# Date 2008-01-16 Time 06:05:11 PST -0800 (1200492311.45 s)
#phil __OFF__

Command line arguments: "../999.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 675
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 999

-------------------------------------------------------------------------------
  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: (71.3037, 46.2261, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.35, per 1000 atoms: 1.19


================================== 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: (71.3037, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.97372
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927597

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   1.9737

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: (71.3037, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.97372
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927597

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.2249 [2212/2238]  1991   221  10.0%
  bin  2:  4.2249 -  3.3653 [2133/2153]  1919   214  10.0%
  bin  3:  3.3653 -  2.9434 [2090/2109]  1884   206   9.9%
  bin  4:  2.9434 -  2.6758 [2074/2104]  1859   215  10.4%
  bin  5:  2.6758 -  2.4849 [2071/2090]  1872   199   9.6%
  bin  6:  2.4849 -  2.3390 [2079/2104]  1868   211  10.1%
  bin  7:  2.3390 -  2.2222 [2021/2049]  1812   209  10.3%
  bin  8:  2.2222 -  2.1257 [2045/2081]  1840   205  10.0%
  bin  9:  2.1257 -  2.0441 [2030/2072]  1838   192   9.5%
  bin 10:  2.0441 -  1.9737 [ 834/2057]   747    87  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2175
        3.04 -     3.66: 4665
        3.66 -     4.28: 8948
        4.28 -     4.90: 12244
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.102 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.195 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28055 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_999/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/model_refine_001.geo

CPU time processing inputs: 8.94


============================ 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 = 71.30375 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4501   r_free= 0.4462   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.259004                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7130 0.99   1435  158 0.3560 0.3280      6.5399      6.4418|
|  2:  4.7130 -  3.7593 0.99   1385  155 0.3728 0.3663      6.7691      6.7205|
|  3:  3.7593 -  3.2896 0.99   1358  147 0.4048 0.3671       6.604      6.5878|
|  4:  3.2896 -  2.9913 0.99   1342  154 0.4424 0.4821      6.4912      6.5152|
|  5:  2.9913 -  2.7783 0.99   1336  152 0.4863 0.4527      6.3378       6.333|
|  6:  2.7783 -  2.6153 0.99   1345  146 0.4651 0.4938      6.2246      6.1988|
|  7:  2.6153 -  2.4849 0.99   1324  143 0.4923 0.4630      6.2167      6.1612|
|  8:  2.4849 -  2.3772 0.98   1314  154 0.5147 0.5160      6.1655      6.1575|
|  9:  2.3772 -  2.2860 0.98   1316  145 0.5046 0.5171      6.1084      6.1646|
| 10:  2.2860 -  2.2073 1.00   1328  145 0.5187 0.5084      6.0783      6.0611|
| 11:  2.2073 -  2.1385 0.98   1308  144 0.5016 0.5361      6.0243      6.0248|
| 12:  2.1385 -  2.0775 0.98   1308  142 0.5220 0.4883      5.9297       5.944|
| 13:  2.0775 -  2.0230 0.92   1228  138 0.5047 0.5114      5.8738      5.7979|
| 14:  2.0230 -  1.9737 0.23    303   36 0.5284 0.5627      5.8607      5.8907|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7130  1435   158  0.77  28.25   0.82     0.80      52313.11|
|  2:  4.7130 -  3.7593  1385   155  0.77  29.52   0.91     0.86      82241.48|
|  3:  3.7593 -  3.2896  1358   147  0.64  40.12   0.93     0.83      93735.77|
|  4:  3.2896 -  2.9913  1342   154  0.55  47.69   0.90     0.73      90527.50|
|  5:  2.9913 -  2.7783  1336   152  0.46  55.21   0.89     0.64      74470.71|
|  6:  2.7783 -  2.6153  1345   146  0.43  57.26   0.91     0.59      64588.42|
|  7:  2.6153 -  2.4849  1324   143  0.42  58.66   0.91     0.57      59535.21|
|  8:  2.4849 -  2.3772  1314   154  0.39  60.35   0.89     0.56      54400.00|
|  9:  2.3772 -  2.2860  1316   145  0.39  60.26   0.92     0.57      51152.48|
| 10:  2.2860 -  2.2073  1328   145  0.39  60.87   0.92     0.57      45615.46|
| 11:  2.2073 -  2.1385  1308   144  0.35  63.46   0.95     0.53      46258.11|
| 12:  2.1385 -  2.0775  1308   142  0.32  66.15   0.90     0.50      42738.86|
| 13:  2.0775 -  2.0230  1228   138  0.30  67.53   0.93     0.50      38459.22|
| 14:  2.0230 -  1.9737   303    36  0.38  61.41   0.92     0.55      29989.62|
|alpha:            min =        0.50 max =            0.86 mean =         0.64|
|beta:             min =    29989.62 max =        93735.77 mean =     60978.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.25|
|phase err.(test): min =        0.00 max =           89.99 mean =        53.38|
|-----------------------------------------------------------------------------|

============================== 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 = 13.487909             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.983   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.357393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.414   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1976 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1848 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2817 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4596 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4352 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5567 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6677 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.207 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4501   r_free= 0.4462   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.259004                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4418   r_free= 0.4421   ksol= 0.35   Bsol= 80.00   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.49,3.17,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.253136                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.327463             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.899   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.095836              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.108   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4418      final r-factor (work) = 0.2779          |
