# Date 2008-01-16 Time 06:19:47 PST -0800 (1200493187.13 s)
#phil __OFF__

Command line arguments: "../1104.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2536
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1104

-------------------------------------------------------------------------------
  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: (71.655, 45.9914, 85.9581, 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: (71.655, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.96392
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9639

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: (71.655, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.96392
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2040 [2193/2220]  1976   217   9.9%
  bin  2:  4.2040 -  3.3486 [2104/2124]  1892   212  10.1%
  bin  3:  3.3486 -  2.9288 [2075/2094]  1866   209  10.1%
  bin  4:  2.9288 -  2.6626 [2051/2081]  1843   208  10.1%
  bin  5:  2.6626 -  2.4726 [2054/2073]  1859   195   9.5%
  bin  6:  2.4726 -  2.3274 [2036/2061]  1822   214  10.5%
  bin  7:  2.3274 -  2.2112 [2033/2061]  1827   206  10.1%
  bin  8:  2.2112 -  2.1152 [2010/2046]  1815   195   9.7%
  bin  9:  2.1152 -  2.0340 [2004/2054]  1805   199   9.9%
  bin 10:  2.0340 -  1.9639 [1029/2061]   925   104  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 31
        2.37 -     3.00: 1955
        3.00 -     3.64: 4643
        3.64 -     4.27: 9174
        4.27 -     4.90: 12584
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.738 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.811 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28382 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_1104/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 71.655 45.9914 85.95805 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: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4446   r_free= 0.4434   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.256415                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.3632 0.3638       6.526      6.5305|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.3777 0.3722      6.7731      6.7319|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.4067 0.3765      6.6228      6.6608|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.4359 0.4663      6.4987      6.4942|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.4649 0.4644      6.3426      6.3678|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.4714 0.4784      6.2487      6.2057|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.4826 0.4580      6.2185      6.1755|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.4871 0.5003      6.1533      6.1655|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.4861 0.4937      6.1064      6.1174|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.4929 0.4733      6.0707      6.0559|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.5009 0.5037      6.0197      6.0556|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.4982 0.5264      5.9434      5.9834|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.5108 0.4848      5.8628      5.8051|
| 14:  2.0129 -  1.9639 0.36    475   55 0.5016 0.5235      5.8463       5.813|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.72  32.67   0.82     0.77      66469.70|
|  2:  4.6898 -  3.7407  1365   149  0.73  32.73   0.92     0.84      94504.06|
|  3:  3.7407 -  3.2733  1339   146  0.62  42.08   0.93     0.80     104322.27|
|  4:  3.2733 -  2.9765  1348   155  0.52  49.94   0.92     0.72      98822.25|
|  5:  2.9765 -  2.7645  1327   146  0.43  57.02   0.90     0.61      81106.36|
|  6:  2.7645 -  2.6023  1329   143  0.42  57.97   0.91     0.60      69185.72|
|  7:  2.6023 -  2.4726  1308   141  0.42  58.32   0.93     0.59      60395.11|
|  8:  2.4726 -  2.3654  1297   153  0.43  57.82   0.92     0.60      53610.12|
|  9:  2.3654 -  2.2746  1308   148  0.42  58.65   0.94     0.59      48542.30|
| 10:  2.2746 -  2.1964  1293   155  0.41  59.34   0.95     0.59      45513.75|
| 11:  2.1964 -  2.1279  1312   128  0.37  61.90   0.97     0.58      45319.67|
| 12:  2.1279 -  2.0672  1281   154  0.36  63.45   0.94     0.55      41938.58|
| 13:  2.0672 -  2.0129  1228   125  0.33  65.30   0.94     0.54      36076.04|
| 14:  2.0129 -  1.9639   475    55  0.39  60.91   0.98     0.55      28832.81|
|alpha:            min =        0.54 max =            0.84 mean =         0.65|
|beta:             min =    28832.81 max =       104322.27 mean =     64544.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.53|
|phase err.(test): min =        0.00 max =           89.91 mean =        53.77|
|-----------------------------------------------------------------------------|

============================== 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 = 17.860862             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.882   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.399251              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.902   (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 |  1.738 -  2.054:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.054 -  2.370:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.370 -  2.686:      117 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.686 -  3.003:     1838 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.003 -  3.319:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.319 -  3.635:     2733 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.635 -  3.951:     4747 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.951 -  4.267:     4427 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.267 -  4.584:     5719 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.584 -  4.900:     6865 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.738 |       0.340 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    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: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4446   r_free= 0.4434   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.256415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4351   r_free= 0.4352   ksol= 0.34   Bsol= 43.45   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,2.29,-1.81,0.00,-0.00,-0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.248203                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.311178             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.160723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.651   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4351      final r-factor (work) = 0.2840          |
| start r-factor (free) = 0.4352      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.9935 = 15.31 * 0.50 * 6.2465 + 1.00 * 0.1731                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.7776 = 15.31 * 0.50 * 6.0874 + 1.00 * 0.1753                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2840      final r-factor (work) = 0.2600          |
| start r-factor (free) = 0.3207      final r-factor (free) = 0.3333          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0718 = 1.16 * 1.00 * 6.0874 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8273 = 1.16 * 1.00 * 5.8672 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.75   18.48    None  None   None       |
|    all(noH): 2823   0      0.00    99.75   18.48    None  None   None       |
|    Sol.    : 438    0      3.02    99.75   42.68    None  None   None       |
|    Mac.    : 2385   0      0.00    73.12   14.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.975:  958   |   5:    49.875 -  59.850:  100        |
|      1:     9.975 -  19.950: 1011   |   6:    59.850 -  69.825:   51        |
|      2:    19.950 -  29.925:  343   |   7:    69.825 -  79.801:   14        |
|      3:    29.925 -  39.900:  202   |   8:    79.801 -  89.776:    6        |
