# Date 2008-01-16 Time 06:41:30 PST -0800 (1200494490.23 s)
#phil __OFF__

Command line arguments: "../1241.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26809
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1241

-------------------------------------------------------------------------------
  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: (72.0062, 46.2261, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3484 1.97425
Completeness in resolution range: 0.920276
Completeness with d_max=infinity: 0.917689

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3484
                             d_min =   1.9742

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: (72.0062, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3484 1.97425
Completeness in resolution range: 0.920276
Completeness with d_max=infinity: 0.917689

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3488 -  4.2266 [2232/2259]  2009   223  10.0%
  bin  2:  4.2266 -  3.3664 [2154/2174]  1941   213   9.9%
  bin  3:  3.3664 -  2.9443 [2106/2125]  1892   214  10.2%
  bin  4:  2.9443 -  2.6766 [2087/2117]  1873   214  10.3%
  bin  5:  2.6766 -  2.4856 [2106/2125]  1902   204   9.7%
  bin  6:  2.4856 -  2.3396 [2080/2105]  1870   210  10.1%
  bin  7:  2.3396 -  2.2228 [2053/2081]  1841   212  10.3%
  bin  8:  2.2228 -  2.1263 [2066/2102]  1861   205   9.9%
  bin  9:  2.1263 -  2.0447 [2038/2092]  1846   192   9.4%
  bin 10:  2.0447 -  1.9742 [ 667/2106]   595    72  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/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: 24
        2.42 -     3.04: 2173
        3.04 -     3.66: 4654
        3.66 -     4.28: 8931
        4.28 -     4.90: 12189
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.102 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.170 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27966 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_1241/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 72.00625 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4785   r_free= 0.4759   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.286107                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.7151 0.99   1448  161 0.3758 0.3530      6.5773      6.5079|
|  2:  4.7151 -  3.7607 0.99   1397  155 0.4138 0.4098      6.8445      6.8182|
|  3:  3.7607 -  3.2906 0.99   1365  152 0.4441 0.4152       6.648      6.6255|
|  4:  3.2906 -  2.9922 0.99   1360  153 0.4777 0.5106      6.5198      6.5173|
|  5:  2.9922 -  2.7791 0.99   1356  150 0.5094 0.4936      6.3664      6.3949|
|  6:  2.7791 -  2.6161 0.99   1343  147 0.4981 0.4925      6.2595      6.2118|
|  7:  2.6161 -  2.4856 0.99   1348  150 0.5256 0.4853      6.2343      6.1791|
|  8:  2.4856 -  2.3778 0.98   1317  148 0.5413 0.5704      6.1783      6.1713|
|  9:  2.3778 -  2.2866 0.98   1340  149 0.5362 0.5425      6.1338       6.176|
| 10:  2.2866 -  2.2079 1.00   1333  153 0.5330 0.5159      6.0641      6.0469|
| 11:  2.2079 -  2.1391 0.98   1315  144 0.5223 0.5441      6.0347      6.0547|
| 12:  2.1391 -  2.0781 0.98   1315  145 0.5383 0.5403      5.9318      5.9273|
| 13:  2.0781 -  2.0235 0.84   1133  123 0.5326 0.5060      5.8756      5.7953|
| 14:  2.0235 -  1.9742 0.19    260   29 0.5161 0.6456      5.8513       5.927|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.7151  1448   161  0.74  30.78   0.81     0.78      61532.17|
|  2:  4.7151 -  3.7607  1397   155  0.73  32.90   0.89     0.83      97848.69|
|  3:  3.7607 -  3.2906  1365   152  0.58  45.38   0.90     0.76     112819.35|
|  4:  3.2906 -  2.9922  1360   153  0.47  54.39   0.87     0.65     109638.27|
|  5:  2.9922 -  2.7791  1356   150  0.37  62.01   0.86     0.54      89339.15|
|  6:  2.7791 -  2.6161  1343   147  0.34  64.32   0.89     0.49      76504.10|
|  7:  2.6161 -  2.4856  1348   150  0.33  65.22   0.88     0.46      67470.92|
|  8:  2.4856 -  2.3778  1317   148  0.31  66.95   0.86     0.45      61911.67|
|  9:  2.3778 -  2.2866  1340   149  0.32  66.25   0.90     0.46      56338.06|
| 10:  2.2866 -  2.2079  1333   153  0.32  66.38   0.89     0.47      50083.67|
| 11:  2.2079 -  2.1391  1315   144  0.31  67.20   0.92     0.46      48783.83|
| 12:  2.1391 -  2.0781  1315   145  0.26  70.86   0.89     0.41      45219.18|
| 13:  2.0781 -  2.0235  1133   123  0.23  73.19   0.90     0.37      41278.09|
| 14:  2.0235 -  1.9742   260    29  0.27  70.23   0.94     0.37      33399.52|
|alpha:            min =        0.37 max =            0.83 mean =         0.55|
|beta:             min =    33399.52 max =       112819.35 mean =     70708.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.59|
|phase err.(test): min =        0.00 max =           89.97 mean =        58.59|
|-----------------------------------------------------------------------------|

============================== 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 = 18.108147             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.074   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.933645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.259   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1975 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1853 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2801 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4579 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4352 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5549 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6640 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.200 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4785   r_free= 0.4759   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.286107                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4718   r_free= 0.4715   ksol= 0.32   Bsol= 72.24   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,-0.39,2.44,-0.00,0.00,0.00); trace/3= 1.12                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.281963                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.469140             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.993   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.364482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.873   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4718      final r-factor (work) = 0.3245          |
| start r-factor (free) = 0.4715      final r-factor (free) = 0.3602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.7134 = 15.47 * 0.50 * 6.2767 + 1.00 * 0.1655                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.7001 = 15.47 * 0.50 * 6.1460 + 1.00 * 0.1634                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3245      final r-factor (work) = 0.2913          |
| start r-factor (free) = 0.3602      final r-factor (free) = 0.3687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3926 = 1.36 * 1.00 * 6.1460 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1681 = 1.36 * 1.00 * 5.9667 + 1.00 * 0.0267                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.54  19.38    None  None   None       |
|    all(noH): 2823   0      0.00    109.54  19.38    None  None   None       |
|    Sol.    : 438    0      0.00    109.54  44.24    None  None   None       |
|    Mac.    : 2385   0      0.00    80.27   14.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.954: 1081   |   5:    54.771 -  65.725:   86        |
|      1:    10.954 -  21.908:  887   |   6:    65.725 -  76.679:   48        |
|      2:    21.908 -  32.862:  379   |   7:    76.679 -  87.633:   19        |
|      3:    32.862 -  43.816:  179   |   8:    87.633 -  98.587:    4        |
|      4:    43.816 -  54.771:  139   |   9:    98.587 - 109.541:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2913 r_free = 0.3687             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2908 r_free = 0.3689             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2908   r_free= 0.3689   ksol= 0.32   Bsol= 72.24   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.32,-0.39,2.44,-0.00,0.00,0.00); trace/3= 1.12                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.979751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2899   r_free= 0.3690   ksol= 0.36   Bsol= 90.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-1.34,1.05,-0.00,0.00,0.00); trace/3= -0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.980608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.450733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.854   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.655374              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.622  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2899      final r-factor (work) = 0.2212          |
