# Date 2008-01-16 Time 04:43:46 PST -0800 (1200487426.99 s)
#phil __OFF__

Command line arguments: "../435.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3853
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 435

-------------------------------------------------------------------------------
  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, 47.1647, 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: 2.74, per 1000 atoms: 0.97


================================== 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, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98066
Completeness in resolution range: 0.958788
Completeness with d_max=infinity: 0.955794

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9040
                             d_min =   1.9807

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, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98066
Completeness in resolution range: 0.958788
Completeness with d_max=infinity: 0.955794

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9044 -  4.2376 [2156/2183]  1939   217  10.1%
  bin  2:  4.2376 -  3.3763 [2049/2065]  1846   203   9.9%
  bin  3:  3.3763 -  2.9533 [2044/2063]  1840   204  10.0%
  bin  4:  2.9533 -  2.6850 [2011/2041]  1811   200   9.9%
  bin  5:  2.6850 -  2.4935 [2000/2019]  1794   206  10.3%
  bin  6:  2.4935 -  2.3471 [2001/2037]  1806   195   9.7%
  bin  7:  2.3471 -  2.2300 [1984/2017]  1786   198  10.0%
  bin  8:  2.2300 -  2.1332 [1974/2009]  1773   201  10.2%
  bin  9:  2.1332 -  2.0513 [1958/1985]  1760   198  10.1%
  bin 10:  2.0513 -  1.9807 [1412/2012]  1275   137   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/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: 16
        2.42 -     3.04: 2207
        3.04 -     3.66: 4653
        3.66 -     4.28: 9053
        4.28 -     4.90: 12370
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.006 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.039 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.046 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.126 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28294 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_435/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/model_refine_001.geo

CPU time processing inputs: 7.62


============================ 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 47.16465 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= 0.2588   r_free= 0.2503   ksol= 0.00   Bsol= 0.00   scale= 0.997    |
|                                                                             |
| 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:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.836317                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1395  154 0.2519 0.2575      6.2633       6.271|
|  2:  4.7261 -  3.7712 0.99   1340  151 0.1941 0.1677      6.1735      6.1004|
|  3:  3.7712 -  3.3004 0.99   1319  148 0.2183 0.2008      6.0931      6.0879|
|  4:  3.3004 -  3.0014 0.99   1300  135 0.2347 0.2513      5.9907      6.0049|
|  5:  3.0014 -  2.7877 0.99   1301  149 0.2646 0.2252      5.8854      5.7798|
|  6:  2.7877 -  2.6243 0.99   1298  147 0.2677 0.2877      5.8163      5.7835|
|  7:  2.6243 -  2.4935 0.99   1277  146 0.2636 0.2303      5.7667      5.6613|
|  8:  2.4935 -  2.3854 0.98   1303  138 0.2799 0.2610      5.7614      5.7372|
|  9:  2.3854 -  2.2939 0.98   1271  145 0.2799 0.2655       5.685      5.6165|
| 10:  2.2939 -  2.2150 0.98   1258  135 0.2871 0.2486      5.7101      5.5554|
| 11:  2.2150 -  2.1460 1.00   1282  147 0.2910 0.2987      5.6621      5.7001|
| 12:  2.1460 -  2.0848 0.97   1270  137 0.2949 0.2928      5.6077      5.6828|
| 13:  2.0848 -  2.0301 0.98   1258  141 0.3052 0.3050      5.5636      5.5032|
| 14:  2.0301 -  1.9807 0.60    758   86 0.3087 0.2842      5.5326       5.398|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7261  1395   154  0.80  24.84   0.88     0.81      38157.91|
|  2:  4.7261 -  3.7712  1340   151  0.88  17.51   1.00     0.94      29373.24|
|  3:  3.7712 -  3.3004  1319   148  0.88  18.16   1.01     0.99      23334.76|
|  4:  3.3004 -  3.0014  1300   135  0.87  19.72   1.01     0.98      20394.70|
|  5:  3.0014 -  2.7877  1301   149  0.82  24.60   1.03     0.97      17747.33|
|  6:  2.7877 -  2.6243  1298   147  0.82  24.82   1.03     0.97      15425.47|
|  7:  2.6243 -  2.4935  1277   146  0.83  23.63   1.04     0.99      13252.58|
|  8:  2.4935 -  2.3854  1303   138  0.84  23.23   1.04     1.02      12046.74|
|  9:  2.3854 -  2.2939  1271   145  0.83  24.07   1.07     1.03      11200.87|
| 10:  2.2939 -  2.2150  1258   135  0.81  25.47   1.09     1.03      11058.12|
| 11:  2.2150 -  2.1460  1282   147  0.81  25.95   1.07     1.06      11201.39|
| 12:  2.1460 -  2.0848  1270   137  0.80  26.83   1.09     1.06      10992.03|
| 13:  2.0848 -  2.0301  1258   141  0.79  27.81   1.08     1.05      10043.53|
| 14:  2.0301 -  1.9807   758    86  0.78  28.39   1.07     1.01       8643.98|
|alpha:            min =        0.81 max =            1.06 mean =         0.99|
|beta:             min =     8643.98 max =        38157.91 mean =     17088.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.99 mean =        23.76|
|phase err.(test): min =        0.00 max =           89.36 mean =        23.61|
|-----------------------------------------------------------------------------|