|      4:    39.900 -  49.875:  137   |   9:    89.776 -  99.751:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2600 r_free = 0.3333             target_work(ml) = 5.885         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2595 r_free = 0.3332             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2595   r_free= 0.3332   ksol= 0.34   Bsol= 43.45   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,2.29,-1.81,0.00,-0.00,-0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.883381                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2568   r_free= 0.3289   ksol= 0.35   Bsol= 63.88   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,-0.76,-1.38,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.874117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.346064              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.593   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.721  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2568      final r-factor (work) = 0.2039          |
| start r-factor (free) = 0.3289      final r-factor (free) = 0.2649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9921 = 3.35 * 0.50 * 5.8678 + 1.00 * 0.1750                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7402 = 3.35 * 0.50 * 5.7892 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2039      final r-factor (work) = 0.1944          |
| start r-factor (free) = 0.2649      final r-factor (free) = 0.2491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4357 = 0.25 * 1.00 * 5.7892 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4641 = 0.25 * 1.00 * 5.6586 + 1.00 * 0.0774                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.38   18.17    None  None   None       |
|    all(noH): 2823   0      0.00    98.38   18.17    None  None   None       |
|    Sol.    : 438    0      5.43    98.38   41.85    None  None   None       |
|    Mac.    : 2385   0      0.00    71.95   13.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.838:  877   |   5:    49.190 -  59.029:  103        |
|      1:     9.838 -  19.676: 1186   |   6:    59.029 -  68.867:   47        |
|      2:    19.676 -  29.514:  274   |   7:    68.867 -  78.705:   15        |
|      3:    29.514 -  39.352:  179   |   8:    78.705 -  88.543:    5        |
|      4:    39.352 -  49.190:  136   |   9:    88.543 -  98.381:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1944 r_free = 0.2491             target_work(ml) = 5.632         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1943 r_free = 0.2490             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1943   r_free= 0.2490   ksol= 0.35   Bsol= 63.88   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,-0.76,-1.38,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.631204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1942   r_free= 0.2476   ksol= 0.34   Bsol= 57.43   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-1.81,-1.19,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.629017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.436630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.842  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.177927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.707   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1942      final r-factor (work) = 0.1492          |
| start r-factor (free) = 0.2476      final r-factor (free) = 0.1987          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7764 = 3.44 * 0.50 * 5.6577 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5397 = 3.44 * 0.50 * 5.5162 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1492      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.1987      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5362 = 1.18 * 1.00 * 5.5162 + 1.00 * 0.0385                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3081 = 1.18 * 1.00 * 5.3456 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.14  18.41    None  None   None       |
|    all(noH): 2823   0      0.00    101.14  18.41    None  None   None       |
|    Sol.    : 438    0      6.61    101.14  45.61    None  None   None       |
|    Mac.    : 2385   0      0.00    89.56   13.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.114: 1026   |   5:    50.571 -  60.685:  103        |
|      1:    10.114 -  20.228: 1100   |   6:    60.685 -  70.799:   75        |
|      2:    20.228 -  30.343:  244   |   7:    70.799 -  80.913:   23        |
|      3:    30.343 -  40.457:  122   |   8:    80.913 -  91.028:   18        |
|      4:    40.457 -  50.571:  111   |   9:    91.028 - 101.142:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1356 r_free = 0.1866             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1355 r_free = 0.1866             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1866   ksol= 0.34   Bsol= 57.43   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-1.81,-1.19,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.310149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1864   ksol= 0.32   Bsol= 57.43   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.58,-1.49,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.309493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.216759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.429   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.374630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.468  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1864      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9890 = 2.22 * 0.50 * 5.3483 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8978 = 2.22 * 0.50 * 5.2727 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9867 = 0.37 * 1.00 * 5.2727 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9670 = 0.37 * 1.00 * 5.2247 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.12    95.68   17.74    None  None   None       |
|    all(noH): 2823   0      0.12    95.68   17.74    None  None   None       |
|    Sol.    : 438    0      6.33    95.62   43.13    None  None   None       |
|    Mac.    : 2385   0      0.12    95.68   13.08    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:     0.121 -   9.678:  950   |   5:    47.903 -  57.459:  104        |
|      1:     9.678 -  19.234: 1176   |   6:    57.459 -  67.016:   64        |
|      2:    19.234 -  28.790:  255   |   7:    67.016 -  76.572:   31        |
|      3:    28.790 -  38.347:  128   |   8:    76.572 -  86.129:   13        |
|      4:    38.347 -  47.903:   94   |   9:    86.129 -  95.685:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1686             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1207 r_free = 0.1686             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1686   ksol= 0.32   Bsol= 57.43   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.58,-1.49,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207943                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1685   ksol= 0.32   Bsol= 57.43   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.74,-1.51,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207713                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.859022              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.423  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506785              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.795  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5222 = 2.86 * 0.50 * 5.2246 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4715 = 2.86 * 0.50 * 5.1811 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6353 = 0.51 * 1.00 * 5.1811 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6236 = 0.51 * 1.00 * 5.1582 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.41   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    99.41   17.52    None  None   None       |
|    Sol.    : 438    0      6.11    92.86   42.19    None  None   None       |
|    Mac.    : 2385   0      0.00    99.41   12.99    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 -   9.941: 1014   |   5:    49.707 -  59.648:   98        |
|      1:     9.941 -  19.883: 1161   |   6:    59.648 -  69.590:   46        |
|      2:    19.883 -  29.824:  229   |   7:    69.590 -  79.531:   23        |
