# Date 2008-01-16 Time 05:14:20 PST -0800 (1200489260.36 s)
#phil __OFF__

Command line arguments: "../654.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30067
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 654

-------------------------------------------------------------------------------
  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: (70.25, 46.6953, 86.39, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.99157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9916

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.99157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2610 [2102/2126]  1892   210  10.0%
  bin  2:  4.2610 -  3.3950 [2027/2047]  1823   204  10.1%
  bin  3:  3.3950 -  2.9696 [1992/2011]  1794   198   9.9%
  bin  4:  2.9696 -  2.6998 [1963/1993]  1765   198  10.1%
  bin  5:  2.6998 -  2.5073 [1977/1996]  1782   195   9.9%
  bin  6:  2.5073 -  2.3600 [1958/1983]  1758   200  10.2%
  bin  7:  2.3600 -  2.2423 [1940/1968]  1748   192   9.9%
  bin  8:  2.2423 -  2.1449 [1932/1968]  1739   193  10.0%
  bin  9:  2.1449 -  2.0626 [1915/1957]  1724   191  10.0%
  bin 10:  2.0626 -  1.9916 [1783/1976]  1605   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2213
        3.04 -     3.66: 4670
        3.66 -     4.28: 9084
        4.28 -     4.90: 12372
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.382 3.040 -x+1,y-1/2,-z+1/2
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28342 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_654/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 86.39 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: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1977   r_free= 0.1976   ksol= 0.00   Bsol= 0.00   scale= 1.015    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.576777                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.2452 0.2369      6.2317      6.1704|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.1556 0.1531      5.9967      5.9814|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.1588 0.1725      5.8342      6.0003|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.1647 0.1737      5.7114       5.744|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.1864 0.1653      5.6095      5.5197|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.1875 0.1955      5.5358      5.4889|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.1945 0.1855       5.506      5.4752|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.1928 0.1913      5.4711      5.4992|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.1909 0.2045      5.3938      5.4111|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.1994 0.1906      5.4187       5.274|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.2018 0.1920       5.376      5.3511|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.2037 0.1943      5.3214       5.407|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.2125 0.2111      5.2584      5.2848|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.2178 0.1977      5.2763      5.0828|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.83  22.55   0.88     0.84      32380.61|
|  2:  4.7522 -  3.7921  1303   146  0.90  15.24   1.00     0.96      23392.85|
|  3:  3.7921 -  3.3186  1287   144  0.91  15.06   1.03     1.02      16689.69|
|  4:  3.3186 -  3.0179  1284   143  0.91  14.73   1.03     1.03      12426.01|
|  5:  3.0179 -  2.8031  1267   138  0.90  16.24   1.05     1.03       9361.15|
|  6:  2.8031 -  2.6388  1272   143  0.90  16.25   1.05     1.03       7685.18|
|  7:  2.6388 -  2.5073  1269   139  0.89  16.96   1.06     1.04       7212.28|
|  8:  2.5073 -  2.3986  1248   141  0.90  17.01   1.08     1.06       6887.58|
|  9:  2.3986 -  2.3066  1255   138  0.90  17.13   1.10     1.07       6349.21|
| 10:  2.3066 -  2.2273  1237   141  0.89  17.16   1.11     1.09       5847.82|
| 11:  2.2273 -  2.1578  1254   135  0.89  18.08   1.12     1.10       5675.34|
| 12:  2.1578 -  2.0963  1246   140  0.89  18.08   1.13     1.11       5470.16|
| 13:  2.0963 -  2.0413  1243   136  0.88  19.16   1.12     1.10       4800.52|
| 14:  2.0413 -  1.9916  1091   123  0.90  17.46   1.13     1.07       3646.30|
|alpha:            min =        0.84 max =            1.11 mean =         1.04|
|beta:             min =     3646.30 max =        32380.61 mean =     10826.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.90 mean =        17.24|
|phase err.(test): min =        0.00 max =           89.44 mean =        17.17|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.446869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.726   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.288103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.468   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      205 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2008 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1831 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2839 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4677 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4407 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5640 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6732 |
|-----------------------------------------------------------------------------|
|-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 |        0.159 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.136 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    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: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1977   r_free= 0.1976   ksol= 0.00   Bsol= 0.00   scale= 1.015    |
|                                                                             |
| 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:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.576777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1767   r_free= 0.1754   ksol= 0.33   Bsol= 50.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-1.92,-1.67,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.527758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.242232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.891   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.149083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.348   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1767      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1471          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4777 = 2.24 * 0.50 * 5.6357 + 1.00 * 0.1594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9609 = 2.24 * 0.50 * 5.2603 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1256      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1471      final r-factor (free) = 0.1474          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7903 = 0.15 * 1.00 * 5.2603 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7911 = 0.15 * 1.00 * 5.1255 + 1.00 * 0.0269                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.27   16.36    None  None   None       |
|    all(noH): 2823   0      0.00    63.27   16.36    None  None   None       |
|    Sol.    : 438    0      5.44    62.72   36.82    None  None   None       |
|    Mac.    : 2385   0      0.00    63.27   12.60    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 -   6.327:  131   |   5:    31.635 -  37.962:  102        |
|      1:     6.327 -  12.654: 1404   |   6:    37.962 -  44.289:  102        |
|      2:    12.654 -  18.981:  647   |   7:    44.289 -  50.616:   74        |
|      3:    18.981 -  25.308:  184   |   8:    50.616 -  56.944:   52        |