| start r-factor (free) = 0.4421      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.5448 = 11.33 * 0.50 * 6.2466 + 1.00 * 0.1655                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5381 = 11.33 * 0.50 * 6.0753 + 1.00 * 0.1290                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2779      final r-factor (work) = 0.2495          |
| start r-factor (free) = 0.3105      final r-factor (free) = 0.3234          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6640 = 1.10 * 1.00 * 6.0753 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4093 = 1.10 * 1.00 * 5.8322 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.98  18.87    None  None   None       |
|    all(noH): 2823   0      0.00    109.98  18.87    None  None   None       |
|    Sol.    : 438    0      1.48    109.98  45.45    None  None   None       |
|    Mac.    : 2385   0      0.00    85.25   13.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.998: 1120   |   5:    54.992 -  65.990:   92        |
|      1:    10.998 -  21.997:  960   |   6:    65.990 -  76.989:   45        |
|      2:    21.997 -  32.995:  301   |   7:    76.989 -  87.987:   18        |
|      3:    32.995 -  43.994:  165   |   8:    87.987 -  98.985:    3        |
|      4:    43.994 -  54.992:  118   |   9:    98.985 - 109.984:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2495 r_free = 0.3234             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2490 r_free = 0.3235             target_work(ml) = 5.850         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2490   r_free= 0.3235   ksol= 0.35   Bsol= 80.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.49,3.17,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.850329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2469   r_free= 0.3228   ksol= 0.36   Bsol= 91.39   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.53,0.79,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.851805                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.176349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.237   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.125  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2469      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.3228      final r-factor (free) = 0.2539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4039 = 3.18 * 0.50 * 5.8399 + 1.00 * 0.1290                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2071 = 3.18 * 0.50 * 5.7614 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1938      final r-factor (work) = 0.1813          |
| start r-factor (free) = 0.2539      final r-factor (free) = 0.2358          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1890 = 0.38 * 1.00 * 5.7614 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1256 = 0.38 * 1.00 * 5.5992 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.09  18.23    None  None   None       |
|    all(noH): 2823   0      0.00    105.09  18.23    None  None   None       |
|    Sol.    : 438    0      4.64    105.09  44.44    None  None   None       |
|    Mac.    : 2385   0      0.00    84.87   13.42    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 -  10.509: 1087   |   5:    52.544 -  63.053:  102        |
|      1:    10.509 -  21.018: 1047   |   6:    63.053 -  73.562:   50        |
|      2:    21.018 -  31.526:  248   |   7:    73.562 -  84.070:   18        |
|      3:    31.526 -  42.035:  136   |   8:    84.070 -  94.579:    5        |
|      4:    42.035 -  52.544:  129   |   9:    94.579 - 105.088:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1813 r_free = 0.2358             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1812 r_free = 0.2356             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1812   r_free= 0.2356   ksol= 0.36   Bsol= 91.39   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.53,0.79,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.562923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1812   r_free= 0.2354   ksol= 0.34   Bsol= 80.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.00,0.05,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.562397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.929455              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.413  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.067   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1812      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2354      final r-factor (free) = 0.1900          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2582 = 2.93 * 0.50 * 5.5991 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0556 = 2.93 * 0.50 * 5.4582 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1422      final r-factor (work) = 0.1334          |
| start r-factor (free) = 0.1900      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8688 = 0.34 * 1.00 * 5.4582 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8206 = 0.34 * 1.00 * 5.3211 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    98.58   17.80    None  None   None       |
|    all(noH): 2823   0      0.29    98.58   17.80    None  None   None       |
|    Sol.    : 438    0      5.71    98.58   43.90    None  None   None       |
|    Mac.    : 2385   0      0.29    85.73   13.01    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:     0.287 -  10.116: 1067   |   5:    49.434 -  59.264:  101        |
|      1:    10.116 -  19.946: 1084   |   6:    59.264 -  69.093:   60        |
|      2:    19.946 -  29.775:  230   |   7:    69.093 -  78.923:   35        |
