " O   HOH Z 171 " =    3.829
peak=    3.367 closest distance to " ND1 HIS A  81 " =    1.666
peak=    3.365 closest distance to " CB  MET A  40 " =    0.863
peak=    3.361 closest distance to " O   HOH Z 209 " =    2.367
peak=    3.361 closest distance to " CA  ALA A 233 " =    1.346
peak=    3.356 closest distance to " OE1 GLU A   2 " =    2.213
peak=    3.356 closest distance to " CG2 ILE A 120 " =    1.262
peak=    3.355 closest distance to " O   ASP A 124 " =    1.085
peak=    3.348 closest distance to " O   HOH Z 407 " =    2.515
peak=    3.347 closest distance to " CB  SER A 212 " =    1.182
peak=    3.345 closest distance to " O   HOH Z   9 " =    2.028
peak=    3.343 closest distance to " ND1 HIS A  86 " =    1.645
peak=    3.339 closest distance to " CG  MET A 185 " =    1.087
peak=    3.337 closest distance to " O   HOH Z 133 " =    2.413
peak=    3.337 closest distance to " O   HOH Z 126 " =    1.674
peak=    3.337 closest distance to " O   ALA A 158 " =    1.373
peak=    3.337 closest distance to " CA  GLY A 211 " =    1.216
peak=    3.335 closest distance to " CD  LYS A 119 " =    1.821
peak=    3.330 closest distance to " O   HOH Z 291 " =    1.583
peak=    3.328 closest distance to " O   HOH Z 128 " =    1.763
peak=    3.328 closest distance to " CB  GLU A  46 " =    1.069
peak=    3.323 closest distance to " O   HOH Z  19 " =    2.233
peak=    3.323 closest distance to " NH2BARG A 145 " =    2.053
peak=    3.323 closest distance to " O   HOH Z 261 " =    2.076
peak=    3.320 closest distance to " NE2 GLN A  58 " =    5.795
peak=    3.319 closest distance to " O   HOH Z 435 " =    1.976
peak=    3.311 closest distance to " CA  VAL A 126 " =    0.898
peak=    3.307 closest distance to " CG  LEU A 167 " =    1.184
peak=    3.303 closest distance to " O   HOH Z 388 " =    2.014
peak=    3.301 closest distance to " O   HOH Z 102 " =    1.270
peak=    3.300 closest distance to " CA  ILE A  33 " =    1.443
peak=    3.299 closest distance to " O   HOH Z 187 " =    2.279
peak=    3.298 closest distance to " C   ALA A 299 " =    0.955
peak=    3.298 closest distance to " O   HOH Z 172 " =    3.830
peak=    3.296 closest distance to " O   HOH Z 116 " =    1.788
peak=    3.295 closest distance to " CB  LEU A 255 " =    0.830
peak=    3.293 closest distance to " N   ARG A 190 " =    1.049
peak=    3.292 closest distance to " CG2 VAL A 257 " =    0.927
peak=    3.290 closest distance to " O   HOH Z 271 " =    1.968
peak=    3.288 closest distance to " O   HOH Z 227 " =    2.046
peak=    3.287 closest distance to " N   ASN A 127 " =    1.260
peak=    3.285 closest distance to " O   HOH Z 366 " =    2.961
peak=    3.285 closest distance to " CG2 THR A 220 " =    0.888
peak=    3.284 closest distance to " O   HOH Z 251 " =    1.703
peak=    3.276 closest distance to " CB  TRP A 150 " =    1.513
peak=    3.268 closest distance to " CA  ALA A 295 " =    1.033
peak=    3.267 closest distance to " CD2 HIS A  81 " =    1.146
peak=    3.262 closest distance to " O   HOH Z 193 " =    1.620
peak=    3.251 closest distance to " O   HOH Z 409 " =    3.368
peak=    3.250 closest distance to " CA  ALA A 158 " =    1.178
peak=    3.250 closest distance to " OG1 THR A 294 " =    1.722
peak=    3.249 closest distance to " O   ASN A 217 " =    1.311
peak=    3.248 closest distance to " O   HOH Z 173 " =    2.155
peak=    3.247 closest distance to " CB  ALA A 161 " =    0.860
peak=    3.238 closest distance to " NZ  LYS A 117 " =    3.335
peak=    3.238 closest distance to " O   HOH Z  48 " =    1.554
peak=    3.237 closest distance to " CA  ALA A 154 " =    1.074
peak=    3.234 closest distance to " CD  PRO A 243 " =    1.387
peak=    3.232 closest distance to " O   HOH Z 185 " =    1.744
peak=    3.230 closest distance to " CB  SER A  26 " =    1.605
peak=    3.230 closest distance to " CB  ARG A  79 " =    0.880
peak=    3.229 closest distance to " O   HOH Z  71 " =    2.211