|      4:    25.308 -  31.635:  108   |   9:    56.944 -  63.271:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1474             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1158 r_free = 0.1476             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1476   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-1.92,-1.67,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128683                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1469   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.53,-1.62,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.128642                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.102857              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.702  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.162958              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.252   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1469      final r-factor (free) = 0.1474          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4521 = 2.10 * 0.50 * 5.1252 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4289 = 2.10 * 0.50 * 5.1030 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1474      final r-factor (free) = 0.1474          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8859 = 0.16 * 1.00 * 5.1030 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8363 = 0.16 * 1.00 * 5.0915 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    67.33   16.47    None  None   None       |
|    all(noH): 2823   0      2.09    67.33   16.47    None  None   None       |
|    Sol.    : 438    0      5.59    67.33   36.58    None  None   None       |
|    Mac.    : 2385   0      2.09    65.37   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.087 -   8.611:  601   |   5:    34.710 -  41.235:  123        |
|      1:     8.611 -  15.136: 1294   |   6:    41.235 -  47.760:   85        |
|      2:    15.136 -  21.661:  375   |   7:    47.760 -  54.285:   81        |
|      3:    21.661 -  28.186:  129   |   8:    54.285 -  60.809:   28        |
|      4:    28.186 -  34.710:  100   |   9:    60.809 -  67.334:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1474             target_work(ml) = 5.094         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1475             target_work(ml) = 5.094         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1475   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.53,-1.62,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.094096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1475   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.46,-1.37,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093925                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.760589              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.612  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.224  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1057          |
| start r-factor (free) = 0.1475      final r-factor (free) = 0.1497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0924 = 2.76 * 0.50 * 5.0924 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0865 = 2.76 * 0.50 * 5.0830 + 1.00 * 0.0704                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1057      final r-factor (work) = 0.1045          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9743 = 0.39 * 1.00 * 5.0830 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9756 = 0.39 * 1.00 * 5.0834 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.20    72.64   16.63    None  None   None       |
|    all(noH): 2823   0      1.20    72.64   16.63    None  None   None       |
|    Sol.    : 438    0      6.34    69.30   37.75    None  None   None       |
|    Mac.    : 2385   0      1.20    72.64   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.203 -   8.347:  587   |   5:    36.922 -  44.065:  105        |
|      1:     8.347 -  15.490: 1331   |   6:    44.065 -  51.209:   87        |
|      2:    15.490 -  22.634:  367   |   7:    51.209 -  58.353:   71        |
|      3:    22.634 -  29.778:  130   |   8:    58.353 -  65.496:   25        |
|      4:    29.778 -  36.922:  112   |   9:    65.496 -  72.640:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1045 r_free = 0.1506             target_work(ml) = 5.088         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1045 r_free = 0.1507             target_work(ml) = 5.088         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1045   r_free= 0.1507   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.46,-1.37,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.088422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1044   r_free= 0.1507   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.31,-1.15,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.088438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.800121              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.392  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308415              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.503  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1044      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1507      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6463 = 1.80 * 0.50 * 5.0845 + 1.00 * 0.0700                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6459 = 1.80 * 0.50 * 5.0989 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1069      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5803 = 0.31 * 1.00 * 5.0989 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5817 = 0.31 * 1.00 * 5.1030 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    72.84   16.49    None  None   None       |
|    all(noH): 2823   0      0.99    72.84   16.49    None  None   None       |
|    Sol.    : 438    0      6.38    69.37   37.66    None  None   None       |
|    Mac.    : 2385   0      0.99    72.84   12.61    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:     0.986 -   8.172:  584   |   5:    36.915 -  44.100:  107        |
|      1:     8.172 -  15.357: 1334   |   6:    44.100 -  51.286:   88        |
|      2:    15.357 -  22.543:  370   |   7:    51.286 -  58.472:   70        |
|      3:    22.543 -  29.729:  127   |   8:    58.472 -  65.657:   23        |
|      4:    29.729 -  36.915:  112   |   9:    65.657 -  72.843:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1517             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1518             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1518   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.31,-1.15,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1518   ksol= 0.33   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.16,-0.98,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.104243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.216494              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 171.188  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.196952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.594  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7128 = 2.22 * 0.50 * 5.1037 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7121 = 2.22 * 0.50 * 5.0987 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3082 = 3.20 * 1.00 * 5.0987 + 1.00 * 0.0078                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.2980 = 3.20 * 1.00 * 5.0950 + 1.00 * 0.0094                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.20   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    83.20   16.67    None  None   None       |
|    Sol.    : 438    0      5.90    74.51   39.07    None  None   None       |
|    Mac.    : 2385   0      0.00    83.20   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.320:  685   |   5:    41.599 -  49.919:  108        |
|      1:     8.320 -  16.640: 1338   |   6:    49.919 -  58.239:   77        |
|      2:    16.640 -  24.960:  304   |   7:    58.239 -  66.559:   45        |
|      3:    24.960 -  33.280:  133   |   8:    66.559 -  74.879:   14        |