|      3:    29.824 -  39.766:  128   |   8:    79.531 -  89.472:   11        |
|      4:    39.766 -  49.707:  106   |   9:    89.472 -  99.414:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1600             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1600             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1600   ksol= 0.32   Bsol= 57.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.74,-1.51,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155995                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.0950 0.1340      5.3547      5.6061|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.0843 0.1081      5.4387      5.6114|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.1103 0.1614      5.4933      5.8548|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.1275 0.1691      5.4722      5.6176|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.1322 0.1750      5.3189      5.5741|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.1202 0.1803      5.1884      5.4308|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.1276 0.1663      5.1692      5.3516|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.1148 0.1826      5.0649      5.3809|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.1194 0.1786      5.0551       5.335|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.1114 0.1687      4.9527      5.1923|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.1150 0.1913      4.9578      5.3558|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.1121 0.1722      4.8745      5.1297|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.1152 0.1621      4.7939      4.9881|
| 14:  2.0129 -  1.9639 0.36    475   55 0.0986 0.1519      4.6418      4.9106|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.94   8.97   0.98     0.95       6988.72|
|  2:  4.6898 -  3.7407  1365   149  0.95   8.14   1.02     1.01       9341.06|
|  3:  3.7407 -  3.2733  1339   146  0.93  11.76   1.03     1.03      10809.17|
|  4:  3.2733 -  2.9765  1348   155  0.91  14.77   1.01     0.98      10703.46|
|  5:  2.9765 -  2.7645  1327   146  0.90  15.45   1.00     0.99       8076.67|
|  6:  2.7645 -  2.6023  1329   143  0.90  15.93   0.99     0.97       6858.36|
|  7:  2.6023 -  2.4726  1308   141  0.90  15.81   1.00     0.98       6311.71|
|  8:  2.4726 -  2.3654  1297   153  0.90  15.77   0.98     0.96       5470.12|
|  9:  2.3654 -  2.2746  1308   148  0.90  16.38   1.01     0.96       5311.65|
| 10:  2.2746 -  2.1964  1293   155  0.90  15.77   1.00     0.97       4474.58|
| 11:  2.1964 -  2.1279  1312   128  0.90  16.66   0.99     0.95       4542.31|
| 12:  2.1279 -  2.0672  1281   154  0.90  16.09   1.01     1.00       4082.73|
| 13:  2.0672 -  2.0129  1228   125  0.90  16.61   1.00     0.98       3426.04|
| 14:  2.0129 -  1.9639   475    55  0.92  14.37   0.98     0.95       2552.01|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2552.01 max =        10809.17 mean =      6585.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.40|
|phase err.(test): min =        0.00 max =           89.46 mean =        13.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1596   ksol= 0.32   Bsol= 57.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.78,-1.49,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1596   ksol= 0.32   Bsol= 57.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.78,-1.49,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.155149                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.6898 0.99   1420  161 0.0956 0.1312      5.3457      5.5793|
|  2:  4.6898 -  3.7407 0.99   1365  149 0.0849 0.1062       5.437      5.5993|
|  3:  3.7407 -  3.2733 0.99   1339  146 0.1103 0.1608      5.4914       5.856|
|  4:  3.2733 -  2.9765 0.99   1348  155 0.1277 0.1697      5.4734      5.6206|
|  5:  2.9765 -  2.7645 0.99   1327  146 0.1325 0.1753      5.3215      5.5741|
|  6:  2.7645 -  2.6023 0.99   1329  143 0.1204 0.1804      5.1891      5.4307|
|  7:  2.6023 -  2.4726 0.99   1308  141 0.1275 0.1661      5.1687      5.3507|
|  8:  2.4726 -  2.3654 0.98   1297  153 0.1146 0.1822      5.0637      5.3789|
|  9:  2.3654 -  2.2746 0.98   1308  148 0.1195 0.1786      5.0548      5.3338|
| 10:  2.2746 -  2.1964 1.00   1293  155 0.1113 0.1689      4.9523      5.1936|
| 11:  2.1964 -  2.1279 0.98   1312  128 0.1149 0.1912       4.958      5.3565|
| 12:  2.1279 -  2.0672 0.98   1281  154 0.1122 0.1723       4.875      5.1305|
| 13:  2.0672 -  2.0129 0.93   1228  125 0.1151 0.1619      4.7934       4.987|
| 14:  2.0129 -  1.9639 0.36    475   55 0.0984 0.1517      4.6404      4.9092|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.6898  1420   161  0.94   8.87   0.97     0.95       6717.21|
|  2:  4.6898 -  3.7407  1365   149  0.95   7.94   1.02     1.01       9035.04|
|  3:  3.7407 -  3.2733  1339   146  0.93  11.63   1.03     1.03      10651.02|
|  4:  3.2733 -  2.9765  1348   155  0.91  14.82   1.01     0.98      10748.16|
|  5:  2.9765 -  2.7645  1327   146  0.90  15.49   1.00     0.99       8128.62|
|  6:  2.7645 -  2.6023  1329   143  0.90  15.92   0.99     0.97       6858.27|
|  7:  2.6023 -  2.4726  1308   141  0.90  15.80   1.00     0.97       6307.24|
|  8:  2.4726 -  2.3654  1297   153  0.90  15.74   0.98     0.96       5454.97|
|  9:  2.3654 -  2.2746  1308   148  0.90  16.36   1.01     0.96       5302.74|
| 10:  2.2746 -  2.1964  1293   155  0.90  15.77   1.00     0.97       4475.42|
| 11:  2.1964 -  2.1279  1312   128  0.90  16.68   0.99     0.95       4547.93|
| 12:  2.1279 -  2.0672  1281   154  0.90  16.11   1.01     1.00       4091.10|
| 13:  2.0672 -  2.0129  1228   125  0.90  16.61   1.00     0.98       3423.78|
| 14:  2.0129 -  1.9639   475    55  0.92  14.35   0.98     0.95       2543.78|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2543.78 max =        10748.16 mean =      6533.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.42   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    99.42   17.53    None  None   None       |
|    Sol.    : 438    0      6.11    92.86   42.19    None  None   None       |
|    Mac.    : 2385   0      0.00    99.42   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.944: 1014   |   5:    49.710 -  59.651:   98        |
|      1:     9.944 -  19.886: 1161   |   6:    59.651 -  69.593:   46        |
|      2:    19.886 -  29.827:  229   |   7:    69.593 -  79.534:   23        |
|      3:    29.827 -  39.769:  128   |   8:    79.534 -  89.475:   11        |
|      4:    39.769 -  49.710:  106   |   9:    89.475 -  99.417:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 4.514
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 311
   mapped sites are within: 0.708 - 4.514

peak=    6.653 closest distance to " NE2 GLN A  11 " =    1.321
peak=    5.570 closest distance to " O   HOH Z   7 " =    1.646
peak=    5.395 closest distance to " O   HOH Z 126 " =    2.195
peak=    5.344 closest distance to " O   HOH Z 417 " =    1.741
peak=    5.223 closest distance to " CG  PRO A  54 " =    1.266
peak=    5.140 closest distance to " O   HOH Z 144 " =    1.598
peak=    5.137 closest distance to " CB  GLN A 223 " =    1.498
peak=    5.113 closest distance to " O   HOH Z 111 " =    1.947
peak=    4.932 closest distance to " O   HOH Z 423 " =    2.060
peak=    4.850 closest distance to " O   HOH Z 369 " =    2.137
peak=    4.846 closest distance to " O   HOH Z 427 " =    2.362
peak=    4.793 closest distance to " CB  SER A  63 " =    1.329
peak=    4.765 closest distance to " O   HOH Z 232 " =    2.241
peak=    4.759 closest distance to " O   HOH Z  63 " =    1.594
peak=    4.757 closest distance to " O   HOH Z 425 " =    1.487
peak=    4.743 closest distance to " O   HOH Z 183 " =    1.555
peak=    4.730 closest distance to " O   HOH Z 298 " =    2.075
peak=    4.602 closest distance to " O   HOH Z 287 " =    1.989
peak=    4.584 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.543 closest distance to " CG  PRO A 213 " =    1.276
peak=    4.500 closest distance to " CB  ASN A 148 " =    1.398
peak=    4.479 closest distance to " CG  PRO A 198 " =    1.304