peak=    3.228 closest distance to " O   ALA A 165 " =    1.398
peak=    3.228 closest distance to " N   SER A 135 " =    1.407
peak=    3.228 closest distance to " O   GLU A   2 " =    1.721
peak=    3.227 closest distance to " N   ARG A 156 " =    1.325
peak=    3.227 closest distance to " O   HOH Z  66 " =    2.270
peak=    3.227 closest distance to " CG AARG A 275 " =    1.227
peak=    3.226 closest distance to " CB  MET A  47 " =    1.115
peak=    3.225 closest distance to " CG  MET A 188 " =    1.100
peak=    3.217 closest distance to " OG BSER A 134 " =    2.975
peak=    3.216 closest distance to " O   HOH Z 374 " =    2.668
peak=    3.215 closest distance to " CB  THR A 157 " =    1.156
peak=    3.213 closest distance to " O   THR A  31 " =    1.469
peak=    3.212 closest distance to " N   SER A  12 " =    1.636
peak=    3.205 closest distance to " OD1 ASP A 231 " =    1.877
peak=    3.205 closest distance to " O   HOH Z 423 " =    3.089
peak=    3.202 closest distance to " O   HOH Z 163 " =    1.834
peak=    3.201 closest distance to " CA  GLN A 194 " =    1.274
peak=    3.200 closest distance to " O   HOH Z 406 " =    1.556
peak=    3.200 closest distance to " O   HOH Z 175 " =    2.175
peak=    3.199 closest distance to " CG2 VAL A 197 " =    1.019
peak=    3.194 closest distance to " O   HOH Z 148 " =    3.186
peak=    3.194 closest distance to " CA  TYR A 116 " =    1.493
peak=    3.193 closest distance to " O   HOH Z 188 " =    2.007
peak=    3.191 closest distance to " CA  ARG A  36 " =    1.104
peak=    3.190 closest distance to " O   HOH Z 213 " =    1.659
peak=    3.189 closest distance to " CB  LYS A 117 " =    1.143
peak=    3.184 closest distance to " O   GLN A 278 " =    1.530
peak=    3.184 closest distance to " O   HOH Z 147 " =    1.696
peak=    3.182 closest distance to " CG1 ILE A 151 " =    1.044
peak=    3.180 closest distance to " O   HOH Z 279 " =    2.168
peak=    3.177 closest distance to " O   HOH Z 334 " =    1.491
peak=    3.177 closest distance to " O   HOH Z 367 " =    3.459
peak=    3.175 closest distance to " O   HOH Z 286 " =    2.471
peak=    3.172 closest distance to " O   HOH Z 417 " =    2.123
peak=    3.170 closest distance to " CB  SER A  28 " =    1.083
peak=    3.167 closest distance to " NH2 ARG A 219 " =    1.797
peak=    3.166 closest distance to " CB  ALA A 100 " =    1.206
peak=    3.165 closest distance to " CG BARG A 275 " =    1.462
peak=    3.165 closest distance to " O   HOH Z 427 " =    3.173
peak=    3.164 closest distance to " O   HOH Z 329 " =    2.684
peak=    3.161 closest distance to " O   HOH Z  90 " =    2.234
peak=    3.157 closest distance to " CB  ASN A 110 " =    1.150
peak=    3.149 closest distance to " OH  TYR A 214 " =    1.148
peak=    3.146 closest distance to " NH1 ARG A 138 " =    1.163
peak=    3.145 closest distance to " CA  ALA A 291 " =    0.970
peak=    3.142 closest distance to " O   HOH Z   4 " =    1.924
peak=    3.137 closest distance to " OE1 GLU A 277 " =    1.939
peak=    3.133 closest distance to " CB  ASN A 215 " =    1.175
peak=    3.131 closest distance to " O   HOH Z 155 " =    3.095
peak=    3.131 closest distance to " CE2 TYR A 186 " =    0.928
peak=    3.128 closest distance to " O   HOH Z 151 " =    1.710
peak=    3.127 closest distance to " CG2 ILE A  20 " =    1.492
peak=    3.127 closest distance to " OD1 ASN A 217 " =    1.673
peak=    3.124 closest distance to " CA  ASN A 217 " =    1.304
peak=    3.118 closest distance to " OE1 GLU A 236 " =    1.688
peak=    3.115 closest distance to " O   HOH Z   1 " =    2.158
peak=    3.114 closest distance to " O   HOH Z 128 " =    1.978
peak=    3.096 closest distance to " O   HOH Z 353 " =    2.755
peak=    3.095 closest distance to " O   HOH Z 213 " =    2.464
peak=    3.087 closest distance to " O   HOH Z 302 " =    1.969
peak=    3.086 closest distance to " O   HOH Z 301 " =    1.869
peak=    3.078 closest distance to " CA  ILE A 106 " =    0.785