|      4:    33.280 -  41.599:  114   |   9:    74.879 -  83.199:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1051 r_free = 0.1536             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1051 r_free = 0.1536             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1051   r_free= 0.1536   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-2.16,-0.98,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.101113                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.0972 0.1268      5.3738      5.5119|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.0818 0.1111      5.4121      5.6105|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.1004 0.1487      5.4433      5.8504|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.1144 0.1492      5.4203      5.5551|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.1235 0.1715       5.292      5.5329|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.1140 0.1841       5.182      5.4554|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.1181 0.1542      5.1171       5.311|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.1068 0.1693      5.0167       5.333|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.1065 0.1649      4.9761      5.2115|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.1021 0.1744      4.9217      5.2486|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.1072 0.1603      4.9075      5.1854|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.1055 0.1730      4.8488      5.2332|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.1014 0.1604      4.7526      5.0192|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.0961 0.1784      4.6238      4.9424|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.94   9.19   0.98     0.95       7115.39|
|  2:  4.7522 -  3.7921  1303   146  0.95   7.70   1.01     1.00       8805.11|
|  3:  3.7921 -  3.3186  1287   144  0.94  10.63   1.02     1.02       9780.91|
|  4:  3.3186 -  3.0179  1284   143  0.92  13.01   1.01     0.99       9843.36|
|  5:  3.0179 -  2.8031  1267   138  0.91  15.24   0.99     0.97       8007.94|
|  6:  2.8031 -  2.6388  1272   143  0.90  15.50   0.99     0.96       6839.76|
|  7:  2.6388 -  2.5073  1269   139  0.91  15.03   0.98     0.96       5772.75|
|  8:  2.5073 -  2.3986  1248   141  0.92  13.91   0.99     0.97       4802.30|
|  9:  2.3986 -  2.3066  1255   138  0.92  14.42   1.00     0.97       4574.05|
| 10:  2.3066 -  2.2273  1237   141  0.91  14.53   0.99     0.95       4097.97|
| 11:  2.2273 -  2.1578  1254   135  0.90  15.82   0.99     0.96       4223.10|
| 12:  2.1578 -  2.0963  1246   140  0.91  14.76   1.00     0.98       3763.91|
| 13:  2.0963 -  2.0413  1243   136  0.91  14.86   0.99     0.98       3185.86|
| 14:  2.0413 -  1.9916  1091   123  0.92  13.86   0.97     0.93       2403.69|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2403.69 max =         9843.36 mean =      6013.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.41|
|phase err.(test): min =        0.00 max =           89.77 mean =        13.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1536   ksol= 0.32   Bsol= 47.86   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.93,-0.75,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.100790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1536   ksol= 0.32   Bsol= 47.86   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-1.93,-0.75,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.100790                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.0968 0.1266      5.3681       5.506|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.0819 0.1110      5.4112      5.6103|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.1004 0.1488      5.4433      5.8509|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.1145 0.1493      5.4205      5.5555|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.1235 0.1715      5.2924      5.5332|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.1140 0.1843      5.1825       5.456|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.1182 0.1543      5.1178      5.3115|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.1069 0.1693      5.0171      5.3334|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.1065 0.1648      4.9763      5.2113|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.1021 0.1745       4.922      5.2493|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.1072 0.1602      4.9076      5.1851|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.1055 0.1730      4.8487      5.2332|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.1014 0.1603      4.7526      5.0191|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.0961 0.1784       4.624      4.9426|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.94   9.11   0.98     0.95       7006.68|
|  2:  4.7522 -  3.7921  1303   146  0.95   7.67   1.02     1.00       8757.48|
|  3:  3.7921 -  3.3186  1287   144  0.94  10.63   1.03     1.02       9782.52|
|  4:  3.3186 -  3.0179  1284   143  0.92  13.02   1.01     1.00       9845.37|
|  5:  3.0179 -  2.8031  1267   138  0.91  15.25   1.00     0.98       8013.68|
|  6:  2.8031 -  2.6388  1272   143  0.90  15.51   0.99     0.97       6846.49|
|  7:  2.6388 -  2.5073  1269   139  0.91  15.05   0.99     0.97       5780.88|
|  8:  2.5073 -  2.3986  1248   141  0.92  13.92   1.00     0.98       4805.92|
|  9:  2.3986 -  2.3066  1255   138  0.92  14.42   1.01     0.98       4577.27|
| 10:  2.3066 -  2.2273  1237   141  0.91  14.54   1.00     0.96       4098.21|
| 11:  2.2273 -  2.1578  1254   135  0.90  15.82   1.00     0.97       4223.80|
| 12:  2.1578 -  2.0963  1246   140  0.91  14.76   1.01     1.00       3763.11|
| 13:  2.0963 -  2.0413  1243   136  0.91  14.86   1.01     0.99       3186.17|
| 14:  2.0413 -  1.9916  1091   123  0.92  13.87   0.98     0.95       2404.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2404.66 max =         9845.37 mean =      6003.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.40|
|phase err.(test): min =        0.00 max =           89.78 mean =        12.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.20   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    83.20   16.67    None  None   None       |
|    Sol.    : 438    0      5.90    74.51   39.07    None  None   None       |
|    Mac.    : 2385   0      0.00    83.20   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.323:  685   |   5:    41.602 -  49.922:  108        |
|      1:     8.323 -  16.643: 1338   |   6:    49.922 -  58.242:   77        |
|      2:    16.643 -  24.963:  304   |   7:    58.242 -  66.562:   45        |
|      3:    24.963 -  33.283:  133   |   8:    66.562 -  74.882:   14        |
|      4:    33.283 -  41.602:  114   |   9:    74.882 -  83.202:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 286         
Filter by distance & map next to the model:
   mapped sites are within: 0.479 - 4.676
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 286
   mapped sites are within: 0.727 - 4.676

peak=    5.931 closest distance to " NH2 ARG A  56 " =    2.201
peak=    5.550 closest distance to " CG  PRO A  54 " =    1.275
peak=    5.376 closest distance to " O   HOH Z 126 " =    1.885
peak=    5.127 closest distance to " NE2 GLN A  11 " =    1.094
peak=    5.082 closest distance to " CB  SER A  63 " =    1.177
peak=    5.061 closest distance to " CB  ARG A 275 " =    0.917
peak=    4.998 closest distance to " O   HOH Z 144 " =    1.736
peak=    4.997 closest distance to " CB  GLN A 223 " =    1.438
peak=    4.971 closest distance to " O   HOH Z 232 " =    2.368
peak=    4.875 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.702 closest distance to " C   PRO A 198 " =    1.440
peak=    4.694 closest distance to " O   HOH Z  15 " =    2.245
peak=    4.651 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.604 closest distance to " CB  ARG A  79 " =    1.328
peak=    4.547 closest distance to " CB  PRO A  54 " =    0.931
