# Date 2008-01-16 Time 04:30:06 PST -0800 (1200486606.28 s)
#phil __OFF__

Command line arguments: "../340.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20591
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 340

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.6339, 88.5498, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9663 1.97093
Completeness in resolution range: 0.922052
Completeness with d_max=infinity: 0.919283

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9663
                             d_min =   1.9709

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: (69.1963, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9663 1.97093
Completeness in resolution range: 0.922052
Completeness with d_max=infinity: 0.919283

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9667 -  4.2175 [2226/2254]  2001   225  10.1%
  bin  2:  4.2175 -  3.3600 [2147/2170]  1930   217  10.1%
  bin  3:  3.3600 -  2.9390 [2115/2140]  1912   203   9.6%
  bin  4:  2.9390 -  2.6719 [2095/2111]  1878   217  10.4%
  bin  5:  2.6719 -  2.4813 [2070/2108]  1860   210  10.1%
  bin  6:  2.4813 -  2.3356 [2070/2103]  1865   205   9.9%
  bin  7:  2.3356 -  2.2190 [2054/2091]  1854   200   9.7%
  bin  8:  2.2190 -  2.1227 [2082/2124]  1876   206   9.9%
  bin  9:  2.1227 -  2.0412 [2008/2068]  1811   197   9.8%
  bin 10:  2.0412 -  1.9709 [ 722/2076]   643    79  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/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: 0.15 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:
        1.49 -     2.17: 19
        2.17 -     2.85: 1101
        2.85 -     3.54: 4378
        3.54 -     4.22: 9145
        4.22 -     4.90: 13354
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.488 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.519 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.538 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.631 3.040 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.698 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27992 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 =====================


==================== 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/noshake/run_340/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 = 69.19625 47.63395 88.54975 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4650   r_free= 0.4644   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.271195                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9667 -  4.7041 0.99   1448  160 0.3568 0.3667      6.5348       6.522|
|  2:  4.7041 -  3.7532 0.99   1401  154 0.3983 0.4347      6.7841      6.8712|
|  3:  3.7532 -  3.2845 0.99   1365  155 0.4455 0.4068      6.6612      6.6117|
|  4:  3.2845 -  2.9868 0.99   1360  144 0.4558 0.4439      6.4828      6.4726|
|  5:  2.9868 -  2.7741 0.98   1338  152 0.4908 0.4680      6.3452       6.373|
|  6:  2.7741 -  2.6115 0.99   1348  151 0.4994 0.5391      6.2686      6.1896|
|  7:  2.6115 -  2.4813 0.99   1321  156 0.4965 0.4551      6.2112      6.1276|
|  8:  2.4813 -  2.3738 0.99   1351  139 0.5136 0.5029      6.1621      6.1393|
|  9:  2.3738 -  2.2827 0.99   1328  148 0.5213 0.5001      6.1128      6.1953|
| 10:  2.2827 -  2.2042 0.98   1327  145 0.5233 0.5451       6.084      6.0767|
| 11:  2.2042 -  2.1355 0.98   1291  157 0.5210 0.5022      6.0151      6.0002|
| 12:  2.1355 -  2.0746 1.00   1350  141 0.5275 0.5310      5.9389      5.9469|
| 13:  2.0746 -  2.0201 0.83   1128  119 0.5288 0.5737      5.8764      5.8622|
| 14:  2.0201 -  1.9709 0.21    274   38 0.4691 0.4610      5.8849      5.7183|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9667 -  4.7041  1448   160  0.72  32.21   0.83     0.74      63352.73|
|  2:  4.7041 -  3.7532  1401   154  0.71  34.05   0.91     0.81      99821.85|
|  3:  3.7532 -  3.2845  1365   155  0.61  42.60   0.89     0.79     105559.34|
|  4:  3.2845 -  2.9868  1360   144  0.53  49.82   0.90     0.70      93266.64|
|  5:  2.9868 -  2.7741  1338   152  0.46  55.46   0.88     0.62      73560.44|
|  6:  2.7741 -  2.6115  1348   151  0.42  58.38   0.89     0.57      66141.09|
|  7:  2.6115 -  2.4813  1321   156  0.42  57.94   0.90     0.57      58782.23|
|  8:  2.4813 -  2.3738  1351   139  0.41  58.99   0.91     0.59      52914.87|
|  9:  2.3738 -  2.2827  1328   148  0.42  58.62   0.90     0.61      49162.07|
| 10:  2.2827 -  2.2042  1327   145  0.40  60.28   0.90     0.57      44781.50|
| 11:  2.2042 -  2.1355  1291   157  0.33  65.57   0.91     0.51      47234.94|
| 12:  2.1355 -  2.0746  1350   141  0.26  70.70   0.92     0.42      45421.77|
| 13:  2.0746 -  2.0201  1128   119  0.24  72.46   0.89     0.39      41768.66|
| 14:  2.0201 -  1.9709   274    38  0.32  65.90   1.03     0.42      31198.07|
|alpha:            min =        0.39 max =            0.81 mean =         0.61|
|beta:             min =    31198.07 max =       105559.34 mean =     64771.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.86|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.02|
|-----------------------------------------------------------------------------|