| start r-factor (free) = 0.3690      final r-factor (free) = 0.2867          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4126 = 6.45 * 0.50 * 5.9681 + 1.00 * 0.1632                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0806 = 6.45 * 0.50 * 5.8928 + 1.00 * 0.0741                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2212      final r-factor (work) = 0.2018          |
| start r-factor (free) = 0.2867      final r-factor (free) = 0.2689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8849 = 0.66 * 1.00 * 5.8928 + 1.00 * 0.0229                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7536 = 0.66 * 1.00 * 5.7049 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.97  18.97    None  None   None       |
|    all(noH): 2823   0      0.00    109.97  18.97    None  None   None       |
|    Sol.    : 438    0      1.88    109.97  46.08    None  None   None       |
|    Mac.    : 2385   0      0.00    80.91   13.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.997: 1156   |   5:    54.985 -  65.982:  101        |
|      1:    10.997 -  21.994:  950   |   6:    65.982 -  76.979:   47        |
|      2:    21.994 -  32.991:  261   |   7:    76.979 -  87.976:   19        |
|      3:    32.991 -  43.988:  144   |   8:    87.976 -  98.974:    4        |
|      4:    43.988 -  54.985:  140   |   9:    98.974 - 109.971:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2018 r_free = 0.2689             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2017 r_free = 0.2686             target_work(ml) = 5.672         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2017   r_free= 0.2686   ksol= 0.36   Bsol= 90.45   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-1.34,1.05,-0.00,0.00,0.00); trace/3= -0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.671599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2018   r_free= 0.2688   ksol= 0.35   Bsol= 85.87   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,-1.73,0.36,-0.00,0.00,0.00); trace/3= -0.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.671189                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.729460              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.287  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.637509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.235  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2018      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2688      final r-factor (free) = 0.2258          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8608 = 2.73 * 0.50 * 5.7057 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6901 = 2.73 * 0.50 * 5.5936 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1562          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.2167          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1742 = 1.64 * 1.00 * 5.5936 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9678 = 1.64 * 1.00 * 5.4668 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.73  19.18    None  None   None       |
|    all(noH): 2823   0      0.00    113.73  19.18    None  None   None       |
|    Sol.    : 438    0      4.98    113.73  49.91    None  None   None       |
|    Mac.    : 2385   0      0.00    91.87   13.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.373: 1277   |   5:    56.863 -  68.236:  103        |
|      1:    11.373 -  22.745:  908   |   6:    68.236 -  79.609:   73        |
|      2:    22.745 -  34.118:  214   |   7:    79.609 -  90.981:   31        |
|      3:    34.118 -  45.491:  113   |   8:    90.981 - 102.354:    6        |
|      4:    45.491 -  56.863:   95   |   9:   102.354 - 113.727:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1562 r_free = 0.2167             target_work(ml) = 5.449         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1561 r_free = 0.2167             target_work(ml) = 5.449         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1561   r_free= 0.2167   ksol= 0.35   Bsol= 85.87   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,-1.73,0.36,-0.00,0.00,0.00); trace/3= -0.75                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.449171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.2173   ksol= 0.34   Bsol= 84.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.18,-0.10,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.451059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.116675              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.371  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.969  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1564      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2173      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8445 = 2.12 * 0.50 * 5.4691 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7788 = 2.12 * 0.50 * 5.4084 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1370          |
| start r-factor (free) = 0.1982      final r-factor (free) = 0.1904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4313 = 0.63 * 1.00 * 5.4084 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3895 = 0.63 * 1.00 * 5.3460 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.06  18.58    None  None   None       |
|    all(noH): 2823   0      0.00    111.06  18.58    None  None   None       |
|    Sol.    : 438    0      5.89    111.06  48.11    None  None   None       |
|    Mac.    : 2385   0      0.00    93.22   13.16    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 -  11.106: 1288   |   5:    55.529 -  66.635:   93        |
|      1:    11.106 -  22.212:  925   |   6:    66.635 -  77.741:   64        |
|      2:    22.212 -  33.318:  203   |   7:    77.741 -  88.847:   34        |
|      3:    33.318 -  44.424:  104   |   8:    88.847 -  99.953:   11        |
|      4:    44.424 -  55.529:   97   |   9:    99.953 - 111.059:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1370 r_free = 0.1904             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1370 r_free = 0.1903             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1903   ksol= 0.34   Bsol= 84.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.18,-0.10,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324974                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1903   ksol= 0.33   Bsol= 80.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.18,-0.10,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.070286              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.122  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.435263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.123  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1370      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1903      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2614 = 3.07 * 0.50 * 5.3458 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1871 = 3.07 * 0.50 * 5.2882 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3148 = 0.44 * 1.00 * 5.2882 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2944 = 0.44 * 1.00 * 5.2451 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.11  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    113.11  17.95    None  None   None       |
|    Sol.    : 438    0      5.61    113.11  45.52    None  None   None       |
|    Mac.    : 2385   0      0.00    96.05   12.89    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 -  11.311: 1351   |   5:    56.555 -  67.866:   80        |
|      1:    11.311 -  22.622:  897   |   6:    67.866 -  79.177:   41        |
|      2:    22.622 -  33.933:  196   |   7:    79.177 -  90.488:   22        |
|      3:    33.933 -  45.244:  128   |   8:    90.488 - 101.799:    6        |
|      4:    45.244 -  56.555:   98   |   9:   101.799 - 113.110:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1234 r_free = 0.1738             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1737             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1737   ksol= 0.33   Bsol= 80.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.18,-0.10,-0.00,-0.00,-0.00); trace/3= -1.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235654                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.7151 0.99   1448  161 0.0953 0.1423      5.3806      5.6283|
|  2:  4.7151 -  3.7607 0.99   1397  155 0.0865 0.1167      5.4643      5.6769|
|  3:  3.7607 -  3.2906 0.99   1365  152 0.1148 0.1643      5.5277      5.8482|
|  4:  3.2906 -  2.9922 0.99   1360  153 0.1410 0.1882      5.5497      5.7002|