peak=    4.533 closest distance to " O   HOH Z 427 " =    2.859
peak=    4.509 closest distance to " O   HOH Z 236 " =    1.992
peak=    4.486 closest distance to " O   HOH Z  78 " =    1.691
peak=    4.455 closest distance to " CB  GLU A 152 " =    1.221
peak=    4.404 closest distance to " O   HOH Z 298 " =    1.884
peak=    4.332 closest distance to " OD1 ASN A  69 " =    2.574
peak=    4.325 closest distance to " O   HOH Z 303 " =    2.102
peak=    4.322 closest distance to " O   HOH Z 369 " =    2.134
peak=    4.274 closest distance to " O   HOH Z 193 " =    1.864
peak=    4.253 closest distance to " O   HOH Z 234 " =    3.645
peak=    4.247 closest distance to " O   HOH Z 250 " =    1.508
peak=    4.235 closest distance to " O   HOH Z  61 " =    1.622
peak=    4.226 closest distance to " CB  TYR A 169 " =    0.745
peak=    4.222 closest distance to " O   HOH Z 203 " =    1.732
peak=    4.218 closest distance to " CB  ARG A 190 " =    1.627
peak=    4.180 closest distance to " CG2 VAL A 257 " =    0.891
peak=    4.170 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.167 closest distance to " ND2 ASN A 187 " =    1.393
peak=    4.160 closest distance to " CB  LEU A 228 " =    1.092
peak=    4.136 closest distance to " O   HOH Z 209 " =    2.320
peak=    4.129 closest distance to " O   HOH Z 158 " =    2.993
peak=    4.104 closest distance to " NZ  LYS A 117 " =    3.268
peak=    4.104 closest distance to " CB  ASP A 140 " =    0.962
peak=    4.099 closest distance to " OG ASER A 258 " =    3.118
peak=    4.094 closest distance to " O   HOH Z 189 " =    2.325
peak=    4.080 closest distance to " CB  VAL A 265 " =    1.273
peak=    4.078 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.077 closest distance to " CA  ASN A 215 " =    1.196
peak=    4.064 closest distance to " O   HOH Z 392 " =    3.186
peak=    4.041 closest distance to " CG  ARG A  66 " =    2.545
peak=    4.005 closest distance to " O   HOH Z 346 " =    1.653
peak=    3.989 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.980 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.933 closest distance to " O   HOH Z  43 " =    1.865
peak=    3.931 closest distance to " O   HOH Z 389 " =    1.868
peak=    3.929 closest distance to " O   HOH Z  40 " =    1.709
peak=    3.917 closest distance to " O   HOH Z 261 " =    2.178
peak=    3.915 closest distance to " CB  GLU A 128 " =    1.055
peak=    3.910 closest distance to " CZ  PHE A 218 " =    1.045
peak=    3.894 closest distance to " CD2 TRP A 179 " =    1.373
peak=    3.874 closest distance to " O   HOH Z 403 " =    1.643
peak=    3.868 closest distance to " CB  SER A   3 " =    1.317
peak=    3.860 closest distance to " O   HOH Z   1 " =    1.906
peak=    3.849 closest distance to " O   HOH Z 245 " =    1.290
peak=    3.825 closest distance to " O   HOH Z 214 " =    2.060
peak=    3.818 closest distance to " O   HOH Z   9 " =    2.053
peak=    3.806 closest distance to " O   HOH Z 368 " =    2.051
peak=    3.799 closest distance to " CG1 ILE A  33 " =    1.214
peak=    3.798 closest distance to " O   SER A  87 " =    2.286
peak=    3.797 closest distance to " O   HOH Z 344 " =    3.206
peak=    3.794 closest distance to " CG  PRO A 243 " =    1.047
peak=    3.776 closest distance to " O   HOH Z  10 " =    1.824
peak=    3.775 closest distance to " CD  ARG A 159 " =    0.727
peak=    3.767 closest distance to " O   HOH Z 425 " =    2.066
peak=    3.766 closest distance to " O   HOH Z  66 " =    2.157
peak=    3.750 closest distance to " O   HOH Z  19 " =    2.545
peak=    3.741 closest distance to " CB  VAL A 202 " =    1.556
peak=    3.738 closest distance to " O   HOH Z 423 " =    1.848
peak=    3.730 closest distance to " O   HOH Z 402 " =    1.398
peak=    3.709 closest distance to " O   HOH Z 193 " =    1.670
peak=    3.705 closest distance to " CB  SER A 212 " =    1.101
peak=    3.699 closest distance to " CB  TRP A 179 " =    1.335
peak=    3.678 closest distance to " CD2 LEU A 297 " =    0.856
peak=    3.673 closest distance to " O   HOH Z 291 " =    1.519
peak=    3.661 closest distance to " O   HOH Z 426 " =    1.641
peak=    3.658 closest distance to " O   HOH Z 407 " =    2.407
peak=    3.641 closest distance to " O   HOH Z 280 " =    2.989
peak=    3.637 closest distance to " O   HOH Z 172 " =    3.261
peak=    3.632 closest distance to " O   HOH Z 305 " =    3.551
peak=    3.632 closest distance to " CB  TYR A 169 " =    0.738
peak=    3.628 closest distance to " O   HOH Z 180 " =    2.200
peak=    3.625 closest distance to " OD2 ASP A 286 " =    2.814
peak=    3.621 closest distance to " CB  GLU A 277 " =    3.562
peak=    3.615 closest distance to " O   HOH Z 132 " =    2.375
peak=    3.607 closest distance to " NH1AARG A 145 " =    1.192
peak=    3.602 closest distance to " O   HOH Z 272 " =    1.781
peak=    3.598 closest distance to " CA  THR A 221 " =    0.987
peak=    3.598 closest distance to " OG BSER A 164 " =    2.293
peak=    3.597 closest distance to " O   HOH Z 248 " =    1.570
peak=    3.592 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.589 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.587 closest distance to " CA  ARG A  36 " =    1.000
peak=    3.587 closest distance to " O   HOH Z 133 " =    2.522
peak=    3.585 closest distance to " O   HOH Z  93 " =    2.667
peak=    3.583 closest distance to " O   HOH Z 371 " =    3.102
peak=    3.578 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.578 closest distance to " O   HOH Z 213 " =    1.795
peak=    3.569 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.563 closest distance to " O   HOH Z 417 " =    3.123
peak=    3.561 closest distance to " O   HOH Z 313 " =    1.961
peak=    3.553 closest distance to " O   MET A 105 " =    1.868
peak=    3.549 closest distance to " O   HOH Z 147 " =    1.792
peak=    3.546 closest distance to " CD1 LEU A 300 " =    1.260
peak=    3.545 closest distance to " CD2 LEU A 255 " =    1.405
peak=    3.545 closest distance to " OG1 THR A 294 " =    2.389
peak=    3.544 closest distance to " N   ARG A 156 " =    1.304
peak=    3.535 closest distance to " O   HOH Z 368 " =    3.624
peak=    3.533 closest distance to " CD  ARG A  66 " =    2.336
peak=    3.532 closest distance to " NE2 GLN A  73 " =    3.794
peak=    3.528 closest distance to " O   HOH Z 298 " =    2.531
peak=    3.520 closest distance to " CB  ARG A 139 " =    0.961
peak=    3.519 closest distance to " CB  ALA A 291 " =    1.400
peak=    3.519 closest distance to " CB  ASN A 142 " =    1.047
peak=    3.519 closest distance to " O   HOH Z 419 " =    2.009
peak=    3.511 closest distance to " CG2 THR A 221 " =    1.142
peak=    3.510 closest distance to " CB  MET A  47 " =    1.032
peak=    3.507 closest distance to " O   HOH Z 371 " =    1.759
peak=    3.507 closest distance to " NH2BARG A 145 " =    2.108
peak=    3.491 closest distance to " CD1 ILE A 106 " =    0.774
peak=    3.484 closest distance to " CG2 ILE A 120 " =    1.128
peak=    3.482 closest distance to " CB  ALA A  34 " =    1.068
peak=    3.482 closest distance to " O   HOH Z 128 " =    2.293
peak=    3.481 closest distance to " CA  ALA A  43 " =    1.253
peak=    3.480 closest distance to " CB  TYR A 116 " =    0.771
peak=    3.472 closest distance to " CG1BVAL A  72 " =    1.584
peak=    3.464 closest distance to " CA  MET A  40 " =    1.102
peak=    3.456 closest distance to " O   HOH Z 175 " =    2.212
peak=    3.447 closest distance to " O   HOH Z  21 " =    1.740
peak=    3.445 closest distance to " CA  ALA A  51 " =    0.884
peak=    3.443 closest distance to " ND2 ASN A 110 " =    1.721
peak=    3.442 closest distance to " CA  ALA A 291 " =    0.826
peak=    3.438 closest distance to " CB  THR A 157 " =    1.099
peak=    3.437 closest distance to " CB  ASN A 110 " =    1.119
peak=    3.436 closest distance to " O   HOH Z 128 " =    2.106
peak=    3.429 closest distance to " CA  ALA A 158 " =    1.246
