# Date 2008-01-16 Time 04:42:32 PST -0800 (1200487352.80 s)
#phil __OFF__

Command line arguments: "../424.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3092
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 424

-------------------------------------------------------------------------------
  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: (69.5475, 46.93, 86.822, 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: 2.77, per 1000 atoms: 0.98


================================== 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: (69.5475, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98064
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9040
                             d_min =   1.9806

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: (69.5475, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98064
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9044 -  4.2375 [2146/2173]  1930   216  10.1%
  bin  2:  4.2375 -  3.3763 [2038/2054]  1836   202   9.9%
  bin  3:  3.3763 -  2.9533 [2036/2055]  1832   204  10.0%
  bin  4:  2.9533 -  2.6850 [2001/2031]  1799   202  10.1%
  bin  5:  2.6850 -  2.4935 [1997/2016]  1796   201  10.1%
  bin  6:  2.4935 -  2.3471 [1983/2008]  1788   195   9.8%
  bin  7:  2.3471 -  2.2299 [1973/2007]  1780   193   9.8%
  bin  8:  2.2299 -  2.1332 [1975/2006]  1774   201  10.2%
  bin  9:  2.1332 -  2.0513 [1938/1979]  1743   195  10.1%
  bin 10:  2.0513 -  1.9806 [1502/2015]  1352   150  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2206
        3.04 -     3.66: 4661
        3.66 -     4.28: 9094
        4.28 -     4.90: 12378
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.983 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.067 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.094 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.205 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28351 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_424/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/model_refine_001.geo

CPU time processing inputs: 7.63


============================ 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 = 69.5475 46.93 86.82195 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: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2308   r_free= 0.2288   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.733577                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7260 0.99   1390  153 0.2448 0.2442      6.2435       6.216|
|  2:  4.7260 -  3.7712 0.99   1326  151 0.1733 0.1624       6.075      6.0658|
|  3:  3.7712 -  3.3004 0.99   1317  146 0.1928 0.1852      5.9948      6.0148|
|  4:  3.3004 -  3.0013 0.99   1298  137 0.2025 0.2249      5.8805      5.9473|
|  5:  3.0013 -  2.7877 0.99   1295  146 0.2262 0.2117      5.7686      5.7034|
|  6:  2.7877 -  2.6243 0.99   1282  148 0.2275 0.2527      5.7031      5.6802|
|  7:  2.6243 -  2.4935 0.99   1285  144 0.2307 0.2091      5.6594      5.5769|
|  8:  2.4935 -  2.3854 0.98   1291  135 0.2419 0.2244      5.6474      5.6106|
|  9:  2.3854 -  2.2939 0.98   1255  146 0.2503 0.2450      5.6011      5.5564|
| 10:  2.2939 -  2.2150 0.98   1267  140 0.2409 0.2335      5.5732      5.4895|
| 11:  2.2150 -  2.1460 0.99   1272  141 0.2547 0.2732      5.5414      5.6157|
| 12:  2.1460 -  2.0848 0.97   1261  138 0.2587 0.2476      5.5218      5.5583|
| 13:  2.0848 -  2.0301 0.99   1268  139 0.2635 0.2546      5.4497       5.364|
| 14:  2.0301 -  1.9806 0.65    823   95 0.2698 0.2520      5.4239      5.2993|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7260  1390   153  0.81  23.73   0.88     0.82      35675.79|
|  2:  4.7260 -  3.7712  1326   151  0.89  16.39   1.00     0.95      26522.21|
|  3:  3.7712 -  3.3004  1317   146  0.89  16.86   1.02     1.00      20372.22|
|  4:  3.3004 -  3.0013  1298   137  0.89  17.82   1.02     1.00      17219.56|
|  5:  3.0013 -  2.7877  1295   146  0.85  21.85   1.04     0.99      14642.20|
|  6:  2.7877 -  2.6243  1282   148  0.85  21.47   1.03     1.00      12262.07|
|  7:  2.6243 -  2.4935  1285   144  0.86  20.87   1.06     1.02      10583.47|
|  8:  2.4935 -  2.3854  1291   135  0.86  20.88   1.06     1.03       9634.32|
|  9:  2.3854 -  2.2939  1255   146  0.86  21.24   1.08     1.05       9242.69|
| 10:  2.2939 -  2.2150  1267   140  0.84  22.62   1.11     1.05       9032.61|
| 11:  2.2150 -  2.1460  1272   141  0.84  23.18   1.08     1.08       8995.25|
| 12:  2.1460 -  2.0848  1261   138  0.84  23.28   1.11     1.10       8535.83|
| 13:  2.0848 -  2.0301  1268   139  0.83  23.79   1.10     1.08       7559.90|
| 14:  2.0301 -  1.9806   823    95  0.83  23.88   1.10     1.02       6141.77|
|alpha:            min =        0.82 max =            1.10 mean =         1.01|
|beta:             min =     6141.77 max =        35675.79 mean =     14438.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.78 mean =        21.19|
|phase err.(test): min =        0.00 max =           89.78 mean =        21.08|
|-----------------------------------------------------------------------------|

============================== 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 = 2.365290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.614   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.313668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.469   (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 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2012 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1851 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2810 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4695 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4399 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5634 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6744 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    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: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2308   r_free= 0.2288   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.733577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2128   r_free= 0.2103   ksol= 0.33   Bsol= 50.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.80,-0.95,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.691763                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.148144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.473   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.177740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.308   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2128      final r-factor (work) = 0.1364          |
| start r-factor (free) = 0.2103      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3419 = 2.15 * 0.50 * 5.7537 + 1.00 * 0.1620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8533 = 2.15 * 0.50 * 5.3965 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1364      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9654 = 0.18 * 1.00 * 5.3965 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9630 = 0.18 * 1.00 * 5.1941 + 1.00 * 0.0398                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.72   16.33    None  None   None       |
|    all(noH): 2823   0      0.00    70.72   16.33    None  None   None       |
|    Sol.    : 438    0      7.49    62.47   36.94    None  None   None       |
|    Mac.    : 2385   0      0.00    70.72   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.072:  248   |   5:    35.361 -  42.433:  110        |
|      1:     7.072 -  14.144: 1524   |   6:    42.433 -  49.505:   73        |
|      2:    14.144 -  21.216:  504   |   7:    49.505 -  56.577:   67        |