peak=    3.074 closest distance to " NZ  LYS A  76 " =    1.260
peak=    3.067 closest distance to " CB  ILE A  20 " =    1.366
peak=    3.066 closest distance to " O   HOH Z 417 " =    2.620
peak=    3.058 closest distance to " O   HOH Z  85 " =    1.486
peak=    3.057 closest distance to " O   HOH Z 420 " =    5.838
peak=    3.056 closest distance to " CD1 ILE A  33 " =    1.583
peak=    3.041 closest distance to " CG  GLN A  89 " =    1.562
peak=    3.033 closest distance to " O   HOH Z 256 " =    2.199
peak=    3.013 closest distance to " CA  ASN A 176 " =    1.044

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.594 - 5.190
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.787 - 5.190

peak=   -5.611 closest distance to " CG2 VAL A 230 " =    0.873
peak=   -4.482 closest distance to " O   HOH Z 290 " =    1.117
peak=   -4.326 closest distance to " CD  ARG A 156 " =    2.009
peak=   -4.299 closest distance to " O   HOH Z 266 " =    4.546
peak=   -4.285 closest distance to " SG  CYS A 254 " =    3.097
peak=   -4.166 closest distance to " CB  ALA A 161 " =    2.571
peak=   -4.105 closest distance to " CG  ASP A 231 " =    0.787
peak=   -4.099 closest distance to " CB  PRO A 243 " =    2.610
peak=   -3.986 closest distance to " CE2 TYR A  30 " =    2.773
peak=   -3.965 closest distance to " O   HOH Z  52 " =    1.533
peak=   -3.914 closest distance to " C   ALA A 158 " =    1.269
peak=   -3.909 closest distance to " CD1 LEU A 101 " =    2.685
peak=   -3.897 closest distance to " CD2 LEU A 300 " =    2.841
peak=   -3.867 closest distance to " C   HIS A 108 " =    1.175
peak=   -3.823 closest distance to " O   HOH Z 351 " =    1.698
peak=   -3.820 closest distance to " CG  GLN A 223 " =    2.060
peak=   -3.810 closest distance to " OG  SER A  97 " =    2.280
peak=   -3.806 closest distance to " CZ3 TRP A 179 " =    1.243
peak=   -3.800 closest distance to " O   HOH Z 166 " =    1.934
peak=   -3.796 closest distance to " CG2 THR A   4 " =    1.936
peak=   -3.792 closest distance to " CG2BVAL A  41 " =    2.677
peak=   -3.791 closest distance to " O   HOH Z  43 " =    1.668
peak=   -3.778 closest distance to " CG  PHE A 283 " =    2.811
peak=   -3.760 closest distance to " NE2 GLN A  88 " =    2.111
peak=   -3.759 closest distance to " N   ALA A  43 " =    2.371
peak=   -3.758 closest distance to " O   PRO A 163 " =    2.022
peak=   -3.750 closest distance to " CD2 LEU A 237 " =    2.768
peak=   -3.733 closest distance to " CD1 LEU A 228 " =    2.361
peak=   -3.732 closest distance to " CB  PRO A 163 " =    2.632
peak=   -3.726 closest distance to " CG1 VAL A 296 " =    1.262
peak=   -3.719 closest distance to " O   HOH Z 241 " =    1.218
peak=   -3.711 closest distance to " O   HOH Z 118 " =    3.023
peak=   -3.711 closest distance to " NH2 ARG A  66 " =    1.881
peak=   -3.710 closest distance to " O   HOH Z  13 " =    1.404
peak=   -3.701 closest distance to " O   HOH Z 103 " =    1.925
peak=   -3.691 closest distance to " OXT GLY A 302 " =    2.832
peak=   -3.690 closest distance to " NH2AARG A 275 " =    5.190
peak=   -3.672 closest distance to " N   GLN A  58 " =    1.719
peak=   -3.669 closest distance to " CD  LYS A 289 " =    2.580
peak=   -3.668 closest distance to " CG  LEU A 101 " =    2.497
peak=   -3.667 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.654 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.653 closest distance to " CG2 VAL A 296 " =    1.231
peak=   -3.650 closest distance to " O   HOH Z  19 " =    2.234
peak=   -3.641 closest distance to " CD  ARG A 139 " =    1.555
peak=   -3.640 closest distance to " CE  MET A 105 " =    2.046
peak=   -3.636 closest distance to " O   HOH Z 231 " =    1.840
peak=   -3.632 closest distance to " O   HOH Z 417 " =    2.776
peak=   -3.616 closest distance to " CG  TRP A 266 " =    1.856
peak=   -3.612 closest distance to " O   VAL A  67 " =    2.590
peak=   -3.607 closest distance to " ND2 ASN A  45 " =    0.988
