# Date 2008-01-16 Time 04:55:16 PST -0800 (1200488116.33 s)
#phil __OFF__

Command line arguments: "../515.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5405
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 515

-------------------------------------------------------------------------------
  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: (69.8988, 46.2261, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.97261
Completeness in resolution range: 0.946009
Completeness with d_max=infinity: 0.943139

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9726

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: (69.8988, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.97261
Completeness in resolution range: 0.946009
Completeness with d_max=infinity: 0.943139

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2214 [2177/2201]  1957   220  10.1%
  bin  2:  4.2214 -  3.3630 [2083/2103]  1875   208  10.0%
  bin  3:  3.3630 -  2.9415 [2071/2090]  1866   205   9.9%
  bin  4:  2.9415 -  2.6742 [2022/2052]  1816   206  10.2%
  bin  5:  2.6742 -  2.4835 [2051/2070]  1851   200   9.8%
  bin  6:  2.4835 -  2.3376 [2009/2034]  1804   205  10.2%
  bin  7:  2.3376 -  2.2209 [2014/2042]  1816   198   9.8%
  bin  8:  2.2209 -  2.1245 [2003/2039]  1800   203  10.1%
  bin  9:  2.1245 -  2.0430 [1992/2034]  1798   194   9.7%
  bin 10:  2.0430 -  1.9726 [1167/2042]  1047   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 12
        2.14 -     2.83: 943
        2.83 -     3.52: 4452
        3.52 -     4.21: 9302
        4.21 -     4.90: 13622
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.449 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.684 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.708 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.892 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28326 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_515/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 = 69.89875 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4228   r_free= 0.4232   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.229745                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.3346 0.3151      6.4996      6.4009|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.3418 0.3633      6.6803      6.6818|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.3791 0.3528      6.5926      6.5741|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.4108 0.4529      6.4629      6.5167|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.4489 0.3830      6.3036      6.2598|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.4468 0.4944       6.214      6.1608|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.4533 0.4371      6.1748      6.1142|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.4783 0.4938      6.1632      6.1602|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.4739 0.4969      6.0827      6.1394|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.4885 0.4572      6.0743      6.0382|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.4838 0.4878      6.0047       6.022|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.4941 0.4407       5.957      5.9209|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.4754 0.5151       5.846      5.8169|
| 14:  2.0218 -  1.9726 0.43    569   61 0.5017 0.4588       5.894       5.777|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7085  1414   154  0.77  27.72   0.84     0.81      50268.78|
|  2:  4.7085 -  3.7565  1359   154  0.77  29.11   0.93     0.88      77643.34|
|  3:  3.7565 -  3.2874  1330   146  0.68  36.77   0.95     0.86      84550.70|
|  4:  3.2874 -  2.9894  1325   150  0.61  42.73   0.93     0.80      78139.35|
|  5:  2.9894 -  2.7765  1310   147  0.55  48.19   0.93     0.73      59917.24|
|  6:  2.7765 -  2.6138  1316   145  0.53  49.77   0.92     0.70      53107.69|
|  7:  2.6138 -  2.4835  1311   143  0.50  51.95   0.94     0.67      49958.39|
|  8:  2.4835 -  2.3758  1291   143  0.48  53.60   0.93     0.65      47468.96|
|  9:  2.3758 -  2.2847  1288   144  0.47  54.52   0.95     0.66      44521.64|
| 10:  2.2847 -  2.2061  1285   145  0.47  54.27   0.94     0.67      40014.54|
| 11:  2.2061 -  2.1373  1294   145  0.46  55.47   0.95     0.70      39980.91|
| 12:  2.1373 -  2.0764  1277   141  0.44  56.59   0.96     0.67      36535.30|
| 13:  2.0764 -  2.0218  1261   141  0.40  59.83   0.95     0.63      33075.18|
| 14:  2.0218 -  1.9726   569    61  0.42  58.68   1.01     0.58      27640.59|
|alpha:            min =        0.58 max =            0.88 mean =         0.72|
|beta:             min =    27640.59 max =        84550.70 mean =     52883.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.82|
|phase err.(test): min =        0.00 max =           89.98 mean =        48.20|
|-----------------------------------------------------------------------------|

============================== 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 = 5.975174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.052   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.569132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.670   (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 |  1.449 -  1.794:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.794 -  2.139:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.139 -  2.484:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.484 -  2.829:      908 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.829 -  3.174:     2020 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.174 -  3.519:     2432 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.519 -  3.865:     4615 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.865 -  4.210:     4687 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.210 -  4.555:     6162 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.555 -  4.900:     7460 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.449 |       0.350 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4228   r_free= 0.4232   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.229745                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4098   r_free= 0.4122   ksol= 0.33   Bsol= 37.75   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,1.32,3.58,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.217058                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.851407              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.922   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.815231              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.505   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4098      final r-factor (work) = 0.2977          |
| start r-factor (free) = 0.4122      final r-factor (free) = 0.3274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2416 = 4.85 * 0.50 * 6.2116 + 1.00 * 0.1741                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7725 = 4.85 * 0.50 * 6.0478 + 1.00 * 0.1024                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2977      final r-factor (work) = 0.2705          |
| start r-factor (free) = 0.3274      final r-factor (free) = 0.3453          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9365 = 0.82 * 1.00 * 6.0478 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8265 = 0.82 * 1.00 * 5.9013 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.53  18.07    None  None   None       |
|    all(noH): 2823   0      0.00    103.53  18.07    None  None   None       |
|    Sol.    : 438    0      1.13    103.53  39.28    None  None   None       |
|    Mac.    : 2385   0      0.00    70.96   14.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.353:  968   |   5:    51.766 -  62.119:   69        |
|      1:    10.353 -  20.707: 1032   |   6:    62.119 -  72.473:   38        |
|      2:    20.707 -  31.060:  400   |   7:    72.473 -  82.826:    9        |
|      3:    31.060 -  41.413:  180   |   8:    82.826 -  93.179:    1        |