|  5:  2.9922 -  2.7791 0.99   1356  150 0.1483 0.1954      5.4143      5.6787|
|  6:  2.7791 -  2.6161 0.99   1343  147 0.1447 0.2082      5.3076      5.5418|
|  7:  2.6161 -  2.4856 0.99   1348  150 0.1419 0.1867      5.2598      5.4198|
|  8:  2.4856 -  2.3778 0.98   1317  148 0.1375 0.1866      5.1793         5.4|
|  9:  2.3778 -  2.2866 0.98   1340  149 0.1344 0.2058      5.1429      5.4052|
| 10:  2.2866 -  2.2079 1.00   1333  153 0.1256 0.1786      5.0159      5.2234|
| 11:  2.2079 -  2.1391 0.98   1315  144 0.1246 0.1867      5.0005      5.3803|
| 12:  2.1391 -  2.0781 0.98   1315  145 0.1284 0.2055      4.9513      5.2005|
| 13:  2.0781 -  2.0235 0.84   1133  123 0.1247 0.1743      4.8676      5.0649|
| 14:  2.0235 -  1.9742 0.19    260   29 0.1040 0.1659      4.7168       5.005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.7151  1448   161  0.94   9.38   0.97     0.94       7707.88|
|  2:  4.7151 -  3.7607  1397   155  0.95   8.66   1.01     0.99       9955.39|
|  3:  3.7607 -  3.2906  1365   152  0.92  12.62   1.03     1.03      11774.58|
|  4:  3.2906 -  2.9922  1360   153  0.90  16.26   1.01     1.00      12510.26|
|  5:  2.9922 -  2.7791  1356   150  0.89  17.21   1.01     0.99       9676.99|
|  6:  2.7791 -  2.6161  1343   147  0.88  18.37   0.99     0.97       8363.05|
|  7:  2.6161 -  2.4856  1348   150  0.89  17.25   1.01     0.98       7505.44|
|  8:  2.4856 -  2.3778  1317   148  0.88  18.01   1.00     0.96       6594.53|
|  9:  2.3778 -  2.2866  1340   149  0.88  18.04   1.01     0.95       6164.09|
| 10:  2.2866 -  2.2079  1333   153  0.89  17.18   1.01     0.97       4972.68|
| 11:  2.2079 -  2.1391  1315   144  0.89  17.50   0.99     0.94       4781.68|
| 12:  2.1391 -  2.0781  1315   145  0.89  17.86   1.01     1.01       4611.72|
| 13:  2.0781 -  2.0235  1133   123  0.88  18.63   0.99     0.97       4051.11|
| 14:  2.0235 -  1.9742   260    29  0.92  14.96   0.98     0.95       3039.79|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3039.79 max =        12510.26 mean =      7596.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.80|
|phase err.(test): min =        0.00 max =           89.46 mean =        15.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1732   ksol= 0.33   Bsol= 73.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.38,-0.27,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.35 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1237   r_free= 0.1732   ksol= 0.33   Bsol= 73.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.38,-0.27,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233620                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3488 -  4.7151 0.99   1448  161 0.0960 0.1355      5.3594      5.5842|
|  2:  4.7151 -  3.7607 0.99   1397  155 0.0866 0.1167      5.4561      5.6771|
|  3:  3.7607 -  3.2906 0.99   1365  152 0.1155 0.1635       5.528      5.8426|
|  4:  3.2906 -  2.9922 0.99   1360  153 0.1411 0.1893      5.5507      5.7046|
|  5:  2.9922 -  2.7791 0.99   1356  150 0.1486 0.1957       5.416      5.6794|
|  6:  2.7791 -  2.6161 0.99   1343  147 0.1447 0.2079      5.3081      5.5413|
|  7:  2.6161 -  2.4856 0.99   1348  150 0.1420 0.1869      5.2605      5.4209|
|  8:  2.4856 -  2.3778 0.98   1317  148 0.1375 0.1868      5.1795      5.4003|
|  9:  2.3778 -  2.2866 0.98   1340  149 0.1344 0.2057      5.1428      5.4053|
| 10:  2.2866 -  2.2079 1.00   1333  153 0.1256 0.1788      5.0162      5.2251|
| 11:  2.2079 -  2.1391 0.98   1315  144 0.1245 0.1866      5.0005      5.3794|
| 12:  2.1391 -  2.0781 0.98   1315  145 0.1284 0.2056      4.9518      5.2008|
| 13:  2.0781 -  2.0235 0.84   1133  123 0.1247 0.1741      4.8674      5.0646|
| 14:  2.0235 -  1.9742 0.19    260   29 0.1041 0.1659      4.7163      5.0045|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3488 -  4.7151  1448   161  0.94   8.86   0.96     0.94       7012.43|
|  2:  4.7151 -  3.7607  1397   155  0.95   8.41   1.01     0.99       9488.84|
|  3:  3.7607 -  3.2906  1365   152  0.92  12.59   1.03     1.03      11695.20|
|  4:  3.2906 -  2.9922  1360   153  0.90  16.26   1.01     0.99      12524.55|
|  5:  2.9922 -  2.7791  1356   150  0.89  17.23   1.00     0.99       9710.66|
|  6:  2.7791 -  2.6161  1343   147  0.88  18.36   0.98     0.96       8372.65|
|  7:  2.6161 -  2.4856  1348   150  0.89  17.25   1.00     0.97       7510.26|
|  8:  2.4856 -  2.3778  1317   148  0.88  18.01   0.99     0.96       6597.33|
|  9:  2.3778 -  2.2866  1340   149  0.88  18.04   1.00     0.94       6168.54|
| 10:  2.2866 -  2.2079  1333   153  0.89  17.19   1.00     0.97       4979.42|
| 11:  2.2079 -  2.1391  1315   144  0.89  17.51   0.99     0.93       4788.74|
| 12:  2.1391 -  2.0781  1315   145  0.89  17.87   1.00     1.00       4616.11|
| 13:  2.0781 -  2.0235  1133   123  0.88  18.63   0.98     0.96       4049.79|
| 14:  2.0235 -  1.9742   260    29  0.92  14.94   0.96     0.94       3035.22|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3035.22 max =        12524.55 mean =      7503.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.77 mean =        15.74|
|phase err.(test): min =        0.00 max =           89.55 mean =        15.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.184)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.11  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    113.11  17.95    None  None   None       |
|    Sol.    : 438    0      5.62    113.11  45.52    None  None   None       |
|    Mac.    : 2385   0      0.00    96.06   12.89    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 -  11.314: 1351   |   5:    56.558 -  67.869:   80        |
|      1:    11.314 -  22.625:  897   |   6:    67.869 -  79.180:   41        |
|      2:    22.625 -  33.936:  196   |   7:    79.180 -  90.491:   22        |
|      3:    33.936 -  45.247:  128   |   8:    90.491 - 101.802:    6        |
|      4:    45.247 -  56.558:   98   |   9:   101.802 - 113.113:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.702 - 4.590
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 338
   mapped sites are within: 0.702 - 4.590

peak=    5.987 closest distance to " O   HOH Z 222 " =    1.412
peak=    5.984 closest distance to " O   HOH Z 103 " =    0.950
peak=    5.826 closest distance to " NE2 GLN A  11 " =    1.201
peak=    5.283 closest distance to " CB  GLN A 223 " =    1.519
peak=    5.211 closest distance to " CG  PRO A  54 " =    1.398
peak=    5.202 closest distance to " O   HOH Z 144 " =    1.990
peak=    5.187 closest distance to " O   HOH Z   7 " =    1.652
peak=    5.154 closest distance to " CB  SER A  63 " =    1.367
peak=    5.066 closest distance to " O   HOH Z  63 " =    1.562
peak=    4.912 closest distance to " O   HOH Z 417 " =    1.886
peak=    4.854 closest distance to " O   HOH Z 232 " =    2.072
peak=    4.841 closest distance to " O   HOH Z 183 " =    1.607
peak=    4.799 closest distance to " O   HOH Z 421 " =    2.309
peak=    4.757 closest distance to " O   HOH Z 369 " =    2.069
peak=    4.596 closest distance to " O   HOH Z 287 " =    2.207
peak=    4.536 closest distance to " NH1AARG A 145 " =    1.252
peak=    4.518 closest distance to " O   HOH Z 403 " =    1.437
peak=    4.496 closest distance to " O   HOH Z 182 " =    1.167
peak=    4.487 closest distance to " CB  PRO A  54 " =    1.042
peak=    4.449 closest distance to " O   HOH Z 295 " =    1.412
peak=    4.385 closest distance to " CG  PRO A 213 " =    1.336
peak=    4.301 closest distance to " CB  ASN A 148 " =    1.410
peak=    4.299 closest distance to " CG  PRO A  90 " =    1.419
peak=    4.269 closest distance to " CG  PRO A 198 " =    1.282
peak=    4.251 closest distance to " CA  ARG A 195 " =    1.426
peak=    4.245 closest distance to " O   HOH Z 126 " =    2.207
peak=    4.224 closest distance to " O   HOH Z  49 " =    1.181
peak=    4.220 closest distance to " O   HOH Z 126 " =    1.609
peak=    4.211 closest distance to " CG2 THR A 221 " =    1.049
peak=    4.195 closest distance to " O   HOH Z  69 " =    1.043
peak=    4.132 closest distance to " CB  TRP A 266 " =    1.032
peak=    4.121 closest distance to " O   HOH Z 427 " =    2.484
peak=    4.112 closest distance to " O   HOH Z 298 " =    2.430
peak=    4.098 closest distance to " O   HOH Z 211 " =    1.408
peak=    4.098 closest distance to " CG  PRO A 280 " =    0.945
peak=    4.092 closest distance to " CB  ARG A 190 " =    1.522
peak=    4.063 closest distance to " O   HOH Z 111 " =    1.796
peak=    4.060 closest distance to " CA  TYR A  30 " =    1.137
peak=    4.058 closest distance to " CB  ASP A 124 " =    0.831
peak=    4.044 closest distance to " O   HOH Z 425 " =    1.506
peak=    4.043 closest distance to " CB  SER A 212 " =    1.245