|      3:    21.216 -  28.289:  137   |   8:    56.577 -  63.649:   25        |
|      4:    28.289 -  35.361:  134   |   9:    63.649 -  70.721:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1268 r_free = 0.1547             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1265 r_free = 0.1545             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1545   ksol= 0.33   Bsol= 50.00   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.80,-0.95,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.199532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1543   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.78,-1.36,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.198794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.967947              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.887  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1485          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7703 = 2.97 * 0.50 * 5.1977 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6934 = 2.97 * 0.50 * 5.1358 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1485      final r-factor (free) = 0.1486          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4033 = 0.22 * 1.00 * 5.1358 + 1.00 * 0.2820                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1197 = 0.22 * 1.00 * 5.0961 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    64.75   16.51    None  None   None       |
|    all(noH): 2823   0      1.70    64.75   16.51    None  None   None       |
|    Sol.    : 438    0      4.98    64.75   37.19    None  None   None       |
|    Mac.    : 2385   0      1.70    61.62   12.71    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:     1.700 -   8.005:  483   |   5:    33.223 -  39.527:  106        |
|      1:     8.005 -  14.309: 1316   |   6:    39.527 -  45.832:   87        |
|      2:    14.309 -  20.614:  426   |   7:    45.832 -  52.136:   95        |
|      3:    20.614 -  26.918:  150   |   8:    52.136 -  58.441:   50        |
|      4:    26.918 -  33.223:   99   |   9:    58.441 -  64.745:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1486             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1485             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1485   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.78,-1.36,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.098170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1485   ksol= 0.33   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.35,-1.07,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.098284                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.957770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.973  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.906652              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.310  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1485      final r-factor (free) = 0.1503          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0619 = 1.96 * 0.50 * 5.0980 + 1.00 * 0.0715                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0537 = 1.96 * 0.50 * 5.1030 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1503      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7367 = 1.91 * 1.00 * 5.1030 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7355 = 1.91 * 1.00 * 5.1014 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.27   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    76.27   16.85    None  None   None       |
|    Sol.    : 438    0      5.73    71.58   39.13    None  None   None       |
|    Mac.    : 2385   0      0.00    76.27   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.627:  486   |   5:    38.133 -  45.760:  108        |
|      1:     7.627 -  15.253: 1412   |   6:    45.760 -  53.387:   84        |
|      2:    15.253 -  22.880:  377   |   7:    53.387 -  61.014:   73        |
|      3:    22.880 -  30.507:  142   |   8:    61.014 -  68.640:   31        |
|      4:    30.507 -  38.133:  103   |   9:    68.640 -  76.267:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1521             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1521             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1521   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.35,-1.07,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110101                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1520   ksol= 0.32   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.09,-0.86,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.367091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.086  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.095642              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.876  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1057          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0972 = 2.37 * 0.50 * 5.1022 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1028 = 2.37 * 0.50 * 5.1033 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1057      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1522          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4971 = 0.10 * 1.00 * 5.1033 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4957 = 0.10 * 1.00 * 5.1193 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.00    70.31   15.89    None  None   None       |
|    all(noH): 2823   0      2.00    70.31   15.89    None  None   None       |
|    Sol.    : 438    0      5.93    67.14   35.04    None  None   None       |
|    Mac.    : 2385   0      2.00    70.31   12.38    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:     1.999 -   8.831:  743   |   5:    36.157 -  42.988:  116        |
|      1:     8.831 -  15.662: 1220   |   6:    42.988 -  49.820:   85        |
|      2:    15.662 -  22.494:  343   |   7:    49.820 -  56.651:   39        |
|      3:    22.494 -  29.325:  122   |   8:    56.651 -  63.483:   15        |
|      4:    29.325 -  36.157:  136   |   9:    63.483 -  70.314:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1522             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1522             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1522   ksol= 0.32   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.09,-0.86,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114315                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1523   ksol= 0.33   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.02,-0.77,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114562                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.391736              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.315629              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 164.088  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6252 = 1.39 * 0.50 * 5.1195 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6173 = 1.39 * 0.50 * 5.1251 + 1.00 * 0.0510                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6237 = 0.32 * 1.00 * 5.1251 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6238 = 0.32 * 1.00 * 5.1205 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    74.15   16.14    None  None   None       |
|    all(noH): 2823   0      0.88    74.15   16.14    None  None   None       |
|    Sol.    : 438    0      5.89    67.29   36.84    None  None   None       |
|    Mac.    : 2385   0      0.88    74.15   12.34    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:     0.879 -   8.206:  639   |   5:    37.514 -  44.840:  114        |
|      1:     8.206 -  15.533: 1307   |   6:    44.840 -  52.167:   88        |