|      4:    41.413 -  51.766:  125   |   9:    93.179 - 103.532:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2705 r_free = 0.3453             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2703 r_free = 0.3453             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2703   r_free= 0.3453   ksol= 0.33   Bsol= 37.75   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.19,1.32,3.58,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.917332                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2690   r_free= 0.3434   ksol= 0.32   Bsol= 51.39   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.65,1.34,-0.00,0.00,0.00); trace/3= -0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.916182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.284341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.779   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.207  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2690      final r-factor (work) = 0.2013          |
| start r-factor (free) = 0.3434      final r-factor (free) = 0.2559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7946 = 3.28 * 0.50 * 5.9020 + 1.00 * 0.1024                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6062 = 3.28 * 0.50 * 5.8047 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2013      final r-factor (work) = 0.1866          |
| start r-factor (free) = 0.2559      final r-factor (free) = 0.2363          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0835 = 0.36 * 1.00 * 5.8047 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0134 = 0.36 * 1.00 * 5.6188 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.62  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    101.62  17.62    None  None   None       |
|    Sol.    : 438    0      4.69    101.62  40.55    None  None   None       |
|    Mac.    : 2385   0      0.00    70.07   13.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.162:  998   |   5:    50.810 -  60.971:   87        |
|      1:    10.162 -  20.324: 1102   |   6:    60.971 -  71.133:   41        |
|      2:    20.324 -  30.486:  286   |   7:    71.133 -  81.295:    6        |
|      3:    30.486 -  40.648:  165   |   8:    81.295 -  91.457:    1        |
|      4:    40.648 -  50.810:  136   |   9:    91.457 - 101.619:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1866 r_free = 0.2363             target_work(ml) = 5.583         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1865 r_free = 0.2359             target_work(ml) = 5.582         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1865   r_free= 0.2359   ksol= 0.32   Bsol= 51.39   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-0.65,1.34,-0.00,0.00,0.00); trace/3= -0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.582311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1865   r_free= 0.2357   ksol= 0.33   Bsol= 58.67   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.51,0.43,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.582598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.034181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.909   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.566848              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.596  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1865      final r-factor (work) = 0.1484          |
| start r-factor (free) = 0.2357      final r-factor (free) = 0.1998          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7900 = 2.03 * 0.50 * 5.6200 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6221 = 2.03 * 0.50 * 5.4747 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.1998      final r-factor (free) = 0.1921          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1143 = 0.57 * 1.00 * 5.4747 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0501 = 0.57 * 1.00 * 5.3618 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.05   17.59    None  None   None       |
|    all(noH): 2823   0      0.00    99.05   17.59    None  None   None       |
|    Sol.    : 438    0      5.31    99.05   43.03    None  None   None       |
|    Mac.    : 2385   0      0.00    80.15   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.905: 1045   |   5:    49.526 -  59.431:   99        |
|      1:     9.905 -  19.810: 1092   |   6:    59.431 -  69.336:   67        |
|      2:    19.810 -  29.715:  245   |   7:    69.336 -  79.241:   21        |
|      3:    29.715 -  39.621:  126   |   8:    79.241 -  89.146:    6        |
|      4:    39.621 -  49.526:  121   |   9:    89.146 -  99.051:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1403 r_free = 0.1921             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1402 r_free = 0.1922             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1402   r_free= 0.1922   ksol= 0.33   Bsol= 58.67   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-1.51,0.43,-0.00,0.00,0.00); trace/3= -1.15                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.342661                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1404   r_free= 0.1916   ksol= 0.33   Bsol= 62.38   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.09,-0.09,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.341508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.758041              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.904   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.784  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1404      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7689 = 1.76 * 0.50 * 5.3640 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7063 = 1.76 * 0.50 * 5.2948 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1724      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5025 = 0.28 * 1.00 * 5.2948 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4830 = 0.28 * 1.00 * 5.2300 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    95.60   17.11    None  None   None       |
|    all(noH): 2823   0      0.52    95.60   17.11    None  None   None       |
|    Sol.    : 438    0      5.51    95.60   41.52    None  None   None       |
|    Mac.    : 2385   0      0.52    83.26   12.63    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:     0.524 -  10.032: 1115   |   5:    48.061 -  57.568:   97        |
|      1:    10.032 -  19.539: 1050   |   6:    57.568 -  67.076:   62        |
|      2:    19.539 -  29.046:  226   |   7:    67.076 -  76.583:   30        |
|      3:    29.046 -  38.554:  129   |   8:    76.583 -  86.090:    8        |
|      4:    38.554 -  48.061:  105   |   9:    86.090 -  95.598:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1681             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1681             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1681   ksol= 0.33   Bsol= 62.38   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.09,-0.09,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1681   ksol= 0.33   Bsol= 62.38   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.11,-0.11,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.480896              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.645  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.406674              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.362  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9245 = 1.48 * 0.50 * 5.2298 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9006 = 1.48 * 0.50 * 5.2012 + 1.00 * 0.0494                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3257 = 1.41 * 1.00 * 5.2012 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3014 = 1.41 * 1.00 * 5.1830 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.32   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    95.32   17.12    None  None   None       |
|    Sol.    : 438    0      5.00    95.32   42.13    None  None   None       |
|    Mac.    : 2385   0      0.00    89.40   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.532: 1048   |   5:    47.661 -  57.193:   91        |
|      1:     9.532 -  19.064: 1110   |   6:    57.193 -  66.725:   70        |
|      2:    19.064 -  28.597:  227   |   7:    66.725 -  76.257:   35        |
|      3:    28.597 -  38.129:  123   |   8:    76.257 -  85.789:   15        |