peak=    3.429 closest distance to " O   HOH Z 148 " =    3.366
peak=    3.424 closest distance to " CA  THR A 264 " =    0.885
peak=    3.421 closest distance to " CD  LYS A 119 " =    1.292
peak=    3.420 closest distance to " O   HOH Z 234 " =    1.868
peak=    3.415 closest distance to " O   HOH Z 173 " =    1.820
peak=    3.414 closest distance to " O   HOH Z  59 " =    1.810
peak=    3.413 closest distance to " OE1 GLU A   2 " =    2.165
peak=    3.411 closest distance to " O   HOH Z 219 " =    2.058
peak=    3.400 closest distance to " CB  ASN A 224 " =    0.987
peak=    3.398 closest distance to " O   HOH Z 193 " =    2.035
peak=    3.397 closest distance to " CB  SER A 141 " =    1.047
peak=    3.396 closest distance to " O   HOH Z  54 " =    1.681
peak=    3.392 closest distance to " O   HOH Z  44 " =    1.702
peak=    3.391 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.390 closest distance to " CG  LEU A 167 " =    1.251
peak=    3.385 closest distance to " N   ASN A  39 " =    1.258
peak=    3.384 closest distance to " O   HOH Z 403 " =    1.336
peak=    3.379 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.378 closest distance to " O   HOH Z 359 " =    1.424
peak=    3.373 closest distance to " O   HOH Z 345 " =    3.392
peak=    3.370 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.366 closest distance to " O   HOH Z 406 " =    1.500
peak=    3.366 closest distance to " ND1 HIS A  86 " =    1.757
peak=    3.363 closest distance to " CB  THR A  31 " =    1.697
peak=    3.362 closest distance to " O  BHOH Z 338 " =    2.345
peak=    3.362 closest distance to " O   HOH Z 435 " =    1.928
peak=    3.357 closest distance to " CA  ALA A  84 " =    1.288
peak=    3.357 closest distance to " CG1 VAL A 153 " =    0.964
peak=    3.356 closest distance to " O   HOH Z 337 " =    3.659
peak=    3.352 closest distance to " O   HOH Z 185 " =    1.766
peak=    3.352 closest distance to " CB  SER A 216 " =    0.857
peak=    3.349 closest distance to " CB  LYS A 290 " =    0.954
peak=    3.343 closest distance to " O   HOH Z  44 " =    3.064
peak=    3.337 closest distance to " O   HOH Z  97 " =    1.998
peak=    3.334 closest distance to " O   HOH Z 353 " =    2.685
peak=    3.331 closest distance to " O   HOH Z  88 " =    2.682
peak=    3.329 closest distance to " O   HOH Z 265 " =    2.461
peak=    3.329 closest distance to " CB  LEU A 255 " =    0.788
peak=    3.328 closest distance to " CG  LYS A  76 " =    0.975
peak=    3.327 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.324 closest distance to " O   HOH Z 411 " =    3.909
peak=    3.324 closest distance to " CZ2 TRP A 179 " =    1.693
peak=    3.321 closest distance to " O   HOH Z 135 " =    1.608
peak=    3.308 closest distance to " CB  ILE A 120 " =    1.277
peak=    3.302 closest distance to " CA  MET A 105 " =    0.983
peak=    3.298 closest distance to " O   HOH Z   1 " =    1.659
peak=    3.294 closest distance to " O   HOH Z 391 " =    2.889
peak=    3.292 closest distance to " NH2 ARG A 156 " =    1.173
peak=    3.290 closest distance to " O   HOH Z 327 " =    1.596
peak=    3.286 closest distance to " O   HOH Z 383 " =    1.747
peak=    3.285 closest distance to " O   HOH Z 433 " =    1.764
peak=    3.283 closest distance to " CG2 ILE A  20 " =    1.380
peak=    3.282 closest distance to " O   HOH Z  85 " =    2.287
peak=    3.282 closest distance to " CB  ALA A 248 " =    1.432
peak=    3.275 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.274 closest distance to " CB  SER A  26 " =    1.631
peak=    3.272 closest distance to " NE2 GLN A  77 " =    3.162
peak=    3.270 closest distance to " CB  GLN A  89 " =    1.373
peak=    3.267 closest distance to " O   HOH Z 285 " =    2.802
peak=    3.261 closest distance to " O   HOH Z 261 " =    1.486
peak=    3.260 closest distance to " O   ALA A   1 " =    1.635
peak=    3.259 closest distance to " OG  SER A  22 " =    2.688
peak=    3.254 closest distance to " O   HOH Z 133 " =    1.505
peak=    3.249 closest distance to " CD1 LEU A  96 " =    0.783
peak=    3.248 closest distance to " O   HOH Z 227 " =    1.669
peak=    3.245 closest distance to " N   ASN A 127 " =    1.215
peak=    3.244 closest distance to " O   HOH Z 286 " =    2.334
peak=    3.243 closest distance to " O   HOH Z 329 " =    3.920
peak=    3.242 closest distance to " O   HOH Z 273 " =    2.789
peak=    3.242 closest distance to " O   HOH Z 261 " =    2.261
peak=    3.238 closest distance to " O   HOH Z 437 " =    1.273
peak=    3.237 closest distance to " O   HOH Z  40 " =    1.930
peak=    3.237 closest distance to " CG  MET A 185 " =    1.144
peak=    3.233 closest distance to " O   HOH Z  64 " =    2.184
peak=    3.232 closest distance to " CB  SER A  62 " =    1.261
peak=    3.230 closest distance to " CA  ALA A 233 " =    1.237
peak=    3.229 closest distance to " CA  TYR A 116 " =    1.317
peak=    3.229 closest distance to " CB  GLU A  46 " =    1.018
peak=    3.226 closest distance to " CB  LYS A 117 " =    1.201
peak=    3.224 closest distance to " O   HOH Z 299 " =    4.471
peak=    3.221 closest distance to " CB  ALA A   9 " =    1.520
peak=    3.219 closest distance to " NH1BARG A 145 " =    1.121
peak=    3.218 closest distance to " CB  ALA A 248 " =    0.876
peak=    3.212 closest distance to " CG  GLN A  77 " =    2.172
peak=    3.211 closest distance to " CB  THR A 235 " =    1.009
peak=    3.210 closest distance to " CA  ARG A 159 " =    1.247
peak=    3.209 closest distance to " CB  MET A  40 " =    0.819
peak=    3.209 closest distance to " CA  ALA A 248 " =    1.197
peak=    3.203 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.199 closest distance to " O   THR A 220 " =    1.288
peak=    3.194 closest distance to " CA  ASP A 162 " =    1.084
peak=    3.193 closest distance to " O   HOH Z 423 " =    2.929
peak=    3.191 closest distance to " CD  LYS A 166 " =    1.202
peak=    3.191 closest distance to " CA  ARG A 102 " =    1.033
peak=    3.190 closest distance to " ND1 HIS A  81 " =    1.612
peak=    3.189 closest distance to " CG1 ILE A  49 " =    1.445
peak=    3.188 closest distance to " CA  SER A 146 " =    1.694
peak=    3.188 closest distance to " O   HOH Z 163 " =    1.707
peak=    3.177 closest distance to " CG2 VAL A 197 " =    1.070
peak=    3.177 closest distance to " CD  ARG A 269 " =    0.928
peak=    3.176 closest distance to " CD2 HIS A  81 " =    1.092
peak=    3.175 closest distance to " NZ  LYS A  76 " =    1.578
peak=    3.174 closest distance to " O   HOH Z 123 " =    2.304
peak=    3.172 closest distance to " CB  ASN A 215 " =    1.103
peak=    3.168 closest distance to " CG  PRO A 213 " =    0.956
peak=    3.167 closest distance to " CG  GLN A  11 " =    1.709
peak=    3.167 closest distance to " CD1 ILE A 263 " =    1.286
peak=    3.162 closest distance to " CG1 VAL A 189 " =    2.092
peak=    3.153 closest distance to " O   HOH Z 116 " =    1.744
peak=    3.152 closest distance to " CB  VAL A 126 " =    1.058
peak=    3.151 closest distance to " O   HOH Z 411 " =    1.732
peak=    3.149 closest distance to " O   HOH Z 365 " =    2.989
peak=    3.149 closest distance to " CA  SER A  87 " =    1.036
peak=    3.137 closest distance to " CB  ALA A   1 " =    4.676
peak=    3.137 closest distance to " N   PHE A 130 " =    1.264
peak=    3.136 closest distance to " O   HOH Z 357 " =    1.860
peak=    3.133 closest distance to " CA  ALA A 154 " =    0.982
peak=    3.131 closest distance to " CB  VAL A 268 " =    0.843
peak=    3.131 closest distance to " CA  ASN A 217 " =    1.195
peak=    3.128 closest distance to " CG  MET A 113 " =    1.242
peak=    3.122 closest distance to " N   GLN A 278 " =    1.227
peak=    3.122 closest distance to " O   THR A 251 " =    1.273
peak=    3.119 closest distance to " O   HOH Z 112 " =    1.588
peak=    3.109 closest distance to " OG  SER A 206 " =    1.291
peak=    3.107 closest distance to " O   HOH Z 409 " =    2.881