============================== 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 = 2.198164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.646   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.130   (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:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      191 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1840 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2813 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4671 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4382 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5612 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6758 |
|-----------------------------------------------------------------------------|
|-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 |   4.113    4.900  1.806 |       0.176 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    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= 0.2588   r_free= 0.2503   ksol= 0.00   Bsol= 0.00   scale= 0.997    |
|                                                                             |
| 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:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.836317                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2438   r_free= 0.2333   ksol= 0.33   Bsol= 50.00   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.77,-0.96,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.802672                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.004984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.469   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208895              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.976   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2438      final r-factor (work) = 0.1480          |
| start r-factor (free) = 0.2333      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0228 = 2.00 * 0.50 * 5.8459 + 1.00 * 0.1623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5567 = 2.00 * 0.50 * 5.4868 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1480      final r-factor (work) = 0.1374          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1526 = 0.21 * 1.00 * 5.4868 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1673 = 0.21 * 1.00 * 5.2683 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.54   16.38    None  None   None       |
|    all(noH): 2823   0      0.00    82.54   16.38    None  None   None       |
|    Sol.    : 438    0      6.95    62.83   37.06    None  None   None       |
|    Mac.    : 2385   0      0.00    82.54   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.254:  491   |   5:    41.268 -  49.522:   98        |
|      1:     8.254 -  16.507: 1520   |   6:    49.522 -  57.775:   80        |
|      2:    16.507 -  24.761:  341   |   7:    57.775 -  66.029:   13        |
|      3:    24.761 -  33.015:  150   |   8:    66.029 -  74.283:    0        |
|      4:    33.015 -  41.268:  129   |   9:    74.283 -  82.536:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1374 r_free = 0.1658             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1370 r_free = 0.1657             target_work(ml) = 5.275         |
| 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= 0.1370   r_free= 0.1657   ksol= 0.33   Bsol= 50.00   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.77,-0.96,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274837                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1652   ksol= 0.33   Bsol= 52.13   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.37,-1.41,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.276064                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.836570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.619   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347808              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.724   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1369      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1505          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5417 = 2.84 * 0.50 * 5.2780 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4260 = 2.84 * 0.50 * 5.1885 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1496          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8490 = 0.35 * 1.00 * 5.1885 + 1.00 * 0.0444                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7864 = 0.35 * 1.00 * 5.1133 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    75.61   16.77    None  None   None       |
|    all(noH): 2823   0      1.25    75.61   16.77    None  None   None       |
|    Sol.    : 438    0      2.74    68.79   38.28    None  None   None       |
|    Mac.    : 2385   0      1.25    75.61   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.249 -   8.685:  679   |   5:    38.428 -  45.863:  113        |
|      1:     8.685 -  16.121: 1288   |   6:    45.863 -  53.299:   90        |
|      2:    16.121 -  23.556:  337   |   7:    53.299 -  60.735:   61        |
|      3:    23.556 -  30.992:  119   |   8:    60.735 -  68.170:   20        |
|      4:    30.992 -  38.428:  112   |   9:    68.170 -  75.606:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1099 r_free = 0.1496             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1495             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1495   ksol= 0.33   Bsol= 52.13   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-2.37,-1.41,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112943                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1493   ksol= 0.33   Bsol= 50.49   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.08,-1.09,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.979503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.141  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.608  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1493      final r-factor (free) = 0.1511          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1300 = 1.98 * 0.50 * 5.1152 + 1.00 * 0.0672                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1179 = 1.98 * 0.50 * 5.1121 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1511      final r-factor (free) = 0.1511          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2972 = 0.25 * 1.00 * 5.1121 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2980 = 0.25 * 1.00 * 5.1156 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    76.60   16.57    None  None   None       |
|    all(noH): 2823   0      1.28    76.60   16.57    None  None   None       |
|    Sol.    : 438    0      2.85    68.63   37.79    None  None   None       |
|    Mac.    : 2385   0      1.28    76.60   12.67    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:     1.284 -   8.816:  743   |   5:    38.944 -  46.475:  108        |
|      1:     8.816 -  16.348: 1249   |   6:    46.475 -  54.007:   84        |
|      2:    16.348 -  23.880:  320   |   7:    54.007 -  61.539:   52        |
|      3:    23.880 -  31.412:  130   |   8:    61.539 -  69.071:   19        |
|      4:    31.412 -  38.944:  115   |   9:    69.071 -  76.603:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1511             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1512             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1512   ksol= 0.33   Bsol= 50.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.08,-1.09,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1512   ksol= 0.33   Bsol= 50.49   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.96,-0.92,-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: 5.116823                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.782128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.275  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.765  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6171 = 1.78 * 0.50 * 5.1162 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6152 = 1.78 * 0.50 * 5.1166 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9434 = 0.18 * 1.00 * 5.1166 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9438 = 0.18 * 1.00 * 5.1207 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    76.52   16.35    None  None   None       |
|    all(noH): 2823   0      1.36    76.52   16.35    None  None   None       |
|    Sol.    : 438    0      5.67    68.16   37.32    None  None   None       |
|    Mac.    : 2385   0      1.36    76.52   12.50    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:     1.365 -   8.880:  800   |   5:    38.941 -  46.456:  105        |
|      1:     8.880 -  16.395: 1216   |   6:    46.456 -  53.972:   84        |
|      2:    16.395 -  23.911:  302   |   7:    53.972 -  61.487:   48        |