|      4:    38.129 -  47.661:  101   |   9:    85.789 -  95.322:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1633             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1633             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1633   ksol= 0.33   Bsol= 62.38   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.11,-0.11,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.0996 0.1256      5.3999      5.5361|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.0874 0.1149      5.4527      5.6496|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.1123 0.1546      5.5163      5.8415|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.1291 0.1759      5.4877      5.6464|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.1371 0.1706      5.3593      5.5635|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.1283 0.2110      5.2469      5.5272|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.1380 0.1644      5.2279       5.363|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.1251 0.1737      5.1395      5.3728|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.1237 0.1902      5.0755      5.3732|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.1194 0.1747      4.9915      5.2155|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.1181 0.1841      4.9671       5.303|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.1258 0.1804      4.9472      5.2372|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.1115 0.1823       4.789       5.036|
| 14:  2.0218 -  1.9726 0.43    569   61 0.0886 0.1517      4.6038      4.8824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7085  1414   154  0.94   9.30   0.97     0.94       7382.20|
|  2:  4.7085 -  3.7565  1359   154  0.95   8.05   1.01     1.00       9270.72|
|  3:  3.7565 -  3.2874  1330   146  0.93  11.70   1.03     1.03      10855.37|
|  4:  3.2874 -  2.9894  1325   150  0.92  14.08   1.01     0.98      10669.59|
|  5:  2.9894 -  2.7765  1310   147  0.90  16.00   1.00     0.98       8751.48|
|  6:  2.7765 -  2.6138  1316   145  0.89  16.85   0.98     0.95       7500.12|
|  7:  2.6138 -  2.4835  1311   143  0.90  16.71   0.99     0.96       6893.82|
|  8:  2.4835 -  2.3758  1291   143  0.90  16.62   0.99     0.96       6180.66|
|  9:  2.3758 -  2.2847  1288   144  0.90  16.15   0.99     0.95       5410.25|
| 10:  2.2847 -  2.2061  1285   145  0.90  16.40   1.00     0.96       4707.00|
| 11:  2.2061 -  2.1373  1294   145  0.89  16.92   0.98     0.94       4634.76|
| 12:  2.1373 -  2.0764  1277   141  0.89  17.06   1.00     0.99       4509.24|
| 13:  2.0764 -  2.0218  1261   141  0.90  16.80   0.99     0.97       3465.21|
| 14:  2.0218 -  1.9726   569    61  0.94  12.02   0.98     0.95       2301.48|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2301.48 max =        10855.37 mean =      6830.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.66|
|phase err.(test): min =        0.00 max =           87.80 mean =        14.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1631   ksol= 0.33   Bsol= 62.39   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.04,-0.02,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1631   ksol= 0.33   Bsol= 62.39   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.04,-0.02,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184595                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7085 0.99   1414  154 0.1002 0.1225      5.3874      5.5119|
|  2:  4.7085 -  3.7565 0.99   1359  154 0.0876 0.1152      5.4523      5.6524|
|  3:  3.7565 -  3.2874 0.99   1330  146 0.1130 0.1534      5.5198      5.8386|
|  4:  3.2874 -  2.9894 0.99   1325  150 0.1291 0.1763      5.4876      5.6491|
|  5:  2.9894 -  2.7765 0.99   1310  147 0.1372 0.1700      5.3585      5.5613|
|  6:  2.7765 -  2.6138 0.99   1316  145 0.1282 0.2105      5.2457      5.5254|
|  7:  2.6138 -  2.4835 0.99   1311  143 0.1379 0.1651      5.2271      5.3655|
|  8:  2.4835 -  2.3758 0.98   1291  143 0.1249 0.1732       5.139      5.3705|
|  9:  2.3758 -  2.2847 0.98   1288  144 0.1237 0.1899      5.0753      5.3733|
| 10:  2.2847 -  2.2061 1.00   1285  145 0.1194 0.1750      4.9916      5.2166|
| 11:  2.2061 -  2.1373 0.98   1294  145 0.1180 0.1838      4.9673      5.3031|
| 12:  2.1373 -  2.0764 0.98   1277  141 0.1258 0.1804      4.9474      5.2369|
| 13:  2.0764 -  2.0218 0.96   1261  141 0.1114 0.1825      4.7886      5.0363|
| 14:  2.0218 -  1.9726 0.43    569   61 0.0887 0.1515      4.6035      4.8811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7085  1414   154  0.94   9.07   0.97     0.95       7065.93|
|  2:  4.7085 -  3.7565  1359   154  0.95   7.96   1.01     1.00       9106.08|
|  3:  3.7565 -  3.2874  1330   146  0.93  11.71   1.03     1.03      10882.05|
|  4:  3.2874 -  2.9894  1325   150  0.92  14.09   1.01     0.99      10669.28|
|  5:  2.9894 -  2.7765  1310   147  0.90  15.98   1.00     0.99       8725.66|
|  6:  2.7765 -  2.6138  1316   145  0.89  16.81   0.98     0.95       7474.33|
|  7:  2.6138 -  2.4835  1311   143  0.90  16.70   0.99     0.96       6880.00|
|  8:  2.4835 -  2.3758  1291   143  0.90  16.62   1.00     0.97       6177.58|
|  9:  2.3758 -  2.2847  1288   144  0.90  16.15   1.00     0.95       5410.11|
| 10:  2.2847 -  2.2061  1285   145  0.90  16.41   1.00     0.97       4713.27|
| 11:  2.2061 -  2.1373  1294   145  0.89  16.93   0.99     0.95       4640.86|
| 12:  2.1373 -  2.0764  1277   141  0.89  17.07   1.00     0.99       4515.12|
| 13:  2.0764 -  2.0218  1261   141  0.90  16.80   0.99     0.97       3461.90|
| 14:  2.0218 -  1.9726   569    61  0.94  12.01   0.98     0.96       2297.47|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2297.47 max =        10882.05 mean =      6789.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.63|
|phase err.(test): min =        0.00 max =           89.08 mean =        14.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.32   17.12    None  None   None       |
|    all(noH): 2823   0      0.00    95.32   17.12    None  None   None       |
|    Sol.    : 438    0      5.00    95.32   42.14    None  None   None       |
|    Mac.    : 2385   0      0.00    89.41   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.535: 1048   |   5:    47.664 -  57.196:   91        |
|      1:     9.535 -  19.067: 1110   |   6:    57.196 -  66.728:   70        |
|      2:    19.067 -  28.600:  227   |   7:    66.728 -  76.260:   35        |
|      3:    28.600 -  38.132:  123   |   8:    76.260 -  85.792:   15        |
|      4:    38.132 -  47.664:  101   |   9:    85.792 -  95.325:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.610 - 4.787
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 302
   mapped sites are within: 0.718 - 4.787

peak=    5.625 closest distance to " CG  PRO A  54 " =    1.409
peak=    5.596 closest distance to " NE2 GLN A  11 " =    1.157
peak=    5.390 closest distance to " O   HOH Z 142 " =    2.033
peak=    5.114 closest distance to " O   HOH Z 287 " =    1.923
peak=    5.099 closest distance to " CB  GLN A 223 " =    1.481
peak=    5.069 closest distance to " O   HOH Z 423 " =    1.647
peak=    4.910 closest distance to " O   HOH Z 369 " =    2.324
peak=    4.857 closest distance to " NH2 ARG A  56 " =    2.072
peak=    4.769 closest distance to " CB  ARG A 275 " =    0.991
peak=    4.764 closest distance to " O   HOH Z 417 " =    1.475
peak=    4.755 closest distance to " O   HOH Z 126 " =    2.046
peak=    4.736 closest distance to " CB  PRO A  54 " =    1.065
peak=    4.721 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.682 closest distance to " CG2 VAL A 257 " =    0.915
peak=    4.636 closest distance to " O   HOH Z 403 " =    1.632
peak=    4.635 closest distance to " O   HOH Z   9 " =    1.583
peak=    4.595 closest distance to " CG  PRO A 198 " =    1.269
peak=    4.552 closest distance to " O   HOH Z 419 " =    2.385
peak=    4.536 closest distance to " CG  PRO A  90 " =    1.215
peak=    4.531 closest distance to " O   HOH Z  78 " =    1.623
peak=    4.523 closest distance to " O   HOH Z 427 " =    2.654
peak=    4.488 closest distance to " O   HOH Z 298 " =    1.957
peak=    4.417 closest distance to " CZ  PHE A 218 " =    1.099
peak=    4.410 closest distance to " O   HOH Z 112 " =    1.125
peak=    4.407 closest distance to " CB  ASN A 148 " =    1.457
peak=    4.396 closest distance to " CG  PRO A 213 " =    1.273