peak=    4.038 closest distance to " O   HOH Z 316 " =    3.095
peak=    4.034 closest distance to " O   HOH Z   9 " =    1.623
peak=    4.029 closest distance to " CD  ARG A 159 " =    0.835
peak=    4.022 closest distance to " NZ  LYS A 119 " =    2.637
peak=    4.011 closest distance to " CB  ARG A 275 " =    1.027
peak=    4.010 closest distance to " O   HOH Z  61 " =    1.715
peak=    4.005 closest distance to " CZ3 TRP A 266 " =    1.161
peak=    4.000 closest distance to " CZ  PHE A 218 " =    1.138
peak=    3.976 closest distance to " O   TYR A 116 " =    1.273
peak=    3.973 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.966 closest distance to " CG  LEU A 167 " =    1.267
peak=    3.958 closest distance to " O   HOH Z 437 " =    1.556
peak=    3.952 closest distance to " O   HOH Z 193 " =    1.735
peak=    3.942 closest distance to " CD1 ILE A  33 " =    1.799
peak=    3.925 closest distance to " O   HOH Z 290 " =    1.293
peak=    3.924 closest distance to " CA  VAL A 125 " =    1.213
peak=    3.922 closest distance to " O   HOH Z  58 " =    1.830
peak=    3.921 closest distance to " O   HOH Z 258 " =    2.076
peak=    3.904 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.881 closest distance to " OE1 GLN A 240 " =    1.572
peak=    3.877 closest distance to " O   ASN A 209 " =    1.493
peak=    3.870 closest distance to " O   HOH Z 214 " =    2.196
peak=    3.859 closest distance to " CB  SER A   3 " =    1.623
peak=    3.856 closest distance to " CB  GLU A 152 " =    1.139
peak=    3.852 closest distance to " O   HOH Z 427 " =    1.161
peak=    3.851 closest distance to " O   HOH Z   1 " =    1.840
peak=    3.817 closest distance to " N   ASN A 127 " =    1.404
peak=    3.810 closest distance to " O   HOH Z 193 " =    2.195
peak=    3.806 closest distance to " CA  ARG A 156 " =    1.104
peak=    3.799 closest distance to " O   HOH Z 272 " =    1.838
peak=    3.797 closest distance to " CG  PRO A 243 " =    1.066
peak=    3.796 closest distance to " O   HOH Z 180 " =    2.107
peak=    3.792 closest distance to " CB  SER A 216 " =    1.049
peak=    3.791 closest distance to " O   HOH Z 380 " =    1.706
peak=    3.788 closest distance to " O   HOH Z 184 " =    1.691
peak=    3.786 closest distance to " NE2 HIS A 207 " =    1.113
peak=    3.773 closest distance to " NH1 ARG A  56 " =    1.251
peak=    3.773 closest distance to " CB  SER A 276 " =    1.092
peak=    3.767 closest distance to " O   HOH Z 362 " =    2.205
peak=    3.763 closest distance to " CB  GLU A 128 " =    1.007
peak=    3.761 closest distance to " CA  ALA A 160 " =    1.045
peak=    3.760 closest distance to " ND1 HIS A  86 " =    1.737
peak=    3.758 closest distance to " CB  SER A 210 " =    0.951
peak=    3.751 closest distance to " CG  TRP A 179 " =    2.332
peak=    3.749 closest distance to " O   HOH Z 352 " =    1.780
peak=    3.748 closest distance to " CD2 TRP A 179 " =    1.235
peak=    3.747 closest distance to " CB  VAL A 265 " =    1.361
peak=    3.731 closest distance to " CB  MET A  40 " =    0.790
peak=    3.720 closest distance to " CB  ASP A 132 " =    3.877
peak=    3.720 closest distance to " O   HOH Z 154 " =    2.169
peak=    3.715 closest distance to " O   PRO A 198 " =    1.560
peak=    3.708 closest distance to " CA  ILE A 234 " =    1.163
peak=    3.698 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.696 closest distance to " O   PRO A 198 " =    1.328
peak=    3.683 closest distance to " CA  MET A 105 " =    0.923
peak=    3.683 closest distance to " CB  ALA A 160 " =    1.501
peak=    3.668 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.667 closest distance to " CA  ASN A 127 " =    1.128
peak=    3.663 closest distance to " CE3 TRP A 274 " =    1.448
peak=    3.655 closest distance to " O   THR A 182 " =    1.495
peak=    3.650 closest distance to " CB  PRO A  90 " =    1.120
peak=    3.649 closest distance to " CB  ASN A  60 " =    0.906
peak=    3.648 closest distance to " OE1 GLN A  11 " =    2.161
peak=    3.642 closest distance to " CB  TYR A 169 " =    0.738
peak=    3.641 closest distance to " ND2 ASN A  60 " =    3.120
peak=    3.641 closest distance to " OG  SER A 135 " =    1.275
peak=    3.639 closest distance to " CA  TYR A 116 " =    1.378
peak=    3.636 closest distance to " O   HOH Z 112 " =    1.343
peak=    3.630 closest distance to " CB  ASP A 140 " =    0.702
peak=    3.629 closest distance to " N   TYR A  15 " =    0.963
peak=    3.629 closest distance to " CA  ARG A 102 " =    1.096
peak=    3.629 closest distance to " O   HOH Z 394 " =    1.730
peak=    3.627 closest distance to " O   HOH Z 122 " =    1.977
peak=    3.627 closest distance to " O   HOH Z 422 " =    2.722
peak=    3.625 closest distance to " CB  GLN A 183 " =    1.225
peak=    3.624 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.617 closest distance to " O   HOH Z 217 " =    2.817
peak=    3.614 closest distance to " O   HOH Z 218 " =    1.521
peak=    3.612 closest distance to " CG1 VAL A 153 " =    1.024
peak=    3.611 closest distance to " OH  TYR A 186 " =    1.162
peak=    3.608 closest distance to " O   HOH Z 393 " =    1.383
peak=    3.603 closest distance to " CG  LYS A  76 " =    1.723
peak=    3.596 closest distance to " CA  GLU A  46 " =    0.888
peak=    3.591 closest distance to " O   HOH Z 251 " =    1.627
peak=    3.591 closest distance to " CD BLYS A 290 " =    1.000
peak=    3.587 closest distance to " CE3 TRP A  85 " =    0.919
peak=    3.581 closest distance to " NE2 GLN A  55 " =    1.015
peak=    3.581 closest distance to " O   HOH Z 207 " =    0.815
peak=    3.579 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.578 closest distance to " CB  LEU A 237 " =    0.851
peak=    3.572 closest distance to " O   HOH Z 218 " =    1.806
peak=    3.570 closest distance to " CB  VAL A 202 " =    1.479
peak=    3.569 closest distance to " CA  ASN A  74 " =    1.380
peak=    3.568 closest distance to " CG  ARG A 159 " =    0.788
peak=    3.563 closest distance to " O   HOH Z 410 " =    1.539
peak=    3.562 closest distance to " O   HOH Z 195 " =    1.328
peak=    3.555 closest distance to " CB  GLU A 277 " =    3.711
peak=    3.554 closest distance to " N   SER A 271 " =    0.973
peak=    3.551 closest distance to " O   HOH Z 124 " =    1.883
peak=    3.549 closest distance to " O   HOH Z 411 " =    3.248
peak=    3.536 closest distance to " O   HOH Z 325 " =    2.243
peak=    3.536 closest distance to " O   HOH Z 170 " =    1.231
peak=    3.534 closest distance to " CA  GLU A 152 " =    1.090
peak=    3.531 closest distance to " O   HOH Z  88 " =    3.287
peak=    3.531 closest distance to " O   HOH Z  97 " =    1.390
peak=    3.530 closest distance to " CB  ASN A 142 " =    0.940
peak=    3.529 closest distance to " CD  ARG A 269 " =    0.919
peak=    3.528 closest distance to " O   HOH Z 148 " =    3.608
peak=    3.527 closest distance to " CA  ARG A  36 " =    1.232
peak=    3.511 closest distance to " O   HOH Z 201 " =    1.661
peak=    3.511 closest distance to " NH2AARG A 190 " =    1.890
peak=    3.508 closest distance to " O   HOH Z 189 " =    3.530
peak=    3.506 closest distance to " O   HOH Z 332 " =    1.648
peak=    3.503 closest distance to " O   HOH Z 434 " =    1.527
peak=    3.498 closest distance to " OG  SER A  62 " =    2.940
peak=    3.497 closest distance to " N   VAL A 296 " =    1.818
peak=    3.488 closest distance to " OD1 ASN A 217 " =    1.470
peak=    3.478 closest distance to " CD  ARG A  66 " =    2.075
peak=    3.474 closest distance to " O   HOH Z   2 " =    1.619
peak=    3.472 closest distance to " CA  GLY A 241 " =    0.873
peak=    3.467 closest distance to " O   HOH Z 145 " =    1.882
peak=    3.467 closest distance to " OE2 GLU A  53 " =    1.437
peak=    3.465 closest distance to " CA  SER A  95 " =    0.938
peak=    3.464 closest distance to " CA  SER A  87 " =    1.074
peak=    3.464 closest distance to " O   HOH Z 298 " =    4.152
peak=    3.459 closest distance to " O   HOH Z 346 " =    1.710
peak=    3.458 closest distance to " O   HOH Z 240 " =    1.936
peak=    3.456 closest distance to " CA  TRP A  92 " =    1.145
peak=    3.455 closest distance to " CA  ASP A 124 " =    0.832
peak=    3.452 closest distance to " O   HOH Z 188 " =    2.595
peak=    3.444 closest distance to " O   HOH Z 366 " =    2.700
peak=    3.441 closest distance to " CG1 ILE A  33 " =    1.178
peak=    3.433 closest distance to " CB  ALA A 104 " =    0.773
peak=    3.432 closest distance to " N   CYS A 260 " =    0.884
peak=    3.431 closest distance to " O   HOH Z 368 " =    1.873
peak=    3.426 closest distance to " O   HOH Z 222 " =    2.367
peak=    3.423 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.423 closest distance to " O   HOH Z 207 " =    2.276