peak=    4.451 closest distance to " O   HOH Z   2 " =    1.733
peak=    4.445 closest distance to " C   PRO A 198 " =    1.519
peak=    4.395 closest distance to " O   HOH Z 209 " =    2.316
peak=    4.373 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.370 closest distance to " O   HOH Z  78 " =    1.633
peak=    4.364 closest distance to " O   HOH Z 133 " =    2.411
peak=    4.361 closest distance to " O   HOH Z 236 " =    1.478
peak=    4.335 closest distance to " CB  GLU A 128 " =    1.035
peak=    4.325 closest distance to " CA  TYR A  30 " =    1.055
peak=    4.290 closest distance to " O   HOH Z 437 " =    2.070
peak=    4.290 closest distance to " CB  SER A   3 " =    1.506
peak=    4.266 closest distance to " O   HOH Z 126 " =    1.488
peak=    4.208 closest distance to " O   HOH Z 380 " =    1.844
peak=    4.203 closest distance to " O   HOH Z 403 " =    1.428
peak=    4.180 closest distance to " ND2 ASN A 187 " =    1.531
peak=    4.141 closest distance to " O   HOH Z   9 " =    2.142
peak=    4.136 closest distance to " O   HOH Z 272 " =    1.853
peak=    4.127 closest distance to " CD  ARG A 159 " =    0.841
peak=    4.100 closest distance to " CG  LEU A 167 " =    1.272
peak=    4.098 closest distance to " O   HOH Z 217 " =    2.659
peak=    4.092 closest distance to " O   HOH Z 193 " =    1.743
peak=    4.091 closest distance to " O   HOH Z 261 " =    1.939
peak=    4.089 closest distance to " OG ASER A 258 " =    3.135
peak=    4.082 closest distance to " O   HOH Z 222 " =    1.178
peak=    4.080 closest distance to " CB  ARG A 275 " =    0.950
peak=    4.050 closest distance to " O   HOH Z   1 " =    1.903
peak=    4.045 closest distance to " ND1 HIS A  86 " =    1.803
peak=    4.040 closest distance to " O   SER A  87 " =    2.310
peak=    4.032 closest distance to " O   HOH Z 419 " =    2.130
peak=    4.017 closest distance to " O   HOH Z 427 " =    1.040
peak=    3.991 closest distance to " O   HOH Z  61 " =    1.557
peak=    3.990 closest distance to " CG  TRP A 179 " =    2.263
peak=    3.977 closest distance to " O   HOH Z 135 " =    1.684
peak=    3.955 closest distance to " O   HOH Z 394 " =    1.676
peak=    3.950 closest distance to " CB  GLU A 152 " =    1.307
peak=    3.935 closest distance to " O   HOH Z 313 " =    1.762
peak=    3.926 closest distance to " CB  ASN A 187 " =    1.028
peak=    3.924 closest distance to " O   HOH Z 282 " =    1.574
peak=    3.903 closest distance to " N   PHE A 130 " =    1.246
peak=    3.886 closest distance to " O   HOH Z 132 " =    2.447
peak=    3.882 closest distance to " OD2 ASP A 286 " =    2.795
peak=    3.880 closest distance to " OD1 ASN A  69 " =    2.601
peak=    3.872 closest distance to " O   HOH Z 214 " =    1.294
peak=    3.868 closest distance to " CB  TRP A 266 " =    1.020
peak=    3.865 closest distance to " CB  LEU A 228 " =    1.065
peak=    3.861 closest distance to " CB  ARG A 190 " =    1.623
peak=    3.859 closest distance to " O   HOH Z 180 " =    2.080
peak=    3.829 closest distance to " CB  SER A 216 " =    0.879
peak=    3.828 closest distance to " CG2 THR A 221 " =    0.999
peak=    3.820 closest distance to " O   HOH Z  88 " =    3.922
peak=    3.806 closest distance to " O   HOH Z  20 " =    1.770
peak=    3.799 closest distance to " O   HOH Z  44 " =    2.773
peak=    3.785 closest distance to " O   HOH Z 115 " =    1.712
peak=    3.781 closest distance to " O   HOH Z 392 " =    1.305
peak=    3.764 closest distance to " O   HOH Z 207 " =    2.176
peak=    3.761 closest distance to " CD  ARG A  66 " =    2.224
peak=    3.752 closest distance to " CB  VAL A 265 " =    1.312
peak=    3.752 closest distance to " O   HOH Z 411 " =    3.692
peak=    3.750 closest distance to " OD1BASN A 224 " =    2.284
peak=    3.741 closest distance to " NE AARG A 275 " =    1.538
peak=    3.739 closest distance to " O   HOH Z  40 " =    2.262
peak=    3.731 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.729 closest distance to " NE2 GLN A  73 " =    3.733
peak=    3.726 closest distance to " CD BLYS A 290 " =    1.042
peak=    3.713 closest distance to " O   HOH Z 175 " =    2.138
peak=    3.697 closest distance to " OG BSER A  99 " =    2.273
peak=    3.692 closest distance to " CB  THR A 157 " =    1.149
peak=    3.689 closest distance to " CE  LYS A  76 " =    0.831
peak=    3.683 closest distance to " CG2 VAL A 257 " =    0.995
peak=    3.677 closest distance to " O   HOH Z 108 " =    2.073
peak=    3.668 closest distance to " O   HOH Z 258 " =    2.182
peak=    3.668 closest distance to " CG  PRO A  90 " =    1.184
peak=    3.668 closest distance to " N   ALA A   1 " =    2.023
peak=    3.667 closest distance to " N   ASN A 127 " =    1.368
peak=    3.664 closest distance to " CG1 ILE A  33 " =    1.232
peak=    3.663 closest distance to " O   HOH Z 234 " =    3.808
peak=    3.658 closest distance to " O   HOH Z  68 " =    2.104
peak=    3.658 closest distance to " CA  GLY A 267 " =    1.312
peak=    3.654 closest distance to " O   ASN A 209 " =    1.410
peak=    3.651 closest distance to " O   HOH Z 193 " =    1.758
peak=    3.643 closest distance to " CB  ASP A 124 " =    0.783
peak=    3.635 closest distance to " O   HOH Z 302 " =    1.643
peak=    3.630 closest distance to " O   HOH Z   3 " =    2.024
peak=    3.624 closest distance to " O   HOH Z 405 " =    1.487
peak=    3.624 closest distance to " O   HOH Z  10 " =    1.731
peak=    3.619 closest distance to " O   HOH Z   1 " =    1.496
peak=    3.619 closest distance to " O   HOH Z 116 " =    2.963
peak=    3.618 closest distance to " O   HOH Z 352 " =    1.753
peak=    3.617 closest distance to " O   HOH Z 171 " =    2.823
peak=    3.612 closest distance to " CA  ILE A 234 " =    1.054
peak=    3.609 closest distance to " CA  ALA A 160 " =    0.866
peak=    3.608 closest distance to " CB  GLU A 236 " =    1.261
peak=    3.604 closest distance to " O   HOH Z  58 " =    1.821
peak=    3.604 closest distance to " O   HOH Z  59 " =    1.989
peak=    3.600 closest distance to " CD1 LEU A 300 " =    1.236
peak=    3.588 closest distance to " CB  ARG A 139 " =    1.050
peak=    3.582 closest distance to " O   HOH Z 365 " =    2.641
peak=    3.582 closest distance to " OG  SER A  62 " =    3.082
peak=    3.577 closest distance to " O   HOH Z 195 " =    1.348
peak=    3.576 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.575 closest distance to " N   TYR A  15 " =    0.905
peak=    3.574 closest distance to " O   HOH Z 327 " =    1.691
peak=    3.569 closest distance to " O   HOH Z 281 " =    4.514
peak=    3.564 closest distance to " CD  LYS A 166 " =    1.384
peak=    3.561 closest distance to " OG  SER A  62 " =    3.065
peak=    3.560 closest distance to " O   HOH Z 213 " =    1.996
peak=    3.552 closest distance to " O   HOH Z 145 " =    1.509
peak=    3.548 closest distance to " O   HOH Z 368 " =    1.960
peak=    3.542 closest distance to " O   HOH Z 128 " =    2.220
peak=    3.541 closest distance to " O   HOH Z 184 " =    1.846
peak=    3.540 closest distance to " CA  ALA A 299 " =    0.887
peak=    3.535 closest distance to " O   HOH Z 422 " =    2.781
peak=    3.533 closest distance to " CB  TYR A 169 " =    0.865
peak=    3.527 closest distance to " NE  ARG A  66 " =    3.503
peak=    3.522 closest distance to " CB  GLU A 277 " =    3.605
peak=    3.521 closest distance to " O   HOH Z 217 " =    1.742
peak=    3.521 closest distance to " O   HOH Z  30 " =    1.607
peak=    3.518 closest distance to " O   HOH Z  68 " =    1.783
peak=    3.502 closest distance to " CB  MET A  47 " =    1.119
peak=    3.498 closest distance to " CA  TYR A 116 " =    1.317
peak=    3.493 closest distance to " O   HOH Z 158 " =    2.796
peak=    3.492 closest distance to " NH1AARG A 145 " =    1.169
peak=    3.488 closest distance to " O   HOH Z 362 " =    2.027
peak=    3.488 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.482 closest distance to " CB  TYR A 116 " =    0.922
peak=    3.476 closest distance to " CA  ASN A 215 " =    1.214
peak=    3.470 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.466 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.465 closest distance to " CB  TRP A 179 " =    1.499