peak=   -3.606 closest distance to " O   GLY A 196 " =    1.123
peak=   -3.592 closest distance to " OG ASER A 134 " =    1.335
peak=   -3.586 closest distance to " O   HOH Z 185 " =    2.369
peak=   -3.584 closest distance to " N   ALA A 226 " =    2.082
peak=   -3.578 closest distance to " OG  SER A  62 " =    1.543
peak=   -3.570 closest distance to " CD1 PHE A  59 " =    1.828
peak=   -3.568 closest distance to " O   HOH Z 436 " =    1.529
peak=   -3.567 closest distance to " O   HOH Z 407 " =    3.174
peak=   -3.557 closest distance to " O   HOH Z 196 " =    2.171
peak=   -3.557 closest distance to " O   HOH Z 353 " =    2.160
peak=   -3.550 closest distance to " O   HOH Z 377 " =    2.239
peak=   -3.548 closest distance to " CG  ASP A  50 " =    2.415
peak=   -3.545 closest distance to " O   HOH Z 311 " =    3.661
peak=   -3.544 closest distance to " O   HOH Z 389 " =    1.846
peak=   -3.543 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.522 closest distance to " CG  ARG A 269 " =    2.330
peak=   -3.507 closest distance to " CB  ALA A 291 " =    2.295
peak=   -3.507 closest distance to " N   THR A 157 " =    1.588
peak=   -3.494 closest distance to " NH2 ARG A  79 " =    1.899
peak=   -3.492 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.487 closest distance to " N   MET A 105 " =    2.654
peak=   -3.481 closest distance to " CZ  TYR A 169 " =    1.670
peak=   -3.475 closest distance to " O   HOH Z 222 " =    1.398
peak=   -3.472 closest distance to " OG  SER A  87 " =    1.401
peak=   -3.468 closest distance to " C   ASP A 231 " =    2.627
peak=   -3.463 closest distance to " CG  LEU A 228 " =    0.949
peak=   -3.461 closest distance to " O   HOH Z  63 " =    0.944
peak=   -3.454 closest distance to " OG  SER A  26 " =    1.279
peak=   -3.449 closest distance to " OG BSER A 134 " =    1.213
peak=   -3.447 closest distance to " O   HOH Z 211 " =    1.672
peak=   -3.447 closest distance to " CA  GLY A 241 " =    3.022
peak=   -3.447 closest distance to " C   MET A 188 " =    1.436
peak=   -3.444 closest distance to " CB  ASN A  39 " =    2.094
peak=   -3.439 closest distance to " O   HOH Z  38 " =    1.600
peak=   -3.436 closest distance to " C   LEU A 222 " =    0.795
peak=   -3.436 closest distance to " O   HOH Z 426 " =    1.568
peak=   -3.431 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.425 closest distance to " O   HOH Z 283 " =    1.777
peak=   -3.424 closest distance to " O   GLY A 211 " =    1.577
peak=   -3.420 closest distance to " O   HOH Z 275 " =    1.523
peak=   -3.415 closest distance to " O   HOH Z  71 " =    0.951
peak=   -3.406 closest distance to " O   HOH Z  60 " =    2.090
peak=   -3.396 closest distance to " O   HOH Z 102 " =    1.662
peak=   -3.391 closest distance to " CG  GLU A  53 " =    1.554
peak=   -3.389 closest distance to " CG2 VAL A 112 " =    2.595
peak=   -3.387 closest distance to " CG  GLU A 277 " =    1.038
peak=   -3.386 closest distance to " NE2 GLN A 103 " =    1.700
peak=   -3.385 closest distance to " OD1 ASN A 148 " =    1.545
peak=   -3.379 closest distance to " N   THR A 235 " =    1.358
peak=   -3.375 closest distance to " NE  ARG A 259 " =    1.160
peak=   -3.374 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.374 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.370 closest distance to " O   HOH Z 372 " =    2.417
peak=   -3.367 closest distance to " C   ASN A 187 " =    1.878
peak=   -3.364 closest distance to " CZ  PHE A  59 " =    1.579
peak=   -3.364 closest distance to " CE3 TRP A 150 " =    2.047
peak=   -3.361 closest distance to " CG2 ILE A 263 " =    2.386
peak=   -3.361 closest distance to " O   ALA A   7 " =    1.550
peak=   -3.360 closest distance to " O   ALA A 161 " =    1.622
peak=   -3.360 closest distance to " CB  ALA A  43 " =    2.404
peak=   -3.355 closest distance to " N   SER A 276 " =    1.296
peak=   -3.347 closest distance to " O   HOH Z 292 " =    4.517
peak=   -3.345 closest distance to " CD  GLN A  58 " =    1.076