============================== 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 = 11.562324             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.925   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.142439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.765   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.488 -  1.829:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.829 -  2.171:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.171 -  2.512:       28 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.512 -  2.853:     1073 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.853 -  3.194:     1922 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.194 -  3.535:     2456 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.535 -  3.876:     4598 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.876 -  4.218:     4547 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.218 -  4.559:     6043 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7311 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.189 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.488 |       0.537 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4650   r_free= 0.4644   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.271195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4568   r_free= 0.4522   ksol= 0.30   Bsol= 39.52   scale= 0.936   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,1.35,4.36,0.00,0.00,0.00); trace/3= 1.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.538443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.135764              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.429   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4568      final r-factor (work) = 0.3293          |
| start r-factor (free) = 0.4522      final r-factor (free) = 0.3549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.0544 = 9.54 * 0.50 * 6.2622 + 1.00 * 0.1885                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.3170 = 9.54 * 0.50 * 6.1170 + 1.00 * 0.1435                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3293      final r-factor (work) = 0.2964          |
| start r-factor (free) = 0.3549      final r-factor (free) = 0.3634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9535 = 1.14 * 1.00 * 6.1170 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7977 = 1.14 * 1.00 * 5.9688 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.33  18.79    None  None   None       |
|    all(noH): 2823   0      0.00    102.33  18.79    None  None   None       |
|    Sol.    : 438    0      0.00    102.33  40.67    None  None   None       |
|    Mac.    : 2385   0      0.00    81.35   14.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.233:  998   |   5:    51.166 -  61.400:   63        |
|      1:    10.233 -  20.467:  917   |   6:    61.400 -  71.633:   40        |
|      2:    20.467 -  30.700:  400   |   7:    71.633 -  81.866:   26        |
|      3:    30.700 -  40.933:  217   |   8:    81.866 -  92.099:    5        |
|      4:    40.933 -  51.166:  152   |   9:    92.099 - 102.333:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2964 r_free = 0.3634             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2960 r_free = 0.3640             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2960   r_free= 0.3640   ksol= 0.30   Bsol= 39.52   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,1.35,4.36,0.00,0.00,0.00); trace/3= 1.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.974796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2936   r_free= 0.3625   ksol= 0.33   Bsol= 61.54   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,0.15,1.77,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.972483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.402721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.670   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.391  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2936      final r-factor (work) = 0.2187          |
| start r-factor (free) = 0.3625      final r-factor (free) = 0.2771          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2665 = 5.40 * 0.50 * 5.9684 + 1.00 * 0.1437                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9377 = 5.40 * 0.50 * 5.8705 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2187      final r-factor (work) = 0.2040          |
| start r-factor (free) = 0.2771      final r-factor (free) = 0.2551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9826 = 0.33 * 1.00 * 5.8705 + 1.00 * 0.0185                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9139 = 0.33 * 1.00 * 5.6899 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.20   17.97    None  None   None       |
|    all(noH): 2823   0      0.00    99.20   17.97    None  None   None       |
|    Sol.    : 438    0      4.87    99.20   40.73    None  None   None       |
|    Mac.    : 2385   0      0.00    78.13   13.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.920:  976   |   5:    49.598 -  59.518:   91        |
|      1:     9.920 -  19.839: 1048   |   6:    59.518 -  69.438:   38        |
|      2:    19.839 -  29.759:  333   |   7:    69.438 -  79.357:   16        |
|      3:    29.759 -  39.679:  171   |   8:    79.357 -  89.277:    5        |
|      4:    39.679 -  49.598:  143   |   9:    89.277 -  99.197:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2040 r_free = 0.2551             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2038 r_free = 0.2551             target_work(ml) = 5.657         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2038   r_free= 0.2551   ksol= 0.33   Bsol= 61.54   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,0.15,1.77,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.656996                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2038   r_free= 0.2540   ksol= 0.33   Bsol= 70.31   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.06,0.41,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.656324                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.057198              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.045   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.874373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.200  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2038      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2540      final r-factor (free) = 0.1991          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6288 = 4.06 * 0.50 * 5.6933 + 1.00 * 0.0794                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3207 = 4.06 * 0.50 * 5.5462 + 1.00 * 0.0696                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.1991      final r-factor (free) = 0.1947          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4059 = 1.87 * 1.00 * 5.5462 + 1.00 * 0.0102                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0835 = 1.87 * 1.00 * 5.3724 + 1.00 * 0.0136                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.05  18.64    None  None   None       |
|    all(noH): 2823   0      0.00    103.05  18.64    None  None   None       |
|    Sol.    : 438    0      5.72    103.05  46.49    None  None   None       |
|    Mac.    : 2385   0      0.00    90.73   13.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.305: 1098   |   5:    51.523 -  61.827:   97        |
|      1:    10.305 -  20.609: 1052   |   6:    61.827 -  72.132:   67        |
|      2:    20.609 -  30.914:  229   |   7:    72.132 -  82.436:   40        |
|      3:    30.914 -  41.218:  109   |   8:    82.436 -  92.741:   14        |
|      4:    41.218 -  51.523:  112   |   9:    92.741 - 103.045:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1947             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1411 r_free = 0.1947             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1947   ksol= 0.33   Bsol= 70.31   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.06,0.41,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357319                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1948   ksol= 0.34   Bsol= 80.58   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.59,-0.23,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357630                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.692437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.353  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161974              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.379  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9948 = 3.69 * 0.50 * 5.3759 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8794 = 3.69 * 0.50 * 5.3109 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8736 = 0.16 * 1.00 * 5.3109 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8611 = 0.16 * 1.00 * 5.2596 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    92.92   17.42    None  None   None       |
|    all(noH): 2823   0      1.34    92.92   17.42    None  None   None       |