peak=    3.464 closest distance to " O   MET A 105 " =    1.782
peak=    3.464 closest distance to " CB  LEU A 143 " =    1.099
peak=    3.462 closest distance to " O   HOH Z   7 " =    3.554
peak=    3.462 closest distance to " OE2 GLU A  53 " =    2.059
peak=    3.458 closest distance to " O   HOH Z  44 " =    1.654
peak=    3.456 closest distance to " O   HOH Z 155 " =    1.529
peak=    3.455 closest distance to " CD2 LEU A 255 " =    1.574
peak=    3.449 closest distance to " O   HOH Z  64 " =    1.967
peak=    3.446 closest distance to " O   HOH Z 122 " =    1.512
peak=    3.445 closest distance to " O   HOH Z 119 " =    1.606
peak=    3.437 closest distance to " CG BARG A 275 " =    1.427
peak=    3.429 closest distance to " O   HOH Z 139 " =    1.188
peak=    3.429 closest distance to " O   HOH Z 188 " =    2.137
peak=    3.425 closest distance to " CA  MET A  40 " =    1.109
peak=    3.423 closest distance to " CB  THR A  82 " =    1.252
peak=    3.420 closest distance to " O   HOH Z 410 " =    1.689
peak=    3.420 closest distance to " CB  ARG A  79 " =    1.291
peak=    3.417 closest distance to " O   HOH Z 153 " =    1.633
peak=    3.416 closest distance to " O   HOH Z  21 " =    1.670
peak=    3.415 closest distance to " O   HOH Z  17 " =    1.771
peak=    3.413 closest distance to " CA  ALA A 233 " =    1.074
peak=    3.412 closest distance to " O   HOH Z 124 " =    2.115
peak=    3.411 closest distance to " CA  ARG A 195 " =    1.352
peak=    3.408 closest distance to " CB  LYS A 117 " =    1.205
peak=    3.407 closest distance to " CB  SER A 276 " =    1.110
peak=    3.403 closest distance to " CZ  PHE A 218 " =    1.077
peak=    3.401 closest distance to " O   HOH Z 227 " =    1.806
peak=    3.400 closest distance to " CG1 ILE A 151 " =    0.984
peak=    3.398 closest distance to " O   HOH Z 289 " =    1.573
peak=    3.395 closest distance to " O   HOH Z 374 " =    2.789
peak=    3.394 closest distance to " CA  THR A 264 " =    0.850
peak=    3.393 closest distance to " CD1 ILE A  33 " =    1.611
peak=    3.387 closest distance to " CB  TRP A 150 " =    1.075
peak=    3.386 closest distance to " CA  ALA A 291 " =    0.907
peak=    3.386 closest distance to " NH2 ARG A 219 " =    1.747
peak=    3.384 closest distance to " CB  ILE A 120 " =    1.289
peak=    3.382 closest distance to " CG  PRO A 243 " =    1.143
peak=    3.382 closest distance to " O   HOH Z 359 " =    1.409
peak=    3.377 closest distance to " O   HOH Z 144 " =    2.276
peak=    3.377 closest distance to " SD  MET A  93 " =    1.321
peak=    3.376 closest distance to " NE2 GLN A  58 " =    3.605
peak=    3.376 closest distance to " CA  TYR A 186 " =    1.540
peak=    3.374 closest distance to " O   HOH Z 368 " =    3.671
peak=    3.371 closest distance to " O   HOH Z 432 " =    1.785
peak=    3.368 closest distance to " O   HOH Z 409 " =    2.233
peak=    3.364 closest distance to " O   THR A 220 " =    1.465
peak=    3.360 closest distance to " N   SER A  97 " =    0.853
peak=    3.360 closest distance to " CG  ARG A 159 " =    0.822
peak=    3.357 closest distance to " CB  LEU A 237 " =    0.774
peak=    3.355 closest distance to " O   HOH Z 288 " =    2.050
peak=    3.352 closest distance to " OG  SER A  22 " =    2.936
peak=    3.351 closest distance to " CB  THR A 235 " =    1.014
peak=    3.349 closest distance to " CA  SER A  87 " =    1.018
peak=    3.349 closest distance to " CA  MET A 105 " =    0.895
peak=    3.344 closest distance to " O   HOH Z 378 " =    1.005
peak=    3.341 closest distance to " CB  SER A 212 " =    1.074
peak=    3.337 closest distance to " O   TYR A 116 " =    1.317
peak=    3.335 closest distance to " CG  GLN A 278 " =    1.293
peak=    3.334 closest distance to " N   SER A 134 " =    1.403
peak=    3.328 closest distance to " O   HOH Z 434 " =    1.336
peak=    3.324 closest distance to " O   HOH Z 193 " =    2.189
peak=    3.321 closest distance to " CZ  PHE A 192 " =    0.945
peak=    3.320 closest distance to " O   HOH Z  51 " =    1.784
peak=    3.320 closest distance to " O   HOH Z 219 " =    2.251
peak=    3.316 closest distance to " O   HOH Z 371 " =    2.773
peak=    3.313 closest distance to " O   HOH Z 373 " =    1.415
peak=    3.309 closest distance to " CG  GLN A 278 " =    3.781
peak=    3.303 closest distance to " CB  ALA A  34 " =    1.242
peak=    3.298 closest distance to " O   HOH Z 345 " =    3.588
peak=    3.298 closest distance to " O   HOH Z 134 " =    1.163
peak=    3.296 closest distance to " O   HOH Z 175 " =    3.670
peak=    3.294 closest distance to " O   HOH Z 371 " =    2.159
peak=    3.293 closest distance to " O   HOH Z 430 " =    1.616
peak=    3.289 closest distance to " CG  MET A 113 " =    1.375
peak=    3.289 closest distance to " O  BHOH Z 338 " =    2.331
peak=    3.287 closest distance to " CB  GLU A 152 " =    1.425
peak=    3.285 closest distance to " CA  ALA A  21 " =    1.195
peak=    3.285 closest distance to " CA  ARG A 102 " =    1.213
peak=    3.275 closest distance to " CG  GLN A  88 " =    1.141
peak=    3.274 closest distance to " O   HOH Z  64 " =    2.306
peak=    3.274 closest distance to " CB  ASN A 142 " =    0.901
peak=    3.273 closest distance to " O   HOH Z 284 " =    3.070
peak=    3.269 closest distance to " N   GLN A 278 " =    1.090
peak=    3.269 closest distance to " CA  LEU A 101 " =    1.633
peak=    3.268 closest distance to " O   HOH Z 329 " =    3.812
peak=    3.266 closest distance to " CG1 VAL A 153 " =    0.928
peak=    3.263 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.261 closest distance to " NH1 ARG A  56 " =    1.223
peak=    3.259 closest distance to " O   HOH Z 425 " =    1.993
peak=    3.253 closest distance to " CB  SER A  62 " =    1.305
peak=    3.253 closest distance to " O   HOH Z 281 " =    1.889
peak=    3.253 closest distance to " O   HOH Z 113 " =    1.817
peak=    3.252 closest distance to " O   HOH Z 147 " =    1.739
peak=    3.251 closest distance to " CB  ALA A  43 " =    0.911
peak=    3.250 closest distance to " O   HOH Z 389 " =    1.936
peak=    3.238 closest distance to " O   ALA A 165 " =    1.311
peak=    3.237 closest distance to " O   HOH Z 271 " =    2.439
peak=    3.232 closest distance to " CB  ARG A 138 " =    0.923
peak=    3.231 closest distance to " CA  ALA A 158 " =    1.093
peak=    3.227 closest distance to " O   HOH Z 386 " =    2.486
peak=    3.227 closest distance to " O   HOH Z 414 " =    1.236
peak=    3.227 closest distance to " O   HOH Z 172 " =    2.763
peak=    3.225 closest distance to " OG BSER A 134 " =    3.169
peak=    3.220 closest distance to " O   HOH Z 393 " =    1.238
peak=    3.219 closest distance to " CD2 TRP A 179 " =    1.207
peak=    3.219 closest distance to " CB  ALA A 114 " =    1.443
peak=    3.213 closest distance to " CA  ALA A 154 " =    0.946
peak=    3.211 closest distance to " CB  THR A  31 " =    1.820
peak=    3.210 closest distance to " O   HOH Z 407 " =    1.488
peak=    3.210 closest distance to " CG1 VAL A 202 " =    1.875
peak=    3.208 closest distance to " CA  SER A  95 " =    1.006
peak=    3.207 closest distance to " O   HOH Z 128 " =    2.029
peak=    3.203 closest distance to " OD1 ASN A 217 " =    1.563
peak=    3.200 closest distance to " O   HOH Z 139 " =    2.315
peak=    3.197 closest distance to " O   HOH Z  59 " =    1.596
peak=    3.187 closest distance to " O   HOH Z 325 " =    3.578
peak=    3.185 closest distance to " O   HOH Z 295 " =    1.541
peak=    3.185 closest distance to " O   HOH Z 207 " =    1.736
peak=    3.184 closest distance to " N   CYS A 260 " =    0.762
peak=    3.183 closest distance to " CA  ASP A 162 " =    1.148
peak=    3.181 closest distance to " CA  ALA A  51 " =    1.068
peak=    3.180 closest distance to " O   HOH Z 286 " =    2.308
peak=    3.178 closest distance to " CB  ALA A 104 " =    0.728
peak=    3.175 closest distance to " O   HOH Z 286 " =    2.262
peak=    3.175 closest distance to " CD  PRO A 243 " =    1.774
peak=    3.174 closest distance to " O   HOH Z 154 " =    1.976
peak=    3.173 closest distance to " O   HOH Z 116 " =    1.682