peak=   -3.344 closest distance to " CB  ALA A 248 " =    2.052
peak=   -3.342 closest distance to " CG  GLU A   2 " =    1.738
peak=   -3.340 closest distance to " O   HOH Z  47 " =    1.599
peak=   -3.335 closest distance to " CB  PHE A 192 " =    1.817
peak=   -3.330 closest distance to " O   HOH Z  98 " =    2.107
peak=   -3.325 closest distance to " O   VAL A 125 " =    2.281
peak=   -3.324 closest distance to " O   SER A 271 " =    2.145
peak=   -3.320 closest distance to " O   HOH Z  10 " =    1.533
peak=   -3.319 closest distance to " CD2 TYR A 293 " =    2.159
peak=   -3.319 closest distance to " O   HOH Z 388 " =    2.114
peak=   -3.311 closest distance to " O   HOH Z 176 " =    0.876
peak=   -3.309 closest distance to " CE BMET A  47 " =    1.971
peak=   -3.308 closest distance to " N   GLY A  23 " =    2.101
peak=   -3.300 closest distance to " NH1 ARG A 195 " =    2.546
peak=   -3.296 closest distance to " CG  PRO A 163 " =    2.615
peak=   -3.292 closest distance to " O   LYS A 117 " =    1.669
peak=   -3.291 closest distance to " N   SER A 212 " =    1.943
peak=   -3.286 closest distance to " O   HOH Z 207 " =    2.143
peak=   -3.284 closest distance to " O   HOH Z 166 " =    1.511
peak=   -3.284 closest distance to " CE2 PHE A 218 " =    2.561
peak=   -3.281 closest distance to " O   HOH Z 359 " =    2.992
peak=   -3.277 closest distance to " ND2 ASN A  60 " =    1.438
peak=   -3.277 closest distance to " O   VAL A 189 " =    2.559
peak=   -3.272 closest distance to " CG  LEU A  83 " =    1.897
peak=   -3.265 closest distance to " C   GLN A 205 " =    2.021
peak=   -3.264 closest distance to " O   HOH Z 435 " =    2.718
peak=   -3.259 closest distance to " CB  TYR A  15 " =    2.235
peak=   -3.256 closest distance to " CB  VAL A 230 " =    0.978
peak=   -3.255 closest distance to " O   HOH Z 313 " =    1.946
peak=   -3.255 closest distance to " O   HOH Z 295 " =    1.458
peak=   -3.253 closest distance to " CG  ARG A 259 " =    2.471
peak=   -3.245 closest distance to " SD BMET A  47 " =    0.845
peak=   -3.239 closest distance to " CG1 VAL A 112 " =    2.720
peak=   -3.235 closest distance to " CG  GLN A  58 " =    1.483
peak=   -3.231 closest distance to " CB  ILE A 239 " =    2.054
peak=   -3.227 closest distance to " CG1 VAL A 296 " =    1.276
peak=   -3.224 closest distance to " O   GLY A 203 " =    2.384
peak=   -3.223 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.223 closest distance to " OG1 THR A 178 " =    1.276
peak=   -3.222 closest distance to " N   PHE A  59 " =    2.177
peak=   -3.220 closest distance to " O   LEU A 167 " =    1.461
peak=   -3.218 closest distance to " CD2 LEU A 167 " =    1.739
peak=   -3.215 closest distance to " O   HOH Z 431 " =    1.709
peak=   -3.215 closest distance to " CB  VAL A 296 " =    1.137
peak=   -3.211 closest distance to " C   ASN A 285 " =    2.504
peak=   -3.204 closest distance to " OG  SER A   3 " =    1.744
peak=   -3.203 closest distance to " O   VAL A 197 " =    1.311
peak=   -3.201 closest distance to " OG  SER A 206 " =    1.717
peak=   -3.198 closest distance to " CD  ARG A 195 " =    5.148
peak=   -3.192 closest distance to " CE3 TRP A 274 " =    2.462
peak=   -3.187 closest distance to " O   HOH Z 165 " =    1.966
peak=   -3.179 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.179 closest distance to " OG1 THR A 246 " =    1.466
peak=   -3.178 closest distance to " O   HOH Z 423 " =    2.231
peak=   -3.176 closest distance to " CD2 LEU A 237 " =    2.676
peak=   -3.175 closest distance to " OD2 ASP A 171 " =    1.799
peak=   -3.173 closest distance to " O   LEU A 222 " =    1.204
peak=   -3.172 closest distance to " O   HOH Z 222 " =    3.318
peak=   -3.170 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.169 closest distance to " CE  MET A  93 " =    1.150
peak=   -3.168 closest distance to " N   VAL A 230 " =    1.181
peak=   -3.168 closest distance to " O   HOH Z 148 " =    2.985