|    Sol.    : 438    0      5.29    92.92   41.60    None  None   None       |
|    Mac.    : 2385   0      1.34    86.99   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.339 -  10.497: 1152   |   5:    47.128 -  56.286:   94        |
|      1:    10.497 -  19.655: 1018   |   6:    56.286 -  65.444:   58        |
|      2:    19.655 -  28.813:  222   |   7:    65.444 -  74.602:   31        |
|      3:    28.813 -  37.971:  119   |   8:    74.602 -  83.760:   13        |
|      4:    37.971 -  47.128:  108   |   9:    83.760 -  92.917:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1700             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1699             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1699   ksol= 0.34   Bsol= 80.58   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.59,-0.23,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239364                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1698   ksol= 0.33   Bsol= 65.11   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.71,-0.34,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238835                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.663459              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.499  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.585317              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.675  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4481 = 1.66 * 0.50 * 5.2587 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4146 = 1.66 * 0.50 * 5.2396 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3155 = 1.59 * 1.00 * 5.2396 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2945 = 1.59 * 1.00 * 5.2249 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.21  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    100.21  17.62    None  None   None       |
|    Sol.    : 438    0      0.00    100.21  43.14    None  None   None       |
|    Mac.    : 2385   0      0.00    92.66   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.021: 1078   |   5:    50.106 -  60.127:   96        |
|      1:    10.021 -  20.042: 1097   |   6:    60.127 -  70.148:   50        |
|      2:    20.042 -  30.063:  221   |   7:    70.148 -  80.169:   28        |
|      3:    30.063 -  40.085:  117   |   8:    80.169 -  90.190:   16        |
|      4:    40.085 -  50.106:  116   |   9:    90.190 - 100.211:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1704             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1705             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1705   ksol= 0.33   Bsol= 65.11   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.71,-0.34,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9667 -  4.7041 0.99   1448  160 0.1008 0.1298       5.409      5.5912|
|  2:  4.7041 -  3.7532 0.99   1401  154 0.0867 0.1062      5.4479      5.6259|
|  3:  3.7532 -  3.2845 0.99   1365  155 0.1162 0.1609      5.5323      5.8648|
|  4:  3.2845 -  2.9868 0.99   1360  144 0.1393 0.1786       5.531      5.6988|
|  5:  2.9868 -  2.7741 0.98   1338  152 0.1478 0.1782      5.4311      5.5953|
|  6:  2.7741 -  2.6115 0.99   1348  151 0.1409 0.2282      5.3181      5.5954|
|  7:  2.6115 -  2.4813 0.99   1321  156 0.1422 0.1800      5.2725      5.4481|
|  8:  2.4813 -  2.3738 0.99   1351  139 0.1328 0.1953       5.194      5.3874|
|  9:  2.3738 -  2.2827 0.99   1328  148 0.1260 0.1920      5.1002      5.3739|
| 10:  2.2827 -  2.2042 0.98   1327  145 0.1262 0.1934      5.0338      5.2385|
| 11:  2.2042 -  2.1355 0.98   1291  157 0.1243 0.1962      4.9751      5.3373|
| 12:  2.1355 -  2.0746 1.00   1350  141 0.1218 0.1580      4.9286      5.1186|
| 13:  2.0746 -  2.0201 0.83   1128  119 0.1172 0.2017      4.8357      5.1258|
| 14:  2.0201 -  1.9709 0.21    274   38 0.1045 0.1808      4.7846      4.9906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9667 -  4.7041  1448   160  0.94   9.47   0.97     0.93       7514.14|
|  2:  4.7041 -  3.7532  1401   154  0.95   8.26   1.01     0.99       9278.95|
|  3:  3.7532 -  3.2845  1365   155  0.93  12.07   1.02     1.02      11239.98|
|  4:  3.2845 -  2.9868  1360   144  0.90  15.72   1.01     0.99      11904.32|
|  5:  2.9868 -  2.7741  1338   152  0.89  17.91   0.99     0.97      10479.89|
|  6:  2.7741 -  2.6115  1348   151  0.88  18.79   0.97     0.94       8881.17|
|  7:  2.6115 -  2.4813  1321   156  0.88  18.08   0.98     0.95       7880.37|
|  8:  2.4813 -  2.3738  1351   139  0.88  18.21   0.99     0.94       7017.60|
|  9:  2.3738 -  2.2827  1328   148  0.89  17.54   0.99     0.94       5876.73|
| 10:  2.2827 -  2.2042  1327   145  0.89  17.46   0.98     0.93       5150.95|
| 11:  2.2042 -  2.1355  1291   157  0.89  17.14   0.98     0.93       4656.45|
| 12:  2.1355 -  2.0746  1350   141  0.89  17.41   0.99     0.99       4470.46|
| 13:  2.0746 -  2.0201  1128   119  0.89  17.95   0.97     0.94       3833.12|
| 14:  2.0201 -  1.9709   274    38  0.91  15.15   0.96     0.91       3225.04|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3225.04 max =        11904.32 mean =      7554.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.73|
|phase err.(test): min =        0.00 max =           89.17 mean =        15.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1704   ksol= 0.33   Bsol= 68.65   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.64,-0.26,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1704   ksol= 0.33   Bsol= 68.65   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.64,-0.26,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232592                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9667 -  4.7041 0.99   1448  160 0.1007 0.1309      5.4039       5.582|
|  2:  4.7041 -  3.7532 0.99   1401  154 0.0879 0.1062      5.4547       5.631|
|  3:  3.7532 -  3.2845 0.99   1365  155 0.1166 0.1610      5.5349       5.862|
|  4:  3.2845 -  2.9868 0.99   1360  144 0.1391 0.1797      5.5301      5.7013|
|  5:  2.9868 -  2.7741 0.98   1338  152 0.1476 0.1781        5.43       5.594|
|  6:  2.7741 -  2.6115 0.99   1348  151 0.1409 0.2274      5.3174      5.5936|
|  7:  2.6115 -  2.4813 0.99   1321  156 0.1421 0.1799      5.2719      5.4483|
|  8:  2.4813 -  2.3738 0.99   1351  139 0.1328 0.1950      5.1936      5.3864|
|  9:  2.3738 -  2.2827 0.99   1328  148 0.1258 0.1921      5.0999      5.3745|
| 10:  2.2827 -  2.2042 0.98   1327  145 0.1262 0.1933      5.0336      5.2379|
| 11:  2.2042 -  2.1355 0.98   1291  157 0.1243 0.1959      4.9751       5.337|
| 12:  2.1355 -  2.0746 1.00   1350  141 0.1218 0.1579      4.9282      5.1182|
| 13:  2.0746 -  2.0201 0.83   1128  119 0.1172 0.2015      4.8356       5.125|
| 14:  2.0201 -  1.9709 0.21    274   38 0.1045 0.1807      4.7849      4.9905|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9667 -  4.7041  1448   160  0.94   9.42   0.96     0.94       7469.38|
|  2:  4.7041 -  3.7532  1401   154  0.95   8.23   1.01     0.99       9258.89|
|  3:  3.7532 -  3.2845  1365   155  0.93  12.10   1.02     1.02      11297.12|
|  4:  3.2845 -  2.9868  1360   144  0.90  15.76   1.01     0.99      11917.23|
|  5:  2.9868 -  2.7741  1338   152  0.89  17.90   0.99     0.97      10463.43|
|  6:  2.7741 -  2.6115  1348   151  0.88  18.76   0.98     0.95       8852.62|
|  7:  2.6115 -  2.4813  1321   156  0.88  18.06   0.99     0.95       7866.83|
|  8:  2.4813 -  2.3738  1351   139  0.88  18.20   1.00     0.95       7012.32|
|  9:  2.3738 -  2.2827  1328   148  0.89  17.53   0.99     0.94       5876.86|
| 10:  2.2827 -  2.2042  1327   145  0.89  17.45   0.98     0.94       5144.69|
| 11:  2.2042 -  2.1355  1291   157  0.89  17.14   0.98     0.93       4652.08|
| 12:  2.1355 -  2.0746  1350   141  0.89  17.41   1.00     0.99       4465.93|
| 13:  2.0746 -  2.0201  1128   119  0.89  17.95   0.98     0.95       3829.81|
| 14:  2.0201 -  1.9709   274    38  0.91  15.15   0.96     0.91       3220.99|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3220.99 max =        11917.23 mean =      7548.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.73|
|phase err.(test): min =        0.00 max =           89.17 mean =        15.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.21  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    100.21  17.62    None  None   None       |
|    Sol.    : 438    0      0.00    100.21  43.14    None  None   None       |
|    Mac.    : 2385   0      0.00    92.66   12.94    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:     0.003 -  10.024: 1078   |   5:    50.109 -  60.130:   96        |
|      1:    10.024 -  20.045: 1097   |   6:    60.130 -  70.151:   50        |
|      2:    20.045 -  30.066:  221   |   7:    70.151 -  80.172:   28        |
|      3:    30.066 -  40.088:  117   |   8:    80.172 -  90.193:   16        |
|      4:    40.088 -  50.109:  116   |   9:    90.193 - 100.214:    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)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 5.555
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 308
   mapped sites are within: 0.705 - 5.555