|      3:    23.911 -  31.426:  131   |   8:    61.487 -  69.002:   17        |
|      4:    31.426 -  38.941:  118   |   9:    69.002 -  76.517:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1526             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1527             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1527   ksol= 0.33   Bsol= 50.49   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.96,-0.92,-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: 5.120085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1516   ksol= 0.32   Bsol= 50.49   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.86,-0.80,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.118914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.970366              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.543  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.638499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.973  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6622 = 2.97 * 0.50 * 5.1214 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6516 = 2.97 * 0.50 * 5.1051 + 1.00 * 0.0695                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2670 = 0.64 * 1.00 * 5.1051 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2662 = 0.64 * 1.00 * 5.1027 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    77.14   16.24    None  None   None       |
|    all(noH): 2823   0      0.39    77.14   16.24    None  None   None       |
|    Sol.    : 438    0      5.61    68.12   37.53    None  None   None       |
|    Mac.    : 2385   0      0.39    77.14   12.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.390 -   8.065:  639   |   5:    38.764 -  46.439:  113        |
|      1:     8.065 -  15.739: 1331   |   6:    46.439 -  54.114:   83        |
|      2:    15.739 -  23.414:  337   |   7:    54.114 -  61.789:   50        |
|      3:    23.414 -  31.089:  129   |   8:    61.789 -  69.464:   18        |
|      4:    31.089 -  38.764:  121   |   9:    69.464 -  77.138:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1539             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1054 r_free = 0.1538             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1538   ksol= 0.32   Bsol= 50.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-1.86,-0.80,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108188                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1395  154 0.0979 0.1263      5.3791      5.5146|
|  2:  4.7261 -  3.7712 0.99   1340  151 0.0833 0.1099      5.4186      5.6141|
|  3:  3.7712 -  3.3004 0.99   1319  148 0.1005 0.1518      5.4334      5.8475|
|  4:  3.3004 -  3.0014 0.99   1300  135 0.1127 0.1434      5.4013        5.55|
|  5:  3.0014 -  2.7877 0.99   1301  149 0.1236 0.1659      5.2793      5.4986|
|  6:  2.7877 -  2.6243 0.99   1298  147 0.1158 0.1966      5.1776      5.4688|
|  7:  2.6243 -  2.4935 0.99   1277  146 0.1156 0.1587      5.1195      5.3125|
|  8:  2.4935 -  2.3854 0.98   1303  138 0.1063 0.1565      5.0238      5.2799|
|  9:  2.3854 -  2.2939 0.98   1271  145 0.1102 0.1797      4.9827      5.2728|
| 10:  2.2939 -  2.2150 0.98   1258  135 0.1057 0.1578      4.9317      5.1649|
| 11:  2.2150 -  2.1460 1.00   1282  147 0.1052 0.1797      4.8978      5.2561|
| 12:  2.1460 -  2.0848 0.97   1270  137 0.1043 0.1598      4.8341      5.1636|
| 13:  2.0848 -  2.0301 0.98   1258  141 0.1023 0.1716      4.7422      4.9969|
| 14:  2.0301 -  1.9807 0.60    758   86 0.0962 0.1768      4.6315      4.9578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7261  1395   154  0.94   9.21   0.98     0.95       7149.17|
|  2:  4.7261 -  3.7712  1340   151  0.95   7.70   1.01     1.00       8745.97|
|  3:  3.7712 -  3.3004  1319   148  0.94  10.78   1.02     1.01       9731.08|
|  4:  3.3004 -  3.0014  1300   135  0.93  12.78   1.00     0.99       9595.96|
|  5:  3.0014 -  2.7877  1301   149  0.90  15.34   0.99     0.96       7770.04|
|  6:  2.7877 -  2.6243  1298   147  0.90  15.86   0.98     0.95       6726.64|
|  7:  2.6243 -  2.4935  1277   146  0.91  14.86   0.98     0.95       5798.60|
|  8:  2.4935 -  2.3854  1303   138  0.92  14.30   0.99     0.97       4998.95|
|  9:  2.3854 -  2.2939  1271   145  0.91  15.03   0.99     0.96       4677.29|
| 10:  2.2939 -  2.2150  1258   135  0.90  15.44   0.99     0.95       4244.69|
| 11:  2.2150 -  2.1460  1282   147  0.91  15.63   0.98     0.95       4203.03|
| 12:  2.1460 -  2.0848  1270   137  0.92  14.64   1.00     0.99       3709.19|
| 13:  2.0848 -  2.0301  1258   141  0.91  15.30   0.99     0.97       3147.53|
| 14:  2.0301 -  1.9807   758    86  0.92  14.14   0.96     0.92       2436.37|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2436.37 max =         9731.08 mean =      6066.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.57|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1539   ksol= 0.32   Bsol= 48.05   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.62,-0.55,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108456                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1539   ksol= 0.32   Bsol= 48.05   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.62,-0.55,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108456                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1395  154 0.0979 0.1262       5.379       5.515|
|  2:  4.7261 -  3.7712 0.99   1340  151 0.0831 0.1097      5.4172      5.6118|
|  3:  3.7712 -  3.3004 0.99   1319  148 0.1004 0.1519      5.4324      5.8479|
|  4:  3.3004 -  3.0014 0.99   1300  135 0.1128 0.1437      5.4018       5.551|
|  5:  3.0014 -  2.7877 0.99   1301  149 0.1237 0.1659      5.2804      5.4992|
|  6:  2.7877 -  2.6243 0.99   1298  147 0.1159 0.1969      5.1786      5.4701|
|  7:  2.6243 -  2.4935 0.99   1277  146 0.1156 0.1589      5.1205      5.3135|
|  8:  2.4935 -  2.3854 0.98   1303  138 0.1063 0.1566      5.0245      5.2804|
|  9:  2.3854 -  2.2939 0.98   1271  145 0.1102 0.1796      4.9831      5.2726|
| 10:  2.2939 -  2.2150 0.98   1258  135 0.1057 0.1579      4.9322      5.1658|
| 11:  2.2150 -  2.1460 1.00   1282  147 0.1052 0.1798      4.8983      5.2564|
| 12:  2.1460 -  2.0848 0.97   1270  137 0.1043 0.1598      4.8342      5.1638|
| 13:  2.0848 -  2.0301 0.98   1258  141 0.1023 0.1717      4.7424      4.9969|
| 14:  2.0301 -  1.9807 0.60    758   86 0.0962 0.1769      4.6322      4.9585|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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 -  4.7261  1395   154  0.94   9.21   0.98     0.95       7143.86|
|  2:  4.7261 -  3.7712  1340   151  0.95   7.69   1.01     1.00       8729.70|
|  3:  3.7712 -  3.3004  1319   148  0.94  10.76   1.02     1.02       9713.53|
|  4:  3.3004 -  3.0014  1300   135  0.93  12.79   1.01     1.00       9606.55|
|  5:  3.0014 -  2.7877  1301   149  0.90  15.36   1.00     0.97       7784.44|
|  6:  2.7877 -  2.6243  1298   147  0.90  15.88   0.98     0.95       6739.72|
|  7:  2.6243 -  2.4935  1277   146  0.91  14.87   0.99     0.96       5810.62|
|  8:  2.4935 -  2.3854  1303   138  0.92  14.32   1.00     0.98       5005.84|
|  9:  2.3854 -  2.2939  1271   145  0.91  15.04   1.00     0.97       4682.27|
| 10:  2.2939 -  2.2150  1258   135  0.90  15.45   1.00     0.96       4246.85|
| 11:  2.2150 -  2.1460  1282   147  0.90  15.64   1.00     0.97       4206.39|
| 12:  2.1460 -  2.0848  1270   137  0.92  14.65   1.01     1.00       3711.80|
| 13:  2.0848 -  2.0301  1258   141  0.91  15.31   1.00     0.99       3150.18|
| 14:  2.0301 -  1.9807   758    86  0.92  14.14   0.97     0.94       2439.42|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2439.42 max =         9713.53 mean =      6068.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.58|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.879)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.38    77.13   16.23    None  None   None       |
|    all(noH): 2823   0      0.38    77.13   16.23    None  None   None       |
|    Sol.    : 438    0      5.60    68.11   37.52    None  None   None       |
|    Mac.    : 2385   0      0.38    77.13   12.32    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:     0.378 -   8.053:  639   |   5:    38.752 -  46.427:  113        |
|      1:     8.053 -  15.728: 1331   |   6:    46.427 -  54.102:   83        |
|      2:    15.728 -  23.403:  337   |   7:    54.102 -  61.777:   50        |
|      3:    23.403 -  31.077:  129   |   8:    61.777 -  69.452:   18        |
|      4:    31.077 -  38.752:  121   |   9:    69.452 -  77.127:    2        |
|                               =>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: 0.513 - 5.389
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 276
   mapped sites are within: 0.709 - 5.389