|      3:    29.775 -  39.605:  128   |   8:    78.923 -  88.752:    7        |
|      4:    39.605 -  49.434:  110   |   9:    88.752 -  98.582:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1334 r_free = 0.1804             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1333 r_free = 0.1805             target_work(ml) = 5.296         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1805   ksol= 0.34   Bsol= 80.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.00,0.05,-0.00,0.00,0.00); trace/3= -1.27                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.295523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1803   ksol= 0.33   Bsol= 72.03   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.53,-0.53,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.293891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.747085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.053  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.228  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3726 = 2.75 * 0.50 * 5.3233 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2809 = 2.75 * 0.50 * 5.2534 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6015 = 0.30 * 1.00 * 5.2534 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5863 = 0.30 * 1.00 * 5.2052 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    92.99   17.46    None  None   None       |
|    all(noH): 2823   0      0.57    92.99   17.46    None  None   None       |
|    Sol.    : 438    0      5.00    92.99   42.24    None  None   None       |
|    Mac.    : 2385   0      0.57    87.45   12.91    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:     0.566 -   9.808:  992   |   5:    46.778 -  56.020:   94        |
|      1:     9.808 -  19.051: 1139   |   6:    56.020 -  65.263:   69        |
|      2:    19.051 -  28.293:  247   |   7:    65.263 -  74.505:   30        |
|      3:    28.293 -  37.535:  134   |   8:    74.505 -  83.747:   19        |
|      4:    37.535 -  46.778:   94   |   9:    83.747 -  92.990:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1652             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1652             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1652   ksol= 0.33   Bsol= 72.03   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.53,-0.53,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.197047                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1651   ksol= 0.32   Bsol= 63.33   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.62,-0.61,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.196895                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.065357              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.753  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.248  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4400 = 2.07 * 0.50 * 5.2047 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4202 = 2.07 * 0.50 * 5.1906 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7710 = 0.15 * 1.00 * 5.1906 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7701 = 0.15 * 1.00 * 5.1964 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    85.08   16.82    None  None   None       |
|    all(noH): 2823   0      1.22    85.08   16.82    None  None   None       |
|    Sol.    : 438    0      6.02    84.38   39.07    None  None   None       |
|    Mac.    : 2385   0      1.22    85.08   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.216 -   9.602:  934   |   5:    43.146 -  51.532:   85        |
|      1:     9.602 -  17.988: 1163   |   6:    51.532 -  59.918:   68        |
|      2:    17.988 -  26.374:  273   |   7:    59.918 -  68.304:   29        |
|      3:    26.374 -  34.760:  130   |   8:    68.304 -  76.690:   16        |
|      4:    34.760 -  43.146:  118   |   9:    76.690 -  85.076:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1634             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1633             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1633   ksol= 0.32   Bsol= 63.33   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.62,-0.61,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195569                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7130 0.99   1435  158 0.0982 0.1314      5.3921      5.5986|
|  2:  4.7130 -  3.7593 0.99   1385  155 0.0886 0.1154      5.4716      5.6594|
|  3:  3.7593 -  3.2896 0.99   1358  147 0.1142 0.1634      5.5165      5.8355|
|  4:  3.2896 -  2.9913 0.99   1342  154 0.1309 0.1773       5.503      5.6493|
|  5:  2.9913 -  2.7783 0.99   1336  152 0.1438 0.1766      5.3781      5.5981|
|  6:  2.7783 -  2.6153 0.99   1345  146 0.1329 0.1994       5.243      5.4949|
|  7:  2.6153 -  2.4849 0.99   1324  143 0.1358 0.1616      5.2236      5.3415|
|  8:  2.4849 -  2.3772 0.98   1314  154 0.1259 0.1835       5.118      5.4088|
|  9:  2.3772 -  2.2860 0.98   1316  145 0.1279 0.1970      5.0965      5.3611|
| 10:  2.2860 -  2.2073 1.00   1328  145 0.1188 0.1685      4.9749       5.187|
| 11:  2.2073 -  2.1385 0.98   1308  144 0.1158 0.1780      4.9581      5.3116|
| 12:  2.1385 -  2.0775 0.98   1308  142 0.1232 0.1765      4.9069      5.1558|
| 13:  2.0775 -  2.0230 0.92   1228  138 0.1166 0.1611      4.8005      5.0107|
| 14:  2.0230 -  1.9737 0.23    303   36 0.1013 0.1588      4.6721      4.9335|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7130  1435   158  0.94   9.13   0.97     0.94       7310.02|
|  2:  4.7130 -  3.7593  1385   155  0.95   8.21   1.00     0.99       9589.98|
|  3:  3.7593 -  3.2896  1358   147  0.93  12.10   1.02     1.01      11133.38|
|  4:  3.2896 -  2.9913  1342   154  0.91  14.90   1.00     0.97      11234.43|
|  5:  2.9913 -  2.7783  1336   152  0.89  16.61   0.99     0.98       8890.23|
|  6:  2.7783 -  2.6153  1345   146  0.89  16.86   0.98     0.96       7373.95|
|  7:  2.6153 -  2.4849  1324   143  0.90  16.03   0.99     0.96       6752.23|