peak=    8.044 closest distance to " O  BHOH Z  74 " =    1.163
peak=    5.304 closest distance to " O   HOH Z 210 " =    1.271
peak=    5.161 closest distance to " O   HOH Z  49 " =    1.404
peak=    4.978 closest distance to " CG  PRO A  54 " =    1.446
peak=    4.913 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.888 closest distance to " O   HOH Z 403 " =    1.956
peak=    4.830 closest distance to " CB  ARG A 275 " =    0.957
peak=    4.812 closest distance to " CG  PRO A  90 " =    1.294
peak=    4.778 closest distance to " CA  TYR A  30 " =    0.957
peak=    4.730 closest distance to " CZ  PHE A 218 " =    1.159
peak=    4.692 closest distance to " O   HOH Z 113 " =    1.872
peak=    4.683 closest distance to " O   HOH Z 255 " =    1.019
peak=    4.641 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.607 closest distance to " CD2 TRP A 179 " =    1.334
peak=    4.564 closest distance to " O   HOH Z 369 " =    2.159
peak=    4.545 closest distance to " CB  ARG A 190 " =    1.683
peak=    4.518 closest distance to " CZ3 TRP A 266 " =    1.094
peak=    4.509 closest distance to " O   HOH Z 117 " =    1.150
peak=    4.473 closest distance to " CA  ARG A  36 " =    1.084
peak=    4.440 closest distance to " O   HOH Z 248 " =    1.377
peak=    4.392 closest distance to " CG  GLN A  58 " =    1.077
peak=    4.391 closest distance to " O   HOH Z 232 " =    2.316
peak=    4.385 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.370 closest distance to " CB  SER A  63 " =    1.096
peak=    4.320 closest distance to " O   HOH Z 188 " =    2.775
peak=    4.299 closest distance to " CZ  PHE A  38 " =    1.184
peak=    4.283 closest distance to " CB  PRO A  54 " =    1.004
peak=    4.274 closest distance to " CG  PRO A 243 " =    1.084
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.231 closest distance to " O   HOH Z 287 " =    1.658
peak=    4.185 closest distance to " O   HOH Z 412 " =    3.800
peak=    4.121 closest distance to " O   HOH Z  63 " =    1.880
peak=    4.118 closest distance to " CD  ARG A 269 " =    1.028
peak=    4.108 closest distance to " NZ  LYS A 117 " =    2.944
peak=    4.091 closest distance to " CB  GLU A 277 " =    3.746
peak=    4.056 closest distance to " ND2 ASN A 187 " =    1.548
peak=    4.053 closest distance to " CA  ALA A  51 " =    0.945
peak=    4.051 closest distance to " O   HOH Z  43 " =    2.222
peak=    4.039 closest distance to " O   HOH Z 142 " =    1.527
peak=    4.024 closest distance to " O   HOH Z 298 " =    1.871
peak=    4.003 closest distance to " O   PRO A 198 " =    1.548
peak=    3.999 closest distance to " O   HOH Z 214 " =    1.409
peak=    3.991 closest distance to " CB  ARG A  79 " =    1.281
peak=    3.980 closest distance to " O   HOH Z 362 " =    3.604
peak=    3.970 closest distance to " CB  ASN A 148 " =    1.426
peak=    3.947 closest distance to " O   HOH Z 251 " =    1.611
peak=    3.947 closest distance to " CB  ASN A 187 " =    1.518
peak=    3.947 closest distance to " CG  ARG A  66 " =    2.604
peak=    3.931 closest distance to " O   HOH Z 346 " =    1.581
peak=    3.928 closest distance to " O   SER A  87 " =    2.301
peak=    3.920 closest distance to " ND2 ASN A 249 " =    0.932
peak=    3.915 closest distance to " O   THR A 220 " =    1.149
peak=    3.901 closest distance to " O   HOH Z  65 " =    0.962
peak=    3.899 closest distance to " O   HOH Z 402 " =    1.428
peak=    3.890 closest distance to " O   HOH Z  40 " =    1.866
peak=    3.879 closest distance to " O   HOH Z  52 " =    1.278
peak=    3.871 closest distance to " CE  LYS A  76 " =    0.903
peak=    3.869 closest distance to " CD1 LEU A  96 " =    0.811
peak=    3.859 closest distance to " CB  TYR A 169 " =    0.705
peak=    3.847 closest distance to " O   HOH Z 265 " =    2.048
peak=    3.841 closest distance to " CG  PRO A 213 " =    1.231
peak=    3.839 closest distance to " CA  ALA A 160 " =    0.869
peak=    3.834 closest distance to " O   HOH Z 234 " =    3.707
peak=    3.818 closest distance to " CA  ARG A 195 " =    1.230
peak=    3.789 closest distance to " O   HOH Z 368 " =    2.186
peak=    3.789 closest distance to " O   HOH Z 227 " =    1.585
peak=    3.781 closest distance to " O   HOH Z 365 " =    2.602
peak=    3.776 closest distance to " CG2 ILE A 120 " =    1.267
peak=    3.761 closest distance to " O   HOH Z 406 " =    1.623
peak=    3.757 closest distance to " O   HOH Z 193 " =    1.247
peak=    3.748 closest distance to " O   HOH Z 394 " =    1.521
peak=    3.739 closest distance to " CG AARG A 275 " =    1.333
peak=    3.734 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.730 closest distance to " NE2 GLN A  11 " =    1.096
peak=    3.730 closest distance to " N   ASN A  39 " =    1.239
peak=    3.718 closest distance to " O   HOH Z  76 " =    1.047
peak=    3.710 closest distance to " CA  ALA A 100 " =    1.011
peak=    3.710 closest distance to " O   HOH Z 209 " =    2.266
peak=    3.708 closest distance to " CE  LYS A 119 " =    1.151
peak=    3.707 closest distance to " CG1 ILE A  20 " =    1.279
peak=    3.707 closest distance to " O   ASN A  74 " =    1.624
peak=    3.694 closest distance to " O   HOH Z 207 " =    1.230
peak=    3.685 closest distance to " CB  PHE A 204 " =    0.786
peak=    3.679 closest distance to " NH1AARG A 145 " =    1.490
peak=    3.675 closest distance to " O   HOH Z 425 " =    1.371
peak=    3.674 closest distance to " O   HOH Z 280 " =    2.965
peak=    3.672 closest distance to " O   ALA A 165 " =    1.451
peak=    3.667 closest distance to " CG2AVAL A 121 " =    2.174
peak=    3.664 closest distance to " CB  SER A 141 " =    1.186
peak=    3.664 closest distance to " CB  PRO A 198 " =    1.324
peak=    3.662 closest distance to " O   HOH Z 199 " =    1.622
peak=    3.661 closest distance to " OG BSER A 164 " =    2.236
peak=    3.659 closest distance to " CA  GLU A 152 " =    0.855
peak=    3.659 closest distance to " O   HOH Z 193 " =    1.786
peak=    3.655 closest distance to " O   HOH Z  21 " =    1.867
peak=    3.652 closest distance to " O   HOH Z 380 " =    1.934
peak=    3.647 closest distance to " O   HOH Z 128 " =    1.512
peak=    3.646 closest distance to " CD  LYS A 166 " =    1.392
peak=    3.644 closest distance to " O   HOH Z 250 " =    1.376
peak=    3.643 closest distance to " O   HOH Z 261 " =    2.432
peak=    3.630 closest distance to " O   TYR A 116 " =    1.432
peak=    3.624 closest distance to " CB  PRO A  90 " =    1.104
peak=    3.619 closest distance to " CG  GLU A  37 " =    0.979
peak=    3.615 closest distance to " CG  GLN A  11 " =    1.476
peak=    3.608 closest distance to " CA  VAL A 125 " =    1.259
peak=    3.606 closest distance to " CB  VAL A 202 " =    1.471
peak=    3.598 closest distance to " O   HOH Z  59 " =    2.219
peak=    3.597 closest distance to " CD1 ILE A 199 " =    1.192
peak=    3.594 closest distance to " O   HOH Z 325 " =    2.179
peak=    3.591 closest distance to " O   HOH Z  78 " =    1.718
peak=    3.591 closest distance to " CB  VAL A 265 " =    1.207
peak=    3.585 closest distance to " CB  ALA A 114 " =    0.830
peak=    3.579 closest distance to " N   CYS A 260 " =    1.011
peak=    3.579 closest distance to " O   HOH Z 303 " =    2.251
peak=    3.572 closest distance to " O   HOH Z 213 " =    1.861
peak=    3.572 closest distance to " O   HOH Z 102 " =    1.296
peak=    3.567 closest distance to " O   HOH Z 126 " =    1.532
peak=    3.564 closest distance to " O   HOH Z 247 " =    1.412
peak=    3.560 closest distance to " CB  GLU A 128 " =    1.052
peak=    3.558 closest distance to " CB  ASN A 142 " =    1.107
peak=    3.558 closest distance to " CB  GLU A  46 " =    1.069
peak=    3.548 closest distance to " CB  ASN A 285 " =    0.954
peak=    3.542 closest distance to " O   HOH Z 299 " =    4.306
peak=    3.541 closest distance to " CB  LEU A  83 " =    0.749
peak=    3.540 closest distance to " CB  SER A  62 " =    0.948
peak=    3.536 closest distance to " CB  ALA A 291 " =    1.099
peak=    3.536 closest distance to " CG2 ILE A  20 " =    1.279
peak=    3.533 closest distance to " O   HOH Z 359 " =    1.804
peak=    3.529 closest distance to " NE  ARG A  56 " =    3.512
peak=    3.524 closest distance to " CG2 VAL A 257 " =    0.795
peak=    3.524 closest distance to " O   HOH Z 423 " =    1.849
peak=    3.521 closest distance to " O   HOH Z 383 " =    2.027
peak=    3.518 closest distance to " CB  THR A  52 " =    0.756
peak=    3.514 closest distance to " O   HOH Z 132 " =    1.008
peak=    3.512 closest distance to " O   HOH Z 427 " =    2.894
peak=    3.510 closest distance to " CB  SER A 210 " =    0.897
peak=    3.509 closest distance to " O   HOH Z  19 " =    1.528
peak=    3.509 closest distance to " O   HOH Z 203 " =    1.734
peak=    3.506 closest distance to " O   HOH Z 357 " =    2.083
peak=    3.503 closest distance to " N   TYR A 116 " =    1.650
peak=    3.497 closest distance to " CA  ASN A 215 " =    0.960
peak=    3.497 closest distance to " O   HOH Z 219 " =    2.055
peak=    3.496 closest distance to " O   HOH Z 417 " =    2.737
peak=    3.496 closest distance to " O   HOH Z 180 " =    2.176
peak=    3.496 closest distance to " CB  ASN A  39 " =    0.842
peak=    3.492 closest distance to " O   HOH Z 298 " =    2.330
peak=    3.492 closest distance to " CB  THR A  31 " =    1.497
peak=    3.489 closest distance to " OG BSER A 212 " =    2.663
peak=    3.486 closest distance to " CB  PRO A 243 " =    1.260
peak=    3.485 closest distance to " O   HOH Z  15 " =    2.369
peak=    3.484 closest distance to " O   THR A 182 " =    1.503
peak=    3.480 closest distance to " O   HOH Z 132 " =    2.637
peak=    3.477 closest distance to " O   HOH Z 214 " =    3.014