peak=    5.468 closest distance to " CB  ARG A 275 " =    0.926
peak=    5.251 closest distance to " NH2 ARG A  56 " =    2.237
peak=    5.086 closest distance to " CG  PRO A  54 " =    1.247
peak=    5.051 closest distance to " CB  GLN A 223 " =    1.427
peak=    5.029 closest distance to " O   HOH Z 232 " =    2.391
peak=    4.999 closest distance to " O   HOH Z 142 " =    1.610
peak=    4.915 closest distance to " O   HOH Z 126 " =    1.836
peak=    4.913 closest distance to " CB  GLU A 152 " =    1.175
peak=    4.802 closest distance to " CB  SER A  63 " =    1.148
peak=    4.799 closest distance to " CB  GLN A 183 " =    1.224
peak=    4.728 closest distance to " CB  ARG A  79 " =    1.342
peak=    4.618 closest distance to " C   PRO A 198 " =    1.443
peak=    4.561 closest distance to " NE2 GLN A  11 " =    1.097
peak=    4.461 closest distance to " CB  ARG A 190 " =    1.707
peak=    4.457 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.419 closest distance to " CB  ASN A 148 " =    1.454
peak=    4.415 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.411 closest distance to " O   HOH Z 250 " =    1.484
peak=    4.392 closest distance to " O   HOH Z  78 " =    1.639
peak=    4.388 closest distance to " CG  PRO A 213 " =    1.173
peak=    4.343 closest distance to " O   HOH Z 369 " =    2.252
peak=    4.340 closest distance to " O   HOH Z  40 " =    1.802
peak=    4.336 closest distance to " O   HOH Z 236 " =    2.138
peak=    4.327 closest distance to " O   HOH Z 427 " =    2.936
peak=    4.314 closest distance to " O   HOH Z 209 " =    2.241
peak=    4.307 closest distance to " O   HOH Z  15 " =    2.154
peak=    4.306 closest distance to " O   HOH Z 298 " =    1.814
peak=    4.268 closest distance to " O   SER A  87 " =    2.168
peak=    4.185 closest distance to " O   HOH Z 193 " =    1.873
peak=    4.173 closest distance to " CD2 TRP A 179 " =    1.351
peak=    4.112 closest distance to " ND2 ASN A 187 " =    1.513
peak=    4.101 closest distance to " O   HOH Z 158 " =    3.055
peak=    4.091 closest distance to " O   HOH Z 234 " =    3.700
peak=    4.082 closest distance to " O   HOH Z 368 " =    2.084
peak=    4.063 closest distance to " CB  PRO A  54 " =    0.882
peak=    4.062 closest distance to " O   HOH Z 403 " =    1.704
peak=    4.061 closest distance to " O   HOH Z 303 " =    2.117
peak=    4.059 closest distance to " O   HOH Z 203 " =    1.648
peak=    4.052 closest distance to " O   HOH Z 346 " =    1.706
peak=    4.043 closest distance to " O   HOH Z  43 " =    1.926
peak=    4.023 closest distance to " CZ  PHE A 218 " =    1.098
peak=    4.017 closest distance to " O   HOH Z  61 " =    1.607
peak=    4.013 closest distance to " CB  TYR A 169 " =    0.817
peak=    4.011 closest distance to " CB  VAL A 265 " =    1.258
peak=    4.009 closest distance to " OD1 ASN A  69 " =    2.534
peak=    3.995 closest distance to " NZ  LYS A 117 " =    3.250
peak=    3.994 closest distance to " O   HOH Z 392 " =    2.949
peak=    3.975 closest distance to " O   HOH Z  63 " =    2.082
peak=    3.961 closest distance to " CB  GLU A 277 " =    3.571
peak=    3.959 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.958 closest distance to " CB  LEU A 228 " =    1.065
peak=    3.951 closest distance to " O   HOH Z 189 " =    2.447
peak=    3.948 closest distance to " O   HOH Z 402 " =    1.418
peak=    3.931 closest distance to " O   HOH Z 128 " =    1.996
peak=    3.929 closest distance to " CG1BVAL A  72 " =    1.672
peak=    3.843 closest distance to " O   HOH Z 147 " =    1.814
peak=    3.838 closest distance to " CG2 ILE A 120 " =    1.043
peak=    3.834 closest distance to " O   HOH Z  97 " =    2.435
peak=    3.832 closest distance to " O   HOH Z 423 " =    2.003
peak=    3.830 closest distance to " CA  ASN A 215 " =    1.109
peak=    3.828 closest distance to " CA  TYR A  30 " =    1.020
peak=    3.826 closest distance to " CA  ARG A  36 " =    1.033
peak=    3.816 closest distance to " CG  ARG A  66 " =    2.443
peak=    3.805 closest distance to " O   HOH Z  44 " =    1.769
peak=    3.800 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.789 closest distance to " O   HOH Z 406 " =    1.543
peak=    3.783 closest distance to " CG2 ILE A  20 " =    1.409
peak=    3.780 closest distance to " O   HOH Z  54 " =    1.715
peak=    3.774 closest distance to " O   HOH Z  66 " =    2.137
peak=    3.762 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.755 closest distance to " O   HOH Z 389 " =    1.862
peak=    3.750 closest distance to " OG ASER A 258 " =    3.071
peak=    3.720 closest distance to " CG2 VAL A 257 " =    0.842
peak=    3.710 closest distance to " CB  SER A   3 " =    1.243
peak=    3.708 closest distance to " O   HOH Z 291 " =    1.565
peak=    3.695 closest distance to " O   HOH Z 261 " =    1.687
peak=    3.683 closest distance to " CG  PRO A  90 " =    1.176
peak=    3.678 closest distance to " O   HOH Z   1 " =    1.985
peak=    3.673 closest distance to " O   HOH Z 344 " =    3.124
peak=    3.670 closest distance to " CG  PRO A 198 " =    1.233
peak=    3.669 closest distance to " O   HOH Z  97 " =    1.940
peak=    3.655 closest distance to " CB  VAL A 202 " =    1.499
peak=    3.647 closest distance to " CG1 ILE A  33 " =    1.199
peak=    3.643 closest distance to " CD2 LEU A 297 " =    0.850
peak=    3.631 closest distance to " O   HOH Z 261 " =    2.074
peak=    3.630 closest distance to " O   HOH Z 417 " =    3.142
peak=    3.630 closest distance to " O  BHOH Z 338 " =    2.265
peak=    3.629 closest distance to " O   HOH Z 337 " =    3.552
peak=    3.627 closest distance to " O   HOH Z  19 " =    2.297
peak=    3.623 closest distance to " CA  ARG A 195 " =    1.305
peak=    3.618 closest distance to " O   HOH Z 280 " =    2.953
peak=    3.614 closest distance to " O   HOH Z 214 " =    2.048
peak=    3.606 closest distance to " CB  SER A  26 " =    1.659
peak=    3.602 closest distance to " CB  GLN A  88 " =    1.167
peak=    3.597 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.595 closest distance to " O   MET A 105 " =    1.912
peak=    3.593 closest distance to " CB  TRP A 179 " =    1.355
peak=    3.592 closest distance to " CB  THR A  31 " =    1.639
peak=    3.590 closest distance to " CA  ALA A  21 " =    1.175
peak=    3.589 closest distance to " O   HOH Z 421 " =    1.653
peak=    3.578 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.575 closest distance to " CB  GLU A  46 " =    0.996
peak=    3.575 closest distance to " CD  ARG A 269 " =    0.925
peak=    3.574 closest distance to " O   HOH Z 180 " =    2.159
peak=    3.574 closest distance to " O   HOH Z 128 " =    2.207
peak=    3.572 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.571 closest distance to " CB  ARG A 139 " =    0.937
peak=    3.567 closest distance to " NH1AARG A 145 " =    1.207
peak=    3.562 closest distance to " O   HOH Z 265 " =    2.216
peak=    3.562 closest distance to " O   HOH Z 299 " =    4.357
peak=    3.560 closest distance to " O   HOH Z 313 " =    1.942
peak=    3.558 closest distance to " O   HOH Z  59 " =    2.092
peak=    3.557 closest distance to " CA  ALA A  51 " =    0.860
peak=    3.548 closest distance to " OG BSER A 164 " =    2.271
peak=    3.538 closest distance to " CG  MET A 185 " =    1.126
peak=    3.535 closest distance to " CB  ASN A  39 " =    0.901
peak=    3.529 closest distance to " CB  ILE A 120 " =    1.270
peak=    3.524 closest distance to " O   HOH Z 172 " =    3.557
peak=    3.518 closest distance to " O   HOH Z 407 " =    2.557
peak=    3.516 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.317
peak=    3.511 closest distance to " CG  PRO A 243 " =    1.028
peak=    3.508 closest distance to " CB  SER A 212 " =    1.072
peak=    3.507 closest distance to " O   HOH Z 245 " =    1.336
peak=    3.502 closest distance to " O   HOH Z 248 " =    1.579
peak=    3.502 closest distance to " OE1 GLU A   2 " =    2.187
peak=    3.497 closest distance to " CB  GLU A 128 " =    1.068
peak=    3.495 closest distance to " O   HOH Z 411 " =    3.872
peak=    3.490 closest distance to " O   HOH Z 371 " =    3.191
peak=    3.486 closest distance to " CA  ASN A 176 " =    1.181
peak=    3.486 closest distance to " NE2 GLN A  77 " =    3.222
peak=    3.485 closest distance to " O   HOH Z 426 " =    1.574
peak=    3.484 closest distance to " O   HOH Z 425 " =    1.979
peak=    3.484 closest distance to " O   HOH Z  21 " =    1.810
peak=    3.482 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.479 closest distance to " CA  ALA A  84 " =    1.256
peak=    3.471 closest distance to " NH2BARG A 145 " =    2.066
peak=    3.470 closest distance to " CB  ASN A 110 " =    1.108