|  8:  2.4849 -  2.3772  1314   154  0.90  16.56   0.99     0.96       5799.77|
|  9:  2.3772 -  2.2860  1316   145  0.89  16.81   0.99     0.95       5627.98|
| 10:  2.2860 -  2.2073  1328   145  0.90  16.04   1.00     0.97       4506.56|
| 11:  2.2073 -  2.1385  1308   144  0.90  16.00   0.98     0.93       4355.76|
| 12:  2.1385 -  2.0775  1308   142  0.90  16.51   1.00     1.01       4096.19|
| 13:  2.0775 -  2.0230  1228   138  0.89  17.04   0.99     0.97       3474.25|
| 14:  2.0230 -  1.9737   303    36  0.93  12.95   0.98     0.95       2566.84|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2566.84 max =        11234.43 mean =      6909.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.72|
|phase err.(test): min =        0.00 max =           88.26 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1633   ksol= 0.31   Bsol= 56.33   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.63,-0.57,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195757                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1633   ksol= 0.31   Bsol= 56.33   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.63,-0.57,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195757                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.7130 0.99   1435  158 0.0978 0.1311      5.3896      5.5956|
|  2:  4.7130 -  3.7593 0.99   1385  155 0.0882 0.1153      5.4682      5.6565|
|  3:  3.7593 -  3.2896 0.99   1358  147 0.1140 0.1630      5.5148      5.8336|
|  4:  3.2896 -  2.9913 0.99   1342  154 0.1310 0.1777       5.504      5.6508|
|  5:  2.9913 -  2.7783 0.99   1336  152 0.1440 0.1769      5.3797      5.6002|
|  6:  2.7783 -  2.6153 0.99   1345  146 0.1332 0.1998      5.2445      5.4964|
|  7:  2.6153 -  2.4849 0.99   1324  143 0.1361 0.1616      5.2253      5.3432|
|  8:  2.4849 -  2.3772 0.98   1314  154 0.1261 0.1838      5.1192      5.4096|
|  9:  2.3772 -  2.2860 0.98   1316  145 0.1279 0.1969      5.0974       5.361|
| 10:  2.2860 -  2.2073 1.00   1328  145 0.1190 0.1688      4.9763      5.1888|
| 11:  2.2073 -  2.1385 0.98   1308  144 0.1158 0.1781      4.9587       5.312|
| 12:  2.1385 -  2.0775 0.98   1308  142 0.1232 0.1765      4.9074      5.1559|
| 13:  2.0775 -  2.0230 0.92   1228  138 0.1167 0.1611      4.8005      5.0107|
| 14:  2.0230 -  1.9737 0.23    303   36 0.1013 0.1591      4.6718      4.9339|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.7130  1435   158  0.94   9.10   0.97     0.94       7262.45|
|  2:  4.7130 -  3.7593  1385   155  0.95   8.17   1.00     0.99       9538.27|
|  3:  3.7593 -  3.2896  1358   147  0.93  12.06   1.02     1.01      11089.90|
|  4:  3.2896 -  2.9913  1342   154  0.91  14.89   1.00     0.97      11238.04|
|  5:  2.9913 -  2.7783  1336   152  0.89  16.63   0.99     0.98       8915.05|
|  6:  2.7783 -  2.6153  1345   146  0.89  16.89   0.98     0.96       7399.25|
|  7:  2.6153 -  2.4849  1324   143  0.90  16.06   0.99     0.96       6775.56|
|  8:  2.4849 -  2.3772  1314   154  0.90  16.58   0.98     0.95       5814.93|
|  9:  2.3772 -  2.2860  1316   145  0.89  16.83   0.99     0.95       5639.52|
| 10:  2.2860 -  2.2073  1328   145  0.90  16.07   1.00     0.97       4518.94|
| 11:  2.2073 -  2.1385  1308   144  0.90  16.03   0.98     0.93       4367.80|
| 12:  2.1385 -  2.0775  1308   142  0.90  16.53   1.00     1.00       4103.57|
| 13:  2.0775 -  2.0230  1228   138  0.89  17.04   0.99     0.97       3475.10|
| 14:  2.0230 -  1.9737   303    36  0.93  12.94   0.97     0.95       2564.95|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2564.95 max =        11238.04 mean =      6908.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.73|
|phase err.(test): min =        0.00 max =           88.42 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.083)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    85.03   16.78    None  None   None       |
|    all(noH): 2823   0      1.17    85.03   16.78    None  None   None       |
|    Sol.    : 438    0      5.98    84.34   39.03    None  None   None       |
|    Mac.    : 2385   0      1.17    85.03   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.174 -   9.560:  934   |   5:    43.103 -  51.489:   85        |
|      1:     9.560 -  17.946: 1163   |   6:    51.489 -  59.875:   68        |
|      2:    17.946 -  26.332:  273   |   7:    59.875 -  68.261:   29        |
|      3:    26.332 -  34.717:  130   |   8:    68.261 -  76.647:   16        |
|      4:    34.717 -  43.103:  118   |   9:    76.647 -  85.033:    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)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.524 - 5.067
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 307
   mapped sites are within: 0.718 - 5.067

peak=    5.794 closest distance to " NE2 GLN A  11 " =    1.236
peak=    5.317 closest distance to " CG  PRO A  54 " =    1.411
peak=    5.303 closest distance to " O   HOH Z 144 " =    1.993
peak=    5.287 closest distance to " O   HOH Z 111 " =    2.050
peak=    5.246 closest distance to " O   HOH Z 423 " =    2.071
peak=    5.226 closest distance to " CB  GLN A 223 " =    1.527
peak=    5.149 closest distance to " O   HOH Z   7 " =    1.538
peak=    5.084 closest distance to " O   HOH Z 417 " =    1.603
peak=    5.022 closest distance to " O   HOH Z 126 " =    2.031
peak=    4.778 closest distance to " O   HOH Z 298 " =    2.135
peak=    4.742 closest distance to " O   HOH Z  63 " =    1.465
peak=    4.729 closest distance to " O   HOH Z 369 " =    2.038
peak=    4.728 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.706 closest distance to " O   HOH Z 232 " =    2.207
peak=    4.636 closest distance to " CG  PRO A 213 " =    1.315
peak=    4.591 closest distance to " CG  PRO A 198 " =    1.322
peak=    4.583 closest distance to " CB  ARG A 275 " =    0.952
peak=    4.524 closest distance to " CD  ARG A 159 " =    0.781
peak=    4.517 closest distance to " ND2 ASN A 187 " =    1.540
peak=    4.512 closest distance to " CG  PRO A  90 " =    1.350
peak=    4.485 closest distance to " CB  SER A  63 " =    1.310