peak=    3.475 closest distance to " O   HOH Z 132 " =    2.624
peak=    3.467 closest distance to " CA  MET A 105 " =    1.122
peak=    3.460 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.459 closest distance to " O   HOH Z 313 " =    2.004
peak=    3.455 closest distance to " O   HOH Z 291 " =    1.428
peak=    3.446 closest distance to " CG1 ILE A  33 " =    1.214
peak=    3.446 closest distance to " NE2 GLN A  77 " =    3.158
peak=    3.440 closest distance to " CD  PRO A  54 " =    0.953
peak=    3.436 closest distance to " O   HOH Z 353 " =    2.725
peak=    3.433 closest distance to " O   HOH Z 134 " =    1.287
peak=    3.432 closest distance to " CG2AVAL A  72 " =    1.891
peak=    3.431 closest distance to " O   HOH Z  80 " =    1.744
peak=    3.430 closest distance to " CE1 TYR A  30 " =    1.040
peak=    3.430 closest distance to " O   HOH Z 361 " =    2.532
peak=    3.428 closest distance to " O   HOH Z  35 " =    2.416
peak=    3.424 closest distance to " O   HOH Z 393 " =    3.083
peak=    3.416 closest distance to " O   HOH Z 371 " =    2.898
peak=    3.414 closest distance to " N   ARG A 156 " =    1.532
peak=    3.409 closest distance to " CA  ILE A 234 " =    0.926
peak=    3.403 closest distance to " O   HOH Z   4 " =    1.591
peak=    3.400 closest distance to " CG2 VAL A 197 " =    1.092
peak=    3.397 closest distance to " CB  ALA A 248 " =    1.408
peak=    3.387 closest distance to " CB  ASP A 124 " =    0.825
peak=    3.387 closest distance to " O   HOH Z  80 " =    1.971
peak=    3.386 closest distance to " O   HOH Z  54 " =    1.074
peak=    3.380 closest distance to " ND2AASN A 224 " =    0.904
peak=    3.376 closest distance to " O   HOH Z  85 " =    1.333
peak=    3.373 closest distance to " O   HOH Z 389 " =    1.933
peak=    3.372 closest distance to " OG1 THR A 264 " =    0.743
peak=    3.371 closest distance to " CD  ARG A 159 " =    0.774
peak=    3.369 closest distance to " O   HOH Z 290 " =    1.118
peak=    3.369 closest distance to " O   HOH Z 139 " =    4.741
peak=    3.368 closest distance to " OG  SER A  28 " =    1.564
peak=    3.368 closest distance to " O   HOH Z  97 " =    1.308
peak=    3.362 closest distance to " O   HOH Z 183 " =    1.783
peak=    3.359 closest distance to " OG  SER A 276 " =    1.492
peak=    3.359 closest distance to " O   HOH Z 146 " =    2.217
peak=    3.358 closest distance to " CA  GLN A  94 " =    0.766
peak=    3.356 closest distance to " CA  SER A  87 " =    1.088
peak=    3.356 closest distance to " O   HOH Z 345 " =    3.719
peak=    3.355 closest distance to " CG2BVAL A  41 " =    0.812
peak=    3.354 closest distance to " O   HOH Z  97 " =    1.826
peak=    3.348 closest distance to " CB  ASP A 191 " =    1.186
peak=    3.342 closest distance to " O   HOH Z 316 " =    3.047
peak=    3.341 closest distance to " CB  TRP A 266 " =    1.070
peak=    3.340 closest distance to " CA  ILE A 106 " =    0.805
peak=    3.338 closest distance to " O   HOH Z  20 " =    1.170
peak=    3.335 closest distance to " CD1 LEU A 167 " =    0.787
peak=    3.333 closest distance to " O   ASP A 124 " =    1.384
peak=    3.331 closest distance to " OG BSER A 134 " =    2.799
peak=    3.327 closest distance to " CA  ALA A 154 " =    1.052
peak=    3.324 closest distance to " CG2 ILE A 239 " =    0.821
peak=    3.323 closest distance to " NE  ARG A  24 " =    0.939
peak=    3.318 closest distance to " OD2 ASP A  50 " =    2.890
peak=    3.318 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.314 closest distance to " O   HOH Z 422 " =    2.623
peak=    3.306 closest distance to " CG2BVAL A 121 " =    0.818
peak=    3.304 closest distance to " NE2 GLN A  58 " =    4.841
peak=    3.294 closest distance to " CB  SER A  26 " =    1.857
peak=    3.288 closest distance to " N   HIS A 108 " =    1.765
peak=    3.287 closest distance to " O   HOH Z 258 " =    1.970
peak=    3.285 closest distance to " CA  ALA A 295 " =    1.030
peak=    3.284 closest distance to " O   HOH Z 345 " =    1.619
peak=    3.281 closest distance to " CG1 VAL A 153 " =    1.112
peak=    3.275 closest distance to " OG  SER A 245 " =    1.534
peak=    3.274 closest distance to " O   HOH Z 375 " =    2.133
peak=    3.273 closest distance to " CB  SER A 273 " =    0.879
peak=    3.273 closest distance to " CB  ALA A 292 " =    0.974
peak=    3.272 closest distance to " O   HOH Z 285 " =    2.075
peak=    3.272 closest distance to " CG  MET A 185 " =    1.189
peak=    3.266 closest distance to " O   HOH Z 285 " =    2.390
peak=    3.266 closest distance to " OG1 THR A  82 " =    0.885
peak=    3.261 closest distance to " CG  LEU A 167 " =    1.195
peak=    3.260 closest distance to " O   LEU A 228 " =    1.875
peak=    3.246 closest distance to " OG  SER A  62 " =    2.775
peak=    3.246 closest distance to " O   HOH Z 394 " =    3.961
peak=    3.241 closest distance to " O   HOH Z 371 " =    1.614
peak=    3.240 closest distance to " O   HOH Z 305 " =    3.660
peak=    3.239 closest distance to " CE1 TYR A 186 " =    1.250
peak=    3.236 closest distance to " CB  SER A  99 " =    1.355
peak=    3.235 closest distance to " CB  ASP A 107 " =    1.316
peak=    3.235 closest distance to " NH1 ARG A 269 " =    0.724
peak=    3.234 closest distance to " O   HOH Z  63 " =    2.205
peak=    3.226 closest distance to " O   HOH Z  44 " =    2.061
peak=    3.223 closest distance to " CE1 HIS A  81 " =    1.456
peak=    3.222 closest distance to " CB  LEU A 228 " =    1.066
peak=    3.221 closest distance to " CG2 THR A 220 " =    0.819
peak=    3.221 closest distance to " O   ASP A 191 " =    1.623
peak=    3.218 closest distance to " CB  ASP A 298 " =    1.151
peak=    3.217 closest distance to " O  BHOH Z 338 " =    2.125
peak=    3.215 closest distance to " CA  ASP A 162 " =    1.066
peak=    3.214 closest distance to " CB  PRO A 198 " =    1.102
peak=    3.212 closest distance to " CE3 TRP A 150 " =    1.148
peak=    3.210 closest distance to " N   SER A 164 " =    1.004
peak=    3.208 closest distance to " CG  ARG A 138 " =    1.365
peak=    3.207 closest distance to " CA  ASN A 127 " =    1.204
peak=    3.206 closest distance to " CH2 TRP A  70 " =    0.866
peak=    3.206 closest distance to " CD2 LEU A 297 " =    0.776
peak=    3.203 closest distance to " CB  ASN A 110 " =    1.103
peak=    3.202 closest distance to " CG2 THR A 221 " =    1.195
peak=    3.201 closest distance to " CA  LEU A  83 " =    1.248
peak=    3.200 closest distance to " OD2 ASP A 286 " =    3.230
peak=    3.199 closest distance to " O   HOH Z 272 " =    1.837
peak=    3.193 closest distance to " O   HOH Z  88 " =    3.186
peak=    3.193 closest distance to " CG1 ILE A  49 " =    1.561
peak=    3.188 closest distance to " CA  ASN A 176 " =    1.179
peak=    3.183 closest distance to " OE1 GLN A  11 " =    2.130
peak=    3.181 closest distance to " OG  SER A 135 " =    1.295
peak=    3.179 closest distance to " O   THR A 251 " =    1.168
peak=    3.177 closest distance to " CE  MET A  40 " =    1.018
peak=    3.176 closest distance to " CA  GLY A 133 " =    3.708
peak=    3.175 closest distance to " CD2 LEU A   5 " =    1.106
peak=    3.172 closest distance to " OE1 GLN A 223 " =    3.533
peak=    3.171 closest distance to " O   HOH Z 162 " =    1.668
peak=    3.171 closest distance to " OE1 GLN A  55 " =    1.471
peak=    3.166 closest distance to " OG  SER A  22 " =    2.632
peak=    3.163 closest distance to " OE2 GLU A  53 " =    1.123
peak=    3.162 closest distance to " O   HOH Z 299 " =    4.601
peak=    3.157 closest distance to " O   HOH Z 336 " =    1.866
peak=    3.151 closest distance to " O   HOH Z  88 " =    1.701
peak=    3.148 closest distance to " O   HOH Z 271 " =    2.500
peak=    3.143 closest distance to " CD  ARG A  66 " =    2.415
peak=    3.134 closest distance to " O   HOH Z 116 " =    1.150
peak=    3.132 closest distance to " CD  ARG A 139 " =    1.210
peak=    3.127 closest distance to " CB  ARG A 138 " =    0.871
peak=    3.126 closest distance to " O   HOH Z 395 " =    3.086
peak=    3.124 closest distance to " CG2 VAL A 268 " =    1.012
peak=    3.122 closest distance to " O   HOH Z 173 " =    2.090
peak=    3.122 closest distance to " N   ASN A 110 " =    1.676
peak=    3.120 closest distance to " CG  LEU A 281 " =    0.950
peak=    3.119 closest distance to " O   HOH Z 327 " =    1.654
peak=    3.114 closest distance to " N   THR A  52 " =    1.102
peak=    3.111 closest distance to " CB  ALA A 299 " =    0.878
peak=    3.108 closest distance to " CB  SER A   3 " =    1.319
peak=    3.108 closest distance to " O   HOH Z 128 " =    1.988
peak=    3.104 closest distance to " N   VAL A 265 " =    1.492
peak=    3.104 closest distance to " CB  SER A 271 " =    1.329
peak=    3.103 closest distance to " O   HOH Z 216 " =    5.020
peak=    3.099 closest distance to " CA  SER A  32 " =    1.617
peak=    3.099 closest distance to " O   HOH Z 258 " =    1.831
peak=    3.096 closest distance to " CA  ARG A 156 " =    1.075
peak=    3.092 closest distance to " CB  ALA A 104 " =    0.807
peak=    3.076 closest distance to " OD1 ASN A  69 " =    2.434
peak=    3.066 closest distance to " CA  ALA A 248 " =    1.216
peak=    3.048 closest distance to " O   HOH Z 420 " =    5.555
peak=    3.045 closest distance to " O   HOH Z 409 " =    3.144
peak=    3.043 closest distance to " CA  THR A 221 " =    1.342
peak=    3.038 closest distance to " O   HOH Z  85 " =    2.093
peak=    3.037 closest distance to " OD1 ASN A 217 " =    1.630
peak=    3.035 closest distance to " OD2 ASP A 298 " =    3.837
peak=    3.021 closest distance to " CA  ASP A 140 " =    1.504
peak=    3.015 closest distance to " CE1 HIS A  81 " =    1.596