peak=    3.167 closest distance to " O   HOH Z 235 " =    1.830
peak=    3.167 closest distance to " O   LEU A 300 " =    1.466
peak=    3.157 closest distance to " O   HOH Z  50 " =    1.916
peak=    3.153 closest distance to " CZ  PHE A  38 " =    1.412
peak=    3.144 closest distance to " CB  ALA A 114 " =    1.148
peak=    3.143 closest distance to " CB  ALA A 184 " =    1.083
peak=    3.137 closest distance to " NZ  LYS A  76 " =    1.574
peak=    3.136 closest distance to " O   HOH Z 110 " =    1.548
peak=    3.131 closest distance to " O   HOH Z 417 " =    1.770
peak=    3.129 closest distance to " O   HOH Z 133 " =    1.660
peak=    3.127 closest distance to " CB  VAL A 250 " =    1.028
peak=    3.121 closest distance to " O   HOH Z 423 " =    1.892
peak=    3.121 closest distance to " O   HOH Z 148 " =    3.309
peak=    3.117 closest distance to " ND1 HIS A  81 " =    1.711
peak=    3.116 closest distance to " CB  LEU A 255 " =    1.461
peak=    3.115 closest distance to " O   HOH Z  88 " =    2.789
peak=    3.114 closest distance to " NH2BARG A 145 " =    2.105
peak=    3.112 closest distance to " CB  ALA A  71 " =    1.454
peak=    3.109 closest distance to " O   GLY A  57 " =    2.620
peak=    3.108 closest distance to " CA  ASN A 217 " =    1.140
peak=    3.103 closest distance to " NZ  LYS A 119 " =    1.228
peak=    3.099 closest distance to " O   GLY A 302 " =    2.273
peak=    3.090 closest distance to " CD2 PHE A  59 " =    1.725
peak=    3.083 closest distance to " ND2 ASN A  60 " =    3.753
peak=    3.079 closest distance to " CD  ARG A 138 " =    0.708
peak=    3.072 closest distance to " O   HOH Z 128 " =    2.031
peak=    3.041 closest distance to " O   HOH Z 213 " =    2.818
peak=    3.034 closest distance to " O   HOH Z 273 " =    2.913
peak=    3.007 closest distance to " O   HOH Z  43 " =    2.317

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 188         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 5.739
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 188
   mapped sites are within: 0.735 - 5.739

peak=   -4.459 closest distance to " O   HOH Z 377 " =    1.862
peak=   -4.365 closest distance to " CB  PRO A 243 " =    2.513
peak=   -4.299 closest distance to " CD  ARG A  14 " =    3.316
peak=   -4.236 closest distance to " CA  GLY A  98 " =    1.882
peak=   -4.227 closest distance to " O   PRO A 198 " =    1.321
peak=   -4.221 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.187 closest distance to " O   HOH Z  65 " =    1.069
peak=   -4.086 closest distance to " O   HOH Z 407 " =    3.261
peak=   -4.029 closest distance to " OG BSER A 134 " =    1.292
peak=   -3.989 closest distance to " O   HOH Z 290 " =    1.270
peak=   -3.985 closest distance to " O   SER A 135 " =    1.436
peak=   -3.948 closest distance to " C   ALA A 158 " =    1.445
peak=   -3.939 closest distance to " O   HOH Z 231 " =    1.963
peak=   -3.878 closest distance to " CZ3 TRP A 179 " =    1.069
peak=   -3.874 closest distance to " CB  ASP A  27 " =    2.374
peak=   -3.839 closest distance to " CG  MET A 105 " =    0.950
peak=   -3.836 closest distance to " O   HOH Z 266 " =    4.743
peak=   -3.818 closest distance to " OE1 GLN A 223 " =    2.274
peak=   -3.791 closest distance to " NH2 ARG A  79 " =    1.891
peak=   -3.783 closest distance to " N   ALA A  43 " =    2.478
peak=   -3.762 closest distance to " O   HOH Z 166 " =    1.308
peak=   -3.752 closest distance to " O   HOH Z 185 " =    2.053
peak=   -3.722 closest distance to " N   THR A 157 " =    1.499
peak=   -3.711 closest distance to " CA  GLY A 203 " =    2.255
peak=   -3.707 closest distance to " CG  GLN A  88 " =    0.830
peak=   -3.700 closest distance to " O   HOH Z 313 " =    1.839
peak=   -3.696 closest distance to " O   HOH Z 372 " =    2.435
peak=   -3.683 closest distance to " O   HOH Z 389 " =    1.994
peak=   -3.679 closest distance to " OG  SER A  87 " =    1.331
peak=   -3.671 closest distance to " O   PHE A 218 " =    1.369
peak=   -3.668 closest distance to " CD2 LEU A 143 " =    2.521
peak=   -3.668 closest distance to " O   HOH Z  13 " =    1.620
peak=   -3.664 closest distance to " CA  GLY A 241 " =    2.226
peak=   -3.659 closest distance to " O   VAL A  67 " =    2.604
peak=   -3.644 closest distance to " CB  ALA A 248 " =    1.951
peak=   -3.631 closest distance to " O   HOH Z 231 " =    0.766
peak=   -3.629 closest distance to " O   HOH Z  38 " =    1.532
peak=   -3.622 closest distance to " O   HOH Z 316 " =    1.905
peak=   -3.621 closest distance to " O   HOH Z 198 " =    2.024
peak=   -3.617 closest distance to " ND2 ASN A 249 " =    2.294
peak=   -3.602 closest distance to " O   PRO A 243 " =    2.348
peak=   -3.595 closest distance to " O   HOH Z 298 " =    1.188
peak=   -3.587 closest distance to " O   HOH Z 351 " =    1.604
peak=   -3.582 closest distance to " CG  PRO A 163 " =    2.377
peak=   -3.581 closest distance to " O   HOH Z 152 " =    5.062
peak=   -3.541 closest distance to " O   ASP A 162 " =    2.294
peak=   -3.535 closest distance to " CD2 LEU A 237 " =    2.781
peak=   -3.518 closest distance to " O   PRO A 163 " =    1.901
peak=   -3.510 closest distance to " O   HOH Z  90 " =    2.839
peak=   -3.501 closest distance to " O   HOH Z 281 " =    2.951
peak=   -3.500 closest distance to " CA  GLY A  23 " =    2.723
peak=   -3.498 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.492 closest distance to " O   HOH Z 168 " =    1.784
peak=   -3.484 closest distance to " C   LEU A 143 " =    1.320
peak=   -3.483 closest distance to " CB  ALA A   9 " =    2.449
peak=   -3.474 closest distance to " CB  ALA A 291 " =    2.138
peak=   -3.472 closest distance to " OE1 GLN A  88 " =    1.181
peak=   -3.471 closest distance to " CE  LYS A  76 " =    2.943
peak=   -3.470 closest distance to " ND2 ASN A 285 " =    2.069
peak=   -3.470 closest distance to " NH2AARG A 275 " =    5.584
peak=   -3.456 closest distance to " CB  PRO A  54 " =    2.393
peak=   -3.455 closest distance to " CB  PHE A 192 " =    1.780
peak=   -3.455 closest distance to " O   HOH Z 198 " =    1.710
peak=   -3.454 closest distance to " C   ASN A 187 " =    1.753
peak=   -3.453 closest distance to " O   ALA A 180 " =    1.273
peak=   -3.447 closest distance to " N   ARG A  14 " =    1.039
peak=   -3.446 closest distance to " O   HOH Z 282 " =    4.392
peak=   -3.441 closest distance to " O   HOH Z   1 " =    1.429
peak=   -3.440 closest distance to " O   HOH Z 191 " =    5.458
peak=   -3.437 closest distance to " CG1 VAL A 197 " =    2.273
peak=   -3.436 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.428 closest distance to " O   HOH Z 292 " =    1.472
peak=   -3.426 closest distance to " OD1 ASN A 148 " =    1.726
peak=   -3.424 closest distance to " CB  TRP A  85 " =    2.485
peak=   -3.420 closest distance to " O   ALA A   1 " =    1.122
peak=   -3.414 closest distance to " CE  MET A  93 " =    1.129
peak=   -3.410 closest distance to " CD1 LEU A 255 " =    3.056
peak=   -3.410 closest distance to " O   HOH Z 131 " =    4.161
peak=   -3.403 closest distance to " N   ASP A 171 " =    2.377
peak=   -3.402 closest distance to " OD1 ASP A 191 " =    1.557
peak=   -3.401 closest distance to " O   HOH Z  52 " =    1.141
peak=   -3.399 closest distance to " N   GLN A  58 " =    1.645
peak=   -3.395 closest distance to " O   HOH Z 211 " =    1.508
peak=   -3.388 closest distance to " C   ASN A 285 " =    2.418
peak=   -3.387 closest distance to " CG1 VAL A 112 " =    2.831
peak=   -3.387 closest distance to " CE1 TYR A 169 " =    2.545
peak=   -3.383 closest distance to " C   LEU A 222 " =    0.735
peak=   -3.378 closest distance to " CG1BVAL A  41 " =    2.695
peak=   -3.377 closest distance to " CB  ASN A  39 " =    2.262
peak=   -3.377 closest distance to " CG1 VAL A  78 " =    2.462
peak=   -3.375 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.372 closest distance to " C   HIS A 108 " =    1.140
peak=   -3.372 closest distance to " NE  ARG A  36 " =    1.945
peak=   -3.372 closest distance to " O   HOH Z 111 " =    2.002
peak=   -3.371 closest distance to " O   ILE A  49 " =    1.724