peak=    4.447 closest distance to " CB  PRO A  54 " =    1.036
peak=    4.444 closest distance to " O   HOH Z 287 " =    2.211
peak=    4.297 closest distance to " CZ  PHE A 218 " =    1.091
peak=    4.273 closest distance to " CB  GLN A 183 " =    1.213
peak=    4.269 closest distance to " CB  ASN A 187 " =    1.032
peak=    4.259 closest distance to " CB  ASN A 142 " =    0.868
peak=    4.254 closest distance to " CB  ARG A 190 " =    1.596
peak=    4.217 closest distance to " CB  ASP A 124 " =    0.841
peak=    4.207 closest distance to " O   HOH Z   9 " =    1.589
peak=    4.176 closest distance to " CB  ARG A  79 " =    1.308
peak=    4.166 closest distance to " CB  LEU A 228 " =    1.059
peak=    4.155 closest distance to " CA  SER A  87 " =    0.989
peak=    4.150 closest distance to " CG  TRP A 179 " =    2.170
peak=    4.136 closest distance to " CD  ARG A  66 " =    2.073
peak=    4.129 closest distance to " O   HOH Z 126 " =    1.474
peak=    4.115 closest distance to " CG  LEU A 167 " =    1.236
peak=    4.082 closest distance to " O   HOH Z  78 " =    1.670
peak=    4.070 closest distance to " O   HOH Z  21 " =    1.772
peak=    4.066 closest distance to " CE  LYS A  76 " =    0.944
peak=    4.056 closest distance to " O   HOH Z 406 " =    1.787
peak=    4.053 closest distance to " O   HOH Z 380 " =    1.804
peak=    4.052 closest distance to " CD2 TRP A 179 " =    1.215
peak=    4.038 closest distance to " NH1AARG A 145 " =    1.281
peak=    4.037 closest distance to " CG2 VAL A 257 " =    0.861
peak=    4.012 closest distance to " O   HOH Z  88 " =    4.077
peak=    3.999 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.983 closest distance to " CB  SER A 210 " =    0.791
peak=    3.979 closest distance to " CB  SER A 212 " =    1.257
peak=    3.978 closest distance to " CA  ARG A 195 " =    1.310
peak=    3.973 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.948 closest distance to " O   TYR A 116 " =    1.327
peak=    3.932 closest distance to " O   HOH Z 222 " =    1.265
peak=    3.927 closest distance to " O   HOH Z 437 " =    1.576
peak=    3.925 closest distance to " O   HOH Z 427 " =    2.791
peak=    3.914 closest distance to " ND1 HIS A  86 " =    1.676
peak=    3.908 closest distance to " CG  PRO A 243 " =    1.103
peak=    3.900 closest distance to " O   HOH Z 425 " =    1.425
peak=    3.899 closest distance to " CB  SER A 216 " =    0.922
peak=    3.883 closest distance to " O   HOH Z 236 " =    2.050
peak=    3.882 closest distance to " O   HOH Z 316 " =    3.098
peak=    3.864 closest distance to " CA  THR A 264 " =    0.877
peak=    3.849 closest distance to " O   HOH Z 362 " =    2.261
peak=    3.840 closest distance to " CD1 LEU A 300 " =    1.144
peak=    3.836 closest distance to " CB  TYR A 169 " =    0.718
peak=    3.823 closest distance to " O   HOH Z 180 " =    2.060
peak=    3.817 closest distance to " O   HOH Z   1 " =    1.814
peak=    3.804 closest distance to " O   ASN A 209 " =    1.348
peak=    3.792 closest distance to " CB  ASN A  39 " =    0.938
peak=    3.791 closest distance to " O   PRO A 198 " =    1.588
peak=    3.787 closest distance to " NH2AARG A 190 " =    1.945
peak=    3.785 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    3.771 closest distance to " O   HOH Z 116 " =    3.196
peak=    3.762 closest distance to " CD  ARG A 269 " =    0.920
peak=    3.754 closest distance to " CB  ALA A 114 " =    0.981
peak=    3.747 closest distance to " CG2 THR A 221 " =    0.921
peak=    3.744 closest distance to " CB  VAL A 265 " =    1.327
peak=    3.743 closest distance to " O   HOH Z 214 " =    2.159
peak=    3.735 closest distance to " N   PHE A 130 " =    1.209
peak=    3.725 closest distance to " O   HOH Z 394 " =    4.062
peak=    3.714 closest distance to " CB  GLU A 128 " =    0.869
peak=    3.713 closest distance to " O   HOH Z   2 " =    1.618
peak=    3.701 closest distance to " NE2 HIS A 207 " =    1.134
peak=    3.691 closest distance to " CG1 ILE A 151 " =    1.174
peak=    3.691 closest distance to " CB  SER A   3 " =    1.495
peak=    3.689 closest distance to " O   HOH Z 419 " =    2.014
peak=    3.684 closest distance to " O   HOH Z 272 " =    1.774
peak=    3.680 closest distance to " O   HOH Z   1 " =    1.822
peak=    3.669 closest distance to " CZ  PHE A  38 " =    1.225
peak=    3.668 closest distance to " O   HOH Z 240 " =    2.172
peak=    3.666 closest distance to " CA  ARG A 102 " =    1.152
peak=    3.664 closest distance to " O   HOH Z 133 " =    2.607
peak=    3.658 closest distance to " CB  GLU A  46 " =    0.944
peak=    3.657 closest distance to " CA  ALA A 158 " =    1.136
peak=    3.656 closest distance to " O   HOH Z  61 " =    1.658
peak=    3.651 closest distance to " CB  GLU A 152 " =    1.185
peak=    3.648 closest distance to " O   HOH Z  40 " =    1.959
peak=    3.645 closest distance to " O   HOH Z 368 " =    3.640
peak=    3.639 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.639 closest distance to " O   HOH Z  78 " =    2.294
peak=    3.635 closest distance to " O   HOH Z 145 " =    1.642
peak=    3.631 closest distance to " O   HOH Z 188 " =    2.760
peak=    3.627 closest distance to " O   HOH Z 258 " =    2.154
peak=    3.622 closest distance to " CB  MET A  40 " =    0.796
peak=    3.614 closest distance to " OG  SER A  62 " =    2.998
peak=    3.607 closest distance to " CA  ALA A 233 " =    1.362
peak=    3.602 closest distance to " CB  ALA A 160 " =    1.382
peak=    3.602 closest distance to " O   ASN A  74 " =    1.432
peak=    3.597 closest distance to " CA  ALA A  51 " =    0.927
peak=    3.584 closest distance to " O   HOH Z 183 " =    1.526
peak=    3.576 closest distance to " O   HOH Z 238 " =    3.740
peak=    3.575 closest distance to " CD  LYS A 166 " =    1.253
peak=    3.571 closest distance to " O   HOH Z 145 " =    1.951
peak=    3.564 closest distance to " O   HOH Z 250 " =    1.569
peak=    3.563 closest distance to " CA  ALA A 154 " =    1.014