peak=    3.469 closest distance to " OD2 ASP A 286 " =    2.833
peak=    3.462 closest distance to " O   HOH Z 419 " =    1.950
peak=    3.458 closest distance to " O   HOH Z 148 " =    3.299
peak=    3.458 closest distance to " O   HOH Z 213 " =    1.738
peak=    3.447 closest distance to " CZ2 TRP A 179 " =    1.755
peak=    3.445 closest distance to " CG AARG A 275 " =    1.075
peak=    3.439 closest distance to " CB  ALA A 291 " =    1.316
peak=    3.433 closest distance to " O   HOH Z  88 " =    3.018
peak=    3.432 closest distance to " O   HOH Z 163 " =    1.925
peak=    3.420 closest distance to " CB  TYR A 169 " =    0.950
peak=    3.410 closest distance to " CB  GLN A  89 " =    1.317
peak=    3.410 closest distance to " CA  LYS A 117 " =    1.247
peak=    3.409 closest distance to " O   HOH Z 365 " =    2.828
peak=    3.405 closest distance to " N   ARG A 156 " =    1.359
peak=    3.400 closest distance to " CD1 LEU A 300 " =    1.290
peak=    3.391 closest distance to " O   HOH Z  66 " =    2.179
peak=    3.378 closest distance to " O   HOH Z 383 " =    1.856
peak=    3.372 closest distance to " ND2 ASN A 110 " =    1.638
peak=    3.370 closest distance to " CA  ALA A 291 " =    0.803
peak=    3.363 closest distance to " CA  ASP A 162 " =    1.074
peak=    3.361 closest distance to " O   HOH Z 133 " =    2.660
peak=    3.354 closest distance to " O   HOH Z 279 " =    2.195
peak=    3.345 closest distance to " O   HOH Z 345 " =    3.217
peak=    3.342 closest distance to " NH2 ARG A 156 " =    1.182
peak=    3.341 closest distance to " O   HOH Z 273 " =    2.788
peak=    3.337 closest distance to " O   HOH Z 327 " =    1.636
peak=    3.336 closest distance to " O   HOH Z 173 " =    1.970
peak=    3.335 closest distance to " CD1 ILE A 106 " =    0.870
peak=    3.333 closest distance to " O   ALA A   1 " =    1.697
peak=    3.331 closest distance to " CB  ASP A 298 " =    1.167
peak=    3.330 closest distance to " O   HOH Z 227 " =    1.552
peak=    3.326 closest distance to " O   HOH Z 126 " =    1.674
peak=    3.316 closest distance to " O   HOH Z 305 " =    3.584
peak=    3.316 closest distance to " CA  ASN A 217 " =    1.222
peak=    3.311 closest distance to " CA  ARG A 275 " =    1.889
peak=    3.309 closest distance to " O   HOH Z 329 " =    3.933
peak=    3.308 closest distance to " O   HOH Z  88 " =    2.427
peak=    3.303 closest distance to " O   HOH Z  61 " =    1.461
peak=    3.290 closest distance to " CB  SER A 141 " =    1.022
peak=    3.289 closest distance to " CB  ASN A 215 " =    1.171
peak=    3.288 closest distance to " OH  TYR A 116 " =    1.060
peak=    3.285 closest distance to " CA  THR A 264 " =    0.923
peak=    3.283 closest distance to " O   HOH Z  85 " =    2.313
peak=    3.283 closest distance to " CA  TYR A 116 " =    1.390
peak=    3.282 closest distance to " CD  LYS A 119 " =    1.362
peak=    3.282 closest distance to " CB  ALA A   9 " =    1.566
peak=    3.280 closest distance to " O   HOH Z 380 " =    1.906
peak=    3.276 closest distance to " CA  ASP A 140 " =    1.132
peak=    3.274 closest distance to " O   HOH Z  30 " =    2.258
peak=    3.272 closest distance to " O   HOH Z 193 " =    2.108
peak=    3.272 closest distance to " O   HOH Z 132 " =    2.503
peak=    3.267 closest distance to " CA  THR A 221 " =    1.002
peak=    3.265 closest distance to " O   HOH Z 433 " =    1.780
peak=    3.263 closest distance to " O   HOH Z 234 " =    1.849
peak=    3.261 closest distance to " N   ASN A  39 " =    1.310
peak=    3.259 closest distance to " O   HOH Z 185 " =    1.792
peak=    3.256 closest distance to " O   HOH Z 353 " =    2.644
peak=    3.253 closest distance to " CB  GLN A 103 " =    0.831
peak=    3.253 closest distance to " CG  LYS A  76 " =    0.965
peak=    3.251 closest distance to " NZ  LYS A  76 " =    1.522
peak=    3.249 closest distance to " N   TYR A 116 " =    1.581
peak=    3.246 closest distance to " CA  MET A 105 " =    0.959
peak=    3.243 closest distance to " ND1 HIS A  81 " =    1.627
peak=    3.234 closest distance to " CG2 THR A 221 " =    1.192
peak=    3.233 closest distance to " CB  GLN A 205 " =    1.142
peak=    3.233 closest distance to " CB  PHE A 204 " =    0.712
peak=    3.233 closest distance to " O   ALA A 165 " =    1.522
peak=    3.229 closest distance to " O   HOH Z 325 " =    2.543
peak=    3.229 closest distance to " CB  TYR A 116 " =    0.753
peak=    3.228 closest distance to " CG  GLN A  77 " =    1.911
peak=    3.227 closest distance to " CB  ALA A   1 " =    4.820
peak=    3.226 closest distance to " CD  ARG A  66 " =    2.432
peak=    3.224 closest distance to " O   HOH Z 391 " =    2.881
peak=    3.223 closest distance to " O   HOH Z 171 " =    1.929
peak=    3.221 closest distance to " CB  ALA A 114 " =    1.176
peak=    3.218 closest distance to " CB  SER A  62 " =    0.894
peak=    3.215 closest distance to " CB  ASN A 142 " =    1.094
peak=    3.208 closest distance to " O   HOH Z 357 " =    1.910
peak=    3.206 closest distance to " O   HOH Z 108 " =    2.633
peak=    3.204 closest distance to " O   HOH Z  35 " =    2.495
peak=    3.204 closest distance to " O   HOH Z 359 " =    1.461
peak=    3.201 closest distance to " O   HOH Z 193 " =    1.582
peak=    3.196 closest distance to " O   THR A 220 " =    1.248
peak=    3.196 closest distance to " O   HOH Z 417 " =    2.057
peak=    3.193 closest distance to " CB  ALA A  34 " =    1.041
peak=    3.193 closest distance to " O   HOH Z 394 " =    3.953
peak=    3.193 closest distance to " O   HOH Z 403 " =    1.313
peak=    3.192 closest distance to " C   TYR A 214 " =    1.456
peak=    3.186 closest distance to " O   HOH Z 175 " =    2.106
peak=    3.186 closest distance to " CG BARG A 102 " =    1.737
peak=    3.179 closest distance to " O   HOH Z 285 " =    2.798
peak=    3.177 closest distance to " O   HOH Z  85 " =    1.860
peak=    3.173 closest distance to " O   HOH Z 261 " =    2.252
peak=    3.166 closest distance to " CA  ALA A 233 " =    1.279
peak=    3.163 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.161 closest distance to " N   VAL A 126 " =    1.337
peak=    3.156 closest distance to " OD1 ASP A 231 " =    1.925
peak=    3.152 closest distance to " O   HOH Z  62 " =    2.150
peak=    3.152 closest distance to " O   HOH Z 214 " =    3.734
peak=    3.150 closest distance to " N   ASN A 127 " =    1.253
peak=    3.149 closest distance to " O   HOH Z 267 " =    2.055
peak=    3.149 closest distance to " O   HOH Z 430 " =    5.389
peak=    3.147 closest distance to " O   HOH Z 234 " =    2.251
peak=    3.146 closest distance to " CA  ARG A 159 " =    1.261
peak=    3.143 closest distance to " CG2 VAL A 197 " =    1.103
peak=    3.141 closest distance to " CD  LYS A  76 " =    1.907
peak=    3.141 closest distance to " O   HOH Z  80 " =    1.633
peak=    3.140 closest distance to " O   HOH Z 188 " =    2.112
peak=    3.138 closest distance to " N   PHE A 130 " =    1.299
peak=    3.135 closest distance to " O   HOH Z 294 " =    1.440
peak=    3.133 closest distance to " O   HOH Z 286 " =    2.196
peak=    3.130 closest distance to " CG  LYS A 119 " =    1.085
peak=    3.129 closest distance to " CG1 ILE A  49 " =    1.456
peak=    3.125 closest distance to " CD1 LEU A  96 " =    0.709
peak=    3.125 closest distance to " O   HOH Z  49 " =    2.089
peak=    3.122 closest distance to " O   HOH Z 336 " =    1.648
peak=    3.122 closest distance to " O   HOH Z 409 " =    3.095
peak=    3.121 closest distance to " CB  PRO A  90 " =    1.175
peak=    3.117 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.112 closest distance to " CD  ARG A  79 " =    2.118
peak=    3.109 closest distance to " N   SER A 135 " =    1.305
peak=    3.098 closest distance to " O   HOH Z 271 " =    2.203
peak=    3.092 closest distance to " CB  GLN A 278 " =    0.848
peak=    3.088 closest distance to " CB  ALA A 248 " =    0.899
peak=    3.088 closest distance to " O   HOH Z 116 " =    1.766
peak=    3.085 closest distance to " OG BSER A  99 " =    2.340
peak=    3.080 closest distance to " N   ASP A 162 " =    1.231
peak=    3.076 closest distance to " CA  SER A  87 " =    1.066
peak=    3.071 closest distance to " CG  GLN A  77 " =    1.876
peak=    3.067 closest distance to " NE2 HIS A 207 " =    1.279
peak=    3.065 closest distance to " OE2 GLU A  53 " =    1.990
peak=    3.063 closest distance to " CA  SER A 146 " =    1.686
peak=    3.056 closest distance to " O   SER A 164 " =    1.121
peak=    3.054 closest distance to " CB  MET A  47 " =    1.190
peak=    3.043 closest distance to " CB  LYS A 290 " =    1.153
peak=    3.019 closest distance to " CB  VAL A 126 " =    1.097