peak=    3.106 closest distance to " CG  GLN A  89 " =    1.501
peak=    3.106 closest distance to " O   HOH Z 336 " =    1.766
peak=    3.104 closest distance to " CA  ASN A 252 " =    1.857
peak=    3.099 closest distance to " O   HOH Z 369 " =    1.656
peak=    3.095 closest distance to " N   CYS A 260 " =    0.868
peak=    3.094 closest distance to " O   HOH Z 302 " =    1.840
peak=    3.083 closest distance to " CD  ARG A 219 " =    1.144
peak=    3.083 closest distance to " CA  ASP A 140 " =    1.129
peak=    3.078 closest distance to " O   HOH Z 171 " =    1.933
peak=    3.076 closest distance to " O   TRP A 274 " =    1.845
peak=    3.063 closest distance to " CB  ARG A 138 " =    0.927
peak=    3.057 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.054 closest distance to " CG  ARG A 159 " =    0.838
peak=    3.043 closest distance to " OG BSER A  99 " =    2.216
peak=    3.037 closest distance to " CE AMET A  47 " =    1.405
peak=    3.006 closest distance to " O   HOH Z 361 " =    3.156

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.808 - 5.577
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.808 - 5.577

peak=   -4.796 closest distance to " O   HOH Z 266 " =    5.027
peak=   -4.610 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.572 closest distance to " CB  PRO A 243 " =    2.647
peak=   -4.487 closest distance to " CG  GLN A 223 " =    1.907
peak=   -4.444 closest distance to " SG  CYS A 254 " =    3.503
peak=   -4.439 closest distance to " O   VAL A  67 " =    2.697
peak=   -4.296 closest distance to " O   HOH Z 377 " =    2.132
peak=   -4.270 closest distance to " OG BSER A 134 " =    1.250
peak=   -4.263 closest distance to " O   HOH Z 198 " =    2.052
peak=   -4.241 closest distance to " C   HIS A 108 " =    1.050
peak=   -4.235 closest distance to " CD  GLN A  58 " =    1.053
peak=   -4.221 closest distance to " O   HOH Z 231 " =    2.276
peak=   -4.187 closest distance to " O   HOH Z 389 " =    1.904
peak=   -4.140 closest distance to " CE  MET A 105 " =    2.400
peak=   -4.087 closest distance to " O   HOH Z 372 " =    2.382
peak=   -4.020 closest distance to " CG1 VAL A 112 " =    2.825
peak=   -4.019 closest distance to " CZ3 TRP A 179 " =    1.150
peak=   -3.998 closest distance to " ND2 ASN A  45 " =    1.778
peak=   -3.978 closest distance to " O   HOH Z 435 " =    2.796
peak=   -3.972 closest distance to " CA  VAL A  67 " =    2.911
peak=   -3.965 closest distance to " CD2 PHE A 192 " =    2.013
peak=   -3.956 closest distance to " CB  ALA A 291 " =    2.267
peak=   -3.909 closest distance to " CD  ARG A 139 " =    1.556
peak=   -3.882 closest distance to " O   ILE A 109 " =    2.545
peak=   -3.877 closest distance to " CB  ALA A 291 " =    2.440
peak=   -3.875 closest distance to " CG2 ILE A 263 " =    2.292
peak=   -3.875 closest distance to " N   ALA A  43 " =    2.647
peak=   -3.851 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.849 closest distance to " O   HOH Z 196 " =    2.054
peak=   -3.831 closest distance to " O   HOH Z 313 " =    1.890
peak=   -3.828 closest distance to " CB  ASN A  39 " =    2.344
peak=   -3.813 closest distance to " O   HOH Z  10 " =    1.483
peak=   -3.810 closest distance to " O   HOH Z 114 " =    3.057
peak=   -3.783 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.777 closest distance to " O   HOH Z 185 " =    2.212
peak=   -3.771 closest distance to " O   HOH Z 126 " =    1.918
peak=   -3.753 closest distance to " O   PRO A 163 " =    2.039
peak=   -3.742 closest distance to " O   HOH Z 407 " =    3.006
peak=   -3.737 closest distance to " CG  ARG A 269 " =    2.390
peak=   -3.732 closest distance to " CZ  PHE A  59 " =    1.528
peak=   -3.730 closest distance to " CE2 PHE A 218 " =    2.432
peak=   -3.725 closest distance to " O   HOH Z  43 " =    1.656
peak=   -3.717 closest distance to " CB  ALA A  43 " =    2.577
peak=   -3.717 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.715 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.713 closest distance to " OD1 ASP A 171 " =    1.623
peak=   -3.694 closest distance to " O   HOH Z 211 " =    1.694
peak=   -3.693 closest distance to " OXT GLY A 302 " =    2.811
peak=   -3.684 closest distance to " CA  GLY A 203 " =    2.341
peak=   -3.682 closest distance to " O   HOH Z 290 " =    1.303
peak=   -3.675 closest distance to " O   HOH Z 198 " =    1.464
peak=   -3.674 closest distance to " OD1 ASN A 187 " =    1.557
peak=   -3.673 closest distance to " O   HOH Z 353 " =    2.173
peak=   -3.665 closest distance to " OD2 ASP A 191 " =    1.445
peak=   -3.629 closest distance to " OG  SER A  97 " =    2.178
peak=   -3.626 closest distance to " NH2AARG A 275 " =    5.275
peak=   -3.618 closest distance to " CB  TYR A  15 " =    2.153
peak=   -3.616 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -3.615 closest distance to " O   HOH Z 351 " =    1.522
peak=   -3.599 closest distance to " O   HOH Z 311 " =    3.633
peak=   -3.595 closest distance to " CA  GLY A 133 " =    2.000
peak=   -3.581 closest distance to " O   ALA A 161 " =    1.694
peak=   -3.580 closest distance to " CG  ASP A 231 " =    0.808
peak=   -3.572 closest distance to " N   ASP A 286 " =    2.397
peak=   -3.535 closest distance to " ND2 ASN A  45 " =    1.139
peak=   -3.522 closest distance to " N   ALA A 248 " =    1.679
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.134
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.361
peak=   -3.496 closest distance to " O   HOH Z 193 " =    2.008
peak=   -3.489 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.489 closest distance to " CD1 LEU A 228 " =    2.176
peak=   -3.482 closest distance to " C   LEU A 143 " =    1.053
peak=   -3.478 closest distance to " O   HOH Z  13 " =    1.598
peak=   -3.469 closest distance to " O   HOH Z 298 " =    1.245
peak=   -3.460 closest distance to " CB  PHE A 208 " =    2.221
peak=   -3.459 closest distance to " O   ARG A 145 " =    1.532
peak=   -3.459 closest distance to " NH2 ARG A  79 " =    1.573
peak=   -3.458 closest distance to " O   SER A 135 " =    1.461
peak=   -3.456 closest distance to " OD1 ASN A 148 " =    1.546
peak=   -3.448 closest distance to " NH2BARG A 275 " =    1.870
peak=   -3.448 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.446 closest distance to " CD1 LEU A 101 " =    2.290
peak=   -3.445 closest distance to " O   HOH Z 292 " =    4.571
peak=   -3.445 closest distance to " O   HOH Z 166 " =    2.006
peak=   -3.433 closest distance to " NH1 ARG A 195 " =    2.581
peak=   -3.421 closest distance to " OD1 ASP A 191 " =    1.513
peak=   -3.414 closest distance to " CA  GLY A 241 " =    3.066
peak=   -3.409 closest distance to " N   SER A 212 " =    2.054
peak=   -3.403 closest distance to " O   PHE A 218 " =    1.561
peak=   -3.399 closest distance to " NE2 GLN A 278 " =    1.727
peak=   -3.398 closest distance to " O   HOH Z  73 " =    2.211
peak=   -3.393 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.385 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.383 closest distance to " CB  ALA A   7 " =    2.157
peak=   -3.380 closest distance to " O   HOH Z 295 " =    1.604
peak=   -3.379 closest distance to " O   HOH Z 102 " =    1.587
peak=   -3.375 closest distance to " N   GLN A  58 " =    1.604
peak=   -3.373 closest distance to " O   HOH Z 394 " =    1.472
peak=   -3.370 closest distance to " CG  GLU A   2 " =    1.907
peak=   -3.368 closest distance to " O   HOH Z  44 " =    2.264
peak=   -3.365 closest distance to " O   HOH Z  51 " =    1.645
peak=   -3.363 closest distance to " O   HOH Z 253 " =    3.916
peak=   -3.362 closest distance to " CD  ARG A 195 " =    5.201
peak=   -3.359 closest distance to " O   HOH Z 123 " =    2.327
peak=   -3.353 closest distance to " CD2 PHE A  61 " =    2.550
peak=   -3.350 closest distance to " OG  SER A  62 " =    1.712
peak=   -3.349 closest distance to " OG BSER A 134 " =    1.720
peak=   -3.348 closest distance to " SG ACYS A 201 " =    1.894