peak=    3.415 closest distance to " O   HOH Z 105 " =    1.083
peak=    3.412 closest distance to " O   HOH Z 216 " =    4.087
peak=    3.405 closest distance to " CB  THR A  82 " =    1.095
peak=    3.399 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.398 closest distance to " O   HOH Z 171 " =    2.617
peak=    3.398 closest distance to " O   HOH Z 302 " =    1.692
peak=    3.391 closest distance to " CA  THR A 264 " =    0.895
peak=    3.391 closest distance to " CB  ASN A 187 " =    1.054
peak=    3.389 closest distance to " CD  ARG A 195 " =    3.501
peak=    3.383 closest distance to " O   HOH Z 394 " =    4.058
peak=    3.380 closest distance to " O   HOH Z  40 " =    1.987
peak=    3.376 closest distance to " O   HOH Z 132 " =    2.507
peak=    3.371 closest distance to " O   HOH Z 185 " =    1.932
peak=    3.366 closest distance to " CB  ASN A  39 " =    0.932
peak=    3.366 closest distance to " O   HOH Z  53 " =    2.439
peak=    3.364 closest distance to " CB  ARG A  79 " =    1.213
peak=    3.364 closest distance to " CA  LEU A 101 " =    1.237
peak=    3.362 closest distance to " O   MET A 105 " =    1.794
peak=    3.362 closest distance to " CB  ARG A 156 " =    1.019
peak=    3.361 closest distance to " O   HOH Z 153 " =    1.599
peak=    3.360 closest distance to " NE AARG A 275 " =    1.696
peak=    3.360 closest distance to " CD2 PHE A  59 " =    1.898
peak=    3.360 closest distance to " CA  ARG A 139 " =    1.104
peak=    3.359 closest distance to " O   HOH Z 391 " =    2.868
peak=    3.358 closest distance to " CB  ALA A   1 " =    4.590
peak=    3.353 closest distance to " O   HOH Z 359 " =    1.415
peak=    3.353 closest distance to " O   HOH Z  80 " =    1.651
peak=    3.348 closest distance to " ND1 HIS A  81 " =    1.840
peak=    3.347 closest distance to " CG1 ILE A 120 " =    1.436
peak=    3.337 closest distance to " CB  ALA A  10 " =    0.956
peak=    3.335 closest distance to " O   THR A 220 " =    1.422
peak=    3.331 closest distance to " N   ARG A 156 " =    1.360
peak=    3.326 closest distance to " O   HOH Z 438 " =    1.894
peak=    3.324 closest distance to " CB  TYR A 169 " =    0.841
peak=    3.322 closest distance to " O   HOH Z  68 " =    1.720
peak=    3.321 closest distance to " CG2 THR A  29 " =    1.550
peak=    3.320 closest distance to " O   ASN A  74 " =    1.420
peak=    3.316 closest distance to " CZ  PHE A  38 " =    1.313
peak=    3.316 closest distance to " CB  TRP A 150 " =    1.044
peak=    3.315 closest distance to " O   HOH Z   7 " =    3.716
peak=    3.308 closest distance to " CG AARG A 275 " =    1.299
peak=    3.307 closest distance to " CB  ARG A 138 " =    0.981
peak=    3.307 closest distance to " CA  ASP A 162 " =    0.994
peak=    3.305 closest distance to " CB  MET A  47 " =    1.081
peak=    3.305 closest distance to " O   HOH Z 280 " =    3.002
peak=    3.303 closest distance to " O   HOH Z 411 " =    1.509
peak=    3.302 closest distance to " CB  ALA A  34 " =    1.214
peak=    3.302 closest distance to " CB  ALA A 114 " =    0.771
peak=    3.295 closest distance to " CG  GLU A 277 " =    1.952
peak=    3.294 closest distance to " O   HOH Z 285 " =    2.213
peak=    3.293 closest distance to " O   HOH Z  78 " =    1.555
peak=    3.292 closest distance to " CB  GLU A 236 " =    1.400
peak=    3.290 closest distance to " OG  SER A  26 " =    1.648
peak=    3.287 closest distance to " O   HOH Z 145 " =    1.697
peak=    3.286 closest distance to " CB  TYR A  15 " =    0.948
peak=    3.284 closest distance to " O   HOH Z 130 " =    3.405
peak=    3.282 closest distance to " OD2 ASP A 286 " =    3.316
peak=    3.281 closest distance to " OG BSER A 134 " =    2.776
peak=    3.279 closest distance to " CG  MET A 113 " =    1.695
peak=    3.278 closest distance to " O   HOH Z 281 " =    1.846
peak=    3.271 closest distance to " O   HOH Z   9 " =    1.901
peak=    3.269 closest distance to " CB  ALA A  43 " =    0.916
peak=    3.269 closest distance to " O   HOH Z  59 " =    1.862
peak=    3.269 closest distance to " O   GLN A  55 " =    1.732
peak=    3.267 closest distance to " CG2 VAL A 257 " =    0.809
peak=    3.263 closest distance to " OG BSER A  99 " =    2.333
peak=    3.262 closest distance to " CB  SER A  22 " =    1.078
peak=    3.261 closest distance to " O   HOH Z  61 " =    1.647
peak=    3.261 closest distance to " CG1 ILE A 151 " =    1.086
peak=    3.259 closest distance to " O  BHOH Z 338 " =    2.169
peak=    3.255 closest distance to " O   HOH Z 235 " =    1.745
peak=    3.250 closest distance to " O   HOH Z  44 " =    2.721
peak=    3.242 closest distance to " CG  ASN A  60 " =    1.139
peak=    3.235 closest distance to " O   HOH Z 188 " =    2.444
peak=    3.231 closest distance to " O   HOH Z 282 " =    1.854
peak=    3.231 closest distance to " CG BARG A 275 " =    1.469
peak=    3.229 closest distance to " CG  ARG A 138 " =    1.201
peak=    3.229 closest distance to " O   HOH Z 238 " =    3.622
peak=    3.228 closest distance to " O   HOH Z 298 " =    2.612
peak=    3.226 closest distance to " CZ3 TRP A 177 " =    1.075
peak=    3.222 closest distance to " CG2 ILE A 151 " =    0.925
peak=    3.221 closest distance to " ND2 ASN A 110 " =    1.658
peak=    3.219 closest distance to " CA  ARG A 159 " =    1.292
peak=    3.217 closest distance to " CE2 TYR A 186 " =    0.886
peak=    3.215 closest distance to " OH  TYR A 116 " =    1.723
peak=    3.215 closest distance to " CD  LYS A 166 " =    1.640
peak=    3.213 closest distance to " CG  GLN A  88 " =    0.989
peak=    3.213 closest distance to " CA  ALA A 100 " =    1.077
peak=    3.213 closest distance to " CG2 VAL A 197 " =    1.245
peak=    3.212 closest distance to " OE1 GLN A 278 " =    0.962
peak=    3.211 closest distance to " NH1 ARG A  66 " =    1.914
peak=    3.210 closest distance to " O   HOH Z 172 " =    2.734
peak=    3.209 closest distance to " CG2 ILE A  20 " =    1.516
peak=    3.207 closest distance to " O   HOH Z  39 " =    1.256
peak=    3.205 closest distance to " O   HOH Z 385 " =    3.866
peak=    3.204 closest distance to " O   THR A 251 " =    1.226
peak=    3.201 closest distance to " N   GLN A 278 " =    1.117
peak=    3.200 closest distance to " CB  LEU A  83 " =    0.769
peak=    3.198 closest distance to " O   HOH Z 345 " =    3.546
peak=    3.198 closest distance to " O   HOH Z 409 " =    2.226
peak=    3.198 closest distance to " O   HOH Z 158 " =    2.781
peak=    3.196 closest distance to " CB  SER A  62 " =    0.877
peak=    3.193 closest distance to " CB  SER A  97 " =    1.075
peak=    3.191 closest distance to " CD1 ILE A 199 " =    1.154
peak=    3.185 closest distance to " O   HOH Z  76 " =    0.996
peak=    3.181 closest distance to " O   HOH Z 115 " =    1.772
peak=    3.177 closest distance to " OD1 ASN A  69 " =    2.583
peak=    3.175 closest distance to " O   HOH Z 265 " =    1.890
peak=    3.172 closest distance to " CB  LYS A 117 " =    1.218
peak=    3.172 closest distance to " CA  GLY A 196 " =    0.962
peak=    3.171 closest distance to " O   HOH Z 148 " =    2.082
peak=    3.168 closest distance to " O   HOH Z 389 " =    1.903
peak=    3.167 closest distance to " O   HOH Z 288 " =    1.855
peak=    3.167 closest distance to " CB  GLN A  89 " =    1.260
peak=    3.166 closest distance to " O   HOH Z 359 " =    4.080
peak=    3.166 closest distance to " O   HOH Z 368 " =    3.827
peak=    3.159 closest distance to " CA  ALA A 129 " =    1.213
peak=    3.157 closest distance to " CB  LYS A 193 " =    0.993
peak=    3.154 closest distance to " O   HOH Z   1 " =    1.652
peak=    3.151 closest distance to " CB  ASN A 285 " =    0.919
peak=    3.151 closest distance to " O   HOH Z 213 " =    2.172
peak=    3.145 closest distance to " O   HOH Z 128 " =    2.075
peak=    3.144 closest distance to " O   HOH Z  21 " =    1.764
peak=    3.143 closest distance to " CB  GLU A  46 " =    0.977
peak=    3.141 closest distance to " C   GLU A 277 " =    1.453
peak=    3.135 closest distance to " NE2 GLN A  73 " =    1.649
peak=    3.134 closest distance to " CB  ASP A  50 " =    1.173
peak=    3.134 closest distance to " O   GLY A 302 " =    2.295
peak=    3.134 closest distance to " CB  ASP A 253 " =    0.972
peak=    3.130 closest distance to " CB  ALA A 100 " =    1.318
peak=    3.128 closest distance to " CB  LEU A 300 " =    0.953
peak=    3.128 closest distance to " CB  ALA A 114 " =    1.515
peak=    3.128 closest distance to " N   GLU A 152 " =    1.505
peak=    3.126 closest distance to " O   HOH Z 294 " =    1.491
peak=    3.123 closest distance to " CG  GLN A 144 " =    0.926
peak=    3.122 closest distance to " O   HOH Z 272 " =    2.544