|      2:    15.533 -  22.860:  354   |   7:    52.167 -  59.494:   54        |
|      3:    22.860 -  30.187:  127   |   8:    59.494 -  66.821:   13        |
|      4:    30.187 -  37.514:  123   |   9:    66.821 -  74.148:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1537             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1094 r_free = 0.1537             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1537   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.02,-0.77,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123504                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7260 0.99   1390  153 0.1037 0.1310      5.4238      5.5472|
|  2:  4.7260 -  3.7712 0.99   1326  151 0.0882 0.1112       5.462      5.6392|
|  3:  3.7712 -  3.3004 0.99   1317  146 0.1050 0.1526      5.4658      5.8603|
|  4:  3.3004 -  3.0013 0.99   1298  137 0.1163 0.1436       5.418      5.5391|
|  5:  3.0013 -  2.7877 0.99   1295  146 0.1268 0.1647      5.2929      5.5147|
|  6:  2.7877 -  2.6243 0.99   1282  148 0.1188 0.1918       5.183      5.4667|
|  7:  2.6243 -  2.4935 0.99   1285  144 0.1199 0.1529      5.1328       5.296|
|  8:  2.4935 -  2.3854 0.98   1291  135 0.1105 0.1643      5.0371      5.2956|
|  9:  2.3854 -  2.2939 0.98   1255  146 0.1136 0.1773      4.9948      5.2743|
| 10:  2.2939 -  2.2150 0.98   1267  140 0.1086 0.1533      4.9377      5.1562|
| 11:  2.2150 -  2.1460 0.99   1272  141 0.1112 0.1825      4.9093      5.2606|
| 12:  2.1460 -  2.0848 0.97   1261  138 0.1092 0.1534      4.8447      5.1398|
| 13:  2.0848 -  2.0301 0.99   1268  139 0.1042 0.1715      4.7521      5.0308|
| 14:  2.0301 -  1.9806 0.65    823   95 0.0974 0.1710      4.6335      4.9236|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7260  1390   153  0.94   9.60   0.98     0.95       7712.25|
|  2:  4.7260 -  3.7712  1326   151  0.95   8.04   1.01     1.00       9257.56|
|  3:  3.7712 -  3.3004  1317   146  0.94  10.98   1.02     1.01      10100.42|
|  4:  3.3004 -  3.0013  1298   137  0.93  12.71   1.00     0.99       9565.73|
|  5:  3.0013 -  2.7877  1295   146  0.91  15.18   0.99     0.96       7704.53|
|  6:  2.7877 -  2.6243  1282   148  0.90  15.52   0.98     0.95       6597.32|
|  7:  2.6243 -  2.4935  1285   144  0.91  14.84   0.98     0.95       5765.45|
|  8:  2.4935 -  2.3854  1291   135  0.92  14.15   0.99     0.97       4926.55|
|  9:  2.3854 -  2.2939  1255   146  0.91  14.81   1.00     0.97       4674.08|
| 10:  2.2939 -  2.2150  1267   140  0.91  15.07   0.99     0.95       4131.21|
| 11:  2.2150 -  2.1460  1272   141  0.90  15.67   0.99     0.96       4143.37|
| 12:  2.1460 -  2.0848  1261   138  0.92  14.63   1.00     0.99       3678.24|
| 13:  2.0848 -  2.0301  1268   139  0.91  14.95   0.99     0.98       3132.83|
| 14:  2.0301 -  1.9806   823    95  0.92  13.98   0.97     0.93       2398.05|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2398.05 max =        10100.42 mean =      6118.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.52|
|phase err.(test): min =        0.00 max =           88.79 mean =        13.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1537   ksol= 0.33   Bsol= 49.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.86,-0.62,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1537   ksol= 0.33   Bsol= 49.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.86,-0.62,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123432                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7260 0.99   1390  153 0.1036 0.1309      5.4228      5.5458|
|  2:  4.7260 -  3.7712 0.99   1326  151 0.0882 0.1112      5.4623      5.6394|
|  3:  3.7712 -  3.3004 0.99   1317  146 0.1050 0.1526      5.4659      5.8602|
|  4:  3.3004 -  3.0013 0.99   1298  137 0.1163 0.1436      5.4178       5.539|
|  5:  3.0013 -  2.7877 0.99   1295  146 0.1268 0.1647      5.2927      5.5145|
|  6:  2.7877 -  2.6243 0.99   1282  148 0.1188 0.1918      5.1829      5.4666|
|  7:  2.6243 -  2.4935 0.99   1285  144 0.1199 0.1529      5.1328       5.296|
|  8:  2.4935 -  2.3854 0.98   1291  135 0.1105 0.1642      5.0371      5.2955|
|  9:  2.3854 -  2.2939 0.98   1255  146 0.1136 0.1773      4.9948      5.2742|
| 10:  2.2939 -  2.2150 0.98   1267  140 0.1086 0.1532      4.9378      5.1562|
| 11:  2.2150 -  2.1460 0.99   1272  141 0.1112 0.1825      4.9092      5.2607|
| 12:  2.1460 -  2.0848 0.97   1261  138 0.1092 0.1534      4.8446      5.1398|
| 13:  2.0848 -  2.0301 0.99   1268  139 0.1042 0.1715      4.7521      5.0307|
| 14:  2.0301 -  1.9806 0.65    823   95 0.0974 0.1710      4.6336      4.9236|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7260  1390   153  0.94   9.59   0.98     0.95       7685.82|
|  2:  4.7260 -  3.7712  1326   151  0.95   8.04   1.01     1.00       9249.40|
|  3:  3.7712 -  3.3004  1317   146  0.94  10.98   1.02     1.01      10102.54|
|  4:  3.3004 -  3.0013  1298   137  0.93  12.70   1.01     0.99       9562.45|
|  5:  3.0013 -  2.7877  1295   146  0.91  15.18   1.00     0.96       7702.58|
|  6:  2.7877 -  2.6243  1282   148  0.90  15.52   0.98     0.96       6595.38|
|  7:  2.6243 -  2.4935  1285   144  0.91  14.83   0.99     0.96       5764.18|
|  8:  2.4935 -  2.3854  1291   135  0.92  14.15   1.00     0.98       4925.74|
|  9:  2.3854 -  2.2939  1255   146  0.91  14.81   1.01     0.97       4673.88|
| 10:  2.2939 -  2.2150  1267   140  0.91  15.07   1.00     0.95       4130.81|
| 11:  2.2150 -  2.1460  1272   141  0.90  15.67   1.00     0.97       4142.68|
| 12:  2.1460 -  2.0848  1261   138  0.92  14.63   1.01     1.00       3677.94|
| 13:  2.0848 -  2.0301  1268   139  0.91  14.95   1.00     0.99       3132.94|
| 14:  2.0301 -  1.9806   823    95  0.92  13.98   0.97     0.94       2398.52|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2398.52 max =        10102.54 mean =      6115.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.52|
|phase err.(test): min =        0.00 max =           88.78 mean =        13.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    74.12   16.11    None  None   None       |
|    all(noH): 2823   0      0.85    74.12   16.11    None  None   None       |
|    Sol.    : 438    0      5.86    67.26   36.81    None  None   None       |
|    Mac.    : 2385   0      0.85    74.12   12.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.849 -   8.176:  639   |   5:    37.484 -  44.810:  114        |
|      1:     8.176 -  15.503: 1307   |   6:    44.810 -  52.137:   88        |
|      2:    15.503 -  22.830:  354   |   7:    52.137 -  59.464:   54        |
|      3:    22.830 -  30.157:  127   |   8:    59.464 -  66.791:   13        |
|      4:    30.157 -  37.484:  123   |   9:    66.791 -  74.118:    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)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 5.447
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 268 from: 276
   mapped sites are within: 0.706 - 5.447

peak=    5.667 closest distance to " CB  ARG A 275 " =    0.953
peak=    5.394 closest distance to " CG  PRO A  54 " =    1.320
peak=    5.143 closest distance to " O   HOH Z 126 " =    1.891
peak=    5.131 closest distance to " CB  GLN A 223 " =    1.387
peak=    5.116 closest distance to " O   HOH Z 232 " =    2.397
peak=    5.112 closest distance to " NH2 ARG A  56 " =    2.193
peak=    4.873 closest distance to " CG  PRO A  90 " =    1.201
peak=    4.872 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.855 closest distance to " O   HOH Z 142 " =    1.669
peak=    4.742 closest distance to " CB  GLU A 152 " =    1.160
peak=    4.679 closest distance to " O   HOH Z  78 " =    1.776
peak=    4.678 closest distance to " CB  SER A  63 " =    1.170