peak=   -3.348 closest distance to " CD1 LEU A 297 " =    2.446
peak=   -3.347 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.347 closest distance to " O   HOH Z 243 " =    2.080
peak=   -3.343 closest distance to " CG1 VAL A 250 " =    2.619
peak=   -3.340 closest distance to " O   HOH Z  52 " =    1.292
peak=   -3.332 closest distance to " NE2 GLN A  88 " =    1.886
peak=   -3.323 closest distance to " O   HOH Z 244 " =    2.092
peak=   -3.320 closest distance to " CD1 ILE A 239 " =    2.340
peak=   -3.313 closest distance to " CG  TRP A 266 " =    1.919
peak=   -3.312 closest distance to " CG  GLU A 277 " =    1.159
peak=   -3.310 closest distance to " NH2 ARG A  79 " =    2.001
peak=   -3.307 closest distance to " CA  GLY A  98 " =    1.928
peak=   -3.306 closest distance to " O   HOH Z 165 " =    2.051
peak=   -3.304 closest distance to " CB  PRO A 163 " =    2.470
peak=   -3.301 closest distance to " O   HOH Z  11 " =    1.740
peak=   -3.299 closest distance to " O   HOH Z 359 " =    3.252
peak=   -3.298 closest distance to " OD2 ASP A 171 " =    2.381
peak=   -3.295 closest distance to " O   HOH Z   6 " =    1.467
peak=   -3.292 closest distance to " O   HOH Z  60 " =    2.335
peak=   -3.283 closest distance to " NE2 GLN A 194 " =    1.701
peak=   -3.279 closest distance to " O   HOH Z  38 " =    1.513
peak=   -3.275 closest distance to " N   THR A 235 " =    1.362
peak=   -3.275 closest distance to " O   HOH Z 310 " =    1.753
peak=   -3.275 closest distance to " O   SER A  95 " =    1.506
peak=   -3.274 closest distance to " CD  GLU A 236 " =    1.051
peak=   -3.265 closest distance to " C   MET A 188 " =    1.347
peak=   -3.257 closest distance to " ND2 ASN A 187 " =    1.564
peak=   -3.251 closest distance to " O   HOH Z 111 " =    2.090
peak=   -3.250 closest distance to " CG1 VAL A 125 " =    2.005
peak=   -3.244 closest distance to " O   ALA A  51 " =    1.340
peak=   -3.238 closest distance to " OD2 ASP A 171 " =    1.778
peak=   -3.237 closest distance to " O   GLY A 211 " =    1.359
peak=   -3.232 closest distance to " O   HOH Z 322 " =    1.632
peak=   -3.231 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.229 closest distance to " O   ALA A 180 " =    1.264
peak=   -3.229 closest distance to " O   ALA A  10 " =    1.668
peak=   -3.228 closest distance to " OD1 ASP A 191 " =    1.785
peak=   -3.220 closest distance to " O   VAL A 189 " =    1.600
peak=   -3.217 closest distance to " O   VAL A 174 " =    2.095
peak=   -3.213 closest distance to " OD1AASN A 224 " =    1.796
peak=   -3.213 closest distance to " O   TRP A  70 " =    1.465
peak=   -3.212 closest distance to " O   HOH Z 134 " =    3.051
peak=   -3.211 closest distance to " O   PRO A 198 " =    1.304
peak=   -3.209 closest distance to " OD2 ASP A  50 " =    1.618
peak=   -3.197 closest distance to " O   HOH Z 414 " =    1.636
peak=   -3.197 closest distance to " CB  ASP A 286 " =    2.222
peak=   -3.194 closest distance to " OH  TYR A 214 " =    1.255
peak=   -3.187 closest distance to " CB  GLN A  11 " =    1.840
peak=   -3.181 closest distance to " CD1 LEU A   5 " =    2.582
peak=   -3.180 closest distance to " O   HOH Z 385 " =    1.882
peak=   -3.180 closest distance to " O   HOH Z 421 " =    2.989
peak=   -3.180 closest distance to " NZ  LYS A 119 " =    3.541
peak=   -3.177 closest distance to " CB  ASP A 286 " =    1.750
peak=   -3.173 closest distance to " CG  GLU A 152 " =    1.239
peak=   -3.163 closest distance to " CG1 VAL A 125 " =    2.371
peak=   -3.161 closest distance to " CG  ARG A 269 " =    2.042
peak=   -3.160 closest distance to " CA  GLY A 241 " =    2.808
peak=   -3.153 closest distance to " O   ALA A  34 " =    2.522
peak=   -3.150 closest distance to " O   ALA A 292 " =    2.050
peak=   -3.144 closest distance to " O   ILE A 106 " =    1.992
peak=   -3.144 closest distance to " CG  ARG A  66 " =    2.370
peak=   -3.140 closest distance to " OE1 GLN A  88 " =    1.141
peak=   -3.139 closest distance to " O   HOH Z 324 " =    2.205
peak=   -3.139 closest distance to " OXT GLY A 302 " =    3.410
peak=   -3.139 closest distance to " CG2 VAL A 189 " =    2.076
peak=   -3.136 closest distance to " O   ALA A 180 " =    1.002
peak=   -3.135 closest distance to " O   HOH Z 191 " =    5.577
peak=   -3.131 closest distance to " O   HOH Z  89 " =    2.946
peak=   -3.128 closest distance to " O   HOH Z 139 " =    2.990
peak=   -3.127 closest distance to " CG  PRO A 163 " =    2.486
peak=   -3.103 closest distance to " N   SER A 276 " =    1.221
peak=   -3.094 closest distance to " OE2 GLU A 152 " =    1.178
peak=   -3.087 closest distance to " O   GLU A 152 " =    1.387
peak=   -3.085 closest distance to " O   HOH Z 137 " =    1.519
peak=   -3.085 closest distance to " CB  ASP A 132 " =    2.371
peak=   -3.083 closest distance to " CE3 TRP A 150 " =    2.141
peak=   -3.082 closest distance to " O   HOH Z  91 " =    1.606
peak=   -3.081 closest distance to " OD1 ASP A 200 " =    1.424
peak=   -3.079 closest distance to " C   VAL A 174 " =    1.784
peak=   -3.078 closest distance to " O   HOH Z 263 " =    3.158
peak=   -3.077 closest distance to " CG1 VAL A  67 " =    3.229
peak=   -3.077 closest distance to " O   HOH Z 262 " =    2.910
peak=   -3.074 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.064 closest distance to " CD2 TYR A 293 " =    2.041
peak=   -3.049 closest distance to " O   HOH Z 234 " =    4.052
peak=   -3.033 closest distance to " CE  LYS A  76 " =    2.841
peak=   -3.022 closest distance to " CD2 LEU A 300 " =    2.885

================= 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    :  0.1977 0.1976   5.576777e+00   5.560660e+00
   1_bss:  0.1767 0.1754   5.527758e+00   5.504015e+00
   1_xyz:  0.1256 0.1471   5.182857e+00   5.312520e+00
   1_adp:  0.1163 0.1474   5.130860e+00   5.324795e+00
   1_occ:  0.1158 0.1476   5.128683e+00   5.324274e+00
   2_bss:  0.1161 0.1469   5.128642e+00   5.320954e+00
   2_xyz:  0.1107 0.1474   5.103722e+00   5.324964e+00
   2_adp:  0.1083 0.1474   5.094111e+00   5.327218e+00
   2_occ:  0.1082 0.1475   5.094096e+00   5.327779e+00
   3_bss:  0.1081 0.1475   5.093925e+00   5.327763e+00
   3_xyz:  0.1057 0.1497   5.089789e+00   5.341061e+00
   3_adp:  0.1045 0.1506   5.088225e+00   5.346281e+00
   3_occ:  0.1045 0.1507   5.088422e+00   5.346713e+00
   4_bss:  0.1044 0.1507   5.088438e+00   5.346795e+00
   4_xyz:  0.1069 0.1517   5.104515e+00   5.356647e+00
   4_adp:  0.1068 0.1517   5.103965e+00   5.356819e+00
   4_occ:  0.1068 0.1518   5.104171e+00   5.357186e+00
   5_bss:  0.1068 0.1518   5.104243e+00   5.357257e+00
   5_xyz:  0.1055 0.1521   5.098456e+00   5.357711e+00
   5_adp:  0.1051 0.1536   5.101014e+00   5.364786e+00
   5_occ:  0.1051 0.1536   5.101113e+00   5.365023e+00
   5_bss:  0.1050 0.1536   5.100790e+00   5.364759e+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:  0.333  50.000  -3.074  -1.921  -1.672  -0.000  -0.000  -0.000
   1_xyz:  0.333  50.000  -3.074  -1.921  -1.672  -0.000  -0.000  -0.000
   1_adp:  0.333  50.000  -3.074  -1.921  -1.672  -0.000  -0.000  -0.000
   1_occ:  0.333  50.000  -3.074  -1.921  -1.672  -0.000  -0.000  -0.000
   2_bss:  0.333  50.000  -3.054  -2.534  -1.617  -0.000  -0.000  -0.000
   2_xyz:  0.333  50.000  -3.054  -2.534  -1.617  -0.000  -0.000  -0.000
   2_adp:  0.333  50.000  -3.054  -2.534  -1.617  -0.000  -0.000  -0.000
   2_occ:  0.333  50.000  -3.054  -2.534  -1.617  -0.000  -0.000  -0.000
   3_bss:  0.333  50.000  -2.781  -2.461  -1.368  -0.000  -0.000  -0.000
   3_xyz:  0.333  50.000  -2.781  -2.461  -1.368  -0.000  -0.000  -0.000
   3_adp:  0.333  50.000  -2.781  -2.461  -1.368  -0.000  -0.000  -0.000
   3_occ:  0.333  50.000  -2.781  -2.461  -1.368  -0.000  -0.000  -0.000
   4_bss:  0.333  50.000  -2.529  -2.310  -1.147  -0.000  -0.000  -0.000
   4_xyz:  0.333  50.000  -2.529  -2.310  -1.147  -0.000  -0.000  -0.000
   4_adp:  0.333  50.000  -2.529  -2.310  -1.147  -0.000  -0.000  -0.000