peak=    3.121 closest distance to " O   HOH Z  28 " =    1.479
peak=    3.120 closest distance to " O   HOH Z 329 " =    4.149
peak=    3.111 closest distance to " CB  GLN A  88 " =    1.396
peak=    3.103 closest distance to " CB  LYS A 290 " =    0.840
peak=    3.099 closest distance to " O   HOH Z  68 " =    1.949
peak=    3.099 closest distance to " OG BSER A 164 " =    2.301
peak=    3.092 closest distance to " CD2 LEU A 167 " =    1.511
peak=    3.086 closest distance to " O   THR A 294 " =    1.106
peak=    3.083 closest distance to " O   HOH Z 215 " =    2.998
peak=    3.075 closest distance to " O   HOH Z 156 " =    2.954
peak=    3.069 closest distance to " O   ALA A 291 " =    1.475
peak=    3.069 closest distance to " O   HOH Z 116 " =    1.866
peak=    3.063 closest distance to " CB  PRO A 243 " =    1.225
peak=    3.059 closest distance to " O   HOH Z 119 " =    3.386
peak=    3.052 closest distance to " O   HOH Z  85 " =    2.114
peak=    3.051 closest distance to " O   HOH Z 225 " =    1.654
peak=    3.048 closest distance to " CA  GLY A 133 " =    4.133
peak=    3.045 closest distance to " O   HOH Z  11 " =    1.067
peak=    3.039 closest distance to " CA  ILE A 106 " =    0.888
peak=    3.033 closest distance to " OG ASER A 212 " =    1.525
peak=    3.030 closest distance to " CA  ALA A 184 " =    1.180
peak=    3.027 closest distance to " O   HOH Z  57 " =    1.379

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.356 - 5.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 225
   mapped sites are within: 0.703 - 5.910

peak=   -4.817 closest distance to " O   PRO A 198 " =    1.299
peak=   -4.641 closest distance to " O   HOH Z 377 " =    1.773
peak=   -4.519 closest distance to " CD  ARG A  14 " =    3.431
peak=   -4.514 closest distance to " OE1 GLN A  88 " =    1.040
peak=   -4.459 closest distance to " CG  GLN A  88 " =    0.923
peak=   -4.365 closest distance to " O   HOH Z 103 " =    0.916
peak=   -4.350 closest distance to " CB  PRO A 243 " =    2.596
peak=   -4.279 closest distance to " OD1 ASN A  60 " =    0.807
peak=   -4.220 closest distance to " O   HOH Z  32 " =    1.432
peak=   -4.132 closest distance to " CG  MET A 105 " =    0.996
peak=   -4.101 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.101 closest distance to " CG2 ILE A  49 " =    2.826
peak=   -4.086 closest distance to " CB  ASP A  27 " =    2.549
peak=   -4.085 closest distance to " O   HOH Z 216 " =    1.374
peak=   -4.047 closest distance to " O   HOH Z 111 " =    1.716
peak=   -4.038 closest distance to " CG  GLN A 223 " =    2.459
peak=   -4.030 closest distance to " O   HOH Z 231 " =    0.703
peak=   -3.996 closest distance to " O   HOH Z  39 " =    0.904
peak=   -3.977 closest distance to " O   HOH Z 389 " =    2.255
peak=   -3.964 closest distance to " O   HOH Z  60 " =    1.376
peak=   -3.935 closest distance to " O   HOH Z  73 " =    1.786
peak=   -3.933 closest distance to " NZ  LYS A 166 " =    1.165
peak=   -3.931 closest distance to " CA  GLY A  98 " =    1.885
peak=   -3.914 closest distance to " CG2 THR A 178 " =    2.235
peak=   -3.903 closest distance to " O   HOH Z 231 " =    2.051
peak=   -3.895 closest distance to " O   HOH Z  65 " =    1.245
peak=   -3.876 closest distance to " O   HOH Z 407 " =    3.417
peak=   -3.864 closest distance to " CZ3 TRP A 179 " =    1.165
peak=   -3.826 closest distance to " O   HOH Z 316 " =    1.897
peak=   -3.811 closest distance to " O   HOH Z 337 " =    1.258
peak=   -3.793 closest distance to " O   HOH Z 290 " =    1.287
peak=   -3.782 closest distance to " CD  LYS A 289 " =    2.279
peak=   -3.778 closest distance to " N   ALA A  43 " =    2.376
peak=   -3.771 closest distance to " O   PRO A 163 " =    1.929
peak=   -3.768 closest distance to " CD2 LEU A 143 " =    2.521
peak=   -3.767 closest distance to " CD1 TRP A 179 " =    1.116
peak=   -3.750 closest distance to " CB  ALA A  43 " =    2.652
peak=   -3.746 closest distance to " O   HOH Z 188 " =    0.848
peak=   -3.745 closest distance to " CA  GLY A  23 " =    2.879
peak=   -3.740 closest distance to " O   SER A 135 " =    1.424
peak=   -3.723 closest distance to " CB  ALA A 291 " =    2.276
peak=   -3.718 closest distance to " O   ALA A  10 " =    1.707
peak=   -3.704 closest distance to " CB  PRO A  54 " =    2.491
peak=   -3.699 closest distance to " CB  ALA A 158 " =    1.633
peak=   -3.685 closest distance to " CE2 TYR A  30 " =    2.600
peak=   -3.671 closest distance to " CD  GLN A  55 " =    1.096
peak=   -3.669 closest distance to " O   VAL A 125 " =    2.256
peak=   -3.666 closest distance to " O   HOH Z 275 " =    1.807
peak=   -3.656 closest distance to " O   HOH Z 318 " =    1.673
peak=   -3.650 closest distance to " CA  GLY A 241 " =    3.110
peak=   -3.639 closest distance to " O   HOH Z  11 " =    1.634
peak=   -3.637 closest distance to " OG  SER A  97 " =    2.178
peak=   -3.636 closest distance to " O   HOH Z 134 " =    1.667
peak=   -3.629 closest distance to " CD1 TYR A 247 " =    2.764
peak=   -3.614 closest distance to " O   HOH Z 351 " =    1.601
peak=   -3.611 closest distance to " OG BSER A 134 " =    1.493
peak=   -3.596 closest distance to " NH2AARG A 275 " =    5.759
peak=   -3.594 closest distance to " CG2 THR A  18 " =    2.812
peak=   -3.592 closest distance to " O   HOH Z 185 " =    2.260
peak=   -3.586 closest distance to " O   HOH Z 131 " =    4.006
peak=   -3.579 closest distance to " O   HOH Z 103 " =    0.778
peak=   -3.560 closest distance to " CA  GLY A 241 " =    2.353
peak=   -3.556 closest distance to " O   HOH Z  69 " =    1.731
peak=   -3.551 closest distance to " CG1 VAL A  78 " =    2.475
peak=   -3.547 closest distance to " O   HOH Z  38 " =    1.177
peak=   -3.540 closest distance to " C   ASN A 285 " =    2.486
peak=   -3.534 closest distance to " O   HOH Z 298 " =    2.469
peak=   -3.533 closest distance to " O   HOH Z 174 " =    2.632
peak=   -3.527 closest distance to " O   HOH Z  52 " =    1.657
peak=   -3.526 closest distance to " OD2 ASP A  27 " =    1.718
peak=   -3.526 closest distance to " CE1 TYR A 169 " =    2.678
peak=   -3.522 closest distance to " CB  GLN A  11 " =    1.624
peak=   -3.515 closest distance to " CA  GLY A 133 " =    1.905
peak=   -3.513 closest distance to " CG1 VAL A 250 " =    2.583
peak=   -3.506 closest distance to " O   HOH Z 166 " =    1.243
peak=   -3.506 closest distance to " N   SER A 141 " =    1.866
peak=   -3.499 closest distance to " O   HOH Z 313 " =    1.691
peak=   -3.489 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.484 closest distance to " CZ2 TRP A 274 " =    0.939
peak=   -3.467 closest distance to " O   HOH Z 281 " =    2.889
peak=   -3.462 closest distance to " O   HOH Z 368 " =    1.389
peak=   -3.457 closest distance to " C   LEU A 222 " =    1.079
peak=   -3.441 closest distance to " O   ILE A  49 " =    1.717
peak=   -3.433 closest distance to " CB  ALA A   9 " =    2.513
peak=   -3.431 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.430 closest distance to " N   ASP A 171 " =    2.426
peak=   -3.427 closest distance to " NE2 GLN A  55 " =    1.089
peak=   -3.426 closest distance to " O   ASP A 253 " =    1.754
peak=   -3.423 closest distance to " CG  LEU A  83 " =    2.145
peak=   -3.414 closest distance to " CD2 TYR A 293 " =    1.898
peak=   -3.410 closest distance to " O   HOH Z 102 " =    1.706
peak=   -3.409 closest distance to " OG ASER A 134 " =    1.229
peak=   -3.398 closest distance to " CG1 VAL A 112 " =    2.585
peak=   -3.393 closest distance to " CB  ALA A 131 " =    2.002
peak=   -3.390 closest distance to " SG BCYS A 201 " =    0.828
peak=   -3.385 closest distance to " CE1 PHE A  59 " =    2.029
peak=   -3.379 closest distance to " OD1 ASP A 171 " =    1.609
peak=   -3.375 closest distance to " OG  SER A  87 " =    1.331
peak=   -3.373 closest distance to " O   GLY A  80 " =    2.508
peak=   -3.370 closest distance to " CE1 PHE A 225 " =    1.969
peak=   -3.366 closest distance to " O   HOH Z 219 " =    4.297
peak=   -3.366 closest distance to " O   ARG A  56 " =    1.886
peak=   -3.360 closest distance to " O   HOH Z 241 " =    1.389
peak=   -3.350 closest distance to " O   GLY A 211 " =    1.263
peak=   -3.347 closest distance to " O   HOH Z 189 " =    2.837
peak=   -3.346 closest distance to " O   HOH Z  51 " =    1.343
peak=   -3.345 closest distance to " O   TYR A 186 " =    1.790
peak=   -3.344 closest distance to " O   GLY A  17 " =    1.104
peak=   -3.341 closest distance to " O   HOH Z 128 " =    2.633
peak=   -3.339 closest distance to " NH2 ARG A  79 " =    2.043
peak=   -3.334 closest distance to " OG  SER A 245 " =    1.388
peak=   -3.331 closest distance to " CA  GLY A 203 " =    2.390