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.796 - 5.959
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 198
   mapped sites are within: 0.796 - 5.959

peak=   -4.718 closest distance to " O   PRO A 198 " =    1.319
peak=   -4.514 closest distance to " CG  GLN A  58 " =    0.954
peak=   -4.427 closest distance to " CG2 ILE A  49 " =    2.829
peak=   -4.416 closest distance to " O   HOH Z  52 " =    1.157
peak=   -4.416 closest distance to " CD  ARG A  14 " =    3.473
peak=   -4.363 closest distance to " CD2 TYR A 293 " =    1.903
peak=   -4.311 closest distance to " O   HOH Z 377 " =    2.044
peak=   -4.212 closest distance to " O   VAL A  67 " =    2.856
peak=   -4.199 closest distance to " O   HOH Z 278 " =    1.045
peak=   -4.193 closest distance to " CE2 PHE A  61 " =    2.716
peak=   -4.131 closest distance to " O   HOH Z 193 " =    0.917
peak=   -4.115 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -4.047 closest distance to " O   HOH Z 266 " =    5.625
peak=   -4.047 closest distance to " CD1 LEU A 101 " =    2.376
peak=   -4.037 closest distance to " CD  GLN A 223 " =    1.549
peak=   -4.030 closest distance to " CA  VAL A  67 " =    3.044
peak=   -4.007 closest distance to " CG  GLN A  58 " =    1.058
peak=   -3.983 closest distance to " CB  ALA A  43 " =    2.604
peak=   -3.955 closest distance to " C   HIS A 108 " =    1.061
peak=   -3.917 closest distance to " CA  ASP A 298 " =    1.098
peak=   -3.903 closest distance to " CD  ARG A 156 " =    2.103
peak=   -3.888 closest distance to " O  BHOH Z  74 " =    0.803
peak=   -3.869 closest distance to " CE  MET A 105 " =    2.920
peak=   -3.855 closest distance to " CB  PRO A 243 " =    2.785
peak=   -3.843 closest distance to " O   HOH Z 166 " =    1.612
peak=   -3.830 closest distance to " CG1 VAL A 112 " =    2.671
peak=   -3.793 closest distance to " O   HOH Z 106 " =    1.970
peak=   -3.770 closest distance to " CA  GLY A 241 " =    2.379
peak=   -3.764 closest distance to " CG  GLN A  11 " =    1.473
peak=   -3.759 closest distance to " O   HOH Z 165 " =    1.918
peak=   -3.746 closest distance to " O   HOH Z 438 " =    3.024
peak=   -3.736 closest distance to " O   ALA A  34 " =    2.494
peak=   -3.725 closest distance to " O   HOH Z 366 " =    1.537
peak=   -3.718 closest distance to " O   HOH Z 394 " =    1.653
peak=   -3.715 closest distance to " O   SER A 210 " =    1.901
peak=   -3.714 closest distance to " CB  HIS A  86 " =    1.139
peak=   -3.709 closest distance to " O   HOH Z 198 " =    1.322
peak=   -3.678 closest distance to " O   HOH Z 150 " =    2.082
peak=   -3.650 closest distance to " OG BSER A 134 " =    1.378
peak=   -3.645 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.645 closest distance to " O   HOH Z 196 " =    2.118
peak=   -3.642 closest distance to " CG1AVAL A  41 " =    2.557
peak=   -3.641 closest distance to " O   HOH Z 211 " =    1.286
peak=   -3.632 closest distance to " CD  ARG A  79 " =    1.264
peak=   -3.628 closest distance to " CG  PRO A 243 " =    1.626
peak=   -3.624 closest distance to " O   HOH Z 374 " =    2.006
peak=   -3.621 closest distance to " CE3 TRP A 150 " =    2.220
peak=   -3.619 closest distance to " CD1 LEU A  25 " =    2.500
peak=   -3.618 closest distance to " CA  GLY A 241 " =    3.204
peak=   -3.617 closest distance to " O   HOH Z  13 " =    1.971
peak=   -3.609 closest distance to " CE2 TYR A  30 " =    2.784
peak=   -3.608 closest distance to " ND2 ASN A  45 " =    1.975
peak=   -3.607 closest distance to " NH2 ARG A  66 " =    1.093
peak=   -3.606 closest distance to " CG  GLN A 103 " =    2.480
peak=   -3.605 closest distance to " O   HOH Z 191 " =    5.959
peak=   -3.605 closest distance to " CH2 TRP A 179 " =    1.283
peak=   -3.601 closest distance to " CB  GLU A 277 " =    1.336
peak=   -3.592 closest distance to " O   HOH Z 102 " =    1.561
peak=   -3.589 closest distance to " CZ  PHE A  38 " =    2.298
peak=   -3.584 closest distance to " O   HOH Z  68 " =    1.649
peak=   -3.576 closest distance to " CD  ARG A 195 " =    5.092
peak=   -3.571 closest distance to " ND2 ASN A 249 " =    2.232
peak=   -3.568 closest distance to " O   HOH Z 348 " =    2.170
peak=   -3.565 closest distance to " O   HOH Z 421 " =    4.009
peak=   -3.559 closest distance to " O   HOH Z 149 " =    1.910
peak=   -3.546 closest distance to " O   TRP A  92 " =    2.036
peak=   -3.540 closest distance to " O   HOH Z 252 " =    3.757
peak=   -3.538 closest distance to " O   HOH Z 154 " =    1.714
peak=   -3.532 closest distance to " N   ALA A  43 " =    2.604
peak=   -3.521 closest distance to " CG1 VAL A 112 " =    2.683
peak=   -3.516 closest distance to " NE2 GLN A 223 " =    1.159
peak=   -3.516 closest distance to " CD2 PHE A 192 " =    2.127
peak=   -3.512 closest distance to " O   HOH Z  64 " =    1.441
peak=   -3.508 closest distance to " C   THR A 279 " =    1.284
peak=   -3.501 closest distance to " N   THR A  52 " =    1.741
peak=   -3.500 closest distance to " CD2 PHE A  61 " =    2.193
peak=   -3.498 closest distance to " SD  MET A 105 " =    1.034
peak=   -3.494 closest distance to " CB  ALA A 129 " =    2.427
peak=   -3.483 closest distance to " CA  ASP A  65 " =    1.329
peak=   -3.482 closest distance to " CB  TRP A  85 " =    2.567
peak=   -3.480 closest distance to " O   HOH Z 171 " =    2.503
peak=   -3.480 closest distance to " CA  GLY A 203 " =    2.310
peak=   -3.479 closest distance to " O   HOH Z 131 " =    4.170
peak=   -3.477 closest distance to " CG  GLU A  53 " =    1.484
peak=   -3.474 closest distance to " O   SER A   3 " =    1.022
peak=   -3.471 closest distance to " O   HOH Z 287 " =    1.986
peak=   -3.470 closest distance to " ND2BASN A 224 " =    1.891
peak=   -3.467 closest distance to " NE2 GLN A 278 " =    1.678
peak=   -3.462 closest distance to " O   HOH Z 174 " =    2.518
peak=   -3.456 closest distance to " O   ALA A  10 " =    1.806
peak=   -3.454 closest distance to " O   HOH Z 244 " =    1.338
peak=   -3.449 closest distance to " CG2 VAL A 189 " =    2.165
peak=   -3.446 closest distance to " CZ  TYR A 169 " =    1.897
peak=   -3.445 closest distance to " O   HOH Z 166 " =    1.631
peak=   -3.444 closest distance to " OD1 ASP A 171 " =    1.560
peak=   -3.437 closest distance to " O   GLU A 152 " =    1.342
peak=   -3.437 closest distance to " CA  GLY A 241 " =    3.009
peak=   -3.430 closest distance to " C   ASN A 285 " =    2.201