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.798
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.793 - 5.798

peak=   -4.865 closest distance to " O   HOH Z 266 " =    5.095
peak=   -4.728 closest distance to " CD  GLN A  58 " =    0.979
peak=   -4.677 closest distance to " O   VAL A  67 " =    2.705
peak=   -4.614 closest distance to " SG  CYS A 254 " =    3.375
peak=   -4.525 closest distance to " CB  PRO A 243 " =    2.638
peak=   -4.510 closest distance to " CD  ARG A 156 " =    2.108
peak=   -4.477 closest distance to " C   HIS A 108 " =    1.151
peak=   -4.245 closest distance to " O   HOH Z 198 " =    1.966
peak=   -4.204 closest distance to " CG  GLN A 223 " =    2.063
peak=   -4.165 closest distance to " O   HOH Z 372 " =    2.313
peak=   -4.131 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -4.099 closest distance to " O   HOH Z 231 " =    2.290
peak=   -4.093 closest distance to " O   HOH Z 196 " =    2.008
peak=   -4.087 closest distance to " CG1 VAL A 112 " =    2.787
peak=   -4.079 closest distance to " C   ILE A 239 " =    2.173
peak=   -4.041 closest distance to " CA  VAL A  67 " =    2.943
peak=   -4.026 closest distance to " OG BSER A 134 " =    1.330
peak=   -3.996 closest distance to " CB  ALA A 161 " =    2.583
peak=   -3.992 closest distance to " O   HOH Z 290 " =    1.128
peak=   -3.961 closest distance to " OG  SER A  97 " =    2.214
peak=   -3.838 closest distance to " N   ALA A  43 " =    2.584
peak=   -3.824 closest distance to " CD  ARG A 139 " =    1.555
peak=   -3.811 closest distance to " CD1 LEU A 101 " =    2.345
peak=   -3.798 closest distance to " CB  PHE A 192 " =    1.959
peak=   -3.797 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.792 closest distance to " OXT GLY A 302 " =    2.760
peak=   -3.791 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.791 closest distance to " CG2 ILE A 263 " =    2.255
peak=   -3.775 closest distance to " CB  ASN A  39 " =    2.358
peak=   -3.759 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.758 closest distance to " O   HOH Z 114 " =    3.165
peak=   -3.757 closest distance to " O   HOH Z 407 " =    2.959
peak=   -3.754 closest distance to " O   HOH Z 211 " =    1.637
peak=   -3.746 closest distance to " O   HOH Z 435 " =    2.804
peak=   -3.744 closest distance to " O   SER A 210 " =    1.949
peak=   -3.741 closest distance to " CB  ALA A 248 " =    2.302
peak=   -3.736 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.687 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.685 closest distance to " CE2 TYR A  30 " =    2.717
peak=   -3.685 closest distance to " O   HOH Z 389 " =    1.840
peak=   -3.678 closest distance to " O   HOH Z  13 " =    1.638
peak=   -3.677 closest distance to " O   HOH Z 126 " =    1.910
peak=   -3.675 closest distance to " N   GLN A  58 " =    1.628
peak=   -3.674 closest distance to " CZ  TYR A 169 " =    1.781
peak=   -3.668 closest distance to " OD1 ASP A 171 " =    1.636
peak=   -3.664 closest distance to " O   HOH Z  10 " =    1.468
peak=   -3.664 closest distance to " O   HOH Z  73 " =    2.351
peak=   -3.650 closest distance to " O   HOH Z 313 " =    1.975
peak=   -3.641 closest distance to " OD2 ASP A 171 " =    2.402
peak=   -3.635 closest distance to " O   PRO A 163 " =    2.103
peak=   -3.625 closest distance to " O   HOH Z 353 " =    2.193
peak=   -3.619 closest distance to " CB  ALA A 291 " =    2.380
peak=   -3.606 closest distance to " ND2 ASN A  45 " =    1.732
peak=   -3.604 closest distance to " OG BSER A 134 " =    1.833
peak=   -3.599 closest distance to " CA  GLY A 203 " =    2.417
peak=   -3.599 closest distance to " O   HOH Z 351 " =    1.512
peak=   -3.575 closest distance to " N   ALA A 248 " =    1.715
peak=   -3.572 closest distance to " CB  PHE A 208 " =    2.259
peak=   -3.568 closest distance to " ND2 ASN A 187 " =    1.466
peak=   -3.565 closest distance to " CG  ARG A  66 " =    2.455
peak=   -3.546 closest distance to " SG ACYS A 201 " =    2.064
peak=   -3.545 closest distance to " CB  ALA A 291 " =    2.245
peak=   -3.541 closest distance to " O   PHE A 218 " =    1.600
peak=   -3.537 closest distance to " CE  MET A 105 " =    2.401
peak=   -3.509 closest distance to " CB  ASP A 286 " =    1.863
peak=   -3.506 closest distance to " CB  ALA A 248 " =    2.194
peak=   -3.503 closest distance to " CG1 VAL A  67 " =    3.184
peak=   -3.483 closest distance to " CB  ALA A  43 " =    2.522
peak=   -3.477 closest distance to " CD  ARG A 195 " =    5.191
peak=   -3.474 closest distance to " CB  TYR A  15 " =    2.201
peak=   -3.470 closest distance to " CG  PHE A 283 " =    2.625
peak=   -3.468 closest distance to " NH2AARG A 275 " =    5.231
peak=   -3.467 closest distance to " O   HOH Z 166 " =    1.922
peak=   -3.465 closest distance to " CD2 TYR A 247 " =    2.458
peak=   -3.463 closest distance to " CG  GLU A 277 " =    1.186
peak=   -3.461 closest distance to " O   SER A  95 " =    1.554
peak=   -3.460 closest distance to " ND2 ASN A  45 " =    1.122
peak=   -3.449 closest distance to " O   HOH Z 394 " =    1.459
peak=   -3.442 closest distance to " O   HOH Z 311 " =    3.684
peak=   -3.440 closest distance to " NE2 GLN A 194 " =    1.824
peak=   -3.434 closest distance to " OD1 ASN A 148 " =    1.531
peak=   -3.427 closest distance to " CD2 LEU A 237 " =    2.705
peak=   -3.420 closest distance to " O   HOH Z 253 " =    3.854
peak=   -3.411 closest distance to " O   ALA A  10 " =    1.730
peak=   -3.408 closest distance to " O   HOH Z 292 " =    4.574
peak=   -3.405 closest distance to " O   HOH Z  60 " =    2.275
peak=   -3.402 closest distance to " CD2 LEU A 300 " =    2.826
peak=   -3.398 closest distance to " CG1 VAL A 250 " =    2.657
peak=   -3.386 closest distance to " O   ALA A 161 " =    1.733
peak=   -3.383 closest distance to " O   HOH Z 165 " =    1.959
peak=   -3.382 closest distance to " C   LEU A 143 " =    1.032
peak=   -3.381 closest distance to " N   ALA A 226 " =    2.011
peak=   -3.381 closest distance to " CE2 PHE A 218 " =    2.407
peak=   -3.379 closest distance to " O   HOH Z 198 " =    1.465
peak=   -3.378 closest distance to " C   PRO A  90 " =    1.495
peak=   -3.376 closest distance to " O   MET A  40 " =    2.778
peak=   -3.375 closest distance to " OD2 ASP A 191 " =    1.433
peak=   -3.366 closest distance to " O   HOH Z  52 " =    1.355
peak=   -3.365 closest distance to " CD2 PHE A  61 " =    2.522
peak=   -3.363 closest distance to " O   HOH Z 191 " =    5.798