peak=   -3.327 closest distance to " OG  SER A  28 " =    2.212
peak=   -3.325 closest distance to " CB  HIS A  86 " =    1.180
peak=   -3.322 closest distance to " CB  PRO A 163 " =    2.482
peak=   -3.321 closest distance to " O   HOH Z 114 " =    1.496
peak=   -3.315 closest distance to " O   VAL A 197 " =    1.763
peak=   -3.314 closest distance to " O   HOH Z 105 " =    1.061
peak=   -3.311 closest distance to " CE  MET A 113 " =    2.302
peak=   -3.311 closest distance to " O   HOH Z 426 " =    1.665
peak=   -3.311 closest distance to " O   ASN A 209 " =    2.101
peak=   -3.308 closest distance to " O   HOH Z 118 " =    1.307
peak=   -3.305 closest distance to " CE1 PHE A  16 " =    2.750
peak=   -3.294 closest distance to " O   PRO A 243 " =    2.385
peak=   -3.293 closest distance to " CD1 LEU A 101 " =    2.381
peak=   -3.290 closest distance to " C   LEU A 143 " =    1.369
peak=   -3.289 closest distance to " ND2 ASN A 217 " =    2.225
peak=   -3.287 closest distance to " O   HOH Z 163 " =    1.623
peak=   -3.285 closest distance to " O   HOH Z 191 " =    5.910
peak=   -3.284 closest distance to " CD2 TRP A 274 " =    2.506
peak=   -3.283 closest distance to " CB  ALA A  10 " =    2.275
peak=   -3.281 closest distance to " O   HOH Z 251 " =    1.466
peak=   -3.281 closest distance to " CG  TRP A 266 " =    1.557
peak=   -3.279 closest distance to " O   HOH Z 198 " =    1.995
peak=   -3.273 closest distance to " NH1AARG A 275 " =    2.028
peak=   -3.271 closest distance to " O   HOH Z 308 " =    2.094
peak=   -3.269 closest distance to " CD2 TYR A 172 " =    2.313
peak=   -3.265 closest distance to " ND2 ASN A 173 " =    1.927
peak=   -3.264 closest distance to " O   HOH Z 132 " =    5.309
peak=   -3.263 closest distance to " CB  SER A  63 " =    3.341
peak=   -3.263 closest distance to " CE3 TRP A 150 " =    2.836
peak=   -3.260 closest distance to " O   HOH Z  24 " =    1.251
peak=   -3.258 closest distance to " O   HOH Z  92 " =    2.371
peak=   -3.256 closest distance to " O   PHE A 218 " =    1.391
peak=   -3.254 closest distance to " CB  CYS A 254 " =    2.059
peak=   -3.252 closest distance to " O   HOH Z 348 " =    2.028
peak=   -3.250 closest distance to " O   HOH Z 394 " =    1.537
peak=   -3.247 closest distance to " C   GLY A  13 " =    0.862
peak=   -3.245 closest distance to " O   HOH Z 145 " =    1.281
peak=   -3.244 closest distance to " CD  PRO A 213 " =    2.143
peak=   -3.242 closest distance to " SG BCYS A 201 " =    2.149
peak=   -3.239 closest distance to " CG1 VAL A 112 " =    2.724
peak=   -3.236 closest distance to " O   HOH Z 275 " =    1.697
peak=   -3.235 closest distance to " N   ASP A 270 " =    1.363
peak=   -3.231 closest distance to " O   ARG A  56 " =    4.354
peak=   -3.231 closest distance to " O   HOH Z  22 " =    1.973
peak=   -3.228 closest distance to " O   SER A 210 " =    1.933
peak=   -3.227 closest distance to " CB  ALA A 100 " =    2.144
peak=   -3.227 closest distance to " CB  ASP A 286 " =    2.018
peak=   -3.214 closest distance to " CG  GLN A  55 " =    1.249
peak=   -3.214 closest distance to " O   HOH Z   9 " =    2.043
peak=   -3.210 closest distance to " CG  LEU A 282 " =    2.407
peak=   -3.206 closest distance to " N   LEU A 282 " =    2.220
peak=   -3.205 closest distance to " O   HOH Z 259 " =    1.003
peak=   -3.205 closest distance to " O   HOH Z 357 " =    1.906
peak=   -3.204 closest distance to " O   ASP A  27 " =    1.755
peak=   -3.203 closest distance to " O   GLU A 152 " =    1.588
peak=   -3.201 closest distance to " O   HOH Z  83 " =    1.477
peak=   -3.199 closest distance to " O   HOH Z 364 " =    2.550
peak=   -3.199 closest distance to " O   HOH Z 264 " =    1.701
peak=   -3.198 closest distance to " CB  ALA A 291 " =    2.400
peak=   -3.190 closest distance to " CG1 VAL A 125 " =    1.832
peak=   -3.190 closest distance to " NE2 GLN A 240 " =    1.479
peak=   -3.185 closest distance to " O   HOH Z  10 " =    1.609
peak=   -3.184 closest distance to " SD  MET A 113 " =    3.007
peak=   -3.184 closest distance to " NH2 ARG A 219 " =    1.793
peak=   -3.183 closest distance to " O   HOH Z 108 " =    1.205
peak=   -3.182 closest distance to " O   VAL A  67 " =    2.761
peak=   -3.180 closest distance to " CD2 TYR A 116 " =    2.206
peak=   -3.178 closest distance to " CG  MET A 188 " =    1.243
peak=   -3.173 closest distance to " CE BMET A  47 " =    1.604
peak=   -3.172 closest distance to " O   HOH Z  28 " =    1.362
peak=   -3.172 closest distance to " CA  GLY A  57 " =    2.035
peak=   -3.170 closest distance to " OE1 GLN A 278 " =    1.139
peak=   -3.169 closest distance to " O   HOH Z 259 " =    4.337
peak=   -3.168 closest distance to " ND2 ASN A 187 " =    1.603
peak=   -3.166 closest distance to " CB  ASP A 200 " =    2.575
peak=   -3.166 closest distance to " CH2 TRP A 179 " =    1.488
peak=   -3.156 closest distance to " CB  ALA A 227 " =    2.407
peak=   -3.152 closest distance to " O   HOH Z 201 " =    1.685
peak=   -3.148 closest distance to " CB  VAL A 189 " =    2.421
peak=   -3.147 closest distance to " C   PHE A  59 " =    1.185
peak=   -3.147 closest distance to " ND2 ASN A 249 " =    2.096
peak=   -3.144 closest distance to " CB  GLU A 277 " =    3.026
peak=   -3.141 closest distance to " O   SER A  87 " =    2.068
peak=   -3.141 closest distance to " CG2BVAL A  41 " =    1.151
peak=   -3.138 closest distance to " O   HOH Z  37 " =    1.379
peak=   -3.134 closest distance to " C   ASN A 176 " =    1.438
peak=   -3.134 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.131 closest distance to " O   HOH Z   1 " =    1.311
peak=   -3.127 closest distance to " CA  ASP A 298 " =    1.091
peak=   -3.120 closest distance to " OE1 GLU A 236 " =    1.120
peak=   -3.117 closest distance to " O   HOH Z 421 " =    3.051
peak=   -3.117 closest distance to " O   HOH Z 198 " =    2.017
peak=   -3.117 closest distance to " O   ALA A   7 " =    1.338
peak=   -3.117 closest distance to " O   ALA A 180 " =    1.218
peak=   -3.113 closest distance to " O   HOH Z 427 " =    1.671
peak=   -3.110 closest distance to " O   HOH Z 128 " =    4.182
peak=   -3.109 closest distance to " O   HOH Z 115 " =    1.640
peak=   -3.107 closest distance to " OE1 GLN A  77 " =    0.966
peak=   -3.105 closest distance to " CE2 TRP A  70 " =    2.424
peak=   -3.098 closest distance to " OD2 ASP A 171 " =    1.809
peak=   -3.094 closest distance to " NE2 GLN A  58 " =    3.302
peak=   -3.093 closest distance to " O   HOH Z 252 " =    3.886
peak=   -3.083 closest distance to " CE  LYS A  76 " =    2.898
peak=   -3.076 closest distance to " O   HOH Z 186 " =    1.264
peak=   -3.060 closest distance to " CD2 PHE A  16 " =    2.400
peak=   -3.057 closest distance to " CB  TYR A  15 " =    2.106
peak=   -3.050 closest distance to " N   ASP A 191 " =    1.149
peak=   -3.043 closest distance to " CB  ASN A  39 " =    2.272
peak=   -3.043 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.002 closest distance to " O   HOH Z 364 " =    1.654

================= 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    :  0.4785 0.4759   6.286107e+00   6.269963e+00
   1_bss:  0.4718 0.4715   6.281963e+00   6.265213e+00
   1_xyz:  0.3245 0.3602   6.027169e+00   6.099073e+00
   1_adp:  0.2913 0.3687   5.979676e+00   6.118930e+00
   1_occ:  0.2908 0.3689   5.979751e+00   6.119366e+00
   2_bss:  0.2899 0.3690   5.980608e+00   6.118899e+00
   2_xyz:  0.2212 0.2867   5.741045e+00   5.923939e+00
   2_adp:  0.2018 0.2689   5.672150e+00   5.868225e+00
   2_occ:  0.2017 0.2686   5.671599e+00   5.868221e+00
   3_bss:  0.2018 0.2688   5.671189e+00   5.866965e+00
   3_xyz:  0.1669 0.2258   5.494501e+00   5.711146e+00
   3_adp:  0.1562 0.2167   5.449261e+00   5.675510e+00
   3_occ:  0.1561 0.2167   5.449171e+00   5.675726e+00
   4_bss:  0.1564 0.2173   5.451059e+00   5.676883e+00
   4_xyz:  0.1407 0.1982   5.354312e+00   5.592435e+00
   4_adp:  0.1370 0.1904   5.325119e+00   5.555197e+00
   4_occ:  0.1370 0.1903   5.324974e+00   5.554922e+00
   5_bss:  0.1370 0.1903   5.324873e+00   5.554764e+00
   5_xyz:  0.1253 0.1770   5.249687e+00   5.491926e+00
   5_adp:  0.1234 0.1738   5.235785e+00   5.476040e+00
   5_occ:  0.1234 0.1737   5.235654e+00   5.475881e+00
   5_bss:  0.1237 0.1732   5.233620e+00   5.472394e+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:  0.322  72.238   1.315  -0.390   2.443  -0.000   0.000   0.000
   1_xyz:  0.322  72.238   1.315  -0.390   2.443  -0.000   0.000   0.000
   1_adp:  0.322  72.238   1.315  -0.390   2.443  -0.000   0.000   0.000
   1_occ:  0.322  72.238   1.315  -0.390   2.443  -0.000   0.000   0.000
   2_bss:  0.355  90.448  -0.291  -1.344   1.054  -0.000   0.000   0.000
   2_xyz:  0.355  90.448  -0.291  -1.344   1.054  -0.000   0.000   0.000