peak=   -3.427 closest distance to " CH2 TRP A 150 " =    1.201
peak=   -3.421 closest distance to " OD2 ASP A 191 " =    1.515
peak=   -3.415 closest distance to " CD  PRO A 243 " =    1.978
peak=   -3.413 closest distance to " O   HOH Z 285 " =    1.539
peak=   -3.412 closest distance to " O   HOH Z 351 " =    1.707
peak=   -3.406 closest distance to " O   HOH Z   5 " =    1.653
peak=   -3.404 closest distance to " CD2 TYR A 247 " =    2.393
peak=   -3.399 closest distance to " O   HOH Z  60 " =    1.971
peak=   -3.398 closest distance to " NH2 ARG A  79 " =    1.549
peak=   -3.398 closest distance to " O   HOH Z 128 " =    2.670
peak=   -3.392 closest distance to " O   HOH Z 145 " =    3.057
peak=   -3.386 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.383 closest distance to " O   HOH Z   6 " =    1.822
peak=   -3.382 closest distance to " CD2 HIS A 207 " =    2.168
peak=   -3.378 closest distance to " CB  ALA A 184 " =    2.365
peak=   -3.369 closest distance to " CB  ALA A  10 " =    2.274
peak=   -3.367 closest distance to " O   HOH Z 216 " =    0.988
peak=   -3.360 closest distance to " O   HOH Z 210 " =    1.910
peak=   -3.359 closest distance to " O   PRO A 163 " =    2.015
peak=   -3.356 closest distance to " O   HOH Z 183 " =    2.282
peak=   -3.350 closest distance to " CD1 ILE A 106 " =    2.310
peak=   -3.347 closest distance to " O   HOH Z 264 " =    1.701
peak=   -3.342 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.333 closest distance to " CG  ARG A 269 " =    2.270
peak=   -3.331 closest distance to " OE1 GLN A 223 " =    2.185
peak=   -3.330 closest distance to " O   VAL A 174 " =    2.138
peak=   -3.321 closest distance to " O   HOH Z  19 " =    2.334
peak=   -3.316 closest distance to " O   ILE A 106 " =    1.709
peak=   -3.308 closest distance to " O   HOH Z 156 " =    3.510
peak=   -3.302 closest distance to " CZ3 TRP A 274 " =    2.357
peak=   -3.299 closest distance to " CB  ALA A 291 " =    2.469
peak=   -3.288 closest distance to " O   ILE A 109 " =    2.570
peak=   -3.286 closest distance to " O   VAL A 257 " =    1.335
peak=   -3.283 closest distance to " O   TRP A  70 " =    1.712
peak=   -3.280 closest distance to " O   HOH Z  63 " =    1.359
peak=   -3.274 closest distance to " NH2 ARG A  79 " =    2.382
peak=   -3.273 closest distance to " O   HOH Z 345 " =    2.936
peak=   -3.269 closest distance to " O   HOH Z 283 " =    2.436
peak=   -3.267 closest distance to " CE BMET A  47 " =    1.611
peak=   -3.258 closest distance to " CG  LEU A  83 " =    2.146
peak=   -3.258 closest distance to " CG  ASP A 286 " =    1.503
peak=   -3.255 closest distance to " CA  GLY A 133 " =    2.071
peak=   -3.252 closest distance to " NE2 GLN A  88 " =    1.083
peak=   -3.244 closest distance to " OD1 ASN A 148 " =    1.304
peak=   -3.241 closest distance to " O   HOH Z   6 " =    1.494
peak=   -3.236 closest distance to " O   HOH Z  17 " =    1.447
peak=   -3.236 closest distance to " O   HOH Z 148 " =    3.885
peak=   -3.228 closest distance to " C   LEU A 143 " =    1.068
peak=   -3.228 closest distance to " O   PHE A 218 " =    1.497
peak=   -3.228 closest distance to " O   HOH Z 407 " =    2.917
peak=   -3.226 closest distance to " OE2 GLU A 152 " =    1.496
peak=   -3.225 closest distance to " OG BSER A  99 " =    1.035
peak=   -3.223 closest distance to " O   HOH Z 174 " =    3.624
peak=   -3.221 closest distance to " CD  GLU A 236 " =    1.169
peak=   -3.220 closest distance to " O   HOH Z 393 " =    1.377
peak=   -3.218 closest distance to " O   ILE A 263 " =    2.225
peak=   -3.215 closest distance to " O   HOH Z 418 " =    1.336
peak=   -3.212 closest distance to " O   HOH Z 281 " =    2.486
peak=   -3.210 closest distance to " CD2 LEU A 282 " =    2.153
peak=   -3.204 closest distance to " SD  MET A 105 " =    2.641
peak=   -3.204 closest distance to " O   HOH Z  38 " =    1.787
peak=   -3.201 closest distance to " O   HOH Z 197 " =    1.901
peak=   -3.198 closest distance to " O   ALA A 227 " =    1.323
peak=   -3.196 closest distance to " O   SER A 276 " =    1.730
peak=   -3.195 closest distance to " OD1 ASP A 191 " =    1.469
peak=   -3.194 closest distance to " O   HOH Z  71 " =    2.874
peak=   -3.192 closest distance to " CD  LYS A 289 " =    2.382
peak=   -3.191 closest distance to " O   HOH Z 210 " =    0.863
peak=   -3.191 closest distance to " O   VAL A 189 " =    1.909
peak=   -3.188 closest distance to " N   ALA A 248 " =    1.727
peak=   -3.185 closest distance to " O   GLY A  17 " =    1.047
peak=   -3.173 closest distance to " O   HOH Z  88 " =    2.598
peak=   -3.173 closest distance to " CE1 TYR A 247 " =    2.725
peak=   -3.170 closest distance to " O   HOH Z 185 " =    2.440
peak=   -3.167 closest distance to " N   ALA A 226 " =    1.902
peak=   -3.167 closest distance to " O   HOH Z 357 " =    2.259
peak=   -3.165 closest distance to " O   HOH Z 423 " =    2.499
peak=   -3.163 closest distance to " NE2 GLN A  88 " =    1.902
peak=   -3.160 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.147 closest distance to " CB  ALA A   9 " =    2.498
peak=   -3.143 closest distance to " O   GLY A  80 " =    1.636
peak=   -3.131 closest distance to " CE  LYS A  76 " =    0.869
peak=   -3.124 closest distance to " CG  ASN A 148 " =    2.317
peak=   -3.111 closest distance to " O   HOH Z 221 " =    1.244
peak=   -3.107 closest distance to " CA  GLY A  57 " =    2.148
peak=   -3.106 closest distance to " CD1 TRP A 150 " =    0.931
peak=   -3.098 closest distance to " O   HOH Z 198 " =    0.796
peak=   -3.097 closest distance to " O   HOH Z 252 " =    4.034
peak=   -3.094 closest distance to " O   GLN A  11 " =    1.154
peak=   -3.086 closest distance to " OD2 ASP A 171 " =    2.525
peak=   -3.085 closest distance to " CB  ASN A  45 " =    2.021
peak=   -3.083 closest distance to " CE1 TYR A 247 " =    2.604
peak=   -3.080 closest distance to " O   HOH Z 113 " =    1.514
peak=   -3.076 closest distance to " CB  SER A 210 " =    1.074
peak=   -3.071 closest distance to " CG1BVAL A  41 " =    2.854
peak=   -3.064 closest distance to " CD1 TRP A  70 " =    1.037
peak=   -3.055 closest distance to " CZ  PHE A  38 " =    2.021
peak=   -3.054 closest distance to " O   HOH Z  37 " =    1.907
peak=   -3.048 closest distance to " O   HOH Z 265 " =    2.447
peak=   -3.032 closest distance to " OH  TYR A 172 " =    1.787