peak=    4.622 closest distance to " CB  GLN A 183 " =    1.205
peak=    4.585 closest distance to " CB  PRO A  54 " =    0.993
peak=    4.578 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.543 closest distance to " O   HOH Z 236 " =    1.946
peak=    4.524 closest distance to " O   HOH Z 250 " =    1.510
peak=    4.458 closest distance to " CG  PRO A 198 " =    1.286
peak=    4.446 closest distance to " CB  ARG A  79 " =    1.295
peak=    4.415 closest distance to " O   HOH Z  15 " =    2.245
peak=    4.403 closest distance to " CG  PRO A 243 " =    1.029
peak=    4.399 closest distance to " NE2 GLN A  11 " =    1.072
peak=    4.389 closest distance to " O   HOH Z 272 " =    1.868
peak=    4.384 closest distance to " C   PRO A 198 " =    1.472
peak=    4.327 closest distance to " CG2 VAL A 257 " =    0.902
peak=    4.323 closest distance to " ND2 ASN A 187 " =    1.521
peak=    4.319 closest distance to " CB  ASN A 148 " =    1.435
peak=    4.295 closest distance to " CB  TYR A 169 " =    0.717
peak=    4.291 closest distance to " O   HOH Z 189 " =    2.388
peak=    4.277 closest distance to " CZ  PHE A 218 " =    1.076
peak=    4.238 closest distance to " O   HOH Z 303 " =    2.082
peak=    4.233 closest distance to " O   HOH Z 234 " =    3.718
peak=    4.230 closest distance to " O   HOH Z 298 " =    1.822
peak=    4.202 closest distance to " CB  ARG A 190 " =    1.706
peak=    4.155 closest distance to " CA  ARG A  36 " =    1.027
peak=    4.154 closest distance to " O   HOH Z 209 " =    2.285
peak=    4.151 closest distance to " CB  VAL A 265 " =    1.219
peak=    4.150 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.140 closest distance to " CB  TRP A 266 " =    0.997
peak=    4.138 closest distance to " CA  ASN A 215 " =    1.070
peak=    4.136 closest distance to " O   HOH Z 427 " =    2.935
peak=    4.135 closest distance to " O   HOH Z 369 " =    2.311
peak=    4.113 closest distance to " O   HOH Z 158 " =    3.017
peak=    4.105 closest distance to " O   HOH Z 346 " =    1.693
peak=    4.092 closest distance to " O   HOH Z  40 " =    1.856
peak=    4.086 closest distance to " O   HOH Z 423 " =    1.916
peak=    4.074 closest distance to " CD2 TRP A 179 " =    1.353
peak=    4.053 closest distance to " O   HOH Z  61 " =    1.640
peak=    4.040 closest distance to " O   HOH Z  43 " =    1.900
peak=    4.034 closest distance to " O   HOH Z 402 " =    1.392
peak=    4.019 closest distance to " O   SER A  87 " =    2.218
peak=    4.012 closest distance to " O   HOH Z 193 " =    1.899
peak=    3.928 closest distance to " CB  GLU A 128 " =    1.000
peak=    3.928 closest distance to " CB  ARG A  79 " =    0.908
peak=    3.923 closest distance to " NZ  LYS A 117 " =    3.204
peak=    3.917 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.910 closest distance to " O   HOH Z  97 " =    2.475
peak=    3.907 closest distance to " O   HOH Z 389 " =    1.832
peak=    3.899 closest distance to " O   HOH Z 392 " =    3.056
peak=    3.897 closest distance to " O   HOH Z 403 " =    1.634
peak=    3.885 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.874 closest distance to " OG ASER A 258 " =    3.103
peak=    3.859 closest distance to " CD  ARG A 159 " =    0.706
peak=    3.849 closest distance to " OD1 ASN A  69 " =    2.540
peak=    3.821 closest distance to " O   HOH Z  19 " =    2.420
peak=    3.801 closest distance to " O   HOH Z 126 " =    2.069
peak=    3.789 closest distance to " O   HOH Z 203 " =    1.682
peak=    3.786 closest distance to " CB  SER A   3 " =    1.275
peak=    3.784 closest distance to " CG2 ILE A 120 " =    1.096
peak=    3.773 closest distance to " CG1BVAL A  72 " =    1.608
peak=    3.769 closest distance to " CB  ALA A 291 " =    1.238
peak=    3.769 closest distance to " O   HOH Z  66 " =    2.180
peak=    3.765 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.762 closest distance to " O   HOH Z 344 " =    3.113
peak=    3.761 closest distance to " O   HOH Z  44 " =    1.785
peak=    3.748 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.736 closest distance to " O   HOH Z  10 " =    1.804
peak=    3.732 closest distance to " O   HOH Z 128 " =    2.028
peak=    3.723 closest distance to " CB  ASP A 140 " =    0.961
peak=    3.711 closest distance to " O   HOH Z 313 " =    1.998
peak=    3.689 closest distance to " CB  GLU A 277 " =    3.548
peak=    3.670 closest distance to " CB  ILE A 120 " =    1.249
peak=    3.665 closest distance to " O   HOH Z  97 " =    1.996
peak=    3.664 closest distance to " O   HOH Z 172 " =    3.389
peak=    3.663 closest distance to " O   HOH Z 291 " =    1.548
peak=    3.654 closest distance to " CB  ASN A 110 " =    1.058
peak=    3.649 closest distance to " O   HOH Z 245 " =    1.318
peak=    3.646 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.641 closest distance to " N   ASN A  39 " =    1.206
peak=    3.638 closest distance to " N   ARG A 156 " =    1.351
peak=    3.634 closest distance to " O   HOH Z 421 " =    1.741
peak=    3.630 closest distance to " OD2 ASP A 286 " =    2.807
peak=    3.627 closest distance to " O   HOH Z   9 " =    2.132
peak=    3.626 closest distance to " O   HOH Z 368 " =    2.049
peak=    3.619 closest distance to " CG  ARG A  66 " =    2.540
peak=    3.618 closest distance to " O   HOH Z 147 " =    1.781
peak=    3.617 closest distance to " O   HOH Z  54 " =    1.701
peak=    3.605 closest distance to " CG1 ILE A  33 " =    1.274
peak=    3.603 closest distance to " O   HOH Z 407 " =    2.446
peak=    3.602 closest distance to " O   HOH Z 128 " =    2.188
peak=    3.594 closest distance to " O   HOH Z 261 " =    2.072
peak=    3.580 closest distance to " NH1AARG A 145 " =    1.213
peak=    3.575 closest distance to " O   HOH Z 248 " =    1.591
peak=    3.560 closest distance to " O   HOH Z 371 " =    3.069
peak=    3.560 closest distance to " O   HOH Z 187 " =    2.278
peak=    3.559 closest distance to " CG2 ILE A  20 " =    1.383
peak=    3.556 closest distance to " CD  ARG A 269 " =    0.947
peak=    3.552 closest distance to " O   HOH Z 173 " =    1.957
peak=    3.540 closest distance to " O   HOH Z 417 " =    3.164
peak=    3.538 closest distance to " CB  ALA A 114 " =    1.075
peak=    3.537 closest distance to " CB  TRP A 179 " =    1.291
peak=    3.535 closest distance to " O   HOH Z 148 " =    3.350
peak=    3.532 closest distance to " O   HOH Z 214 " =    2.119
peak=    3.523 closest distance to " CD2 LEU A 297 " =    0.856
peak=    3.518 closest distance to " CA  ASP A 162 " =    1.047
peak=    3.510 closest distance to " O   HOH Z 265 " =    2.301
peak=    3.508 closest distance to " N   TYR A 116 " =    1.483
peak=    3.504 closest distance to " O   ASN A  74 " =    1.562
peak=    3.503 closest distance to " CB  SER A 212 " =    1.106
peak=    3.498 closest distance to " CD1 LEU A 300 " =    1.256
peak=    3.496 closest distance to " O   HOH Z 280 " =    2.992
peak=    3.493 closest distance to " O   HOH Z   1 " =    2.046
peak=    3.491 closest distance to " O   HOH Z  21 " =    1.806
peak=    3.482 closest distance to " CA  SER A  87 " =    1.015
peak=    3.470 closest distance to " O   HOH Z 261 " =    1.711
peak=    3.466 closest distance to " CB  THR A  31 " =    1.623
peak=    3.464 closest distance to " CD1 ILE A 106 " =    0.840
peak=    3.455 closest distance to " CB  ALA A 248 " =    1.331
peak=    3.450 closest distance to " O   HOH Z 403 " =    1.382
peak=    3.445 closest distance to " O   HOH Z 180 " =    2.198
peak=    3.439 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.435 closest distance to " O   HOH Z 337 " =    3.599
peak=    3.435 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.432 closest distance to " CA  THR A 264 " =    0.889