peak=   -3.164 closest distance to " O   HOH Z 369 " =    2.222
peak=   -3.163 closest distance to " CB  ASP A 132 " =    2.255
peak=   -3.163 closest distance to " O   HOH Z 128 " =    4.223
peak=   -3.163 closest distance to " O   HOH Z  22 " =    2.474
peak=   -3.162 closest distance to " O   HOH Z 128 " =    2.492
peak=   -3.162 closest distance to " CA  GLY A 203 " =    2.291
peak=   -3.158 closest distance to " CA  GLY A  98 " =    1.948
peak=   -3.139 closest distance to " NE2 GLN A  88 " =    0.968
peak=   -3.137 closest distance to " O   HOH Z 252 " =    3.998
peak=   -3.136 closest distance to " O   HOH Z 231 " =    1.269
peak=   -3.127 closest distance to " O   HOH Z  37 " =    2.153
peak=   -3.124 closest distance to " SG ACYS A 201 " =    2.234
peak=   -3.124 closest distance to " CG1 VAL A 230 " =    1.846
peak=   -3.122 closest distance to " O   HOH Z 234 " =    4.267
peak=   -3.115 closest distance to " CD1 LEU A 297 " =    2.428
peak=   -3.113 closest distance to " O   HOH Z 189 " =    1.790
peak=   -3.108 closest distance to " CD2 PHE A  61 " =    2.350
peak=   -3.099 closest distance to " CA  GLY A 133 " =    2.203
peak=   -3.060 closest distance to " O   HOH Z 298 " =    2.832
peak=   -3.058 closest distance to " ND2 ASN A 249 " =    2.395
peak=   -3.044 closest distance to " O   HOH Z 396 " =    1.727
peak=   -3.035 closest distance to " O   HOH Z 417 " =    2.769
peak=   -3.013 closest distance to " O   HOH Z 193 " =    1.788

================= 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    :  0.4446 0.4361   6.241859e+00   6.230405e+00
   1_bss:  0.4361 0.4260   6.240705e+00   6.222313e+00
   1_xyz:  0.3353 0.3700   6.058007e+00   6.116265e+00
   1_adp:  0.2808 0.3336   5.921472e+00   6.042356e+00
   1_occ:  0.2804 0.3342   5.921092e+00   6.043282e+00
   2_bss:  0.2761 0.3283   5.919204e+00   6.038485e+00
   2_xyz:  0.1865 0.2409   5.584901e+00   5.777877e+00
   2_adp:  0.1689 0.2183   5.489033e+00   5.689987e+00
   2_occ:  0.1687 0.2182   5.488035e+00   5.689222e+00
   3_bss:  0.1675 0.2160   5.486929e+00   5.686460e+00
   3_xyz:  0.1289 0.1716   5.255533e+00   5.478187e+00
   3_adp:  0.1207 0.1655   5.208277e+00   5.443099e+00
   3_occ:  0.1206 0.1654   5.207926e+00   5.442888e+00
   4_bss:  0.1209 0.1658   5.210263e+00   5.444467e+00
   4_xyz:  0.1119 0.1595   5.159618e+00   5.409499e+00
   4_adp:  0.1128 0.1579   5.157614e+00   5.399153e+00
   4_occ:  0.1127 0.1577   5.156915e+00   5.398448e+00
   5_bss:  0.1127 0.1577   5.156902e+00   5.398355e+00
   5_xyz:  0.1121 0.1572   5.153060e+00   5.395118e+00
   5_adp:  0.1118 0.1574   5.152770e+00   5.396708e+00
   5_occ:  0.1118 0.1575   5.152743e+00   5.396807e+00
   5_bss:  0.1118 0.1575   5.152751e+00   5.396817e+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:  0.340  14.279   7.874   8.382   8.760   0.000   0.000   0.000
   1_xyz:  0.340  14.279   7.874   8.382   8.760   0.000   0.000   0.000
   1_adp:  0.340  14.279   7.874   8.382   8.760   0.000   0.000   0.000
   1_occ:  0.340  14.279   7.874   8.382   8.760   0.000   0.000   0.000
   2_bss:  0.335  40.874   4.281   4.505   5.568   0.000   0.000   0.000
   2_xyz:  0.335  40.874   4.281   4.505   5.568   0.000   0.000   0.000
   2_adp:  0.335  40.874   4.281   4.505   5.568   0.000   0.000   0.000
   2_occ:  0.335  40.874   4.281   4.505   5.568   0.000   0.000   0.000
   3_bss:  0.328  42.355   2.895   3.180   3.799   0.000   0.000   0.000
   3_xyz:  0.328  42.355   2.895   3.180   3.799   0.000   0.000   0.000
   3_adp:  0.328  42.355   2.895   3.180   3.799   0.000   0.000   0.000
   3_occ:  0.328  42.355   2.895   3.180   3.799   0.000   0.000   0.000
   4_bss:  0.319  42.355   2.659   2.874   3.351   0.000   0.000   0.000
   4_xyz:  0.319  42.355   2.659   2.874   3.351   0.000   0.000   0.000
   4_adp:  0.319  42.355   2.659   2.874   3.351   0.000   0.000   0.000
   4_occ:  0.319  42.355   2.659   2.874   3.351   0.000   0.000   0.000