================= 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    :  0.4650 0.4644   6.271195e+00   6.260647e+00
   1_bss:  0.4568 0.4522   6.264923e+00   6.250681e+00
   1_xyz:  0.3293 0.3549   6.026784e+00   6.097261e+00
   1_adp:  0.2964 0.3634   5.974875e+00   6.110930e+00
   1_occ:  0.2960 0.3640   5.974796e+00   6.112229e+00
   2_bss:  0.2936 0.3625   5.972483e+00   6.111309e+00
   2_xyz:  0.2187 0.2771   5.718726e+00   5.901333e+00
   2_adp:  0.2040 0.2551   5.657344e+00   5.838491e+00
   2_occ:  0.2038 0.2551   5.656996e+00   5.838574e+00
   3_bss:  0.2038 0.2540   5.656324e+00   5.837216e+00
   3_xyz:  0.1545 0.1991   5.415603e+00   5.621573e+00
   3_adp:  0.1412 0.1947   5.357528e+00   5.587698e+00
   3_occ:  0.1411 0.1947   5.357319e+00   5.587458e+00
   4_bss:  0.1415 0.1948   5.357630e+00   5.586020e+00
   4_xyz:  0.1258 0.1767   5.259238e+00   5.497814e+00
   4_adp:  0.1246 0.1700   5.240071e+00   5.463309e+00
   4_occ:  0.1244 0.1699   5.239364e+00   5.462582e+00
   5_bss:  0.1242 0.1698   5.238835e+00   5.462121e+00
   5_xyz:  0.1241 0.1677   5.233599e+00   5.450952e+00
   5_adp:  0.1223 0.1704   5.232572e+00   5.461311e+00
   5_occ:  0.1222 0.1705   5.232646e+00   5.461464e+00
   5_bss:  0.1223 0.1704   5.232592e+00   5.460669e+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:  0.303  39.522  -2.223   1.347   4.355   0.000   0.000   0.000
   1_xyz:  0.303  39.522  -2.223   1.347   4.355   0.000   0.000   0.000
   1_adp:  0.303  39.522  -2.223   1.347   4.355   0.000   0.000   0.000
   1_occ:  0.303  39.522  -2.223   1.347   4.355   0.000   0.000   0.000
   2_bss:  0.332  61.536  -2.071   0.149   1.774   0.000   0.000   0.000
   2_xyz:  0.332  61.536  -2.071   0.149   1.774   0.000   0.000   0.000
   2_adp:  0.332  61.536  -2.071   0.149   1.774   0.000   0.000   0.000
   2_occ:  0.332  61.536  -2.071   0.149   1.774   0.000   0.000   0.000
   3_bss:  0.332  70.309  -2.789  -1.057   0.413  -0.000   0.000   0.000
   3_xyz:  0.332  70.309  -2.789  -1.057   0.413  -0.000   0.000   0.000
   3_adp:  0.332  70.309  -2.789  -1.057   0.413  -0.000   0.000   0.000
   3_occ:  0.332  70.309  -2.789  -1.057   0.413  -0.000   0.000   0.000
   4_bss:  0.338  80.579  -3.063  -1.586  -0.234  -0.000  -0.000  -0.000
   4_xyz:  0.338  80.579  -3.063  -1.586  -0.234  -0.000  -0.000  -0.000
   4_adp:  0.338  80.579  -3.063  -1.586  -0.234  -0.000  -0.000  -0.000
   4_occ:  0.338  80.579  -3.063  -1.586  -0.234  -0.000  -0.000  -0.000
   5_bss:  0.328  65.110  -2.980  -1.712  -0.336  -0.000  -0.000  -0.000
   5_xyz:  0.328  65.110  -2.980  -1.712  -0.336  -0.000  -0.000  -0.000
   5_adp:  0.328  65.110  -2.980  -1.712  -0.336  -0.000  -0.000  -0.000
   5_occ:  0.328  65.110  -2.980  -1.712  -0.336  -0.000  -0.000  -0.000
   5_bss:  0.327  68.649  -2.854  -1.643  -0.259  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.872 0.4592  0.6073    64763.562
   1_bss:  53.661 0.4732  0.6540    61783.061
   1_xyz:  38.728 0.6580  0.8797    35594.966
   1_adp:  39.620 0.6466  0.8684    36966.830
   1_occ:  39.675 0.6459  0.8673    37089.024
   2_bss:  39.343 0.6499  0.8401    36749.994
   2_xyz:  28.510 0.7729  0.9605    20168.775
   2_adp:  25.777 0.8033  0.9770    17364.441
   2_occ:  25.788 0.8032  0.9767    17377.180
   3_bss:  25.663 0.8044  0.9415    17272.949
   3_xyz:  19.355 0.8675  0.9839    10446.058
   3_adp:  18.542 0.8754  0.9789     9935.897
   3_occ:  18.532 0.8755  0.9789     9930.483
   4_bss:  18.479 0.8759  0.9631     9892.067
   4_xyz:  16.577 0.8929  0.9692     8121.100
   4_adp:  15.790 0.9002  0.9668     7646.636
   4_occ:  15.780 0.9002  0.9669     7632.352
   5_bss:  15.778 0.9002  0.9655     7621.067
   5_xyz:  15.459 0.9031  0.9672     7398.224
   5_adp:  15.683 0.9013  0.9590     7551.050
   5_occ:  15.686 0.9013  0.9588     7553.943
   5_bss:  15.679 0.9014  0.9619     7547.838
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8854e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8854e-01
   1_xyz:   1.638  0.012  0.097 15.630  0.006  4.107   1.4354e-01
   1_adp:   1.638  0.012  0.097 15.630  0.006  4.107   1.4354e-01
   1_occ:   1.638  0.012  0.097 15.630  0.006  4.107   1.4354e-01
   2_bss:   1.638  0.012  0.097 15.630  0.006  4.107   1.4354e-01
   2_xyz:   1.192  0.009  0.083 14.651  0.005  4.111   7.9387e-02
   2_adp:   1.192  0.009  0.083 14.651  0.005  4.111   7.9387e-02
   2_occ:   1.192  0.009  0.083 14.651  0.005  4.111   7.9387e-02
   3_bss:   1.192  0.009  0.083 14.651  0.005  4.111   7.9387e-02
   3_xyz:   1.110  0.009  0.077 14.760  0.004  4.127   6.9613e-02
   3_adp:   1.110  0.009  0.077 14.760  0.004  4.127   6.9613e-02
   3_occ:   1.110  0.009  0.077 14.760  0.004  4.127   6.9613e-02
   4_bss:   1.110  0.009  0.077 14.760  0.004  4.127   6.9613e-02
   4_xyz:   1.149  0.010  0.083 14.743  0.004  4.114   7.4287e-02
   4_adp:   1.149  0.010  0.083 14.743  0.004  4.114   7.4287e-02
   4_occ:   1.149  0.010  0.083 14.743  0.004  4.114   7.4287e-02
   5_bss:   1.149  0.010  0.083 14.743  0.004  4.114   7.4287e-02
   5_xyz:   0.987  0.007  0.074 14.369  0.004  4.116   5.6638e-02
   5_adp:   0.987  0.007  0.074 14.369  0.004  4.116   5.6638e-02
   5_occ:   0.987  0.007  0.074 14.369  0.004  4.116   5.6638e-02
   5_bss:   0.987  0.007  0.074 14.369  0.004  4.116   5.6638e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.488   2.4440e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.488   2.4440e-01
   1_xyz:  10.071  0.082  0.332 85.133  0.042  2.014   2.0278e-01
   1_adp:  10.071  0.082  0.332 85.133  0.042  2.014   2.0278e-01
   1_occ:  10.071  0.082  0.332 85.133  0.042  2.014   2.0278e-01
   2_bss:  10.071  0.082  0.332 85.133  0.042  2.014   2.0278e-01
   2_xyz:   7.621  0.051  0.341 79.318  0.045  2.340   1.0817e-01
   2_adp:   7.621  0.051  0.341 79.318  0.045  2.340   1.0817e-01
   2_occ:   7.621  0.051  0.341 79.318  0.045  2.340   1.0817e-01
   3_bss:   7.621  0.051  0.341 79.318  0.045  2.340   1.0817e-01
   3_xyz:   8.509  0.048  0.239 82.588  0.041  2.189   5.9351e-02
   3_adp:   8.509  0.048  0.239 82.588  0.041  2.189   5.9351e-02
   3_occ:   8.509  0.048  0.239 82.588  0.041  2.189   5.9351e-02
   4_bss:   8.509  0.048  0.239 82.588  0.041  2.189   5.9351e-02
   4_xyz:   8.206  0.053  0.274 83.358  0.045  2.248   5.5744e-02
   4_adp:   8.206  0.053  0.274 83.358  0.045  2.248   5.5744e-02
   4_occ:   8.206  0.053  0.274 83.358  0.045  2.248   5.5744e-02
   5_bss:   8.206  0.053  0.274 83.358  0.045  2.248   5.5744e-02
   5_xyz:   7.215  0.045  0.249 81.073  0.035  2.346   3.4525e-02
   5_adp:   7.215  0.045  0.249 81.073  0.035  2.346   3.4525e-02
   5_occ:   7.215  0.045  0.249 81.073  0.035  2.346   3.4525e-02
   5_bss:   7.215  0.045  0.249 81.073  0.035  2.346   3.4525e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 102.33   0.00  18.79  81.35   0.00  14.77 102.33   0.00  40.67
   1_occ: 102.33   0.00  18.79  81.35   0.00  14.77 102.33   0.00  40.67
   2_bss: 102.33   0.00  18.79  81.35   0.00  14.77 102.33   0.00  40.67
   2_xyz: 102.33   0.00  18.79  81.35   0.00  14.77 102.33   0.00  40.67
   2_adp:  99.20   0.00  17.97  78.13   0.00  13.78  99.20   4.87  40.73
   2_occ:  99.20   0.00  17.97  78.13   0.00  13.78  99.20   4.87  40.73
   3_bss:  99.20   0.00  17.97  78.13   0.00  13.78  99.20   4.87  40.73
   3_xyz:  99.20   0.00  17.97  78.13   0.00  13.78  99.20   4.87  40.73
   3_adp: 103.05   0.00  18.64  90.73   0.00  13.53 103.05   5.72  46.49
   3_occ: 103.05   0.00  18.64  90.73   0.00  13.53 103.05   5.72  46.49
   4_bss: 103.05   0.00  18.64  90.73   0.00  13.53 103.05   5.72  46.49
   4_xyz: 103.05   0.00  18.64  90.73   0.00  13.53 103.05   5.72  46.49
   4_adp:  92.92   1.34  17.42  86.99   1.34  12.98  92.92   5.29  41.60
   4_occ:  92.92   1.34  17.42  86.99   1.34  12.98  92.92   5.29  41.60
   5_bss:  92.92   1.34  17.42  86.99   1.34  12.98  92.92   5.29  41.60
   5_xyz:  92.92   1.34  17.42  86.99   1.34  12.98  92.92   5.29  41.60
   5_adp: 100.21   0.00  17.62  92.66   0.00  12.93 100.21   0.00  43.14
   5_occ: 100.21   0.00  17.62  92.66   0.00  12.93 100.21   0.00  43.14
   5_bss: 100.21   0.00  17.62  92.66   0.00  12.94 100.21   0.00  43.14
------------------------------------------------------------------------
 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:    2.307    0.020    0.437
   1_adp:    2.307    0.020    0.437
   1_occ:    2.307    0.020    0.437
   2_bss:    2.307    0.020    0.437
   2_xyz:    2.048    0.051    0.566
   2_adp:    2.048    0.051    0.566
   2_occ:    2.048    0.051    0.566
   3_bss:    2.048    0.051    0.566
   3_xyz:    1.839    0.042    0.692
   3_adp:    1.839    0.042    0.692
   3_occ:    1.839    0.042    0.692
   4_bss:    1.839    0.042    0.692
   4_xyz:    1.647    0.100    0.728
   4_adp:    1.647    0.100    0.728
   4_occ:    1.647    0.100    0.728
   5_bss:    1.647    0.100    0.728
   5_xyz:    1.482    0.096    0.740
   5_adp:    1.482    0.096    0.740
   5_occ:    1.482    0.096    0.740
   5_bss:    1.482    0.096    0.740
------------------------------------------------------------------------

CPU time actual refinement: 334.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/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/noshake/run_340/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_340/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.13 
  Macro-tasks:
    bulk solvent and scale       = 42.28  
    individual site refinement   = 132.84 
    weights calculation          = 30.10  
    collect and process          = 6.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 211.91 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 105.28 
    alpha_beta                      = 8.21   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 112.70 
    fmodel                         = 6.79   
    r_factors                      = 0.30   
    phase_errors                   = 10.45  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 247.64 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.805 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    626 calls, 104.88 s
gradients_fft:          571 calls,  99.98 s

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

# Date 2008-01-16 Time 04:35:53 PST -0800 (1200486953.54 s)
Start R-work = 0.4650, R-free = 0.4644 (no bulk solvent and anisotropic scale)
Final R-work = 0.1446, R-free = 0.1876 (no bulk solvent and anisotropic scale)

Start R-work = 0.4568, R-free = 0.4522
Final R-work = 0.1223, R-free = 0.1704