peak=    3.423 closest distance to " CE1 TYR A 186 " =    1.332
peak=    3.419 closest distance to " NH2BARG A 145 " =    2.015
peak=    3.416 closest distance to " CA  ALA A  51 " =    0.862
peak=    3.415 closest distance to " O   HOH Z 425 " =    1.959
peak=    3.415 closest distance to " CA  ALA A  84 " =    1.176
peak=    3.413 closest distance to " O   HOH Z  88 " =    2.643
peak=    3.407 closest distance to " O   THR A 220 " =    1.255
peak=    3.406 closest distance to " CB  ALA A 242 " =    0.894
peak=    3.401 closest distance to " O   HOH Z 383 " =    1.741
peak=    3.400 closest distance to " O   HOH Z 305 " =    3.648
peak=    3.399 closest distance to " O   HOH Z 234 " =    1.944
peak=    3.398 closest distance to " CB  SER A  26 " =    1.658
peak=    3.397 closest distance to " O   ALA A   1 " =    1.700
peak=    3.397 closest distance to " CB  ARG A 139 " =    0.964
peak=    3.396 closest distance to " O   HOH Z 359 " =    1.495
peak=    3.389 closest distance to " O   HOH Z  59 " =    1.955
peak=    3.387 closest distance to " CB  HIS A 108 " =    0.823
peak=    3.380 closest distance to " CB  TYR A 116 " =    0.752
peak=    3.373 closest distance to " CD  LYS A 119 " =    1.379
peak=    3.373 closest distance to " O   HOH Z 175 " =    2.133
peak=    3.372 closest distance to " O  BHOH Z 338 " =    2.308
peak=    3.367 closest distance to " O   HOH Z 132 " =    2.465
peak=    3.366 closest distance to " O   HOH Z 411 " =    3.845
peak=    3.362 closest distance to " CA  MET A 105 " =    0.988
peak=    3.361 closest distance to " O   HOH Z 329 " =    3.908
peak=    3.361 closest distance to " CA  ALA A  21 " =    1.108
peak=    3.360 closest distance to " CD BLYS A 290 " =    1.074
peak=    3.356 closest distance to " O   MET A 105 " =    1.877
peak=    3.354 closest distance to " O   HOH Z 213 " =    1.752
peak=    3.352 closest distance to " O   HOH Z 193 " =    2.017
peak=    3.351 closest distance to " CB  ASN A 215 " =    1.173
peak=    3.348 closest distance to " CG  LEU A 167 " =    1.253
peak=    3.346 closest distance to " CG AARG A 275 " =    1.121
peak=    3.345 closest distance to " ND2 ASN A 249 " =    0.897
peak=    3.335 closest distance to " CZ2 TRP A 179 " =    1.776
peak=    3.335 closest distance to " CB  PRO A 198 " =    1.140
peak=    3.333 closest distance to " O   HOH Z 227 " =    1.489
peak=    3.331 closest distance to " CB  LYS A 290 " =    0.996
peak=    3.328 closest distance to " CA  LYS A 117 " =    1.229
peak=    3.327 closest distance to " NE2 GLN A  77 " =    3.198
peak=    3.325 closest distance to " O   HOH Z 185 " =    1.746
peak=    3.320 closest distance to " OE1 GLU A   2 " =    2.216
peak=    3.317 closest distance to " O   HOH Z 302 " =    2.027
peak=    3.316 closest distance to " O   HOH Z 426 " =    1.654
peak=    3.314 closest distance to " O   HOH Z 327 " =    1.652
peak=    3.310 closest distance to " OG1 THR A 294 " =    2.424
peak=    3.306 closest distance to " O   HOH Z 188 " =    2.057
peak=    3.300 closest distance to " OG BSER A 164 " =    2.328
peak=    3.299 closest distance to " O   HOH Z  44 " =    3.182
peak=    3.299 closest distance to " O   HOH Z 133 " =    2.814
peak=    3.293 closest distance to " CG  GLN A  11 " =    1.604
peak=    3.292 closest distance to " O   HOH Z 435 " =    1.942
peak=    3.285 closest distance to " CE1 PHE A  38 " =    1.303
peak=    3.285 closest distance to " CD  LYS A 166 " =    1.223
peak=    3.282 closest distance to " CD1 LEU A  96 " =    0.748
peak=    3.282 closest distance to " CA  GLY A  80 " =    0.737
peak=    3.277 closest distance to " CG  LYS A  76 " =    0.942
peak=    3.270 closest distance to " O   HOH Z 336 " =    1.708
peak=    3.266 closest distance to " CB  MET A  47 " =    1.192
peak=    3.264 closest distance to " CB  ASN A 142 " =    1.059
peak=    3.261 closest distance to " CA  THR A 221 " =    0.975
peak=    3.257 closest distance to " O   HOH Z 219 " =    1.940
peak=    3.255 closest distance to " O   ALA A 165 " =    1.516
peak=    3.255 closest distance to " CB  GLN A  89 " =    1.339
peak=    3.251 closest distance to " CB  ALA A  34 " =    0.949
peak=    3.249 closest distance to " CB  SER A  62 " =    0.973
peak=    3.248 closest distance to " N   PHE A 130 " =    1.256
peak=    3.246 closest distance to " ND2 ASN A 110 " =    1.644
peak=    3.241 closest distance to " CG  GLU A  37 " =    0.860
peak=    3.240 closest distance to " CB  GLN A 278 " =    0.829
peak=    3.239 closest distance to " O   HOH Z 353 " =    2.618
peak=    3.236 closest distance to " CB  VAL A 126 " =    1.007
peak=    3.233 closest distance to " O   HOH Z 273 " =    2.774
peak=    3.233 closest distance to " CB  PRO A  90 " =    1.080
peak=    3.230 closest distance to " CB  LEU A 300 " =    0.948
peak=    3.230 closest distance to " O   HOH Z 419 " =    1.993
peak=    3.225 closest distance to " CA  MET A  40 " =    1.120
peak=    3.222 closest distance to " O   HOH Z 325 " =    2.523
peak=    3.218 closest distance to " CG  MET A 185 " =    1.066
peak=    3.216 closest distance to " O   HOH Z 298 " =    2.508
peak=    3.213 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.211 closest distance to " CB  SER A  62 " =    1.313
peak=    3.210 closest distance to " O   HOH Z 261 " =    2.276
peak=    3.209 closest distance to " O   HOH Z  88 " =    1.900
peak=    3.207 closest distance to " CA  ALA A 248 " =    1.152
peak=    3.201 closest distance to " CG1 ILE A  49 " =    1.449
peak=    3.198 closest distance to " O   HOH Z  61 " =    1.445
peak=    3.197 closest distance to " O   HOH Z 406 " =    1.505
peak=    3.196 closest distance to " CG  GLN A  77 " =    1.925
peak=    3.195 closest distance to " N   SER A 135 " =    1.256
peak=    3.195 closest distance to " CA  ILE A 234 " =    0.873
peak=    3.191 closest distance to " O   TRP A 274 " =    1.857
peak=    3.191 closest distance to " CB  SER A 141 " =    0.981
peak=    3.190 closest distance to " CB  GLN A  88 " =    1.152
peak=    3.187 closest distance to " CD1AILE A 234 " =    0.954
peak=    3.186 closest distance to " CB  PRO A 243 " =    1.588
peak=    3.183 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.183 closest distance to " CA  TYR A 116 " =    1.346
peak=    3.181 closest distance to " CA  ALA A 233 " =    1.253
peak=    3.178 closest distance to " O   HOH Z  88 " =    2.539
peak=    3.178 closest distance to " O   HOH Z 433 " =    1.833
peak=    3.167 closest distance to " O   HOH Z 299 " =    4.417
peak=    3.162 closest distance to " O   HOH Z 193 " =    1.624
peak=    3.159 closest distance to " O   HOH Z 371 " =    1.651
peak=    3.159 closest distance to " O   HOH Z 285 " =    2.756
peak=    3.157 closest distance to " O   HOH Z 365 " =    2.913
peak=    3.156 closest distance to " CA  ILE A  33 " =    1.408
peak=    3.153 closest distance to " O   HOH Z 380 " =    1.818
peak=    3.152 closest distance to " CG2 THR A 221 " =    1.067
peak=    3.150 closest distance to " CD  ARG A  36 " =    0.978
peak=    3.149 closest distance to " CA  ASP A 140 " =    1.138
peak=    3.142 closest distance to " O   HOH Z 430 " =    5.447
peak=    3.142 closest distance to " N   GLY A  98 " =    1.006
peak=    3.141 closest distance to " O   HOH Z 325 " =    3.901
peak=    3.138 closest distance to " CA  ALA A 291 " =    0.794
peak=    3.137 closest distance to " NH1BARG A 145 " =    1.172
peak=    3.132 closest distance to " CB  MET A  40 " =    0.778
peak=    3.132 closest distance to " N   ASN A 127 " =    1.219
peak=    3.131 closest distance to " O   SER A 164 " =    1.211
peak=    3.128 closest distance to " C   TYR A 214 " =    1.450