peak=   -3.366 closest distance to " O   HOH Z  51 " =    0.980
peak=   -3.365 closest distance to " O   HOH Z  73 " =    2.140
peak=   -3.363 closest distance to " N   GLN A 122 " =    1.442
peak=   -3.354 closest distance to " CE  MET A 105 " =    2.520
peak=   -3.349 closest distance to " CB  PRO A  90 " =    1.507
peak=   -3.347 closest distance to " OD1 ASN A 187 " =    1.518
peak=   -3.347 closest distance to " OD2 ASP A 191 " =    1.475
peak=   -3.342 closest distance to " CG  GLN A 240 " =    2.440
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.447
peak=   -3.339 closest distance to " CE2 PHE A 218 " =    2.434
peak=   -3.338 closest distance to " CB  ALA A  43 " =    2.421
peak=   -3.337 closest distance to " O   HOH Z  60 " =    2.134
peak=   -3.335 closest distance to " O   HOH Z 409 " =    5.739
peak=   -3.331 closest distance to " O   HOH Z 102 " =    1.565
peak=   -3.331 closest distance to " O   MET A  47 " =    2.650
peak=   -3.330 closest distance to " O   HOH Z 298 " =    2.485
peak=   -3.330 closest distance to " O   HOH Z  49 " =    1.367
peak=   -3.326 closest distance to " OD2 ASP A 171 " =    1.804
peak=   -3.320 closest distance to " CD  LYS A 289 " =    2.352
peak=   -3.317 closest distance to " CE2 TYR A  30 " =    2.638
peak=   -3.312 closest distance to " OXT GLY A 302 " =    3.118
peak=   -3.311 closest distance to " O   SER A  62 " =    2.281
peak=   -3.303 closest distance to " OG  SER A 245 " =    1.191
peak=   -3.297 closest distance to " CG2 VAL A 232 " =    2.039
peak=   -3.296 closest distance to " O   HOH Z 337 " =    1.441
peak=   -3.294 closest distance to " OG  SER A  97 " =    2.153
peak=   -3.293 closest distance to " CG1 VAL A 250 " =    2.648
peak=   -3.287 closest distance to " CZ BARG A 275 " =    1.633
peak=   -3.284 closest distance to " CD1 LEU A 228 " =    2.350
peak=   -3.281 closest distance to " O   HOH Z  22 " =    2.493
peak=   -3.280 closest distance to " O   HOH Z  43 " =    1.675
peak=   -3.279 closest distance to " ND2 ASN A  45 " =    2.015
peak=   -3.278 closest distance to " CZ  PHE A  59 " =    1.531
peak=   -3.277 closest distance to " CE3 TRP A 123 " =    1.412
peak=   -3.274 closest distance to " CB  CYS A 254 " =    2.065
peak=   -3.272 closest distance to " O   HOH Z 118 " =    1.336
peak=   -3.270 closest distance to " CD2 LEU A  25 " =    2.229
peak=   -3.270 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.268 closest distance to " ND2BASN A 224 " =    1.122
peak=   -3.267 closest distance to " O   GLY A  80 " =    2.370
peak=   -3.266 closest distance to " ND2 ASN A  45 " =    1.167
peak=   -3.256 closest distance to " CD1 LEU A 101 " =    2.297
peak=   -3.251 closest distance to " CD1 ILE A 239 " =    2.303
peak=   -3.250 closest distance to " CG  PHE A 283 " =    2.726
peak=   -3.249 closest distance to " CG  GLU A 152 " =    1.670
peak=   -3.229 closest distance to " O   HOH Z 318 " =    1.913
peak=   -3.229 closest distance to " O   HOH Z 134 " =    2.880
peak=   -3.227 closest distance to " O   HOH Z 134 " =    1.695
peak=   -3.221 closest distance to " O   GLY A  17 " =    1.133
peak=   -3.216 closest distance to " NH2 ARG A 219 " =    1.848
peak=   -3.214 closest distance to " CA  GLY A 133 " =    1.991
peak=   -3.208 closest distance to " CE1 PHE A  59 " =    2.210
peak=   -3.201 closest distance to " O   HOH Z 350 " =    2.070
peak=   -3.200 closest distance to " CB  PHE A 130 " =    1.231
peak=   -3.197 closest distance to " CB  ALA A 131 " =    1.963
peak=   -3.196 closest distance to " O   HOH Z 427 " =    1.815
peak=   -3.196 closest distance to " N   ASP A 270 " =    1.402
peak=   -3.194 closest distance to " OG BSER A 134 " =    1.635
peak=   -3.194 closest distance to " O   HOH Z 193 " =    1.639
peak=   -3.193 closest distance to " O   HOH Z 140 " =    1.597
peak=   -3.191 closest distance to " O   HOH Z  53 " =    1.787
peak=   -3.187 closest distance to " O   HOH Z 388 " =    1.988
peak=   -3.186 closest distance to " CB  PRO A 163 " =    2.403
peak=   -3.183 closest distance to " CD2 TYR A 293 " =    1.889
peak=   -3.177 closest distance to " CD  PRO A 213 " =    2.119
peak=   -3.174 closest distance to " CB  ALA A 114 " =    2.524
peak=   -3.160 closest distance to " O   ASN A 301 " =    1.392
peak=   -3.159 closest distance to " O   HOH Z 174 " =    2.571
peak=   -3.159 closest distance to " O   HOH Z 111 " =    1.135
peak=   -3.158 closest distance to " OE1 GLN A  58 " =    3.023
peak=   -3.149 closest distance to " O   HOH Z 412 " =    4.398
peak=   -3.143 closest distance to " CD  PRO A 198 " =    1.723
peak=   -3.141 closest distance to " O   HOH Z 414 " =    1.831
peak=   -3.136 closest distance to " CB  ALA A 248 " =    2.371
peak=   -3.131 closest distance to " O   HOH Z 345 " =    2.370
peak=   -3.131 closest distance to " CG  ARG A 269 " =    2.549
peak=   -3.129 closest distance to " O   HOH Z 186 " =    1.074
peak=   -3.128 closest distance to " O   HOH Z 234 " =    4.148
peak=   -3.126 closest distance to " O   VAL A 197 " =    1.514
peak=   -3.117 closest distance to " C   ALA A 114 " =    2.200
peak=   -3.105 closest distance to " OH  TYR A 247 " =    1.776
peak=   -3.103 closest distance to " O   ALA A  84 " =    1.690
peak=   -3.102 closest distance to " OG ASER A 134 " =    1.176
peak=   -3.101 closest distance to " O   HOH Z 426 " =    2.287
peak=   -3.094 closest distance to " CE  LYS A  76 " =    2.788
peak=   -3.087 closest distance to " OG ASER A 216 " =    1.038
peak=   -3.086 closest distance to " O   ARG A 145 " =    1.392
peak=   -3.077 closest distance to " CB  TYR A  15 " =    2.124
peak=   -3.060 closest distance to " O   HOH Z 147 " =    1.370
peak=   -3.045 closest distance to " ND2 ASN A  45 " =    1.430
peak=   -3.042 closest distance to " O   GLN A 240 " =    1.679
peak=   -3.018 closest distance to " CA  GLY A  57 " =    2.044

================= 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    :  0.4446 0.4434   6.256415e+00   6.253545e+00
   1_bss:  0.4351 0.4352   6.248203e+00   6.242653e+00
   1_xyz:  0.2840 0.3207   5.929977e+00   6.006981e+00
   1_adp:  0.2600 0.3333   5.884690e+00   6.043939e+00
   1_occ:  0.2595 0.3332   5.883381e+00   6.043019e+00
   2_bss:  0.2568 0.3289   5.874117e+00   6.032975e+00
   2_xyz:  0.2039 0.2649   5.675215e+00   5.867729e+00
   2_adp:  0.1944 0.2491   5.631583e+00   5.816081e+00
   2_occ:  0.1943 0.2490   5.631204e+00   5.815957e+00
   3_bss:  0.1942 0.2476   5.629017e+00   5.813172e+00
   3_xyz:  0.1492 0.1987   5.389308e+00   5.606528e+00
   3_adp:  0.1356 0.1866   5.310365e+00   5.542486e+00
   3_occ:  0.1355 0.1866   5.310149e+00   5.542408e+00
   4_bss:  0.1358 0.1864   5.309493e+00   5.541667e+00
   4_xyz:  0.1236 0.1742   5.232495e+00   5.474841e+00
   4_adp:  0.1208 0.1686   5.208184e+00   5.447742e+00
   4_occ:  0.1207 0.1686   5.207943e+00   5.447470e+00
   5_bss:  0.1207 0.1685   5.207713e+00   5.447232e+00
   5_xyz:  0.1135 0.1613   5.161846e+00   5.412517e+00
   5_adp:  0.1123 0.1600   5.155972e+00   5.408767e+00
   5_occ:  0.1123 0.1600   5.155995e+00   5.408891e+00
   5_bss:  0.1125 0.1596   5.155149e+00   5.405867e+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:  0.339  43.451   0.735   2.295  -1.814   0.000  -0.000  -0.000
   1_xyz:  0.339  43.451   0.735   2.295  -1.814   0.000  -0.000  -0.000
   1_adp:  0.339  43.451   0.735   2.295  -1.814   0.000  -0.000  -0.000
   1_occ:  0.339  43.451   0.735   2.295  -1.814   0.000  -0.000  -0.000
   2_bss:  0.347  63.883  -0.823  -0.757  -1.381  -0.000  -0.000  -0.000
   2_xyz:  0.347  63.883  -0.823  -0.757  -1.381  -0.000  -0.000  -0.000
   2_adp:  0.347  63.883  -0.823  -0.757  -1.381  -0.000  -0.000  -0.000
   2_occ:  0.347  63.883  -0.823  -0.757  -1.381  -0.000  -0.000  -0.000
   3_bss:  0.337  57.431  -1.455  -1.810  -1.194  -0.000  -0.000  -0.000
   3_xyz:  0.337  57.431  -1.455  -1.810  -1.194  -0.000  -0.000  -0.000
   3_adp:  0.337  57.431  -1.455  -1.810  -1.194  -0.000  -0.000  -0.000
   3_occ:  0.337  57.431  -1.455  -1.810  -1.194  -0.000  -0.000  -0.000
   4_bss:  0.323  57.431  -1.884  -2.581  -1.493  -0.000  -0.000  -0.000
   4_xyz:  0.323  57.431  -1.884  -2.581  -1.493  -0.000  -0.000  -0.000