   2_adp:  0.355  90.448  -0.291  -1.344   1.054  -0.000   0.000   0.000
   2_occ:  0.355  90.448  -0.291  -1.344   1.054  -0.000   0.000   0.000
   3_bss:  0.346  85.871  -0.871  -1.728   0.363  -0.000   0.000   0.000
   3_xyz:  0.346  85.871  -0.871  -1.728   0.363  -0.000   0.000   0.000
   3_adp:  0.346  85.871  -0.871  -1.728   0.363  -0.000   0.000   0.000
   3_occ:  0.346  85.871  -0.871  -1.728   0.363  -0.000   0.000   0.000
   4_bss:  0.337  84.985  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   4_xyz:  0.337  84.985  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   4_adp:  0.337  84.985  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   4_occ:  0.337  84.985  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   5_bss:  0.333  80.000  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   5_xyz:  0.333  80.000  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   5_adp:  0.333  80.000  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   5_occ:  0.333  80.000  -1.389  -2.176  -0.102  -0.000  -0.000  -0.000
   5_bss:  0.326  73.549  -1.549  -2.379  -0.272  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.592 0.4108  0.5526    70713.616
   1_bss:  58.136 0.4159  0.5898    69890.382
   1_xyz:  38.826 0.6570  0.8781    36256.418
   1_adp:  40.570 0.6351  0.8543    38912.371
   1_occ:  40.673 0.6339  0.8519    38991.461
   2_bss:  40.604 0.6347  0.8166    38937.110
   2_xyz:  29.605 0.7606  0.9445    21597.233
   2_adp:  27.021 0.7896  0.9579    18844.139
   2_occ:  27.015 0.7896  0.9575    18825.592
   3_bss:  26.961 0.7900  0.9393    18746.391
   3_xyz:  21.822 0.8429  0.9784    12730.749
   3_adp:  20.803 0.8535  0.9764    11899.587
   3_occ:  20.809 0.8534  0.9762    11903.508
   4_bss:  20.837 0.8532  0.9602    11963.527
   4_xyz:  18.575 0.8747  0.9722     9743.489
   4_adp:  17.625 0.8840  0.9723     9081.279
   4_occ:  17.621 0.8840  0.9722     9077.980
   5_bss:  17.619 0.8840  0.9721     9074.546
   5_xyz:  16.147 0.8969  0.9803     7834.946
   5_adp:  15.739 0.9007  0.9780     7603.727
   5_occ:  15.737 0.9007  0.9779     7597.398
   5_bss:  15.675 0.9011  0.9721     7503.715
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6546e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6546e-01
   1_xyz:   1.685  0.014  0.115 16.666  0.007  4.115   1.6338e-01
   1_adp:   1.685  0.014  0.115 16.666  0.007  4.115   1.6338e-01
   1_occ:   1.685  0.014  0.115 16.666  0.007  4.115   1.6338e-01
   2_bss:   1.685  0.014  0.115 16.666  0.007  4.115   1.6338e-01
   2_xyz:   1.178  0.008  0.086 14.484  0.004  4.110   7.4130e-02
   2_adp:   1.178  0.008  0.086 14.484  0.004  4.110   7.4130e-02
   2_occ:   1.178  0.008  0.086 14.484  0.004  4.110   7.4130e-02
   3_bss:   1.178  0.008  0.086 14.484  0.004  4.110   7.4130e-02
   3_xyz:   0.964  0.007  0.068 14.279  0.004  4.122   5.6343e-02
   3_adp:   0.964  0.007  0.068 14.279  0.004  4.122   5.6343e-02
   3_occ:   0.964  0.007  0.068 14.279  0.004  4.122   5.6343e-02
   4_bss:   0.964  0.007  0.068 14.279  0.004  4.122   5.6343e-02
   4_xyz:   0.969  0.007  0.073 14.076  0.003  4.112   5.4862e-02
   4_adp:   0.969  0.007  0.073 14.076  0.003  4.112   5.4862e-02
   4_occ:   0.969  0.007  0.073 14.076  0.003  4.112   5.4862e-02
   5_bss:   0.969  0.007  0.073 14.076  0.003  4.112   5.4862e-02
   5_xyz:   1.087  0.010  0.079 14.388  0.004  4.119   6.8989e-02
   5_adp:   1.087  0.010  0.079 14.388  0.004  4.119   6.8989e-02
   5_occ:   1.087  0.010  0.079 14.388  0.004  4.119   6.8989e-02
   5_bss:   1.087  0.010  0.079 14.388  0.004  4.119   6.8989e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4314e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4314e-01
   1_xyz:  10.289  0.097  0.404 82.815  0.065  1.915   1.1944e-01
   1_adp:  10.289  0.097  0.404 82.815  0.065  1.915   1.1944e-01
   1_occ:  10.289  0.097  0.404 82.815  0.065  1.915   1.1944e-01
   2_bss:  10.289  0.097  0.404 82.815  0.065  1.915   1.1944e-01
   2_xyz:   7.012  0.057  0.295 78.407  0.036  2.202   7.3615e-02
   2_adp:   7.012  0.057  0.295 78.407  0.036  2.202   7.3615e-02
   2_occ:   7.012  0.057  0.295 78.407  0.036  2.202   7.3615e-02
   3_bss:   7.012  0.057  0.295 78.407  0.036  2.202   7.3615e-02
   3_xyz:   9.368  0.035  0.310 78.439  0.031  2.377   7.5617e-02
   3_adp:   9.368  0.035  0.310 78.439  0.031  2.377   7.5617e-02
   3_occ:   9.368  0.035  0.310 78.439  0.031  2.377   7.5617e-02
   4_bss:   9.368  0.035  0.310 78.439  0.031  2.377   7.5617e-02
   4_xyz:   8.282  0.052  0.265 80.439  0.032  2.358   3.8818e-02
   4_adp:   8.282  0.052  0.265 80.439  0.032  2.358   3.8818e-02
   4_occ:   8.282  0.052  0.265 80.439  0.032  2.358   3.8818e-02
   5_bss:   8.282  0.052  0.265 80.439  0.032  2.358   3.8818e-02
   5_xyz:   8.825  0.055  0.257 82.735  0.028  2.341   4.9454e-02
   5_adp:   8.825  0.055  0.257 82.735  0.028  2.341   4.9454e-02
   5_occ:   8.825  0.055  0.257 82.735  0.028  2.341   4.9454e-02
   5_bss:   8.825  0.055  0.257 82.735  0.028  2.341   4.9454e-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: 109.54   0.00  19.38  80.27   0.00  14.81 109.54   0.00  44.24
   1_occ: 109.54   0.00  19.38  80.27   0.00  14.81 109.54   0.00  44.24
   2_bss: 109.54   0.00  19.38  80.27   0.00  14.81 109.54   0.00  44.24
   2_xyz: 109.54   0.00  19.38  80.27   0.00  14.81 109.54   0.00  44.24
   2_adp: 109.97   0.00  18.97  80.91   0.00  13.99 109.97   1.88  46.08
   2_occ: 109.97   0.00  18.97  80.91   0.00  13.99 109.97   1.88  46.08
   3_bss: 109.97   0.00  18.97  80.91   0.00  13.99 109.97   1.88  46.08
   3_xyz: 109.97   0.00  18.97  80.91   0.00  13.99 109.97   1.88  46.08
   3_adp: 113.73   0.00  19.18  91.87   0.00  13.53 113.73   4.98  49.91
   3_occ: 113.73   0.00  19.18  91.87   0.00  13.53 113.73   4.98  49.91
   4_bss: 113.73   0.00  19.18  91.87   0.00  13.53 113.73   4.98  49.91
   4_xyz: 113.73   0.00  19.18  91.87   0.00  13.53 113.73   4.98  49.91
   4_adp: 111.06   0.00  18.58  93.22   0.00  13.16 111.06   5.89  48.11
   4_occ: 111.06   0.00  18.58  93.22   0.00  13.16 111.06   5.89  48.11
   5_bss: 111.06   0.00  18.58  93.22   0.00  13.16 111.06   5.89  48.11
   5_xyz: 111.06   0.00  18.58  93.22   0.00  13.16 111.06   5.89  48.11
   5_adp: 113.11   0.00  17.95  96.05   0.00  12.89 113.11   5.61  45.52
   5_occ: 113.11   0.00  17.95  96.05   0.00  12.89 113.11   5.61  45.52
   5_bss: 113.11   0.00  17.95  96.06   0.00  12.89 113.11   5.62  45.52
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.540    0.024    0.500
   1_adp:    1.540    0.024    0.500
   1_occ:    1.540    0.024    0.500
   2_bss:    1.540    0.024    0.500
   2_xyz:    1.480    0.016    0.604
   2_adp:    1.480    0.016    0.604
   2_occ:    1.480    0.016    0.604
   3_bss:    1.480    0.016    0.604
   3_xyz:    1.412    0.027    0.696
   3_adp:    1.412    0.027    0.696
   3_occ:    1.412    0.027    0.696
   4_bss:    1.412    0.027    0.696
   4_xyz:    1.465    0.038    0.729
   4_adp:    1.465    0.038    0.729
   4_occ:    1.465    0.038    0.729
   5_bss:    1.465    0.038    0.729
   5_xyz:    1.582    0.077    0.759
   5_adp:    1.582    0.077    0.759
   5_occ:    1.582    0.077    0.759
   5_bss:    1.582    0.077    0.759
------------------------------------------------------------------------

CPU time actual refinement: 372.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/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_1241/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1241/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 372.54 
  Macro-tasks:
    bulk solvent and scale       = 60.68  
    individual site refinement   = 143.29 
    weights calculation          = 30.43  
    collect and process          = 6.62   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 241.16 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 115.69 
    alpha_beta                      = 8.56   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 122.42 
    fmodel                         = 9.73   
    r_factors                      = 0.50   
    phase_errors                   = 10.60  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 271.35 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.252 micro seconds
Total CPU time: 6.44 minutes
from_scatterers_fft:    647 calls, 115.26 s
gradients_fft:          592 calls, 109.60 s

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

# Date 2008-01-16 Time 06:47:55 PST -0800 (1200494875.71 s)
Start R-work = 0.4785, R-free = 0.4759 (no bulk solvent and anisotropic scale)
Final R-work = 0.1441, R-free = 0.1908 (no bulk solvent and anisotropic scale)

Start R-work = 0.4718, R-free = 0.4715
Final R-work = 0.1237, R-free = 0.1732