peak=    3.119 closest distance to " O   HOH Z 345 " =    3.264
peak=    3.118 closest distance to " CA  SER A 146 " =    1.707
peak=    3.115 closest distance to " CB  GLN A 103 " =    0.811
peak=    3.113 closest distance to " CB  LEU A  83 " =    0.759
peak=    3.113 closest distance to " O   HOH Z  85 " =    2.356
peak=    3.091 closest distance to " O   HOH Z  62 " =    2.115
peak=    3.091 closest distance to " CD1 ILE A 199 " =    1.049
peak=    3.087 closest distance to " CB  SER A 216 " =    0.760
peak=    3.087 closest distance to " CB  ASP A 191 " =    1.185
peak=    3.068 closest distance to " CA  LYS A 290 " =    1.256
peak=    3.066 closest distance to " CA  ASN A 252 " =    1.791
peak=    3.059 closest distance to " N   ASP A 162 " =    1.199
peak=    3.028 closest distance to " O   HOH Z 423 " =    3.043
peak=    3.024 closest distance to " O   HOH Z  47 " =    1.784

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.539 - 5.927
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 182 from: 185
   mapped sites are within: 0.763 - 5.927

peak=   -4.824 closest distance to " CD  GLN A  58 " =    0.990
peak=   -4.763 closest distance to " O   HOH Z 266 " =    5.180
peak=   -4.564 closest distance to " CB  PRO A 243 " =    2.678
peak=   -4.504 closest distance to " C   HIS A 108 " =    1.107
peak=   -4.493 closest distance to " O   VAL A  67 " =    2.652
peak=   -4.445 closest distance to " SG  CYS A 254 " =    3.466
peak=   -4.337 closest distance to " CD  ARG A 156 " =    2.076
peak=   -4.253 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -4.199 closest distance to " CZ3 TRP A 179 " =    1.188
peak=   -4.181 closest distance to " OG BSER A 134 " =    1.246
peak=   -4.177 closest distance to " O   HOH Z 372 " =    2.254
peak=   -4.170 closest distance to " O   HOH Z 290 " =    1.086
peak=   -4.141 closest distance to " CB  PHE A 192 " =    2.049
peak=   -4.069 closest distance to " CG  GLN A 223 " =    1.886
peak=   -4.022 closest distance to " CA  VAL A  67 " =    2.882
peak=   -3.995 closest distance to " O   HOH Z 231 " =    2.250
peak=   -3.982 closest distance to " O   HOH Z 377 " =    2.048
peak=   -3.969 closest distance to " O   PRO A 198 " =    1.236
peak=   -3.954 closest distance to " O   HOH Z 198 " =    1.897
peak=   -3.953 closest distance to " ND2 ASN A  45 " =    1.618
peak=   -3.914 closest distance to " CB  ALA A 161 " =    2.519
peak=   -3.871 closest distance to " O   HOH Z 389 " =    1.872
peak=   -3.860 closest distance to " O   HOH Z 435 " =    2.825
peak=   -3.833 closest distance to " CE  MET A 105 " =    2.387
peak=   -3.813 closest distance to " CD  ARG A 139 " =    1.520
peak=   -3.798 closest distance to " CE2 TYR A  30 " =    2.769
peak=   -3.796 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.793 closest distance to " CG2 ILE A 263 " =    2.317
peak=   -3.791 closest distance to " O   HOH Z 185 " =    2.408
peak=   -3.789 closest distance to " O   HOH Z 407 " =    2.937
peak=   -3.785 closest distance to " CB  ALA A 291 " =    2.248
peak=   -3.777 closest distance to " CD1 LEU A 101 " =    2.296
peak=   -3.758 closest distance to " N   ALA A  43 " =    2.552
peak=   -3.757 closest distance to " O   HOH Z 114 " =    3.088
peak=   -3.748 closest distance to " CB  ASN A  39 " =    2.323
peak=   -3.747 closest distance to " OG  SER A  97 " =    2.261
peak=   -3.734 closest distance to " OXT GLY A 302 " =    2.733
peak=   -3.728 closest distance to " ND2 ASN A 187 " =    1.482
peak=   -3.716 closest distance to " CG  ASP A 231 " =    0.788
peak=   -3.679 closest distance to " O   HOH Z 211 " =    1.694
peak=   -3.675 closest distance to " OD1 ASP A 171 " =    1.590
peak=   -3.672 closest distance to " CZ  TYR A 169 " =    1.784
peak=   -3.669 closest distance to " O   HOH Z 196 " =    1.989
peak=   -3.665 closest distance to " ND2 ASN A  45 " =    1.057
peak=   -3.664 closest distance to " O   HOH Z 353 " =    2.156
peak=   -3.651 closest distance to " N   SER A 212 " =    1.987
peak=   -3.641 closest distance to " O   HOH Z 429 " =    2.185
peak=   -3.631 closest distance to " CA  GLY A 203 " =    2.384
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.307
peak=   -3.625 closest distance to " CG1 VAL A 112 " =    2.588
peak=   -3.623 closest distance to " CB  ALA A  43 " =    2.458
peak=   -3.606 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.602 closest distance to " CG  ASP A 132 " =    2.293
peak=   -3.582 closest distance to " CG  ARG A 269 " =    2.297
peak=   -3.564 closest distance to " O   HOH Z  44 " =    2.286
peak=   -3.556 closest distance to " CG  ARG A  66 " =    2.499
peak=   -3.556 closest distance to " O   PRO A 163 " =    2.040
peak=   -3.553 closest distance to " OD2 ASP A 191 " =    1.417
peak=   -3.550 closest distance to " CB  ALA A 291 " =    2.389
peak=   -3.540 closest distance to " ND2 ASN A 249 " =    2.175
peak=   -3.539 closest distance to " O   HOH Z 313 " =    1.845
peak=   -3.537 closest distance to " O   HOH Z 126 " =    1.951
peak=   -3.534 closest distance to " O   HOH Z  73 " =    2.373
peak=   -3.530 closest distance to " NH2AARG A 275 " =    5.152
peak=   -3.526 closest distance to " O   ALA A 161 " =    1.650
peak=   -3.521 closest distance to " CG  PHE A 283 " =    2.667
peak=   -3.516 closest distance to " OD1 ASN A 148 " =    1.476
peak=   -3.507 closest distance to " CD1 PHE A  59 " =    1.902
peak=   -3.483 closest distance to " CG  GLU A 277 " =    1.215
peak=   -3.480 closest distance to " N   ALA A 248 " =    1.709
peak=   -3.478 closest distance to " O   HOH Z  63 " =    1.642
peak=   -3.465 closest distance to " O   HOH Z 166 " =    2.040
peak=   -3.449 closest distance to " CD2 TYR A 293 " =    2.045
peak=   -3.447 closest distance to " O   LEU A 101 " =    2.729
peak=   -3.441 closest distance to " CZ  PHE A 155 " =    1.152
peak=   -3.440 closest distance to " CG1 VAL A  78 " =    3.219
peak=   -3.432 closest distance to " O   HOH Z  43 " =    1.701
peak=   -3.432 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.429 closest distance to " N   GLN A  58 " =    1.741
peak=   -3.427 closest distance to " NE2 GLN A 278 " =    1.750
peak=   -3.426 closest distance to " O   HOH Z 102 " =    1.571
peak=   -3.422 closest distance to " CB  ASP A 286 " =    1.812
peak=   -3.413 closest distance to " OG  SER A   3 " =    1.698
peak=   -3.399 closest distance to " C   LEU A 143 " =    0.987
peak=   -3.399 closest distance to " CD  ARG A 195 " =    5.173
peak=   -3.396 closest distance to " CA  GLY A 241 " =    3.190
peak=   -3.386 closest distance to " CE2 PHE A 218 " =    2.431
peak=   -3.384 closest distance to " CB  PRO A 163 " =    2.477
peak=   -3.382 closest distance to " O   HOH Z 311 " =    3.643
peak=   -3.380 closest distance to " CA  GLY A 133 " =    2.000
peak=   -3.380 closest distance to " CD1 ILE A 239 " =    2.316
peak=   -3.377 closest distance to " CG1 VAL A 230 " =    2.043
peak=   -3.377 closest distance to " NE2 GLN A 194 " =    1.825
peak=   -3.374 closest distance to " O   HOH Z 292 " =    4.561
peak=   -3.371 closest distance to " C   MET A 188 " =    1.340
peak=   -3.367 closest distance to " CD1 LEU A   5 " =    2.440
peak=   -3.364 closest distance to " O   HOH Z 362 " =    5.927
peak=   -3.359 closest distance to " O   SER A  95 " =    1.543
peak=   -3.349 closest distance to " O   PHE A 218 " =    1.582
peak=   -3.345 closest distance to " NH2 ARG A  79 " =    1.562
peak=   -3.342 closest distance to " CD1 LEU A 228 " =    2.134
peak=   -3.339 closest distance to " CZ3 TRP A 274 " =    1.076
peak=   -3.337 closest distance to " C   ALA A 158 " =    1.386
peak=   -3.327 closest distance to " O   GLN A 240 " =    2.100
peak=   -3.327 closest distance to " CD  GLU A 236 " =    1.023