   5_bss:  0.323  42.255   2.592   2.825   3.269   0.000   0.000   0.000
   5_xyz:  0.323  42.255   2.592   2.825   3.269   0.000   0.000   0.000
   5_adp:  0.323  42.255   2.592   2.825   3.269   0.000   0.000   0.000
   5_occ:  0.323  42.255   2.592   2.825   3.269   0.000   0.000   0.000
   5_bss:  0.323  45.170  -0.301  -0.074   0.375   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.456 0.5155  0.5886    56967.221
   1_bss:  50.829 0.5079  0.7371    54691.669
   1_xyz:  40.623 0.6333  0.9039    37647.669
   1_adp:  34.946 0.7013  1.0017    29611.798
   1_occ:  35.017 0.7005  1.0004    29735.106
   2_bss:  34.692 0.7041  0.8871    29306.542
   2_xyz:  23.916 0.8220  0.9944    14896.640
   2_adp:  20.981 0.8524  1.0173    12184.113
   2_occ:  20.965 0.8525  1.0172    12153.554
   3_bss:  20.878 0.8533  0.9634    12063.936
   3_xyz:  15.998 0.8980  0.9871     7658.918
   3_adp:  15.267 0.9044  0.9889     7171.072
   3_occ:  15.258 0.9045  0.9889     7168.076
   4_bss:  15.297 0.9042  0.9764     7226.524
   4_xyz:  14.510 0.9109  0.9780     6663.476
   4_adp:  14.237 0.9133  0.9782     6541.377
   4_occ:  14.221 0.9134  0.9782     6536.777
   5_bss:  14.218 0.9134  0.9759     6534.596
   5_xyz:  14.123 0.9143  0.9751     6465.506
   5_adp:  14.158 0.9140  0.9732     6486.513
   5_occ:  14.160 0.9140  0.9731     6489.974
   5_bss:  14.160 0.9140  0.9738     6490.093
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3722e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3722e+01
   1_xyz:   1.616  0.012  0.105 17.894  0.007  4.112   1.2866e-01
   1_adp:   1.616  0.012  0.105 17.894  0.007  4.112   1.2866e-01
   1_occ:   1.616  0.012  0.105 17.894  0.007  4.112   1.2866e-01
   2_bss:   1.616  0.012  0.105 17.894  0.007  4.112   1.2866e-01
   2_xyz:   1.016  0.007  0.073 15.995  0.004  4.128   6.4779e-02
   2_adp:   1.016  0.007  0.073 15.995  0.004  4.128   6.4779e-02
   2_occ:   1.016  0.007  0.073 15.995  0.004  4.128   6.4779e-02
   3_bss:   1.016  0.007  0.073 15.995  0.004  4.128   6.4779e-02
   3_xyz:   1.103  0.008  0.085 15.814  0.004  4.126   7.0591e-02
   3_adp:   1.103  0.008  0.085 15.814  0.004  4.126   7.0591e-02
   3_occ:   1.103  0.008  0.085 15.814  0.004  4.126   7.0591e-02
   4_bss:   1.103  0.008  0.085 15.814  0.004  4.126   7.0591e-02
   4_xyz:   1.129  0.009  0.091 15.740  0.004  4.122   7.5259e-02
   4_adp:   1.129  0.009  0.091 15.740  0.004  4.122   7.5259e-02
   4_occ:   1.129  0.009  0.091 15.740  0.004  4.122   7.5259e-02
   5_bss:   1.129  0.009  0.091 15.740  0.004  4.122   7.5259e-02
   5_xyz:   1.060  0.008  0.086 15.394  0.004  4.121   6.7112e-02
   5_adp:   1.060  0.008  0.086 15.394  0.004  4.121   6.7112e-02
   5_occ:   1.060  0.008  0.086 15.394  0.004  4.121   6.7112e-02
   5_bss:   1.060  0.008  0.086 15.394  0.004  4.121   6.7112e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9652e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9652e+00
   1_xyz:  14.205  0.154  0.474 86.351  0.049  2.252   9.5420e-02
   1_adp:  14.205  0.154  0.474 86.351  0.049  2.252   9.5420e-02
   1_occ:  14.205  0.154  0.474 86.351  0.049  2.252   9.5420e-02
   2_bss:  14.205  0.154  0.474 86.351  0.049  2.252   9.5420e-02
   2_xyz:   6.226  0.064  0.257 88.257  0.038  2.284   4.6264e-02
   2_adp:   6.226  0.064  0.257 88.257  0.038  2.284   4.6264e-02
   2_occ:   6.226  0.064  0.257 88.257  0.038  2.284   4.6264e-02
   3_bss:   6.226  0.064  0.257 88.257  0.038  2.284   4.6264e-02
   3_xyz:   9.128  0.053  0.556 82.397  0.034  2.351   5.1696e-02
   3_adp:   9.128  0.053  0.556 82.397  0.034  2.351   5.1696e-02
   3_occ:   9.128  0.053  0.556 82.397  0.034  2.351   5.1696e-02
   4_bss:   9.128  0.053  0.556 82.397  0.034  2.351   5.1696e-02
   4_xyz:   7.232  0.049  0.685 82.817  0.034  2.303   7.3228e-02
   4_adp:   7.232  0.049  0.685 82.817  0.034  2.303   7.3228e-02
   4_occ:   7.232  0.049  0.685 82.817  0.034  2.303   7.3228e-02