peak=    4.338 closest distance to " CB  VAL A 265 " =    1.243
peak=    4.326 closest distance to " CB  SER A  63 " =    1.238
peak=    4.322 closest distance to " O   HOH Z  63 " =    1.516
peak=    4.291 closest distance to " CA  ARG A 195 " =    1.246
peak=    4.287 closest distance to " CB  ARG A 190 " =    1.521
peak=    4.238 closest distance to " O   HOH Z 380 " =    1.689
peak=    4.211 closest distance to " ND2 ASN A 187 " =    1.660
peak=    4.165 closest distance to " CB  ARG A  79 " =    1.376
peak=    4.161 closest distance to " CB  GLU A 277 " =    3.623
peak=    4.115 closest distance to " CZ3 TRP A 266 " =    1.159
peak=    4.112 closest distance to " NH2AARG A 190 " =    1.942
peak=    4.102 closest distance to " O   HOH Z   1 " =    1.829
peak=    4.097 closest distance to " NZ  LYS A 119 " =    2.380
peak=    4.094 closest distance to " NH1AARG A 145 " =    1.257
peak=    4.085 closest distance to " O   HOH Z  49 " =    1.104
peak=    4.058 closest distance to " CG  TRP A 179 " =    2.199
peak=    4.038 closest distance to " CA  TYR A  30 " =    1.011
peak=    4.029 closest distance to " O   HOH Z 362 " =    2.453
peak=    4.027 closest distance to " O   HOH Z  40 " =    1.623
peak=    4.026 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.012 closest distance to " O   HOH Z  69 " =    0.909
peak=    4.011 closest distance to " CD  ARG A 159 " =    0.758
peak=    4.011 closest distance to " CB  ASN A 142 " =    0.950
peak=    4.002 closest distance to " CG  PRO A 243 " =    1.058
peak=    3.986 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.955 closest distance to " O   HOH Z   7 " =    1.331
peak=    3.952 closest distance to " CD2 TRP A 179 " =    1.276
peak=    3.943 closest distance to " O   HOH Z 352 " =    1.733
peak=    3.928 closest distance to " O   HOH Z 406 " =    1.629
peak=    3.908 closest distance to " OG ASER A 258 " =    3.126
peak=    3.900 closest distance to " O   HOH Z 188 " =    2.743
peak=    3.890 closest distance to " NE2 HIS A 207 " =    1.091
peak=    3.888 closest distance to " CA  VAL A 125 " =    1.158
peak=    3.882 closest distance to " CB  SER A 216 " =    0.958
peak=    3.876 closest distance to " CB  GLU A 128 " =    0.971
peak=    3.872 closest distance to " O   HOH Z 368 " =    3.612
peak=    3.869 closest distance to " O   HOH Z 425 " =    1.350
peak=    3.866 closest distance to " CG2 ILE A 120 " =    1.271
peak=    3.859 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.847 closest distance to " CB  SER A 212 " =    1.252
peak=    3.847 closest distance to " CE  LYS A 119 " =    1.229
peak=    3.838 closest distance to " O   HOH Z 405 " =    1.428
peak=    3.831 closest distance to " O   ASN A  74 " =    1.476
peak=    3.828 closest distance to " O   HOH Z 236 " =    1.380
peak=    3.819 closest distance to " O   HOH Z 214 " =    2.366
peak=    3.818 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.814 closest distance to " CA  ALA A  51 " =    0.957
peak=    3.802 closest distance to " O   HOH Z 365 " =    2.733
peak=    3.787 closest distance to " O   HOH Z 272 " =    1.785
peak=    3.784 closest distance to " CB  VAL A 202 " =    1.616
peak=    3.776 closest distance to " O   HOH Z 359 " =    1.508
peak=    3.773 closest distance to " O   HOH Z   2 " =    1.539
peak=    3.757 closest distance to " O   HOH Z 193 " =    1.717
peak=    3.755 closest distance to " CB  LEU A 228 " =    1.097
peak=    3.753 closest distance to " OD1 ASN A  69 " =    2.572
peak=    3.751 closest distance to " OE2 GLU A  53 " =    2.113
peak=    3.751 closest distance to " O   SER A  87 " =    2.239
peak=    3.745 closest distance to " O   HOH Z 375 " =    1.069
peak=    3.743 closest distance to " O   HOH Z  30 " =    1.813
peak=    3.735 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.734 closest distance to " CB  ASN A  39 " =    0.986
peak=    3.734 closest distance to " NZ  LYS A 117 " =    2.915
peak=    3.729 closest distance to " CB  THR A  31 " =    1.540
peak=    3.729 closest distance to " CG AARG A 275 " =    1.172
peak=    3.724 closest distance to " CA  ASN A 127 " =    1.094
peak=    3.721 closest distance to " O   HOH Z 394 " =    1.707
peak=    3.719 closest distance to " CB  PRO A  90 " =    1.048
peak=    3.712 closest distance to " N   TYR A 116 " =    1.429
peak=    3.708 closest distance to " CA  SER A  87 " =    1.069
peak=    3.699 closest distance to " O   HOH Z 180 " =    2.217
peak=    3.696 closest distance to " CB  ARG A  79 " =    0.948
peak=    3.694 closest distance to " O   HOH Z 250 " =    1.502
peak=    3.688 closest distance to " O   HOH Z   1 " =    1.857
peak=    3.687 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.683 closest distance to " O   HOH Z 172 " =    2.904
peak=    3.679 closest distance to " O   HOH Z 422 " =    2.524
peak=    3.673 closest distance to " O   HOH Z 346 " =    1.652
peak=    3.673 closest distance to " CA  ALA A 160 " =    1.244
peak=    3.672 closest distance to " O   HOH Z  44 " =    1.741
peak=    3.668 closest distance to " O   HOH Z   3 " =    2.055
peak=    3.665 closest distance to " CA  ASP A 124 " =    0.773
peak=    3.660 closest distance to " CB  SER A 210 " =    0.791
peak=    3.658 closest distance to " ND1 HIS A  86 " =    1.719
peak=    3.655 closest distance to " O   HOH Z 286 " =    2.437
peak=    3.652 closest distance to " OG BSER A 164 " =    2.271
peak=    3.650 closest distance to " CD  ARG A 269 " =    0.965
peak=    3.649 closest distance to " O   HOH Z 258 " =    2.117
peak=    3.648 closest distance to " O   HOH Z 437 " =    1.468
peak=    3.643 closest distance to " CG  GLN A  58 " =    1.010
peak=    3.642 closest distance to " O   HOH Z 215 " =    1.417
peak=    3.642 closest distance to " O   HOH Z  59 " =    1.705
peak=    3.616 closest distance to " CB  ASN A 187 " =    1.126
peak=    3.613 closest distance to " O   HOH Z 327 " =    1.552
peak=    3.612 closest distance to " CB  TRP A 266 " =    1.089
peak=    3.610 closest distance to " O   HOH Z  61 " =    1.722
peak=    3.608 closest distance to " O   ASN A  74 " =    2.072
peak=    3.604 closest distance to " CB  GLU A  46 " =    1.044
peak=    3.603 closest distance to " CZ  PHE A  38 " =    1.218
peak=    3.598 closest distance to " OG  SER A  62 " =    2.922
peak=    3.596 closest distance to " CB  SER A  62 " =    1.061
peak=    3.595 closest distance to " O   HOH Z 290 " =    1.074
peak=    3.589 closest distance to " CB  LYS A 117 " =    1.253
peak=    3.587 closest distance to " O   HOH Z 261 " =    1.909
peak=    3.581 closest distance to " CE3 TRP A 150 " =    1.144
peak=    3.571 closest distance to " O   HOH Z 116 " =    2.962
peak=    3.566 closest distance to " O   TYR A 116 " =    1.271
peak=    3.562 closest distance to " O   HOH Z 421 " =    2.145
peak=    3.556 closest distance to " CB  ALA A 114 " =    0.861
peak=    3.556 closest distance to " O   HOH Z 213 " =    2.330
peak=    3.556 closest distance to " CA  ILE A 234 " =    1.034
peak=    3.551 closest distance to " O   HOH Z 132 " =    2.397
peak=    3.550 closest distance to " O   HOH Z 126 " =    1.523
peak=    3.549 closest distance to " O   HOH Z 158 " =    3.029
peak=    3.537 closest distance to " CB  SER A   3 " =    1.287
peak=    3.534 closest distance to " O   HOH Z 394 " =    3.800
peak=    3.521 closest distance to " O   HOH Z  68 " =    2.234
peak=    3.519 closest distance to " O   HOH Z 285 " =    2.149
peak=    3.513 closest distance to " NZ  LYS A 166 " =    1.017
peak=    3.508 closest distance to " O   HOH Z 368 " =    4.250
peak=    3.505 closest distance to " O   HOH Z 402 " =    1.393
peak=    3.497 closest distance to " N   GLN A 278 " =    1.377
peak=    3.488 closest distance to " CB  ASP A 124 " =    0.829
peak=    3.487 closest distance to " ND2BASN A 224 " =    0.845
peak=    3.477 closest distance to " OG1 THR A 264 " =    0.718
peak=    3.471 closest distance to " O   HOH Z 325 " =    2.224
peak=    3.463 closest distance to " O   HOH Z 234 " =    3.639
peak=    3.462 closest distance to " O   PRO A 198 " =    1.238
peak=    3.460 closest distance to " CB  TRP A 179 " =    1.424
peak=    3.458 closest distance to " O  BHOH Z 338 " =    2.371
peak=    3.454 closest distance to " CB  LEU A 300 " =    0.944