peak=   -3.317 closest distance to " O   ALA A  10 " =    1.693
peak=   -3.313 closest distance to " O   HOH Z 322 " =    1.701
peak=   -3.309 closest distance to " NE2 GLN A  88 " =    1.767
peak=   -3.308 closest distance to " N   ALA A 226 " =    1.995
peak=   -3.298 closest distance to " O   SER A 135 " =    1.446
peak=   -3.298 closest distance to " SG ACYS A 201 " =    1.939
peak=   -3.294 closest distance to " O   HOH Z  13 " =    1.524
peak=   -3.294 closest distance to " CA  ASP A 298 " =    1.103
peak=   -3.294 closest distance to " O   HOH Z 295 " =    1.624
peak=   -3.294 closest distance to " O   HOH Z 385 " =    2.101
peak=   -3.292 closest distance to " CD1 LEU A 297 " =    2.395
peak=   -3.285 closest distance to " N   THR A  52 " =    1.685
peak=   -3.278 closest distance to " O   VAL A 189 " =    2.648
peak=   -3.278 closest distance to " O   HOH Z 317 " =    1.490
peak=   -3.275 closest distance to " O   HOH Z  38 " =    1.626
peak=   -3.271 closest distance to " CZ  PHE A  59 " =    1.515
peak=   -3.268 closest distance to " O   HOH Z 377 " =    1.721
peak=   -3.268 closest distance to " OD2 ASP A 171 " =    2.423
peak=   -3.267 closest distance to " O   ARG A 145 " =    1.542
peak=   -3.259 closest distance to " CD2 PHE A  61 " =    2.528
peak=   -3.258 closest distance to " CB  PHE A 208 " =    2.258
peak=   -3.258 closest distance to " O   GLN A  89 " =    1.555
peak=   -3.254 closest distance to " O   HOH Z 253 " =    3.842
peak=   -3.250 closest distance to " O   ALA A  34 " =    2.521
peak=   -3.248 closest distance to " OE1 GLN A  88 " =    1.107
peak=   -3.244 closest distance to " O   VAL A 174 " =    2.046
peak=   -3.243 closest distance to " O   HOH Z 174 " =    4.196
peak=   -3.241 closest distance to " OD2 ASP A  50 " =    2.217
peak=   -3.238 closest distance to " CG  GLN A  11 " =    1.693
peak=   -3.238 closest distance to " O   HOH Z 134 " =    3.075
peak=   -3.230 closest distance to " C   ASP A 231 " =    2.543
peak=   -3.229 closest distance to " CB  TRP A  85 " =    2.538
peak=   -3.228 closest distance to " OD2 ASP A  50 " =    1.540
peak=   -3.224 closest distance to " O   HOH Z 165 " =    1.971
peak=   -3.224 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.223 closest distance to " CB  TYR A  15 " =    2.177
peak=   -3.216 closest distance to " O   HOH Z 210 " =    1.128
peak=   -3.207 closest distance to " N   ASP A 286 " =    2.346
peak=   -3.201 closest distance to " NH2 ARG A  79 " =    2.049
peak=   -3.197 closest distance to " CG  GLU A 152 " =    0.763
peak=   -3.191 closest distance to " O   HOH Z 177 " =    1.751
peak=   -3.189 closest distance to " NE2 GLN A  88 " =    1.042
peak=   -3.189 closest distance to " OG BSER A 134 " =    1.819
peak=   -3.184 closest distance to " CD2 LEU A 237 " =    2.787
peak=   -3.183 closest distance to " CG1 VAL A 250 " =    2.648
peak=   -3.172 closest distance to " O   HOH Z  11 " =    1.698
peak=   -3.167 closest distance to " O   ALA A 180 " =    1.245
peak=   -3.153 closest distance to " CA  GLY A 241 " =    2.296
peak=   -3.151 closest distance to " CB  ASN A  69 " =    1.161
peak=   -3.145 closest distance to " O   ALA A 292 " =    1.989
peak=   -3.136 closest distance to " CZ  PHE A 130 " =    0.967
peak=   -3.134 closest distance to " O   ALA A  51 " =    1.305
peak=   -3.130 closest distance to " O   HOH Z  76 " =    1.893
peak=   -3.126 closest distance to " O   HOH Z 233 " =    2.423
peak=   -3.124 closest distance to " O   LEU A 167 " =    1.383
peak=   -3.120 closest distance to " O   HOH Z 421 " =    3.130
peak=   -3.118 closest distance to " O   HOH Z  71 " =    2.022
peak=   -3.117 closest distance to " CE3 TRP A 150 " =    2.162
peak=   -3.117 closest distance to " OXT GLY A 302 " =    3.382
peak=   -3.115 closest distance to " O   TRP A  70 " =    1.436
peak=   -3.113 closest distance to " CG  TRP A 266 " =    1.991
peak=   -3.108 closest distance to " O   HOH Z 298 " =    2.471
peak=   -3.103 closest distance to " O   ALA A 180 " =    1.000
peak=   -3.101 closest distance to " O   HOH Z 244 " =    2.098
peak=   -3.097 closest distance to " O   HOH Z 357 " =    2.016
peak=   -3.094 closest distance to " CG1 VAL A 197 " =    2.278
peak=   -3.094 closest distance to " CA  GLY A  98 " =    1.899
peak=   -3.092 closest distance to " CB  ASP A 132 " =    2.396
peak=   -3.084 closest distance to " CG2 THR A 221 " =    2.196
peak=   -3.083 closest distance to " O   HOH Z 123 " =    2.206
peak=   -3.073 closest distance to " CG2 VAL A 189 " =    2.116
peak=   -3.061 closest distance to " O   HOH Z  60 " =    2.304
peak=   -3.060 closest distance to " C   ALA A 114 " =    2.242
peak=   -3.057 closest distance to " N   GLY A  23 " =    2.313
peak=   -3.055 closest distance to " O   HOH Z 166 " =    1.636
peak=   -3.038 closest distance to " CG1AVAL A  41 " =    2.863
peak=   -3.037 closest distance to " O   HOH Z 353 " =    2.086

================= 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    :  0.2308 0.2288   5.733577e+00   5.707714e+00
   1_bss:  0.2128 0.2103   5.691763e+00   5.659574e+00
   1_xyz:  0.1364 0.1536   5.250995e+00   5.351543e+00
   1_adp:  0.1268 0.1547   5.200846e+00   5.368841e+00
   1_occ:  0.1265 0.1545   5.199532e+00   5.368608e+00
   2_bss:  0.1262 0.1543   5.198794e+00   5.366817e+00
   2_xyz:  0.1118 0.1485   5.113948e+00   5.329897e+00
   2_adp:  0.1082 0.1486   5.098560e+00   5.331958e+00
   2_occ:  0.1081 0.1485   5.098170e+00   5.331804e+00
   3_bss:  0.1080 0.1485   5.098284e+00   5.331666e+00
   3_xyz:  0.1089 0.1503   5.109084e+00   5.345126e+00
   3_adp:  0.1075 0.1521   5.110022e+00   5.356589e+00
   3_occ:  0.1075 0.1521   5.110101e+00   5.356855e+00
   4_bss:  0.1073 0.1520   5.110033e+00   5.356601e+00
   4_xyz:  0.1057 0.1534   5.106146e+00   5.362679e+00
   4_adp:  0.1086 0.1522   5.114057e+00   5.357049e+00
   4_occ:  0.1085 0.1522   5.114315e+00   5.357725e+00
   5_bss:  0.1085 0.1523   5.114562e+00   5.358045e+00
   5_xyz:  0.1110 0.1534   5.129591e+00   5.365896e+00
   5_adp:  0.1094 0.1537   5.123245e+00   5.367805e+00
   5_occ:  0.1094 0.1537   5.123504e+00   5.368260e+00
   5_bss:  0.1093 0.1537   5.123432e+00   5.368111e+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:  0.335  50.001  -2.011  -2.801  -0.947  -0.000  -0.000  -0.000
   1_xyz:  0.335  50.001  -2.011  -2.801  -0.947  -0.000  -0.000  -0.000
   1_adp:  0.335  50.001  -2.011  -2.801  -0.947  -0.000  -0.000  -0.000
   1_occ:  0.335  50.001  -2.011  -2.801  -0.947  -0.000  -0.000  -0.000
   2_bss:  0.327  50.001  -3.022  -2.779  -1.362  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.001  -3.022  -2.779  -1.362  -0.000  -0.000  -0.000
   2_adp:  0.327  50.001  -3.022  -2.779  -1.362  -0.000  -0.000  -0.000
   2_occ:  0.327  50.001  -3.022  -2.779  -1.362  -0.000  -0.000  -0.000
   3_bss:  0.328  50.001  -2.829  -2.354  -1.070  -0.000  -0.000  -0.000
   3_xyz:  0.328  50.001  -2.829  -2.354  -1.070  -0.000  -0.000  -0.000
   3_adp:  0.328  50.001  -2.829  -2.354  -1.070  -0.000  -0.000  -0.000
   3_occ:  0.328  50.001  -2.829  -2.354  -1.070  -0.000  -0.000  -0.000
   4_bss:  0.323  50.001  -2.630  -2.093  -0.860  -0.000  -0.000  -0.000
   4_xyz:  0.323  50.001  -2.630  -2.093  -0.860  -0.000  -0.000  -0.000
   4_adp:  0.323  50.001  -2.630  -2.093  -0.860  -0.000  -0.000  -0.000
   4_occ:  0.323  50.001  -2.630  -2.093  -0.860  -0.000  -0.000  -0.000
   5_bss:  0.329  50.001  -2.594  -2.022  -0.773  -0.000  -0.000  -0.000
   5_xyz:  0.329  50.001  -2.594  -2.022  -0.773  -0.000  -0.000  -0.000
   5_adp:  0.329  50.001  -2.594  -2.022  -0.773  -0.000  -0.000  -0.000
   5_occ:  0.329  50.001  -2.594  -2.022  -0.773  -0.000  -0.000  -0.000