peak=    3.559 closest distance to " CA  PRO A  54 " =    1.374
peak=    3.554 closest distance to " O   HOH Z 286 " =    2.152
peak=    3.553 closest distance to " CB  ASN A 110 " =    0.980
peak=    3.550 closest distance to " CG2AVAL A  72 " =    1.585
peak=    3.545 closest distance to " O   HOH Z 148 " =    3.468
peak=    3.543 closest distance to " CA  TYR A 116 " =    1.388
peak=    3.535 closest distance to " O   HOH Z 132 " =    2.562
peak=    3.533 closest distance to " O   HOH Z 332 " =    1.574
peak=    3.504 closest distance to " CG2 ILE A 151 " =    0.815
peak=    3.502 closest distance to " CB  PRO A  90 " =    1.084
peak=    3.499 closest distance to " O   THR A 220 " =    1.378
peak=    3.480 closest distance to " NZ  LYS A 117 " =    3.119
peak=    3.477 closest distance to " N   ASN A 127 " =    1.286
peak=    3.473 closest distance to " O   HOH Z 158 " =    2.868
peak=    3.467 closest distance to " O   HOH Z  58 " =    1.826
peak=    3.463 closest distance to " OH  TYR A 186 " =    1.089
peak=    3.462 closest distance to " O   HOH Z  69 " =    2.256
peak=    3.462 closest distance to " O   HOH Z  44 " =    2.748
peak=    3.461 closest distance to " CA  VAL A 125 " =    1.173
peak=    3.460 closest distance to " O   HOH Z 422 " =    2.755
peak=    3.460 closest distance to " O   HOH Z 365 " =    2.784
peak=    3.457 closest distance to " O   HOH Z 273 " =    2.891
peak=    3.456 closest distance to " O   HOH Z 184 " =    1.559
peak=    3.453 closest distance to " N   VAL A 296 " =    1.698
peak=    3.448 closest distance to " O   HOH Z 411 " =    3.626
peak=    3.448 closest distance to " CB  GLU A 277 " =    3.684
peak=    3.447 closest distance to " OG  SER A 135 " =    1.251
peak=    3.442 closest distance to " O   HOH Z 128 " =    1.775
peak=    3.440 closest distance to " CD  LYS A  76 " =    2.113
peak=    3.437 closest distance to " CB  ARG A 138 " =    0.989
peak=    3.425 closest distance to " O   HOH Z 359 " =    4.165
peak=    3.424 closest distance to " O   HOH Z 291 " =    1.554
peak=    3.421 closest distance to " O   HOH Z 345 " =    1.869
peak=    3.420 closest distance to " O   HOH Z 389 " =    1.844
peak=    3.419 closest distance to " N   ARG A 156 " =    1.336
peak=    3.416 closest distance to " O   HOH Z 218 " =    1.645
peak=    3.415 closest distance to " O   HOH Z 434 " =    1.472
peak=    3.414 closest distance to " CB  ILE A 120 " =    1.263
peak=    3.412 closest distance to " O   HOH Z 285 " =    2.114
peak=    3.408 closest distance to " O   HOH Z 201 " =    1.609
peak=    3.408 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.407 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.404 closest distance to " CB  ALA A   1 " =    4.675
peak=    3.402 closest distance to " CA  ILE A 106 " =    0.789
peak=    3.397 closest distance to " O   HOH Z 130 " =    3.611
peak=    3.397 closest distance to " O   HOH Z 346 " =    1.630
peak=    3.395 closest distance to " CD2 TYR A 186 " =    1.112
peak=    3.393 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.393 closest distance to " O   HOH Z 294 " =    1.578
peak=    3.393 closest distance to " O   HOH Z 371 " =    1.867
peak=    3.385 closest distance to " O   HOH Z 193 " =    2.179
peak=    3.384 closest distance to " CA  SER A  95 " =    0.940
peak=    3.384 closest distance to " O   HOH Z 248 " =    1.674
peak=    3.378 closest distance to " O   HOH Z 391 " =    2.946
peak=    3.377 closest distance to " CB  THR A 157 " =    1.175
peak=    3.358 closest distance to " N   TYR A  15 " =    0.810
peak=    3.358 closest distance to " OD1 ASN A  69 " =    2.573
peak=    3.345 closest distance to " CG  PHE A 204 " =    1.056
peak=    3.343 closest distance to " CA  ASN A 127 " =    1.101
peak=    3.343 closest distance to " CG AARG A 275 " =    1.326
peak=    3.342 closest distance to " CB  LEU A  83 " =    0.750
peak=    3.338 closest distance to " CA  ARG A 159 " =    1.295
peak=    3.334 closest distance to " O   HOH Z 305 " =    3.713
peak=    3.332 closest distance to " CA  GLY A 136 " =    0.892
peak=    3.332 closest distance to " CB  VAL A 202 " =    1.583
peak=    3.331 closest distance to " CA  ILE A 234 " =    0.979
peak=    3.331 closest distance to " O   HOH Z 368 " =    4.354
peak=    3.330 closest distance to " CZ3 TRP A 123 " =    1.415
peak=    3.329 closest distance to " CA  ASP A 162 " =    1.001
peak=    3.326 closest distance to " O   HOH Z 219 " =    4.565
peak=    3.316 closest distance to " CD BLYS A 290 " =    1.024
peak=    3.315 closest distance to " N   CYS A 260 " =    0.818
peak=    3.314 closest distance to " O   HOH Z 213 " =    2.199
peak=    3.314 closest distance to " CB  PRO A 243 " =    1.249
peak=    3.313 closest distance to " O   HOH Z 128 " =    2.253
peak=    3.312 closest distance to " CG  GLU A  37 " =    0.900
peak=    3.312 closest distance to " O   HOH Z 302 " =    1.856
peak=    3.309 closest distance to " CB  TRP A 150 " =    1.222
peak=    3.308 closest distance to " O   HOH Z 116 " =    1.768
peak=    3.306 closest distance to " CB  LYS A 117 " =    1.224
peak=    3.306 closest distance to " NE AARG A 275 " =    1.408
peak=    3.305 closest distance to " O   HOH Z 371 " =    2.803
peak=    3.301 closest distance to " O   HOH Z 234 " =    3.778
peak=    3.292 closest distance to " CA  CYS A 201 " =    1.561
peak=    3.289 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.287 closest distance to " O   HOH Z 153 " =    1.706
peak=    3.287 closest distance to " O   HOH Z  49 " =    1.006
peak=    3.283 closest distance to " O   HOH Z 147 " =    1.885
peak=    3.283 closest distance to " CB  TYR A  30 " =    1.257
peak=    3.281 closest distance to " O   HOH Z 274 " =    2.166
peak=    3.274 closest distance to " CA  GLU A  46 " =    0.936
peak=    3.270 closest distance to " O   HOH Z 153 " =    3.720
peak=    3.268 closest distance to " N   ALA A   1 " =    1.988
peak=    3.265 closest distance to " O   HOH Z  85 " =    2.223
peak=    3.260 closest distance to " O   HOH Z 403 " =    1.493