   4_adp:  0.323  57.431  -1.884  -2.581  -1.493  -0.000  -0.000  -0.000
   4_occ:  0.323  57.431  -1.884  -2.581  -1.493  -0.000  -0.000  -0.000
   5_bss:  0.323  57.431  -1.994  -2.736  -1.510  -0.000  -0.000  -0.000
   5_xyz:  0.323  57.431  -1.994  -2.736  -1.510  -0.000  -0.000  -0.000
   5_adp:  0.323  57.431  -1.994  -2.736  -1.510  -0.000  -0.000  -0.000
   5_occ:  0.323  57.431  -1.994  -2.736  -1.510  -0.000  -0.000  -0.000
   5_bss:  0.323  57.434  -2.008  -2.777  -1.485  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.556 0.4765  0.6458    64540.831
   1_bss:  52.794 0.4849  0.6704    62147.948
   1_xyz:  33.004 0.7256  0.9396    27866.867
   1_adp:  35.277 0.6981  0.9126    30440.485
   1_occ:  35.266 0.6981  0.9116    30333.135
   2_bss:  34.543 0.7061  0.8786    29256.537
   2_xyz:  27.092 0.7883  0.9519    18498.162
   2_adp:  24.839 0.8133  0.9706    16415.563
   2_occ:  24.848 0.8131  0.9701    16416.279
   3_bss:  24.729 0.8142  0.9535    16247.076
   3_xyz:  19.027 0.8700  0.9925     9998.116
   3_adp:  17.450 0.8852  0.9943     8789.797
   3_occ:  17.448 0.8853  0.9942     8785.834
   4_bss:  17.419 0.8854  0.9768     8758.343
   4_xyz:  15.825 0.8996  0.9819     7554.761
   4_adp:  15.142 0.9058  0.9808     7164.899
   4_occ:  15.138 0.9058  0.9808     7158.494
   5_bss:  15.130 0.9058  0.9776     7154.555
   5_xyz:  14.474 0.9111  0.9810     6645.174
   5_adp:  14.349 0.9123  0.9780     6584.772
   5_occ:  14.351 0.9123  0.9780     6585.372
   5_bss:  14.324 0.9123  0.9781     6533.741
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7306e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7306e-01
   1_xyz:   1.709  0.015  0.124 16.257  0.008  4.115   1.7526e-01
   1_adp:   1.709  0.015  0.124 16.257  0.008  4.115   1.7526e-01
   1_occ:   1.709  0.015  0.124 16.257  0.008  4.115   1.7526e-01
   2_bss:   1.709  0.015  0.124 16.257  0.008  4.115   1.7526e-01
   2_xyz:   0.947  0.006  0.070 14.369  0.003  4.115   5.4690e-02
   2_adp:   0.947  0.006  0.070 14.369  0.003  4.115   5.4690e-02
   2_occ:   0.947  0.006  0.070 14.369  0.003  4.115   5.4690e-02
   3_bss:   0.947  0.006  0.070 14.369  0.003  4.115   5.4690e-02
   3_xyz:   0.985  0.007  0.071 14.454  0.004  4.107   6.1072e-02
   3_adp:   0.985  0.007  0.071 14.454  0.004  4.107   6.1072e-02
   3_occ:   0.985  0.007  0.071 14.454  0.004  4.107   6.1072e-02
   4_bss:   0.985  0.007  0.071 14.454  0.004  4.107   6.1072e-02
   4_xyz:   0.936  0.006  0.070 14.388  0.004  4.111   5.3630e-02
   4_adp:   0.936  0.006  0.070 14.388  0.004  4.111   5.3630e-02
   4_occ:   0.936  0.006  0.070 14.388  0.004  4.111   5.3630e-02
   5_bss:   0.936  0.006  0.070 14.388  0.004  4.111   5.3630e-02
   5_xyz:   1.049  0.008  0.077 14.706  0.004  4.114   6.5066e-02
   5_adp:   1.049  0.008  0.077 14.706  0.004  4.114   6.5066e-02
   5_occ:   1.049  0.008  0.077 14.706  0.004  4.114   6.5066e-02
   5_bss:   1.049  0.008  0.077 14.706  0.004  4.114   6.5066e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.738   2.4063e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.738   2.4063e-01
   1_xyz:  10.206  0.123  0.479 85.606  0.054  2.018   2.6648e-01
   1_adp:  10.206  0.123  0.479 85.606  0.054  2.018   2.6648e-01
   1_occ:  10.206  0.123  0.479 85.606  0.054  2.018   2.6648e-01
   2_bss:  10.206  0.123  0.479 85.606  0.054  2.018   2.6648e-01
   2_xyz:   7.375  0.040  0.243 83.536  0.034  2.301   4.6769e-02
   2_adp:   7.375  0.040  0.243 83.536  0.034  2.301   4.6769e-02
   2_occ:   7.375  0.040  0.243 83.536  0.034  2.301   4.6769e-02
   3_bss:   7.375  0.040  0.243 83.536  0.034  2.301   4.6769e-02
   3_xyz:   8.070  0.049  0.229 80.432  0.029  2.276   1.1807e-01
   3_adp:   8.070  0.049  0.229 80.432  0.029  2.276   1.1807e-01
   3_occ:   8.070  0.049  0.229 80.432  0.029  2.276   1.1807e-01
   4_bss:   8.070  0.049  0.229 80.432  0.029  2.276   1.1807e-01
   4_xyz:   7.964  0.040  0.202 85.321  0.037  2.316   3.7939e-02
   4_adp:   7.964  0.040  0.202 85.321  0.037  2.316   3.7939e-02
   4_occ:   7.964  0.040  0.202 85.321  0.037  2.316   3.7939e-02
   5_bss:   7.964  0.040  0.202 85.321  0.037  2.316   3.7939e-02
   5_xyz:   8.465  0.043  0.236 84.452  0.040  2.256   5.1547e-02
   5_adp:   8.465  0.043  0.236 84.452  0.040  2.256   5.1547e-02
   5_occ:   8.465  0.043  0.236 84.452  0.040  2.256   5.1547e-02
   5_bss:   8.465  0.043  0.236 84.452  0.040  2.256   5.1547e-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:  99.75   0.00  18.48  73.12   0.00  14.04  99.75   3.02  42.68
   1_occ:  99.75   0.00  18.48  73.12   0.00  14.04  99.75   3.02  42.68
   2_bss:  99.75   0.00  18.48  73.12   0.00  14.04  99.75   3.02  42.68
   2_xyz:  99.75   0.00  18.48  73.12   0.00  14.04  99.75   3.02  42.68
   2_adp:  98.38   0.00  18.17  71.95   0.00  13.83  98.38   5.43  41.85
   2_occ:  98.38   0.00  18.17  71.95   0.00  13.83  98.38   5.43  41.85
   3_bss:  98.38   0.00  18.17  71.95   0.00  13.83  98.38   5.43  41.85
   3_xyz:  98.38   0.00  18.17  71.95   0.00  13.83  98.38   5.43  41.85
   3_adp: 101.14   0.00  18.41  89.56   0.00  13.41 101.14   6.61  45.61
   3_occ: 101.14   0.00  18.41  89.56   0.00  13.41 101.14   6.61  45.61
   4_bss: 101.14   0.00  18.41  89.56   0.00  13.41 101.14   6.61  45.61
   4_xyz: 101.14   0.00  18.41  89.56   0.00  13.41 101.14   6.61  45.61
   4_adp:  95.68   0.12  17.74  95.68   0.12  13.08  95.62   6.33  43.13
   4_occ:  95.68   0.12  17.74  95.68   0.12  13.08  95.62   6.33  43.13
   5_bss:  95.68   0.12  17.74  95.68   0.12  13.08  95.62   6.33  43.13
   5_xyz:  95.68   0.12  17.74  95.68   0.12  13.08  95.62   6.33  43.13
   5_adp:  99.41   0.00  17.52  99.41   0.00  12.99  92.86   6.11  42.19
   5_occ:  99.41   0.00  17.52  99.41   0.00  12.99  92.86   6.11  42.19
   5_bss:  99.42   0.00  17.53  99.42   0.00  13.00  92.86   6.11  42.19
------------------------------------------------------------------------
 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:    1.634    0.023    0.537
   1_adp:    1.634    0.023    0.537
   1_occ:    1.634    0.023    0.537
   2_bss:    1.634    0.023    0.537
   2_xyz:    1.285    0.047    0.567
   2_adp:    1.285    0.047    0.567
   2_occ:    1.285    0.047    0.567
   3_bss:    1.285    0.047    0.567
   3_xyz:    1.490    0.070    0.682
   3_adp:    1.490    0.070    0.682
   3_occ:    1.490    0.070    0.682
   4_bss:    1.490    0.070    0.682
   4_xyz:    1.621    0.061    0.702
   4_adp:    1.621    0.061    0.702
   4_occ:    1.621    0.061    0.702
   5_bss:    1.621    0.061    0.702
   5_xyz:    1.746    0.097    0.723
   5_adp:    1.746    0.097    0.723
   5_occ:    1.746    0.097    0.723
   5_bss:    1.746    0.097    0.723
------------------------------------------------------------------------

CPU time actual refinement: 346.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/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_1104/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1104/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.02 
  Macro-tasks:
    bulk solvent and scale       = 36.38  
    individual site refinement   = 145.15 
    weights calculation          = 30.86  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 219.13 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 113.79 
    alpha_beta                      = 8.36   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 122.20 
    fmodel                         = 6.49   
    r_factors                      = 0.22   
    phase_errors                   = 10.80  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 265.75 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.907 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    641 calls, 113.52 s
gradients_fft:          586 calls, 108.54 s

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

# Date 2008-01-16 Time 06:25:47 PST -0800 (1200493547.15 s)
Start R-work = 0.4446, R-free = 0.4434 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1804 (no bulk solvent and anisotropic scale)

Start R-work = 0.4351, R-free = 0.4352
Final R-work = 0.1125, R-free = 0.1596