peak=   -3.349 closest distance to " OG  SER A  62 " =    1.637
peak=   -3.349 closest distance to " O   HOH Z 123 " =    2.379
peak=   -3.345 closest distance to " CZ  PHE A 155 " =    1.212
peak=   -3.343 closest distance to " CB  PRO A 163 " =    2.444
peak=   -3.343 closest distance to " CG  ARG A 269 " =    2.332
peak=   -3.341 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.339 closest distance to " O   ALA A  34 " =    2.461
peak=   -3.333 closest distance to " O   HOH Z 102 " =    1.551
peak=   -3.328 closest distance to " O   HOH Z   6 " =    1.484
peak=   -3.325 closest distance to " O   VAL A 174 " =    2.081
peak=   -3.323 closest distance to " CE3 TRP A 150 " =    2.252
peak=   -3.319 closest distance to " O   HOH Z 244 " =    1.680
peak=   -3.318 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.307 closest distance to " O   HOH Z  43 " =    1.727
peak=   -3.306 closest distance to " O   HOH Z 243 " =    1.943
peak=   -3.305 closest distance to " O   HOH Z 357 " =    2.080
peak=   -3.303 closest distance to " NE2 GLN A 278 " =    1.743
peak=   -3.302 closest distance to " CB  TRP A  85 " =    2.618
peak=   -3.299 closest distance to " N   MET A 105 " =    2.614
peak=   -3.294 closest distance to " ND2 ASN A 249 " =    2.306
peak=   -3.293 closest distance to " CZ  PHE A  59 " =    1.544
peak=   -3.289 closest distance to " CG  ASP A 231 " =    0.793
peak=   -3.285 closest distance to " N   ASP A 286 " =    2.318
peak=   -3.281 closest distance to " O   HOH Z 166 " =    1.520
peak=   -3.278 closest distance to " NE2 GLN A  11 " =    1.850
peak=   -3.276 closest distance to " CA  GLY A 133 " =    2.052
peak=   -3.276 closest distance to " N   PHE A  59 " =    2.091
peak=   -3.276 closest distance to " O   HOH Z  44 " =    2.227
peak=   -3.275 closest distance to " CE  MET A 105 " =    2.274
peak=   -3.272 closest distance to " NE2 GLN A  88 " =    1.777
peak=   -3.264 closest distance to " CA  GLY A 241 " =    3.172
peak=   -3.263 closest distance to " CG2 ILE A  20 " =    2.934
peak=   -3.258 closest distance to " CD1 LEU A 228 " =    2.134
peak=   -3.255 closest distance to " CB  ASN A  69 " =    1.141
peak=   -3.249 closest distance to " NH2 ARG A 159 " =    2.380
peak=   -3.247 closest distance to " O   HOH Z  11 " =    1.733
peak=   -3.245 closest distance to " O   GLN A 240 " =    2.056
peak=   -3.244 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.243 closest distance to " O   HOH Z 234 " =    4.034
peak=   -3.242 closest distance to " N   THR A  52 " =    1.734
peak=   -3.241 closest distance to " OD2 ASP A  50 " =    2.176
peak=   -3.229 closest distance to " O   HOH Z  38 " =    1.620
peak=   -3.229 closest distance to " O   HOH Z  37 " =    1.848
peak=   -3.226 closest distance to " O   HOH Z  63 " =    1.590
peak=   -3.224 closest distance to " C   SER A 206 " =    1.572
peak=   -3.223 closest distance to " O   HOH Z 134 " =    3.034
peak=   -3.218 closest distance to " O   HOH Z   6 " =    2.165
peak=   -3.216 closest distance to " O   HOH Z 177 " =    1.702
peak=   -3.208 closest distance to " O   HOH Z 339 " =    1.779
peak=   -3.206 closest distance to " O   LEU A 167 " =    1.556
peak=   -3.206 closest distance to " CG  GLU A  53 " =    1.555
peak=   -3.203 closest distance to " C   MET A 188 " =    1.395
peak=   -3.199 closest distance to " NH2 ARG A  79 " =    2.030
peak=   -3.195 closest distance to " NH2 ARG A  79 " =    1.609
peak=   -3.195 closest distance to " CD2 TYR A 293 " =    2.043
peak=   -3.194 closest distance to " O   SER A 135 " =    1.499
peak=   -3.194 closest distance to " ND2 ASN A  60 " =    1.357
peak=   -3.192 closest distance to " CG  GLU A 152 " =    0.868
peak=   -3.180 closest distance to " CA  SER A  62 " =    2.640
peak=   -3.179 closest distance to " O   HOH Z 174 " =    4.179
peak=   -3.176 closest distance to " CG1 VAL A 197 " =    2.219
peak=   -3.176 closest distance to " N   GLY A  23 " =    2.281
peak=   -3.175 closest distance to " OE1 GLN A 223 " =    1.993
peak=   -3.175 closest distance to " CA  GLY A 241 " =    2.368
peak=   -3.174 closest distance to " N   ALA A 248 " =    2.295
peak=   -3.174 closest distance to " C   ASP A 231 " =    2.633
peak=   -3.174 closest distance to " CG  GLU A   2 " =    1.938
peak=   -3.172 closest distance to " O   HOH Z 193 " =    1.881
peak=   -3.170 closest distance to " O   ALA A   1 " =    1.732
peak=   -3.168 closest distance to " CG2 VAL A 189 " =    2.151
peak=   -3.167 closest distance to " C   ALA A 114 " =    2.184
peak=   -3.166 closest distance to " O   HOH Z 414 " =    1.527
peak=   -3.159 closest distance to " CD1 ILE A 199 " =    2.431
peak=   -3.158 closest distance to " C   GLY A 262 " =    1.846
peak=   -3.157 closest distance to " CD1 LEU A 297 " =    2.233
peak=   -3.155 closest distance to " O   HOH Z 171 " =    1.955
peak=   -3.154 closest distance to " O   HOH Z 421 " =    3.251
peak=   -3.152 closest distance to " O   ALA A 292 " =    1.981
peak=   -3.145 closest distance to " OE1 GLN A 194 " =    1.722
peak=   -3.142 closest distance to " C   ALA A 158 " =    1.293
peak=   -3.137 closest distance to " O   ALA A  51 " =    1.279
peak=   -3.137 closest distance to " O   HOH Z 377 " =    1.780
peak=   -3.137 closest distance to " NE2 GLN A  88 " =    1.031
peak=   -3.135 closest distance to " CZ3 TRP A 274 " =    2.468
peak=   -3.114 closest distance to " CG1 VAL A 125 " =    1.983
peak=   -3.113 closest distance to " CG2 THR A 221 " =    2.273
peak=   -3.108 closest distance to " O   LEU A 101 " =    2.282
peak=   -3.107 closest distance to " O   HOH Z 396 " =    1.817
peak=   -3.107 closest distance to " NH2BARG A 275 " =    2.145
peak=   -3.105 closest distance to " SD  MET A 188 " =    2.178
peak=   -3.085 closest distance to " OG  SER A  97 " =    2.085
peak=   -3.084 closest distance to " OE2 GLU A 152 " =    1.230
peak=   -3.081 closest distance to " CE  LYS A  76 " =    2.754
peak=   -3.077 closest distance to " O   HOH Z 407 " =    3.060
peak=   -3.074 closest distance to " O   TRP A  70 " =    1.487
peak=   -3.071 closest distance to " O   HOH Z 200 " =    3.477
peak=   -3.069 closest distance to " N   SER A 276 " =    1.319
peak=   -3.064 closest distance to " CG  PRO A 163 " =    2.671
peak=   -3.061 closest distance to " OD1 ASN A 301 " =    1.949
peak=   -3.059 closest distance to " O   HOH Z 210 " =    1.155
peak=   -3.056 closest distance to " O   HOH Z 283 " =    5.615
peak=   -3.013 closest distance to " CA  GLY A 241 " =    2.814