peak=    3.450 closest distance to " CA  ASN A 215 " =    0.982
peak=    3.445 closest distance to " CB  ASN A 110 " =    1.088
peak=    3.445 closest distance to " O   HOH Z 294 " =    1.500
peak=    3.434 closest distance to " N   ARG A 156 " =    1.335
peak=    3.429 closest distance to " O   HOH Z 248 " =    1.531
peak=    3.429 closest distance to " CB  ASN A 215 " =    1.139
peak=    3.425 closest distance to " O   HOH Z 265 " =    1.985
peak=    3.423 closest distance to " O   HOH Z 193 " =    2.077
peak=    3.423 closest distance to " CA  ASN A 217 " =    1.211
peak=    3.410 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.407 closest distance to " CA  ARG A  36 " =    1.004
peak=    3.407 closest distance to " O   HOH Z 368 " =    1.877
peak=    3.405 closest distance to " CA  ARG A 156 " =    1.036
peak=    3.404 closest distance to " CB  GLU A 152 " =    1.216
peak=    3.401 closest distance to " CA  GLU A  46 " =    1.014
peak=    3.398 closest distance to " CB  TYR A 116 " =    0.885
peak=    3.395 closest distance to " O   HOH Z  10 " =    1.712
peak=    3.392 closest distance to " O   THR A 220 " =    1.304
peak=    3.390 closest distance to " CG1BVAL A  72 " =    1.574
peak=    3.390 closest distance to " O   HOH Z 344 " =    3.136
peak=    3.390 closest distance to " O   HOH Z 188 " =    1.512
peak=    3.388 closest distance to " N   PHE A 130 " =    1.247
peak=    3.387 closest distance to " CA  ALA A 158 " =    1.233
peak=    3.384 closest distance to " CB  HIS A 108 " =    0.824
peak=    3.382 closest distance to " O   HOH Z 218 " =    1.567
peak=    3.381 closest distance to " O   HOH Z  90 " =    2.203
peak=    3.381 closest distance to " O   HOH Z 391 " =    2.895
peak=    3.376 closest distance to " CB  SER A 273 " =    0.866
peak=    3.374 closest distance to " O   HOH Z 305 " =    3.589
peak=    3.373 closest distance to " CD  ARG A  66 " =    2.162
peak=    3.371 closest distance to " O   HOH Z 411 " =    3.763
peak=    3.366 closest distance to " CB  PHE A 130 " =    0.933
peak=    3.361 closest distance to " CB  ALA A 291 " =    1.247
peak=    3.359 closest distance to " O   PHE A 192 " =    1.383
peak=    3.357 closest distance to " NZ  LYS A 119 " =    1.349
peak=    3.354 closest distance to " O   HOH Z  97 " =    2.168
peak=    3.353 closest distance to " O   HOH Z 251 " =    1.500
peak=    3.348 closest distance to " CA  THR A 264 " =    0.849
peak=    3.341 closest distance to " O   HOH Z 357 " =    2.059
peak=    3.338 closest distance to " O   PRO A 198 " =    1.554
peak=    3.336 closest distance to " CG1 ILE A 151 " =    0.993
peak=    3.333 closest distance to " CD1 LEU A 300 " =    1.103
peak=    3.333 closest distance to " NE2 GLN A  73 " =    1.685
peak=    3.332 closest distance to " CB  ILE A 120 " =    1.409
peak=    3.330 closest distance to " O   HOH Z 371 " =    1.940
peak=    3.330 closest distance to " CD1 LEU A  96 " =    0.771
peak=    3.324 closest distance to " CG1 VAL A 153 " =    0.970
peak=    3.324 closest distance to " CB  GLN A  89 " =    1.315
peak=    3.323 closest distance to " O   HOH Z 425 " =    1.967
peak=    3.321 closest distance to " O   HOH Z 128 " =    1.991
peak=    3.320 closest distance to " NE  ARG A  56 " =    3.543
peak=    3.315 closest distance to " CA  MET A 105 " =    0.929
peak=    3.315 closest distance to " CG  MET A 113 " =    1.036
peak=    3.306 closest distance to " CG2 ILE A 239 " =    0.761
peak=    3.305 closest distance to " O   HOH Z 261 " =    1.704
peak=    3.299 closest distance to " NH1 ARG A 138 " =    1.012
peak=    3.298 closest distance to " CB  ARG A 139 " =    1.188
peak=    3.296 closest distance to " O   HOH Z 128 " =    2.095
peak=    3.292 closest distance to " CB  TYR A  30 " =    1.437
peak=    3.291 closest distance to " O   HOH Z 153 " =    3.729
peak=    3.290 closest distance to " N   ASN A  39 " =    1.237
peak=    3.289 closest distance to " CB  ARG A 219 " =    0.924
peak=    3.284 closest distance to " O   HOH Z 244 " =    1.735
peak=    3.280 closest distance to " CB  SER A  62 " =    0.801
peak=    3.280 closest distance to " OG BSER A 134 " =    2.898
peak=    3.275 closest distance to " CB  ALA A 114 " =    0.987
peak=    3.274 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.263 closest distance to " O   HOH Z 201 " =    1.358
peak=    3.263 closest distance to " CA  ALA A 129 " =    1.268
peak=    3.261 closest distance to " O   THR A 182 " =    1.398
peak=    3.254 closest distance to " CB  ALA A   1 " =    4.725
peak=    3.254 closest distance to " CB  LEU A  83 " =    0.760
peak=    3.254 closest distance to " O   HOH Z  49 " =    3.425
peak=    3.251 closest distance to " CA  ARG A 102 " =    1.182
peak=    3.251 closest distance to " O   HOH Z  43 " =    1.729
peak=    3.249 closest distance to " CD2 LEU A 297 " =    0.991
peak=    3.245 closest distance to " O   HOH Z   9 " =    1.806
peak=    3.243 closest distance to " CA  ALA A 233 " =    1.288
peak=    3.242 closest distance to " CB  PRO A 243 " =    1.345
peak=    3.234 closest distance to " O   HOH Z 216 " =    4.009
peak=    3.233 closest distance to " CG  GLU A 277 " =    2.024
peak=    3.229 closest distance to " O   CYS A 168 " =    1.334
peak=    3.227 closest distance to " N   VAL A 296 " =    1.788
peak=    3.226 closest distance to " OH  TYR A 116 " =    1.004
peak=    3.220 closest distance to " O   HOH Z  47 " =    1.845
peak=    3.220 closest distance to " NZ  LYS A 117 " =    1.269
peak=    3.218 closest distance to " CB  THR A 157 " =    1.102
peak=    3.218 closest distance to " O   HOH Z 434 " =    1.397
peak=    3.216 closest distance to " CA  SER A  95 " =    1.007
peak=    3.214 closest distance to " CB  ARG A 138 " =    0.862
peak=    3.213 closest distance to " O   HOH Z  26 " =    1.284
peak=    3.202 closest distance to " CB  PHE A 204 " =    0.729
peak=    3.201 closest distance to " O   HOH Z 156 " =    2.651
peak=    3.200 closest distance to " O   HOH Z  88 " =    3.758
peak=    3.197 closest distance to " N   GLU A   2 " =    1.491
peak=    3.192 closest distance to " CG2 VAL A 232 " =    0.844
peak=    3.192 closest distance to " CG2 ILE A  20 " =    1.529
peak=    3.187 closest distance to " CB  MET A  40 " =    0.810
peak=    3.180 closest distance to " O   HOH Z  42 " =    1.535
peak=    3.180 closest distance to " O   HOH Z 272 " =    2.197
peak=    3.180 closest distance to " CB  ASP A 140 " =    1.045
peak=    3.178 closest distance to " O   HOH Z 285 " =    2.677
peak=    3.177 closest distance to " CB  TYR A 169 " =    0.941
peak=    3.176 closest distance to " O  BHOH Z  74 " =    1.329
peak=    3.175 closest distance to " O   THR A 251 " =    1.092
peak=    3.172 closest distance to " O   HOH Z 298 " =    2.619
peak=    3.171 closest distance to " NH1 ARG A  14 " =    1.164
peak=    3.168 closest distance to " CG1 ILE A  33 " =    1.280
peak=    3.162 closest distance to " CE3 TRP A  85 " =    0.991
peak=    3.161 closest distance to " N   GLU A  44 " =    1.147
peak=    3.160 closest distance to " CA  ARG A 159 " =    1.258
peak=    3.160 closest distance to " O   HOH Z 371 " =    2.901
peak=    3.158 closest distance to " OG BSER A  99 " =    2.350
peak=    3.158 closest distance to " CG1 ILE A 120 " =    1.111
peak=    3.153 closest distance to " CD1 ILE A 199 " =    1.163
peak=    3.150 closest distance to " CA  LEU A 101 " =    1.541
peak=    3.143 closest distance to " O   HOH Z 193 " =    1.528
peak=    3.140 closest distance to " CG2 VAL A 197 " =    1.021
peak=    3.140 closest distance to " O   HOH Z 343 " =    3.166
peak=    3.137 closest distance to " O   HOH Z 106 " =    2.203
peak=    3.135 closest distance to " O   HOH Z  88 " =    2.664
peak=    3.133 closest distance to " N   ASP A 162 " =    1.048
peak=    3.133 closest distance to " N   CYS A 260 " =    0.862
peak=    3.132 closest distance to " O   HOH Z 299 " =    2.596
peak=    3.131 closest distance to " CE  LYS A  48 " =    1.152
peak=    3.130 closest distance to " CA  ALA A 291 " =    0.812
peak=    3.128 closest distance to " O   MET A 105 " =    1.882
peak=    3.127 closest distance to " O   HOH Z 194 " =    2.382
peak=    3.119 closest distance to " NH1BARG A 145 " =    1.207
peak=    3.113 closest distance to " O   HOH Z 109 " =    2.582