peak=    3.258 closest distance to " CG  ARG A 159 " =    0.854
peak=    3.256 closest distance to " O   HOH Z 394 " =    1.661
peak=    3.255 closest distance to " CA  GLN A  94 " =    0.774
peak=    3.253 closest distance to " O   HOH Z 130 " =    2.151
peak=    3.247 closest distance to " O   HOH Z 132 " =    4.045
peak=    3.247 closest distance to " CA  ALA A 299 " =    0.888
peak=    3.244 closest distance to " O   HOH Z 380 " =    5.067
peak=    3.239 closest distance to " CA  MET A 105 " =    0.861
peak=    3.239 closest distance to " CE3 TRP A  85 " =    0.975
peak=    3.235 closest distance to " O   HOH Z 405 " =    1.533
peak=    3.232 closest distance to " O   HOH Z 343 " =    3.403
peak=    3.230 closest distance to " CG2 ILE A 120 " =    1.330
peak=    3.228 closest distance to " O   SER A  87 " =    2.379
peak=    3.228 closest distance to " CG  ARG A 138 " =    1.171
peak=    3.227 closest distance to " O   THR A 294 " =    1.016
peak=    3.227 closest distance to " O  BHOH Z  74 " =    1.282
peak=    3.226 closest distance to " O   HOH Z  68 " =    1.981
peak=    3.222 closest distance to " O   HOH Z 426 " =    2.069
peak=    3.219 closest distance to " CG  LYS A 119 " =    1.129
peak=    3.217 closest distance to " N   SER A 271 " =    0.991
peak=    3.216 closest distance to " CG  GLN A 144 " =    0.857
peak=    3.214 closest distance to " CB  ALA A 248 " =    0.996
peak=    3.214 closest distance to " CA  ARG A 156 " =    1.122
peak=    3.212 closest distance to " O   HOH Z 188 " =    2.239
peak=    3.211 closest distance to " CB  TYR A 116 " =    0.994
peak=    3.210 closest distance to " O   HOH Z 402 " =    1.474
peak=    3.207 closest distance to " O   HOH Z 193 " =    1.666
peak=    3.207 closest distance to " CG  GLN A 278 " =    1.364
peak=    3.206 closest distance to " CA  LEU A 282 " =    1.103
peak=    3.205 closest distance to " O   HOH Z 172 " =    2.741
peak=    3.204 closest distance to " O   THR A 251 " =    1.176
peak=    3.204 closest distance to " CG  MET A 113 " =    1.436
peak=    3.203 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.202 closest distance to " CB  SER A 276 " =    1.171
peak=    3.201 closest distance to " O   HOH Z 327 " =    1.849
peak=    3.200 closest distance to " CB  THR A  31 " =    1.597
peak=    3.199 closest distance to " CB  ASP A 140 " =    0.878
peak=    3.197 closest distance to " CB  THR A  82 " =    1.372
peak=    3.194 closest distance to " O   HOH Z 415 " =    3.906
peak=    3.194 closest distance to " CD2 LEU A   5 " =    1.421
peak=    3.192 closest distance to " CA  THR A 221 " =    0.933
peak=    3.190 closest distance to " CG2 ILE A  20 " =    1.363
peak=    3.187 closest distance to " CB  GLN A  89 " =    1.334
peak=    3.184 closest distance to " O   PHE A 192 " =    1.315
peak=    3.184 closest distance to " CG BARG A 102 " =    1.901
peak=    3.183 closest distance to " CB  SER A 245 " =    3.255
peak=    3.180 closest distance to " CZ  PHE A 192 " =    0.878
peak=    3.178 closest distance to " O   ARG A 145 " =    1.667
peak=    3.177 closest distance to " CB  SER A  62 " =    1.069
peak=    3.177 closest distance to " CD2 LEU A 297 " =    0.933
peak=    3.174 closest distance to " CB  ALA A 291 " =    0.835
peak=    3.173 closest distance to " O   HOH Z  53 " =    2.443
peak=    3.172 closest distance to " O   HOH Z 260 " =    2.395
peak=    3.170 closest distance to " O   HOH Z 409 " =    3.304
peak=    3.164 closest distance to " CB  ALA A 114 " =    1.119
peak=    3.160 closest distance to " N   SER A 135 " =    1.343
peak=    3.159 closest distance to " CA  ILE A 263 " =    1.036
peak=    3.158 closest distance to " O   HOH Z  88 " =    3.348
peak=    3.158 closest distance to " CG BARG A 275 " =    1.448
peak=    3.155 closest distance to " CA  ALA A 160 " =    1.133
peak=    3.154 closest distance to " O   HOH Z 213 " =    2.051
peak=    3.153 closest distance to " CG  GLU A 277 " =    1.934
peak=    3.152 closest distance to " O  BHOH Z 338 " =    2.370
peak=    3.150 closest distance to " NE  ARG A  79 " =    1.166
peak=    3.150 closest distance to " O   HOH Z 368 " =    1.853
peak=    3.149 closest distance to " O   HOH Z 352 " =    1.638
peak=    3.149 closest distance to " CB  ALA A  10 " =    0.814
peak=    3.143 closest distance to " CB  ALA A  43 " =    0.827
peak=    3.137 closest distance to " O   HOH Z 193 " =    1.905
peak=    3.137 closest distance to " O   HOH Z 244 " =    1.675
peak=    3.134 closest distance to " O   HOH Z 409 " =    2.330
peak=    3.133 closest distance to " O   HOH Z 282 " =    2.006
peak=    3.129 closest distance to " O   HOH Z  57 " =    1.199
peak=    3.128 closest distance to " O   HOH Z 124 " =    1.983
peak=    3.127 closest distance to " CB  GLU A  37 " =    0.880
peak=    3.125 closest distance to " CD1 ILE A 263 " =    1.272
peak=    3.123 closest distance to " CA  ASN A 217 " =    1.201
peak=    3.122 closest distance to " CB  LEU A 237 " =    0.786
peak=    3.120 closest distance to " O   MET A 105 " =    1.625
peak=    3.119 closest distance to " OG BSER A  99 " =    2.308
peak=    3.115 closest distance to " OE2 GLU A  53 " =    2.093
peak=    3.111 closest distance to " O   HOH Z 357 " =    2.026
peak=    3.110 closest distance to " O   HOH Z 233 " =    1.626
peak=    3.103 closest distance to " NH2BARG A 190 " =    1.427
peak=    3.098 closest distance to " CD1 ILE A 106 " =    0.880
peak=    3.096 closest distance to " O   HOH Z 299 " =    2.539
peak=    3.084 closest distance to " O   HOH Z 234 " =    2.306
peak=    3.084 closest distance to " CA  ALA A 100 " =    1.103
peak=    3.084 closest distance to " O   HOH Z 128 " =    1.987
peak=    3.083 closest distance to " CB  LEU A 255 " =    1.376
peak=    3.081 closest distance to " C   GLU A 277 " =    1.418
peak=    3.070 closest distance to " CB  HIS A 108 " =    0.731
peak=    3.022 closest distance to " CA  ALA A 129 " =    1.171

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.418 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 214