================= 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    :  0.2588 0.2503   5.836317e+00   5.793368e+00
   1_bss:  0.2438 0.2333   5.802672e+00   5.752750e+00
   1_xyz:  0.1480 0.1645   5.326554e+00   5.415681e+00
   1_adp:  0.1374 0.1658   5.275772e+00   5.436352e+00
   1_occ:  0.1370 0.1657   5.274837e+00   5.436563e+00
   2_bss:  0.1369 0.1652   5.276064e+00   5.434976e+00
   2_xyz:  0.1147 0.1505   5.136917e+00   5.343495e+00
   2_adp:  0.1099 0.1496   5.113413e+00   5.340691e+00
   2_occ:  0.1098 0.1495   5.112943e+00   5.340337e+00
   3_bss:  0.1096 0.1493   5.113114e+00   5.340492e+00
   3_xyz:  0.1092 0.1511   5.117416e+00   5.352525e+00
   3_adp:  0.1090 0.1511   5.116510e+00   5.353397e+00
   3_occ:  0.1089 0.1512   5.116725e+00   5.353862e+00
   4_bss:  0.1088 0.1512   5.116823e+00   5.353933e+00
   4_xyz:  0.1088 0.1531   5.120245e+00   5.361837e+00
   4_adp:  0.1091 0.1526   5.119839e+00   5.359468e+00
   4_occ:  0.1090 0.1527   5.120085e+00   5.360040e+00
   5_bss:  0.1091 0.1516   5.118914e+00   5.355610e+00
   5_xyz:  0.1059 0.1527   5.106379e+00   5.358361e+00
   5_adp:  0.1054 0.1539   5.108214e+00   5.365940e+00
   5_occ:  0.1054 0.1538   5.108188e+00   5.365970e+00
   5_bss:  0.1053 0.1539   5.108456e+00   5.366282e+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:  0.330  50.000  -2.152  -1.770  -0.965  -0.000  -0.000  -0.000
   1_xyz:  0.330  50.000  -2.152  -1.770  -0.965  -0.000  -0.000  -0.000
   1_adp:  0.330  50.000  -2.152  -1.770  -0.965  -0.000  -0.000  -0.000
   1_occ:  0.330  50.000  -2.152  -1.770  -0.965  -0.000  -0.000  -0.000
   2_bss:  0.328  52.128  -3.109  -2.366  -1.405  -0.000  -0.000  -0.000
   2_xyz:  0.328  52.128  -3.109  -2.366  -1.405  -0.000  -0.000  -0.000
   2_adp:  0.328  52.128  -3.109  -2.366  -1.405  -0.000  -0.000  -0.000
   2_occ:  0.328  52.128  -3.109  -2.366  -1.405  -0.000  -0.000  -0.000
   3_bss:  0.326  50.493  -2.823  -2.083  -1.091  -0.000  -0.000  -0.000
   3_xyz:  0.326  50.493  -2.823  -2.083  -1.091  -0.000  -0.000  -0.000
   3_adp:  0.326  50.493  -2.823  -2.083  -1.091  -0.000  -0.000  -0.000
   3_occ:  0.326  50.493  -2.823  -2.083  -1.091  -0.000  -0.000  -0.000
   4_bss:  0.326  50.493  -2.692  -1.959  -0.920  -0.000  -0.000  -0.000
   4_xyz:  0.326  50.493  -2.692  -1.959  -0.920  -0.000  -0.000  -0.000
   4_adp:  0.326  50.493  -2.692  -1.959  -0.920  -0.000  -0.000  -0.000
   4_occ:  0.326  50.493  -2.692  -1.959  -0.920  -0.000  -0.000  -0.000
   5_bss:  0.322  50.493  -2.594  -1.859  -0.797  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.493  -2.594  -1.859  -0.797  -0.000  -0.000  -0.000
   5_adp:  0.322  50.493  -2.594  -1.859  -0.797  -0.000  -0.000  -0.000
   5_occ:  0.322  50.493  -2.594  -1.859  -0.797  -0.000  -0.000  -0.000
   5_bss:  0.319  48.054  -2.343  -1.616  -0.553  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.743 0.8286  0.9922    17087.405
   1_bss:  22.319 0.8413  0.9525    14061.132
   1_xyz:  14.663 0.9101  0.9957     6809.051
   1_adp:  15.085 0.9064  0.9905     7015.856
   1_occ:  15.103 0.9062  0.9900     7016.955
   2_bss:  15.060 0.9066  0.9664     6991.465
   2_xyz:  13.259 0.9208  0.9712     5848.429
   2_adp:  13.232 0.9209  0.9658     5784.376
   2_occ:  13.225 0.9209  0.9658     5777.333
   3_bss:  13.230 0.9209  0.9760     5778.070
   3_xyz:  13.324 0.9206  0.9759     5933.923
   3_adp:  13.319 0.9206  0.9706     5947.020
   3_occ:  13.328 0.9206  0.9704     5950.862
   4_bss:  13.330 0.9206  0.9754     5952.471
   4_xyz:  13.444 0.9197  0.9748     6053.995
   4_adp:  13.392 0.9201  0.9696     6028.108
   4_occ:  13.401 0.9200  0.9695     6033.681
   5_bss:  13.337 0.9205  0.9730     5931.843
   5_xyz:  13.387 0.9201  0.9736     5996.616
   5_adp:  13.528 0.9190  0.9664     6065.360
   5_occ:  13.528 0.9190  0.9663     6065.751
   5_bss:  13.536 0.9189  0.9744     6068.232
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6231e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6231e-01
   1_xyz:   0.973  0.006  0.068 14.926  0.004  4.114   5.6290e-02
   1_adp:   0.973  0.006  0.068 14.926  0.004  4.114   5.6290e-02
   1_occ:   0.973  0.006  0.068 14.926  0.004  4.114   5.6290e-02
   2_bss:   0.973  0.006  0.068 14.926  0.004  4.114   5.6290e-02
   2_xyz:   1.067  0.009  0.081 14.908  0.005  4.123   6.7200e-02
   2_adp:   1.067  0.009  0.081 14.908  0.005  4.123   6.7200e-02
   2_occ:   1.067  0.009  0.081 14.908  0.005  4.123   6.7200e-02
   3_bss:   1.067  0.009  0.081 14.908  0.005  4.123   6.7200e-02
   3_xyz:   0.978  0.007  0.076 14.663  0.004  4.123   5.8214e-02
   3_adp:   0.978  0.007  0.076 14.663  0.004  4.123   5.8214e-02
   3_occ:   0.978  0.007  0.076 14.663  0.004  4.123   5.8214e-02
   4_bss:   0.978  0.007  0.076 14.663  0.004  4.123   5.8214e-02
   4_xyz:   0.965  0.007  0.075 14.478  0.004  4.124   5.5978e-02
   4_adp:   0.965  0.007  0.075 14.478  0.004  4.124   5.5978e-02
   4_occ:   0.965  0.007  0.075 14.478  0.004  4.124   5.5978e-02
   5_bss:   0.965  0.007  0.075 14.478  0.004  4.124   5.5978e-02
   5_xyz:   1.080  0.009  0.083 14.812  0.005  4.126   6.9540e-02
   5_adp:   1.080  0.009  0.083 14.812  0.005  4.126   6.9540e-02
   5_occ:   1.080  0.009  0.083 14.812  0.005  4.126   6.9540e-02
   5_bss:   1.080  0.009  0.083 14.812  0.005  4.126   6.9540e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4089e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4089e-01
   1_xyz:   6.588  0.036  0.251 83.674  0.042  2.295   7.5597e-02
   1_adp:   6.588  0.036  0.251 83.674  0.042  2.295   7.5597e-02
   1_occ:   6.588  0.036  0.251 83.674  0.042  2.295   7.5597e-02
   2_bss:   6.588  0.036  0.251 83.674  0.042  2.295   7.5597e-02
   2_xyz:   7.491  0.047  0.277 83.127  0.039  2.336   5.7763e-02
   2_adp:   7.491  0.047  0.277 83.127  0.039  2.336   5.7763e-02
   2_occ:   7.491  0.047  0.277 83.127  0.039  2.336   5.7763e-02
   3_bss:   7.491  0.047  0.277 83.127  0.039  2.336   5.7763e-02
   3_xyz:   7.038  0.049  0.246 82.481  0.038  2.370   4.2264e-02
   3_adp:   7.038  0.049  0.246 82.481  0.038  2.370   4.2264e-02
   3_occ:   7.038  0.049  0.246 82.481  0.038  2.370   4.2264e-02
   4_bss:   7.038  0.049  0.246 82.481  0.038  2.370   4.2264e-02
   4_xyz:   6.914  0.047  0.242 83.083  0.037  2.359   3.7147e-02
   4_adp:   6.914  0.047  0.242 83.083  0.037  2.359   3.7147e-02
   4_occ:   6.914  0.047  0.242 83.083  0.037  2.359   3.7147e-02
   5_bss:   6.914  0.047  0.242 83.083  0.037  2.359   3.7147e-02
   5_xyz:   7.552  0.055  0.276 83.410  0.037  2.276   5.5086e-02
   5_adp:   7.552  0.055  0.276 83.410  0.037  2.276   5.5086e-02
   5_occ:   7.552  0.055  0.276 83.410  0.037  2.276   5.5086e-02
   5_bss:   7.552  0.055  0.276 83.410  0.037  2.276   5.5086e-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:  82.54   0.00  16.38  82.54   0.00  12.59  62.83   6.95  37.06
   1_occ:  82.54   0.00  16.38  82.54   0.00  12.59  62.83   6.95  37.06
   2_bss:  82.54   0.00  16.38  82.54   0.00  12.59  62.83   6.95  37.06
   2_xyz:  82.54   0.00  16.38  82.54   0.00  12.59  62.83   6.95  37.06
   2_adp:  75.61   1.25  16.77  75.61   1.25  12.82  68.79   2.74  38.28
   2_occ:  75.61   1.25  16.77  75.61   1.25  12.82  68.79   2.74  38.28
   3_bss:  75.61   1.25  16.77  75.61   1.25  12.82  68.79   2.74  38.28
   3_xyz:  75.61   1.25  16.77  75.61   1.25  12.82  68.79   2.74  38.28
   3_adp:  76.60   1.28  16.57  76.60   1.28  12.67  68.63   2.85  37.79
   3_occ:  76.60   1.28  16.57  76.60   1.28  12.67  68.63   2.85  37.79
   4_bss:  76.60   1.28  16.57  76.60   1.28  12.67  68.63   2.85  37.79
   4_xyz:  76.60   1.28  16.57  76.60   1.28  12.67  68.63   2.85  37.79
   4_adp:  76.52   1.36  16.35  76.52   1.36  12.50  68.16   5.67  37.32
   4_occ:  76.52   1.36  16.35  76.52   1.36  12.50  68.16   5.67  37.32
   5_bss:  76.52   1.36  16.35  76.52   1.36  12.50  68.16   5.67  37.32
   5_xyz:  76.52   1.36  16.35  76.52   1.36  12.50  68.16   5.67  37.32
   5_adp:  77.14   0.39  16.24  77.14   0.39  12.33  68.12   5.61  37.53
   5_occ:  77.14   0.39  16.24  77.14   0.39  12.33  68.12   5.61  37.53
   5_bss:  77.13   0.38  16.23  77.13   0.38  12.32  68.11   5.60  37.52
------------------------------------------------------------------------
 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:    0.891    0.018    0.225
   1_adp:    0.891    0.018    0.225
   1_occ:    0.891    0.018    0.225
   2_bss:    0.891    0.018    0.225
   2_xyz:    0.707    0.028    0.260
   2_adp:    0.707    0.028    0.260
   2_occ:    0.707    0.028    0.260
   3_bss:    0.707    0.028    0.260
   3_xyz:    0.934    0.012    0.270
   3_adp:    0.934    0.012    0.270
   3_occ:    0.934    0.012    0.270
   4_bss:    0.934    0.012    0.270
   4_xyz:    1.034    0.019    0.278
   4_adp:    1.034    0.019    0.278
   4_occ:    1.034    0.019    0.278
   5_bss:    1.034    0.019    0.278
   5_xyz:    1.054    0.020    0.283
   5_adp:    1.054    0.020    0.283
   5_occ:    1.054    0.020    0.283
   5_bss:    1.054    0.020    0.283
------------------------------------------------------------------------

CPU time actual refinement: 265.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/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_435/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_435/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 265.29 
  Macro-tasks:
    bulk solvent and scale       = 32.80  
    individual site refinement   = 109.39 
    weights calculation          = 24.13  
    collect and process          = 5.47   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 171.88 
  Micro-tasks:
    mask                            = 0.96   
    f_calc                          = 82.93  
    alpha_beta                      = 6.95   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 91.40  
    fmodel                         = 5.10   
    r_factors                      = 0.11   
    phase_errors                   = 9.29   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 198.02 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.761 micro seconds
Total CPU time: 4.61 minutes
from_scatterers_fft:    637 calls, 82.74 s
gradients_fft:          582 calls, 79.65 s

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

# Date 2008-01-16 Time 04:48:22 PST -0800 (1200487702.83 s)
Start R-work = 0.2588, R-free = 0.2503 (no bulk solvent and anisotropic scale)
Final R-work = 0.1287, R-free = 0.1727 (no bulk solvent and anisotropic scale)

Start R-work = 0.2438, R-free = 0.2333
Final R-work = 0.1053, R-free = 0.1539