peak=    3.108 closest distance to " O   HOH Z 145 " =    1.176
peak=    3.102 closest distance to " O   HOH Z 183 " =    1.371
peak=    3.102 closest distance to " O   HOH Z 213 " =    1.906
peak=    3.098 closest distance to " O   HOH Z 172 " =    4.787
peak=    3.088 closest distance to " O   HOH Z 181 " =    2.094
peak=    3.074 closest distance to " O   HOH Z  94 " =    2.384
peak=    3.060 closest distance to " CA  ALA A 299 " =    0.928
peak=    3.059 closest distance to " O   HOH Z 113 " =    2.129
peak=    3.057 closest distance to " O   PRO A  90 " =    1.566
peak=    3.055 closest distance to " N   TYR A  15 " =    1.091
peak=    3.048 closest distance to " N   ASN A 127 " =    1.310
peak=    3.023 closest distance to " CB  ARG A 156 " =    1.081
peak=    3.013 closest distance to " O   THR A 294 " =    0.988

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.845 - 5.558
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.845 - 5.558

peak=   -4.716 closest distance to " CD  ARG A  14 " =    3.379
peak=   -4.557 closest distance to " O   HOH Z 377 " =    2.040
peak=   -4.505 closest distance to " CD  ARG A 156 " =    2.079
peak=   -4.480 closest distance to " O   PRO A 198 " =    1.186
peak=   -4.344 closest distance to " OG BSER A 134 " =    1.313
peak=   -4.187 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.159 closest distance to " O   HOH Z 231 " =    2.126
peak=   -4.135 closest distance to " C   HIS A 108 " =    1.153
peak=   -4.031 closest distance to " O   HOH Z  69 " =    1.682
peak=   -4.013 closest distance to " CB  ALA A  43 " =    2.518
peak=   -3.991 closest distance to " O   HOH Z  60 " =    1.610
peak=   -3.986 closest distance to " CB  PHE A 192 " =    2.003
peak=   -3.978 closest distance to " O   VAL A  67 " =    2.561
peak=   -3.915 closest distance to " CG  GLN A  58 " =    1.036
peak=   -3.913 closest distance to " CB  ALA A 291 " =    2.239
peak=   -3.892 closest distance to " CD2 TYR A 293 " =    1.835
peak=   -3.881 closest distance to " O   HOH Z 351 " =    1.588
peak=   -3.855 closest distance to " O   ALA A  10 " =    1.632
peak=   -3.853 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.849 closest distance to " CE BMET A  47 " =    1.167
peak=   -3.829 closest distance to " O   HOH Z 131 " =    4.039
peak=   -3.828 closest distance to " CE  MET A 105 " =    2.514
peak=   -3.823 closest distance to " O   HOH Z 185 " =    2.189
peak=   -3.805 closest distance to " CG  MET A 105 " =    1.025
peak=   -3.795 closest distance to " CD1 LEU A 255 " =    2.883
peak=   -3.787 closest distance to " O   HOH Z 211 " =    1.149
peak=   -3.778 closest distance to " ND2 ASN A 249 " =    2.212
peak=   -3.773 closest distance to " N   THR A 157 " =    1.537
peak=   -3.766 closest distance to " CA  GLY A 241 " =    2.275
peak=   -3.756 closest distance to " O   GLU A 152 " =    1.385
peak=   -3.725 closest distance to " CG2 THR A 178 " =    2.208
peak=   -3.720 closest distance to " CB  ASN A  39 " =    2.357
peak=   -3.709 closest distance to " O   HOH Z 266 " =    5.530
peak=   -3.688 closest distance to " OD1 ASP A 171 " =    1.588
peak=   -3.679 closest distance to " O   HOH Z 102 " =    1.496
peak=   -3.676 closest distance to " O   HOH Z 198 " =    1.344
peak=   -3.664 closest distance to " CZ3 TRP A 179 " =    1.262
peak=   -3.652 closest distance to " CE2 TYR A  30 " =    2.603
peak=   -3.648 closest distance to " O   HOH Z 313 " =    1.647
peak=   -3.638 closest distance to " O   HOH Z 278 " =    1.164
peak=   -3.632 closest distance to " O   HOH Z 298 " =    2.602
peak=   -3.616 closest distance to " O   HOH Z 166 " =    1.716
peak=   -3.616 closest distance to " CB  ASP A  27 " =    2.375
peak=   -3.609 closest distance to " O   TYR A 247 " =    2.796
peak=   -3.598 closest distance to " O   HOH Z 286 " =    1.630
peak=   -3.595 closest distance to " CG2 ILE A  20 " =    2.976
peak=   -3.592 closest distance to " O   SER A 135 " =    1.428
peak=   -3.587 closest distance to " OD2 ASP A 191 " =    1.348
peak=   -3.572 closest distance to " N   ALA A  43 " =    2.592
peak=   -3.569 closest distance to " O   HOH Z 348 " =    2.116
peak=   -3.568 closest distance to " CZ2 TRP A  92 " =    2.870
peak=   -3.567 closest distance to " CB  GLN A  11 " =    1.711
peak=   -3.564 closest distance to " O   PRO A 243 " =    2.579
peak=   -3.563 closest distance to " CD1 LEU A 101 " =    2.235
peak=   -3.561 closest distance to " O   ILE A  49 " =    1.710
peak=   -3.556 closest distance to " O   TYR A 186 " =    1.528
peak=   -3.556 closest distance to " O   HOH Z 290 " =    1.027
peak=   -3.545 closest distance to " O   PHE A 218 " =    1.406
peak=   -3.543 closest distance to " CG  GLN A 223 " =    1.966
peak=   -3.519 closest distance to " CE2 PHE A 218 " =    2.422
peak=   -3.513 closest distance to " OG  SER A  97 " =    2.181
peak=   -3.511 closest distance to " O   HOH Z  65 " =    1.210
peak=   -3.511 closest distance to " O   SER A 210 " =    1.968
peak=   -3.501 closest distance to " CA  ASN A 127 " =    1.335
peak=   -3.495 closest distance to " CG2 ILE A 151 " =    2.611
peak=   -3.495 closest distance to " O   HOH Z 174 " =    2.654
peak=   -3.494 closest distance to " CA  ASP A 298 " =    1.106
peak=   -3.488 closest distance to " CZ2 TRP A 274 " =    0.947
peak=   -3.477 closest distance to " O   HOH Z  24 " =    1.128
peak=   -3.477 closest distance to " O   ARG A 145 " =    1.326
peak=   -3.469 closest distance to " O   HOH Z 318 " =    1.856
peak=   -3.469 closest distance to " O   PRO A 163 " =    1.860
peak=   -3.463 closest distance to " OG  SER A  87 " =    1.565
peak=   -3.463 closest distance to " O   HOH Z 191 " =    5.558
peak=   -3.460 closest distance to " CG  GLU A 277 " =    1.299
peak=   -3.459 closest distance to " O   HOH Z 216 " =    1.385
peak=   -3.454 closest distance to " NE2 GLN A 278 " =    1.515
peak=   -3.454 closest distance to " ND2 ASN A  45 " =    2.112
peak=   -3.453 closest distance to " CG2 THR A  18 " =    2.775
peak=   -3.448 closest distance to " CG1 VAL A 112 " =    3.020
peak=   -3.446 closest distance to " O   HOH Z  64 " =    1.250
peak=   -3.437 closest distance to " O   HOH Z   1 " =    1.346
peak=   -3.436 closest distance to " CA  GLY A  98 " =    1.826
peak=   -3.426 closest distance to " OD1 ASP A 191 " =    1.738
peak=   -3.424 closest distance to " O   HOH Z 372 " =    2.373
peak=   -3.413 closest distance to " O   HOH Z 407 " =    2.922
peak=   -3.406 closest distance to " CB  ALA A   7 " =    2.084
peak=   -3.405 closest distance to " O   HOH Z 295 " =    1.816
peak=   -3.404 closest distance to " O   ASN A 249 " =    1.671
peak=   -3.404 closest distance to " O   HOH Z  49 " =    1.168
peak=   -3.394 closest distance to " O   HOH Z 389 " =    2.097
peak=   -3.394 closest distance to " CA  GLY A 203 " =    2.389
peak=   -3.384 closest distance to " O   HOH Z 385 " =    1.945
peak=   -3.383 closest distance to " CD  LYS A 166 " =    2.579
peak=   -3.382 closest distance to " ND2 ASN A 187 " =    1.525
peak=   -3.381 closest distance to " O   HOH Z 394 " =    1.600
peak=   -3.381 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.379 closest distance to " O   HOH Z  32 " =    2.058
peak=   -3.379 closest distance to " OXT GLY A 302 " =    3.111
peak=   -3.379 closest distance to " CG  PRO A 198 " =    1.824
peak=   -3.378 closest distance to " OE1 GLN A  88 " =    1.130
peak=   -3.378 closest distance to " O   HOH Z 429 " =    1.940
peak=   -3.377 closest distance to " CD2 PHE A  61 " =    2.046
peak=   -3.377 closest distance to " O   HOH Z  15 " =    1.500
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.322
peak=   -3.365 closest distance to " O   HOH Z  39 " =    1.050
peak=   -3.355 closest distance to " O   GLN A 240 " =    1.989
peak=   -3.351 closest distance to " CB  TYR A  15 " =    2.227
peak=   -3.350 closest distance to " O   HOH Z 219 " =    4.518
peak=   -3.346 closest distance to " O   HOH Z 359 " =    3.048
peak=   -3.346 closest distance to " O   HOH Z 285 " =    1.803
peak=   -3.336 closest distance to " O   HOH Z  28 " =    1.490
peak=   -3.332 closest distance to " CD1 ILE A 199 " =    2.490
peak=   -3.330 closest distance to " CE2 PHE A  61 " =    2.734