   5_bss:   7.232  0.049  0.685 82.817  0.034  2.303   7.3228e-02
   5_xyz:   7.219  0.040  0.597 82.758  0.032  2.300   4.8316e-02
   5_adp:   7.219  0.040  0.597 82.758  0.032  2.300   4.8316e-02
   5_occ:   7.219  0.040  0.597 82.758  0.032  2.300   4.8316e-02
   5_bss:   7.219  0.040  0.597 82.758  0.032  2.300   4.8316e-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:  72.33   0.00  11.15  68.46   0.00   8.11  72.33   0.00  27.68
   1_occ:  72.33   0.00  11.15  68.46   0.00   8.11  72.33   0.00  27.68
   2_bss:  72.33   0.00  11.15  68.46   0.00   8.11  72.33   0.00  27.68
   2_xyz:  72.33   0.00  11.15  68.46   0.00   8.11  72.33   0.00  27.68
   2_adp:  72.00   0.00  11.57  69.30   0.00   7.87  72.00   1.46  31.76
   2_occ:  72.00   0.00  11.57  69.30   0.00   7.87  72.00   1.46  31.76
   3_bss:  72.00   0.00  11.57  69.30   0.00   7.87  72.00   1.46  31.76
   3_xyz:  72.00   0.00  11.57  69.30   0.00   7.87  72.00   1.46  31.76
   3_adp:  84.90   0.00  12.31  84.90   0.00   8.01  73.57   1.14  35.72
   3_occ:  84.90   0.00  12.31  84.90   0.00   8.01  73.57   1.14  35.72
   4_bss:  84.90   0.00  12.31  84.90   0.00   8.01  73.57   1.14  35.72
   4_xyz:  84.90   0.00  12.31  84.90   0.00   8.01  73.57   1.14  35.72
   4_adp:  81.44   0.00  11.67  81.44   0.00   7.81  69.21   1.24  32.75
   4_occ:  81.44   0.00  11.67  81.44   0.00   7.81  69.21   1.24  32.75
   5_bss:  81.44   0.00  11.67  81.44   0.00   7.81  69.21   1.24  32.75
   5_xyz:  81.44   0.00  11.67  81.44   0.00   7.81  69.21   1.24  32.75
   5_adp:  81.84   0.00  11.60  81.84   0.00   7.79  65.87   1.45  32.40
   5_occ:  81.84   0.00  11.60  81.84   0.00   7.79  65.87   1.45  32.40
   5_bss:  84.75   2.92  14.52  84.75   2.92  10.70  68.78   4.37  35.31
------------------------------------------------------------------------
 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:    1.203    0.014    0.410
   1_adp:    1.203    0.014    0.410
   1_occ:    1.203    0.014    0.410
   2_bss:    1.203    0.014    0.410
   2_xyz:    1.470    0.044    0.536
   2_adp:    1.470    0.044    0.536
   2_occ:    1.470    0.044    0.536
   3_bss:    1.470    0.044    0.536
   3_xyz:    1.444    0.044    0.585
   3_adp:    1.444    0.044    0.585
   3_occ:    1.444    0.044    0.585
   4_bss:    1.444    0.044    0.585
   4_xyz:    1.506    0.059    0.604
   4_adp:    1.506    0.059    0.604
   4_occ:    1.506    0.059    0.604
   5_bss:    1.506    0.059    0.604
   5_xyz:    1.590    0.061    0.612
   5_adp:    1.590    0.061    0.612
   5_occ:    1.590    0.061    0.612
   5_bss:    1.590    0.061    0.612
------------------------------------------------------------------------

CPU time actual refinement: 315.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/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_915/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_915/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.90 
  Macro-tasks:
    bulk solvent and scale       = 40.03  
    individual site refinement   = 123.28 
    weights calculation          = 32.67  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 202.67 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 95.18  
    alpha_beta                      = 8.13   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 104.23 
    fmodel                         = 6.90   
    r_factors                      = 0.23   
    phase_errors                   = 10.86  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 228.66 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.515 micro seconds
Total CPU time: 5.47 minutes
from_scatterers_fft:    624 calls, 94.83 s
gradients_fft:          568 calls, 91.72 s

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

# Date 2008-01-16 Time 02:44:05 PST -0800 (1200480245.14 s)
Start R-work = 0.4446, R-free = 0.4361 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.4361, R-free = 0.4260
Final R-work = 0.1118, R-free = 0.1575