   5_bss:  0.327  49.970  -2.432  -1.860  -0.619  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  21.181 0.8543  1.0125    14437.537
   1_bss:  19.642 0.8677  0.9621    11382.255
   1_xyz:  13.338 0.9205  0.9929     6019.872
   1_adp:  13.698 0.9174  0.9892     6155.996
   1_occ:  13.697 0.9174  0.9889     6142.809
   2_bss:  13.659 0.9178  0.9717     6121.718
   2_xyz:  12.851 0.9241  0.9723     5679.108
   2_adp:  12.907 0.9235  0.9671     5669.615
   2_occ:  12.905 0.9236  0.9670     5664.840
   3_bss:  12.909 0.9235  0.9775     5665.289
   3_xyz:  13.084 0.9225  0.9771     5855.813
   3_adp:  13.331 0.9206  0.9695     5947.049
   3_occ:  13.337 0.9205  0.9694     5949.712
   4_bss:  13.335 0.9205  0.9772     5944.971
   4_xyz:  13.432 0.9198  0.9769     6029.865
   4_adp:  13.260 0.9211  0.9733     5998.190
   4_occ:  13.272 0.9210  0.9732     6006.014
   5_bss:  13.279 0.9209  0.9754     6013.722
   5_xyz:  13.404 0.9201  0.9751     6109.239
   5_adp:  13.472 0.9196  0.9699     6112.353
   5_occ:  13.478 0.9195  0.9698     6118.148
   5_bss:  13.477 0.9195  0.9743     6114.848
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6200e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6200e-01
   1_xyz:   0.972  0.006  0.070 15.080  0.004  4.111   5.7035e-02
   1_adp:   0.972  0.006  0.070 15.080  0.004  4.111   5.7035e-02
   1_occ:   0.972  0.006  0.070 15.080  0.004  4.111   5.7035e-02
   2_bss:   0.972  0.006  0.070 15.080  0.004  4.111   5.7035e-02
   2_xyz:   1.094  0.009  0.083 15.080  0.005  4.114   7.1934e-02
   2_adp:   1.094  0.009  0.083 15.080  0.005  4.114   7.1934e-02
   2_occ:   1.094  0.009  0.083 15.080  0.005  4.114   7.1934e-02
   3_bss:   1.094  0.009  0.083 15.080  0.005  4.114   7.1934e-02
   3_xyz:   0.978  0.007  0.076 14.678  0.004  4.116   5.8492e-02
   3_adp:   0.978  0.007  0.076 14.678  0.004  4.116   5.8492e-02
   3_occ:   0.978  0.007  0.076 14.678  0.004  4.116   5.8492e-02
   4_bss:   0.978  0.007  0.076 14.678  0.004  4.116   5.8492e-02
   4_xyz:   1.024  0.008  0.079 14.718  0.004  4.117   6.2748e-02
   4_adp:   1.024  0.008  0.079 14.718  0.004  4.117   6.2748e-02
   4_occ:   1.024  0.008  0.079 14.718  0.004  4.117   6.2748e-02
   5_bss:   1.024  0.008  0.079 14.718  0.004  4.117   6.2748e-02
   5_xyz:   0.903  0.006  0.071 14.436  0.004  4.116   5.0954e-02
   5_adp:   0.903  0.006  0.071 14.436  0.004  4.116   5.0954e-02
   5_occ:   0.903  0.006  0.071 14.436  0.004  4.116   5.0954e-02
   5_bss:   0.903  0.006  0.071 14.436  0.004  4.116   5.0954e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4050e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4050e-01
   1_xyz:   6.810  0.038  0.231 83.593  0.040  2.276   6.3393e-02
   1_adp:   6.810  0.038  0.231 83.593  0.040  2.276   6.3393e-02
   1_occ:   6.810  0.038  0.231 83.593  0.040  2.276   6.3393e-02
   2_bss:   6.810  0.038  0.231 83.593  0.040  2.276   6.3393e-02
   2_xyz:   7.031  0.050  0.285 82.999  0.039  2.292   5.9922e-02
   2_adp:   7.031  0.050  0.285 82.999  0.039  2.292   5.9922e-02
   2_occ:   7.031  0.050  0.285 82.999  0.039  2.292   5.9922e-02
   3_bss:   7.031  0.050  0.285 82.999  0.039  2.292   5.9922e-02
   3_xyz:   6.620  0.048  0.249 83.279  0.040  2.354   4.7723e-02
   3_adp:   6.620  0.048  0.249 83.279  0.040  2.354   4.7723e-02
   3_occ:   6.620  0.048  0.249 83.279  0.040  2.354   4.7723e-02
   4_bss:   6.620  0.048  0.249 83.279  0.040  2.354   4.7723e-02
   4_xyz:   6.756  0.051  0.263 82.570  0.037  2.335   4.6401e-02
   4_adp:   6.756  0.051  0.263 82.570  0.037  2.335   4.6401e-02
   4_occ:   6.756  0.051  0.263 82.570  0.037  2.335   4.6401e-02
   5_bss:   6.756  0.051  0.263 82.570  0.037  2.335   4.6401e-02
   5_xyz:   6.248  0.044  0.220 83.063  0.036  2.362   3.0429e-02
   5_adp:   6.248  0.044  0.220 83.063  0.036  2.362   3.0429e-02
   5_occ:   6.248  0.044  0.220 83.063  0.036  2.362   3.0429e-02
   5_bss:   6.248  0.044  0.220 83.063  0.036  2.362   3.0429e-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:  70.72   0.00  16.33  70.72   0.00  12.55  62.47   7.49  36.94
   1_occ:  70.72   0.00  16.33  70.72   0.00  12.55  62.47   7.49  36.94
   2_bss:  70.72   0.00  16.33  70.72   0.00  12.55  62.47   7.49  36.94
   2_xyz:  70.72   0.00  16.33  70.72   0.00  12.55  62.47   7.49  36.94
   2_adp:  64.75   1.70  16.51  61.62   1.70  12.71  64.75   4.98  37.19
   2_occ:  64.75   1.70  16.51  61.62   1.70  12.71  64.75   4.98  37.19
   3_bss:  64.75   1.70  16.51  61.62   1.70  12.71  64.75   4.98  37.19
   3_xyz:  64.75   1.70  16.51  61.62   1.70  12.71  64.75   4.98  37.19
   3_adp:  76.27   0.00  16.85  76.27   0.00  12.76  71.58   5.73  39.13
   3_occ:  76.27   0.00  16.85  76.27   0.00  12.76  71.58   5.73  39.13
   4_bss:  76.27   0.00  16.85  76.27   0.00  12.76  71.58   5.73  39.13
   4_xyz:  76.27   0.00  16.85  76.27   0.00  12.76  71.58   5.73  39.13
   4_adp:  70.31   2.00  15.89  70.31   2.00  12.38  67.14   5.93  35.04
   4_occ:  70.31   2.00  15.89  70.31   2.00  12.38  67.14   5.93  35.04
   5_bss:  70.31   2.00  15.89  70.31   2.00  12.38  67.14   5.93  35.04
   5_xyz:  70.31   2.00  15.89  70.31   2.00  12.38  67.14   5.93  35.04
   5_adp:  74.15   0.88  16.14  74.15   0.88  12.34  67.29   5.89  36.84
   5_occ:  74.15   0.88  16.14  74.15   0.88  12.34  67.29   5.89  36.84
   5_bss:  74.12   0.85  16.11  74.12   0.85  12.31  67.26   5.86  36.81
------------------------------------------------------------------------
 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:    0.568    0.006    0.185
   1_adp:    0.568    0.006    0.185
   1_occ:    0.568    0.006    0.185
   2_bss:    0.568    0.006    0.185
   2_xyz:    0.767    0.007    0.212
   2_adp:    0.767    0.007    0.212
   2_occ:    0.767    0.007    0.212
   3_bss:    0.767    0.007    0.212
   3_xyz:    0.995    0.018    0.219
   3_adp:    0.995    0.018    0.219
   3_occ:    0.995    0.018    0.219
   4_bss:    0.995    0.018    0.219
   4_xyz:    1.050    0.013    0.225
   4_adp:    1.050    0.013    0.225
   4_occ:    1.050    0.013    0.225
   5_bss:    1.050    0.013    0.225
   5_xyz:    1.111    0.020    0.226
   5_adp:    1.111    0.020    0.226
   5_occ:    1.111    0.020    0.226
   5_bss:    1.111    0.020    0.226
------------------------------------------------------------------------

CPU time actual refinement: 272.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/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_424/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_424/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 272.64 
  Macro-tasks:
    bulk solvent and scale       = 30.26  
    individual site refinement   = 114.14 
    weights calculation          = 25.02  
    collect and process          = 5.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 175.09 
  Micro-tasks:
    mask                            = 0.50   
    f_calc                          = 86.70  
    alpha_beta                      = 6.92   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 95.44  
    fmodel                         = 5.40   
    r_factors                      = 0.13   
    phase_errors                   = 9.26   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 205.56 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 3.850 micro seconds
Total CPU time: 4.73 minutes
from_scatterers_fft:    651 calls, 86.31 s
gradients_fft:          596 calls, 83.47 s

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

# Date 2008-01-16 Time 04:47:15 PST -0800 (1200487635.81 s)
Start R-work = 0.2308, R-free = 0.2288 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.2128, R-free = 0.2103
Final R-work = 0.1093, R-free = 0.1537