peak=   -3.320 closest distance to " OE1 GLN A 183 " =    1.616
peak=   -3.317 closest distance to " O   HOH Z 231 " =    1.272
peak=   -3.312 closest distance to " O   HOH Z 389 " =    1.426
peak=   -3.312 closest distance to " CG2 ILE A 263 " =    2.389
peak=   -3.308 closest distance to " O   HOH Z  11 " =    1.637
peak=   -3.301 closest distance to " O   VAL A 189 " =    2.621
peak=   -3.290 closest distance to " CB  PRO A  54 " =    2.484
peak=   -3.287 closest distance to " O   TRP A  70 " =    1.410
peak=   -3.282 closest distance to " OH  TYR A 172 " =    1.875
peak=   -3.282 closest distance to " O   HOH Z   9 " =    1.706
peak=   -3.278 closest distance to " O   HOH Z 418 " =    1.584
peak=   -3.275 closest distance to " O   HOH Z 298 " =    1.158
peak=   -3.272 closest distance to " NE2 GLN A 194 " =    1.851
peak=   -3.272 closest distance to " O   HOH Z 351 " =    1.718
peak=   -3.267 closest distance to " O   HOH Z 412 " =    4.037
peak=   -3.266 closest distance to " C   PHE A  59 " =    1.233
peak=   -3.266 closest distance to " CB  GLN A  55 " =    1.208
peak=   -3.264 closest distance to " N   GLN A  58 " =    1.338
peak=   -3.263 closest distance to " CB  ALA A 114 " =    2.603
peak=   -3.260 closest distance to " OG BSER A 134 " =    1.845
peak=   -3.260 closest distance to " O   HOH Z 165 " =    2.235
peak=   -3.257 closest distance to " O   HOH Z  71 " =    1.139
peak=   -3.256 closest distance to " CB  ALA A 291 " =    2.037
peak=   -3.253 closest distance to " O   SER A  22 " =    2.526
peak=   -3.249 closest distance to " OD2 ASP A 171 " =    2.249
peak=   -3.248 closest distance to " ND2 ASN A  69 " =    1.797
peak=   -3.243 closest distance to " O   HOH Z 317 " =    1.551
peak=   -3.240 closest distance to " O   ALA A 161 " =    1.658
peak=   -3.240 closest distance to " CG  GLN A  88 " =    0.845
peak=   -3.239 closest distance to " CZ  TYR A 169 " =    1.719
peak=   -3.238 closest distance to " O   HOH Z 276 " =    1.621
peak=   -3.238 closest distance to " O   HOH Z 111 " =    1.864
peak=   -3.237 closest distance to " O   GLY A  17 " =    1.115
peak=   -3.237 closest distance to " O   HOH Z 364 " =    1.522
peak=   -3.236 closest distance to " CG1 VAL A  78 " =    2.666
peak=   -3.231 closest distance to " O   HOH Z 421 " =    2.951
peak=   -3.230 closest distance to " O   ALA A 180 " =    1.258
peak=   -3.224 closest distance to " C   ASN A 285 " =    2.309
peak=   -3.223 closest distance to " O   HOH Z  38 " =    1.894
peak=   -3.223 closest distance to " CE3 TRP A 150 " =    2.239
peak=   -3.221 closest distance to " CB  SER A 210 " =    1.089
peak=   -3.220 closest distance to " CE1 TYR A 247 " =    2.738
peak=   -3.220 closest distance to " O   PRO A 198 " =    1.431
peak=   -3.216 closest distance to " O   ARG A  24 " =    1.780
peak=   -3.215 closest distance to " O   HOH Z 393 " =    4.907
peak=   -3.215 closest distance to " O   ALA A   1 " =    1.599
peak=   -3.211 closest distance to " O   HOH Z 252 " =    4.018
peak=   -3.204 closest distance to " O   HOH Z 414 " =    1.390
peak=   -3.202 closest distance to " CG  LEU A 167 " =    0.998
peak=   -3.202 closest distance to " O   HOH Z 100 " =    1.340
peak=   -3.200 closest distance to " CE3 TRP A 274 " =    2.307
peak=   -3.199 closest distance to " O   HOH Z 281 " =    2.710
peak=   -3.198 closest distance to " O   HOH Z  63 " =    2.176
peak=   -3.196 closest distance to " O   HOH Z 253 " =    3.813
peak=   -3.194 closest distance to " O   HOH Z 193 " =    1.270
peak=   -3.193 closest distance to " CA  GLY A  57 " =    2.124
peak=   -3.192 closest distance to " CB  ALA A  10 " =    2.322
peak=   -3.186 closest distance to " OD1 ASN A 187 " =    1.634
peak=   -3.184 closest distance to " O   HOH Z 292 " =    1.557
peak=   -3.183 closest distance to " CD2 PHE A 225 " =    1.051
peak=   -3.182 closest distance to " ND2 ASN A  45 " =    1.191
peak=   -3.181 closest distance to " CG  ARG A 269 " =    2.470
peak=   -3.180 closest distance to " O   HOH Z 256 " =    1.342
peak=   -3.180 closest distance to " O   HOH Z 140 " =    1.281
peak=   -3.178 closest distance to " ND2BASN A 224 " =    1.818
peak=   -3.168 closest distance to " O   HOH Z 108 " =    1.442
peak=   -3.167 closest distance to " O   HOH Z 134 " =    3.981
peak=   -3.167 closest distance to " CB  ALA A   9 " =    2.391
peak=   -3.166 closest distance to " CD  GLU A 236 " =    1.136
peak=   -3.160 closest distance to " O   HOH Z 345 " =    2.111
peak=   -3.154 closest distance to " O   HOH Z  90 " =    2.519
peak=   -3.154 closest distance to " CB  ASP A 286 " =    2.279
peak=   -3.152 closest distance to " O   HOH Z  20 " =    1.657
peak=   -3.149 closest distance to " CD  GLN A 223 " =    1.828
peak=   -3.148 closest distance to " CG  LEU A  83 " =    2.130
peak=   -3.133 closest distance to " O   HOH Z  52 " =    1.436
peak=   -3.132 closest distance to " O   LEU A 101 " =    2.175
peak=   -3.120 closest distance to " CB  TRP A  85 " =    2.373
peak=   -3.112 closest distance to " O   HOH Z 390 " =    2.358
peak=   -3.109 closest distance to " CD  GLN A  77 " =    1.427
peak=   -3.105 closest distance to " CB  ALA A 158 " =    1.771
peak=   -3.103 closest distance to " CE  LYS A  76 " =    2.669
peak=   -3.103 closest distance to " O   HOH Z 364 " =    2.106
peak=   -3.090 closest distance to " O   LYS A  76 " =    2.021
peak=   -3.086 closest distance to " C   ALA A 114 " =    2.281
peak=   -3.080 closest distance to " NZ  LYS A 166 " =    1.491
peak=   -3.077 closest distance to " N   ASP A 270 " =    1.420
peak=   -3.077 closest distance to " CA  GLY A 241 " =    3.166
peak=   -3.073 closest distance to " O   HOH Z 346 " =    1.743
peak=   -3.069 closest distance to " O   HOH Z  68 " =    1.359
peak=   -3.059 closest distance to " O   HOH Z 110 " =    1.321
peak=   -3.045 closest distance to " CB  ASN A  39 " =    2.112
peak=   -3.041 closest distance to " OG  SER A 245 " =    1.454
peak=   -3.037 closest distance to " CB  ALA A 100 " =    2.245
peak=   -3.034 closest distance to " CG  TRP A 266 " =    1.767
peak=   -3.014 closest distance to " N   GLY A 118 " =    1.974

================= 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    :  0.4228 0.4232   6.229745e+00   6.207774e+00
   1_bss:  0.4098 0.4122   6.217058e+00   6.191972e+00
   1_xyz:  0.2977 0.3274   5.964040e+00   6.021524e+00
   1_adp:  0.2705 0.3453   5.917413e+00   6.054984e+00
   1_occ:  0.2703 0.3453   5.917332e+00   6.055192e+00
   2_bss:  0.2690 0.3434   5.916182e+00   6.054665e+00
   2_xyz:  0.2013 0.2559   5.651897e+00   5.833639e+00
   2_adp:  0.1866 0.2363   5.583281e+00   5.759426e+00
   2_occ:  0.1865 0.2359   5.582311e+00   5.758373e+00
   3_bss:  0.1865 0.2357   5.582598e+00   5.758678e+00
   3_xyz:  0.1484 0.1998   5.389512e+00   5.603673e+00
   3_adp:  0.1403 0.1921   5.342714e+00   5.566447e+00
   3_occ:  0.1402 0.1922   5.342661e+00   5.566665e+00
   4_bss:  0.1404 0.1916   5.341508e+00   5.563697e+00
   4_xyz:  0.1253 0.1724   5.237266e+00   5.465218e+00
   4_adp:  0.1230 0.1681   5.217185e+00   5.440153e+00
   4_occ:  0.1229 0.1681   5.217113e+00   5.440216e+00
   5_bss:  0.1229 0.1681   5.216961e+00   5.440184e+00
   5_xyz:  0.1184 0.1631   5.189090e+00   5.419274e+00
   5_adp:  0.1171 0.1633   5.185804e+00   5.422357e+00
   5_occ:  0.1170 0.1633   5.185646e+00   5.422256e+00
   5_bss:  0.1171 0.1631   5.184595e+00   5.420338e+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:  0.326  37.746  -3.187   1.323   3.578   0.000   0.000   0.000
   1_xyz:  0.326  37.746  -3.187   1.323   3.578   0.000   0.000   0.000
   1_adp:  0.326  37.746  -3.187   1.323   3.578   0.000   0.000   0.000
   1_occ:  0.326  37.746  -3.187   1.323   3.578   0.000   0.000   0.000
   2_bss:  0.323  51.392  -2.488  -0.652   1.340  -0.000   0.000   0.000
   2_xyz:  0.323  51.392  -2.488  -0.652   1.340  -0.000   0.000   0.000
   2_adp:  0.323  51.392  -2.488  -0.652   1.340  -0.000   0.000   0.000
   2_occ:  0.323  51.392  -2.488  -0.652   1.340  -0.000   0.000   0.000
   3_bss:  0.330  58.671  -2.353  -1.515   0.427  -0.000   0.000   0.000
   3_xyz:  0.330  58.671  -2.353  -1.515   0.427  -0.000   0.000   0.000
   3_adp:  0.330  58.671  -2.353  -1.515   0.427  -0.000   0.000   0.000
   3_occ:  0.330  58.671  -2.353  -1.515   0.427  -0.000   0.000   0.000