   4_occ:  0.333  50.000  -2.529  -2.310  -1.147  -0.000  -0.000  -0.000
   5_bss:  0.333  50.000  -2.357  -2.161  -0.983  -0.000  -0.000  -0.000
   5_xyz:  0.333  50.000  -2.357  -2.161  -0.983  -0.000  -0.000  -0.000
   5_adp:  0.333  50.000  -2.357  -2.161  -0.983  -0.000  -0.000  -0.000
   5_occ:  0.333  50.000  -2.357  -2.161  -0.983  -0.000  -0.000  -0.000
   5_bss:  0.322  47.859  -2.095  -1.930  -0.749  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  17.234 0.8908  1.0364    10826.821
   1_bss:  15.691 0.9033  0.9701     7913.965
   1_xyz:  12.397 0.9280  0.9828     5538.103
   1_adp:  12.686 0.9253  0.9823     5627.384
   1_occ:  12.666 0.9255  0.9821     5596.659
   2_bss:  12.593 0.9260  0.9764     5532.381
   2_xyz:  12.567 0.9265  0.9752     5590.678
   2_adp:  12.643 0.9257  0.9708     5575.104
   2_occ:  12.657 0.9256  0.9706     5579.833
   3_bss:  12.653 0.9256  0.9779     5579.928
   3_xyz:  12.894 0.9239  0.9776     5781.064
   3_adp:  13.018 0.9229  0.9716     5813.775
   3_occ:  13.028 0.9228  0.9715     5818.759
   4_bss:  13.029 0.9228  0.9789     5820.128
   4_xyz:  13.185 0.9218  0.9781     5928.389
   4_adp:  13.195 0.9217  0.9719     5931.083
   4_occ:  13.202 0.9216  0.9718     5935.635
   5_bss:  13.203 0.9216  0.9776     5936.780
   5_xyz:  13.209 0.9215  0.9778     5951.705
   5_adp:  13.365 0.9203  0.9702     6010.305
   5_occ:  13.368 0.9203  0.9701     6013.589
   5_bss:  13.362 0.9203  0.9787     6003.921
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5936e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5936e-01
   1_xyz:   0.997  0.008  0.077 15.326  0.004  4.110   6.3402e-02
   1_adp:   0.997  0.008  0.077 15.326  0.004  4.110   6.3402e-02
   1_occ:   0.997  0.008  0.077 15.326  0.004  4.110   6.3402e-02
   2_bss:   0.997  0.008  0.077 15.326  0.004  4.110   6.3402e-02
   2_xyz:   1.008  0.008  0.079 15.261  0.004  4.110   6.3409e-02
   2_adp:   1.008  0.008  0.079 15.261  0.004  4.110   6.3409e-02
   2_occ:   1.008  0.008  0.079 15.261  0.004  4.110   6.3409e-02
   3_bss:   1.008  0.008  0.079 15.261  0.004  4.110   6.3409e-02
   3_xyz:   1.057  0.009  0.082 15.356  0.004  4.112   7.0446e-02
   3_adp:   1.057  0.009  0.082 15.356  0.004  4.112   7.0446e-02
   3_occ:   1.057  0.009  0.082 15.356  0.004  4.112   7.0446e-02
   4_bss:   1.057  0.009  0.082 15.356  0.004  4.112   7.0446e-02
   4_xyz:   0.941  0.007  0.074 15.115  0.004  4.117   5.6570e-02
   4_adp:   0.941  0.007  0.074 15.115  0.004  4.117   5.6570e-02
   4_occ:   0.941  0.007  0.074 15.115  0.004  4.117   5.6570e-02
   5_bss:   0.941  0.007  0.074 15.115  0.004  4.117   5.6570e-02
   5_xyz:   0.990  0.007  0.077 15.170  0.004  4.117   6.1511e-02
   5_adp:   0.990  0.007  0.077 15.170  0.004  4.117   6.1511e-02
   5_occ:   0.990  0.007  0.077 15.170  0.004  4.117   6.1511e-02
   5_bss:   0.990  0.007  0.077 15.170  0.004  4.117   6.1511e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4051e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4051e-01
   1_xyz:   6.924  0.042  0.224 85.517  0.034  2.311   8.8436e-02
   1_adp:   6.924  0.042  0.224 85.517  0.034  2.311   8.8436e-02
   1_occ:   6.924  0.042  0.224 85.517  0.034  2.311   8.8436e-02
   2_bss:   6.924  0.042  0.224 85.517  0.034  2.311   8.8436e-02
   2_xyz:   6.776  0.038  0.261 84.181  0.035  2.286   4.6806e-02
   2_adp:   6.776  0.038  0.261 84.181  0.035  2.286   4.6806e-02
   2_occ:   6.776  0.038  0.261 84.181  0.035  2.286   4.6806e-02
   3_bss:   6.776  0.038  0.261 84.181  0.035  2.286   4.6806e-02
   3_xyz:   6.754  0.047  0.279 83.895  0.037  2.260   5.5977e-02
   3_adp:   6.754  0.047  0.279 83.895  0.037  2.260   5.5977e-02
   3_occ:   6.754  0.047  0.279 83.895  0.037  2.260   5.5977e-02
   4_bss:   6.754  0.047  0.279 83.895  0.037  2.260   5.5977e-02
   4_xyz:   6.474  0.042  0.233 83.462  0.034  2.344   3.7474e-02
   4_adp:   6.474  0.042  0.233 83.462  0.034  2.344   3.7474e-02
   4_occ:   6.474  0.042  0.233 83.462  0.034  2.344   3.7474e-02
   5_bss:   6.474  0.042  0.233 83.462  0.034  2.344   3.7474e-02
   5_xyz:   6.445  0.044  0.253 83.432  0.035  2.291   4.3443e-02
   5_adp:   6.445  0.044  0.253 83.432  0.035  2.291   4.3443e-02
   5_occ:   6.445  0.044  0.253 83.432  0.035  2.291   4.3443e-02
   5_bss:   6.445  0.044  0.253 83.432  0.035  2.291   4.3443e-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:  63.27   0.00  16.36  63.27   0.00  12.60  62.72   5.44  36.82
   1_occ:  63.27   0.00  16.36  63.27   0.00  12.60  62.72   5.44  36.82
   2_bss:  63.27   0.00  16.36  63.27   0.00  12.60  62.72   5.44  36.82
   2_xyz:  63.27   0.00  16.36  63.27   0.00  12.60  62.72   5.44  36.82
   2_adp:  67.33   2.09  16.47  65.37   2.09  12.77  67.33   5.59  36.58
   2_occ:  67.33   2.09  16.47  65.37   2.09  12.77  67.33   5.59  36.58
   3_bss:  67.33   2.09  16.47  65.37   2.09  12.77  67.33   5.59  36.58
   3_xyz:  67.33   2.09  16.47  65.37   2.09  12.77  67.33   5.59  36.58
   3_adp:  72.64   1.20  16.63  72.64   1.20  12.75  69.30   6.34  37.75
   3_occ:  72.64   1.20  16.63  72.64   1.20  12.75  69.30   6.34  37.75
   4_bss:  72.64   1.20  16.63  72.64   1.20  12.75  69.30   6.34  37.75
   4_xyz:  72.64   1.20  16.63  72.64   1.20  12.75  69.30   6.34  37.75
   4_adp:  72.84   0.99  16.49  72.84   0.99  12.61  69.37   6.38  37.66
   4_occ:  72.84   0.99  16.49  72.84   0.99  12.61  69.37   6.38  37.66
   5_bss:  72.84   0.99  16.49  72.84   0.99  12.61  69.37   6.38  37.66
   5_xyz:  72.84   0.99  16.49  72.84   0.99  12.61  69.37   6.38  37.66
   5_adp:  83.20   0.00  16.67  83.20   0.00  12.55  74.51   5.90  39.07
   5_occ:  83.20   0.00  16.67  83.20   0.00  12.55  74.51   5.90  39.07
   5_bss:  83.20   0.00  16.67  83.20   0.00  12.55  74.51   5.90  39.07
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.426    0.006    0.147
   1_adp:    0.426    0.006    0.147
   1_occ:    0.426    0.006    0.147
   2_bss:    0.426    0.006    0.147
   2_xyz:    0.690    0.015    0.167
   2_adp:    0.690    0.015    0.167
   2_occ:    0.690    0.015    0.167
   3_bss:    0.690    0.015    0.167
   3_xyz:    0.892    0.020    0.178
   3_adp:    0.892    0.020    0.178
   3_occ:    0.892    0.020    0.178
   4_bss:    0.892    0.020    0.178
   4_xyz:    0.992    0.013    0.181
   4_adp:    0.992    0.013    0.181
   4_occ:    0.992    0.013    0.181
   5_bss:    0.992    0.013    0.181
   5_xyz:    1.080    0.011    0.183
   5_adp:    1.080    0.011    0.183
   5_occ:    1.080    0.011    0.183
   5_bss:    1.080    0.011    0.183
------------------------------------------------------------------------

CPU time actual refinement: 308.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/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_654/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_654/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 308.11 
  Macro-tasks:
    bulk solvent and scale       = 35.26  
    individual site refinement   = 120.89 
    weights calculation          = 29.07  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 191.83 
  Micro-tasks:
    mask                            = 0.58   
    f_calc                          = 98.15  
    alpha_beta                      = 8.04   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 105.51 
    fmodel                         = 6.41   
    r_factors                      = 0.15   
    phase_errors                   = 11.30  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 231.55 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.464 micro seconds
Total CPU time: 5.36 minutes
from_scatterers_fft:    634 calls, 97.89 s
gradients_fft:          579 calls, 92.73 s

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

# Date 2008-01-16 Time 05:19:40 PST -0800 (1200489580.72 s)
Start R-work = 0.1977, R-free = 0.1976 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.1767, R-free = 0.1754
Final R-work = 0.1050, R-free = 0.1536