   4_bss:  0.328  62.384  -2.510  -2.090  -0.085  -0.000  -0.000  -0.000
   4_xyz:  0.328  62.384  -2.510  -2.090  -0.085  -0.000  -0.000  -0.000
   4_adp:  0.328  62.384  -2.510  -2.090  -0.085  -0.000  -0.000  -0.000
   4_occ:  0.328  62.384  -2.510  -2.090  -0.085  -0.000  -0.000  -0.000
   5_bss:  0.328  62.384  -2.381  -2.114  -0.114  -0.000  -0.000  -0.000
   5_xyz:  0.328  62.384  -2.381  -2.114  -0.114  -0.000  -0.000  -0.000
   5_adp:  0.328  62.384  -2.381  -2.114  -0.114  -0.000  -0.000  -0.000
   5_occ:  0.328  62.384  -2.381  -2.114  -0.114  -0.000  -0.000  -0.000
   5_bss:  0.328  62.387  -2.215  -2.045  -0.018  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.857 0.5482  0.7227    52889.290
   1_bss:  46.650 0.5615  0.7569    49728.192
   1_xyz:  33.678 0.7172  0.9245    28516.573
   1_adp:  35.863 0.6908  0.8985    31732.707
   1_occ:  35.934 0.6899  0.8968    31771.966
   2_bss:  35.606 0.6939  0.8681    31499.008
   2_xyz:  25.561 0.8047  0.9703    16776.498
   2_adp:  22.815 0.8342  0.9833    14206.880
   2_occ:  22.776 0.8345  0.9834    14162.477
   3_bss:  22.729 0.8351  0.9658    14173.406
   3_xyz:  19.040 0.8704  0.9868    10168.251
   3_adp:  17.984 0.8807  0.9809     9400.931
   3_occ:  17.989 0.8807  0.9807     9403.106
   4_bss:  17.913 0.8813  0.9670     9324.808
   4_xyz:  15.691 0.9008  0.9775     7468.736
   4_adp:  15.107 0.9060  0.9740     7167.247
   4_occ:  15.108 0.9060  0.9739     7163.631
   5_bss:  15.103 0.9061  0.9749     7163.446
   5_xyz:  14.610 0.9102  0.9767     6816.547
   5_adp:  14.624 0.9103  0.9694     6835.871
   5_occ:  14.619 0.9103  0.9694     6830.745
   5_bss:  14.591 0.9105  0.9736     6790.561
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7407e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7407e-01
   1_xyz:   1.391  0.010  0.090 15.605  0.006  4.107   1.0243e-01
   1_adp:   1.391  0.010  0.090 15.605  0.006  4.107   1.0243e-01
   1_occ:   1.391  0.010  0.090 15.605  0.006  4.107   1.0243e-01
   2_bss:   1.391  0.010  0.090 15.605  0.006  4.107   1.0243e-01
   2_xyz:   1.169  0.008  0.081 14.625  0.004  4.112   7.3896e-02
   2_adp:   1.169  0.008  0.081 14.625  0.004  4.112   7.3896e-02
   2_occ:   1.169  0.008  0.081 14.625  0.004  4.112   7.3896e-02
   3_bss:   1.169  0.008  0.081 14.625  0.004  4.112   7.3896e-02
   3_xyz:   0.919  0.006  0.066 14.620  0.003  4.116   5.3820e-02
   3_adp:   0.919  0.006  0.066 14.620  0.003  4.116   5.3820e-02
   3_occ:   0.919  0.006  0.066 14.620  0.003  4.116   5.3820e-02
   4_bss:   0.919  0.006  0.066 14.620  0.003  4.116   5.3820e-02
   4_xyz:   0.937  0.006  0.072 14.495  0.003  4.112   5.2055e-02
   4_adp:   0.937  0.006  0.072 14.495  0.003  4.112   5.2055e-02
   4_occ:   0.937  0.006  0.072 14.495  0.003  4.112   5.2055e-02
   5_bss:   0.937  0.006  0.072 14.495  0.003  4.112   5.2055e-02
   5_xyz:   0.891  0.006  0.068 14.387  0.003  4.114   4.9433e-02
   5_adp:   0.891  0.006  0.068 14.387  0.003  4.114   4.9433e-02
   5_occ:   0.891  0.006  0.068 14.387  0.003  4.114   4.9433e-02
   5_bss:   0.891  0.006  0.068 14.387  0.003  4.114   4.9433e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.449   2.4120e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.449   2.4120e-01
   1_xyz:   8.655  0.062  0.318 85.416  0.047  1.933   8.6253e-02
   1_adp:   8.655  0.062  0.318 85.416  0.047  1.933   8.6253e-02
   1_occ:   8.655  0.062  0.318 85.416  0.047  1.933   8.6253e-02
   2_bss:   8.655  0.062  0.318 85.416  0.047  1.933   8.6253e-02
   2_xyz:   7.524  0.062  0.253 82.117  0.034  2.387   1.4491e-01
   2_adp:   7.524  0.062  0.253 82.117  0.034  2.387   1.4491e-01
   2_occ:   7.524  0.062  0.253 82.117  0.034  2.387   1.4491e-01
   3_bss:   7.524  0.062  0.253 82.117  0.034  2.387   1.4491e-01
   3_xyz:   6.736  0.040  0.216 79.905  0.028  2.428   9.4977e-02
   3_adp:   6.736  0.040  0.216 79.905  0.028  2.428   9.4977e-02
   3_occ:   6.736  0.040  0.216 79.905  0.028  2.428   9.4977e-02
   4_bss:   6.736  0.040  0.216 79.905  0.028  2.428   9.4977e-02
   4_xyz:   6.633  0.037  0.222 81.579  0.030  2.385   3.2929e-02
   4_adp:   6.633  0.037  0.222 81.579  0.030  2.385   3.2929e-02
   4_occ:   6.633  0.037  0.222 81.579  0.030  2.385   3.2929e-02
   5_bss:   6.633  0.037  0.222 81.579  0.030  2.385   3.2929e-02
   5_xyz:   6.709  0.040  0.227 83.135  0.034  2.397   3.1587e-02
   5_adp:   6.709  0.040  0.227 83.135  0.034  2.397   3.1587e-02
   5_occ:   6.709  0.040  0.227 83.135  0.034  2.397   3.1587e-02
   5_bss:   6.709  0.040  0.227 83.135  0.034  2.397   3.1587e-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: 103.53   0.00  18.07  70.96   0.00  14.17 103.53   1.13  39.28
   1_occ: 103.53   0.00  18.07  70.96   0.00  14.17 103.53   1.13  39.28
   2_bss: 103.53   0.00  18.07  70.96   0.00  14.17 103.53   1.13  39.28
   2_xyz: 103.53   0.00  18.07  70.96   0.00  14.17 103.53   1.13  39.28
   2_adp: 101.62   0.00  17.62  70.07   0.00  13.41 101.62   4.69  40.55
   2_occ: 101.62   0.00  17.62  70.07   0.00  13.41 101.62   4.69  40.55
   3_bss: 101.62   0.00  17.62  70.07   0.00  13.41 101.62   4.69  40.55
   3_xyz: 101.62   0.00  17.62  70.07   0.00  13.41 101.62   4.69  40.55
   3_adp:  99.05   0.00  17.59  80.15   0.00  12.92  99.05   5.31  43.03
   3_occ:  99.05   0.00  17.59  80.15   0.00  12.92  99.05   5.31  43.03
   4_bss:  99.05   0.00  17.59  80.15   0.00  12.92  99.05   5.31  43.03
   4_xyz:  99.05   0.00  17.59  80.15   0.00  12.92  99.05   5.31  43.03
   4_adp:  95.60   0.52  17.11  83.26   0.52  12.63  95.60   5.51  41.52
   4_occ:  95.60   0.52  17.11  83.26   0.52  12.63  95.60   5.51  41.52
   5_bss:  95.60   0.52  17.11  83.26   0.52  12.63  95.60   5.51  41.52
   5_xyz:  95.60   0.52  17.11  83.26   0.52  12.63  95.60   5.51  41.52
   5_adp:  95.32   0.00  17.12  89.40   0.00  12.53  95.32   5.00  42.13
   5_occ:  95.32   0.00  17.12  89.40   0.00  12.53  95.32   5.00  42.13
   5_bss:  95.32   0.00  17.12  89.41   0.00  12.53  95.32   5.00  42.14
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.095    0.017    0.322
   1_adp:    2.095    0.017    0.322
   1_occ:    2.095    0.017    0.322
   2_bss:    2.095    0.017    0.322
   2_xyz:    1.672    0.014    0.467
   2_adp:    1.672    0.014    0.467
   2_occ:    1.672    0.014    0.467
   3_bss:    1.672    0.014    0.467
   3_xyz:    1.451    0.034    0.562
   3_adp:    1.451    0.034    0.562
   3_occ:    1.451    0.034    0.562
   4_bss:    1.451    0.034    0.562
   4_xyz:    1.375    0.064    0.601
   4_adp:    1.375    0.064    0.601
   4_occ:    1.375    0.064    0.601
   5_bss:    1.375    0.064    0.601
   5_xyz:    1.539    0.060    0.622
   5_adp:    1.539    0.060    0.622
   5_occ:    1.539    0.060    0.622
   5_bss:    1.539    0.060    0.622
------------------------------------------------------------------------

CPU time actual refinement: 319.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/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_515/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_515/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.80 
  Macro-tasks:
    bulk solvent and scale       = 39.46  
    individual site refinement   = 127.40 
    weights calculation          = 28.83  
    collect and process          = 6.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.26 
  Micro-tasks:
    mask                            = 2.29   
    f_calc                          = 100.49 
    alpha_beta                      = 8.19   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 108.34 
    fmodel                         = 6.31   
    r_factors                      = 0.17   
    phase_errors                   = 10.91  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 238.08 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.598 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    635 calls, 100.21 s
gradients_fft:          580 calls,  95.80 s

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

# Date 2008-01-16 Time 05:00:48 PST -0800 (1200488448.17 s)
Start R-work = 0.4228, R-free = 0.4232 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1809 (no bulk solvent and anisotropic scale)

Start R-work = 0.4098, R-free = 0.4122
Final R-work = 0.1171, R-free = 0.1631