   mapped sites are within: 0.753 - 5.980

peak=   -4.736 closest distance to " O   HOH Z 231 " =    0.794
peak=   -4.734 closest distance to " O   HOH Z 290 " =    0.922
peak=   -4.498 closest distance to " O   PRO A 198 " =    1.241
peak=   -4.469 closest distance to " CB  PRO A 243 " =    2.592
peak=   -4.288 closest distance to " CD  ARG A  14 " =    3.412
peak=   -4.260 closest distance to " O   HOH Z 211 " =    0.800
peak=   -4.219 closest distance to " O   HOH Z 377 " =    1.817
peak=   -4.185 closest distance to " O   HOH Z 351 " =    1.477
peak=   -4.171 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -4.147 closest distance to " CB  ALA A  43 " =    2.569
peak=   -4.091 closest distance to " CD  ARG A 156 " =    2.138
peak=   -4.056 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -4.004 closest distance to " CG2 ILE A  49 " =    2.753
peak=   -3.998 closest distance to " O   HOH Z  38 " =    1.371
peak=   -3.961 closest distance to " O   HOH Z  60 " =    1.208
peak=   -3.930 closest distance to " O   HOH Z  52 " =    1.320
peak=   -3.928 closest distance to " O   HOH Z 231 " =    2.060
peak=   -3.892 closest distance to " O   HOH Z  73 " =    2.048
peak=   -3.866 closest distance to " O   HOH Z 389 " =    2.159
peak=   -3.861 closest distance to " CA  GLY A  98 " =    1.866
peak=   -3.860 closest distance to " CE BMET A  47 " =    1.527
peak=   -3.853 closest distance to " CD1 LEU A 255 " =    2.990
peak=   -3.831 closest distance to " CD2 TYR A 293 " =    1.904
peak=   -3.828 closest distance to " ND2 ASN A 249 " =    2.180
peak=   -3.817 closest distance to " CG  MET A 105 " =    1.024
peak=   -3.814 closest distance to " OG BSER A 134 " =    1.456
peak=   -3.792 closest distance to " O   VAL A  67 " =    2.696
peak=   -3.779 closest distance to " O   HOH Z 394 " =    1.528
peak=   -3.775 closest distance to " CB  ALA A 158 " =    1.683
peak=   -3.774 closest distance to " O   PRO A 163 " =    1.937
peak=   -3.762 closest distance to " N   ALA A  43 " =    2.528
peak=   -3.755 closest distance to " CD  GLN A  88 " =    0.864
peak=   -3.747 closest distance to " O   TYR A 247 " =    2.884
peak=   -3.729 closest distance to " O   HOH Z 407 " =    3.245
peak=   -3.727 closest distance to " O   ALA A  10 " =    1.705
peak=   -3.702 closest distance to " O   HOH Z 185 " =    2.255
peak=   -3.701 closest distance to " N   THR A 157 " =    1.620
peak=   -3.700 closest distance to " CA  GLY A 133 " =    2.072
peak=   -3.683 closest distance to " CE2 TYR A  30 " =    2.706
peak=   -3.675 closest distance to " O   HOH Z 140 " =    1.258
peak=   -3.672 closest distance to " O   SER A  22 " =    2.662
peak=   -3.666 closest distance to " NH2AARG A 275 " =    5.511
peak=   -3.649 closest distance to " CA  GLY A 241 " =    3.122
peak=   -3.648 closest distance to " O   HOH Z 377 " =    0.867
peak=   -3.628 closest distance to " O   HOH Z 298 " =    2.477
peak=   -3.624 closest distance to " O   HOH Z  65 " =    1.166
peak=   -3.618 closest distance to " CE2 PHE A  61 " =    2.761
peak=   -3.616 closest distance to " O   HOH Z 357 " =    2.027
peak=   -3.612 closest distance to " O   HOH Z 191 " =    5.532
peak=   -3.611 closest distance to " CA  GLY A 241 " =    2.305
peak=   -3.610 closest distance to " O   GLY A 203 " =    2.555
peak=   -3.609 closest distance to " CD  GLN A  58 " =    0.787
peak=   -3.605 closest distance to " O   HOH Z 411 " =    5.314
peak=   -3.603 closest distance to " CB  ALA A 291 " =    2.284
peak=   -3.596 closest distance to " CB  ALA A   9 " =    2.463
peak=   -3.593 closest distance to " NZ  LYS A 166 " =    1.081
peak=   -3.589 closest distance to " CG1 VAL A 112 " =    3.100
peak=   -3.577 closest distance to " CB  TRP A  85 " =    2.496
peak=   -3.566 closest distance to " OG  SER A  97 " =    2.238
peak=   -3.562 closest distance to " O   ILE A  49 " =    1.702
peak=   -3.559 closest distance to " O   HOH Z 111 " =    1.589
peak=   -3.558 closest distance to " CD2 LEU A 143 " =    2.596
peak=   -3.544 closest distance to " OE1 GLN A  88 " =    1.134
peak=   -3.537 closest distance to " O   HOH Z  22 " =    2.364
peak=   -3.528 closest distance to " OD1 ASP A 191 " =    1.770
peak=   -3.527 closest distance to " CD  ARG A  79 " =    1.125
peak=   -3.522 closest distance to " CD2 PHE A  61 " =    2.076
peak=   -3.521 closest distance to " O   HOH Z 131 " =    4.041
peak=   -3.521 closest distance to " O   HOH Z 216 " =    1.199
peak=   -3.515 closest distance to " O   HOH Z 275 " =    1.730
peak=   -3.511 closest distance to " O   HOH Z 368 " =    1.572
peak=   -3.505 closest distance to " CG2 ILE A 263 " =    2.408
peak=   -3.503 closest distance to " CD1 LEU A 101 " =    2.345
peak=   -3.498 closest distance to " ND2 ASN A  45 " =    2.178
peak=   -3.497 closest distance to " CG  GLN A 223 " =    2.307
peak=   -3.492 closest distance to " CB  PRO A  54 " =    2.523
peak=   -3.488 closest distance to " O   HOH Z 359 " =    3.231
peak=   -3.488 closest distance to " O   HOH Z   9 " =    1.879
peak=   -3.485 closest distance to " O   HOH Z 152 " =    5.029
peak=   -3.484 closest distance to " O   VAL A 189 " =    2.566
peak=   -3.471 closest distance to " O   HOH Z 114 " =    0.879
peak=   -3.460 closest distance to " O   HOH Z  53 " =    1.721
peak=   -3.458 closest distance to " O   HOH Z 118 " =    1.270
peak=   -3.457 closest distance to " O   HOH Z 281 " =    2.712
peak=   -3.451 closest distance to " CG  PHE A 283 " =    2.762
peak=   -3.448 closest distance to " O   HOH Z 295 " =    1.719
peak=   -3.447 closest distance to " CG2 THR A 178 " =    2.301
peak=   -3.446 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -3.439 closest distance to " O   HOH Z 100 " =    1.115
peak=   -3.438 closest distance to " ND2 ASN A  60 " =    4.071
peak=   -3.432 closest distance to " CE1 TYR A 172 " =    1.930
peak=   -3.431 closest distance to " CG  LEU A 282 " =    2.469
peak=   -3.430 closest distance to " O   PRO A 243 " =    2.427
peak=   -3.419 closest distance to " ND2 ASN A  45 " =    1.352
peak=   -3.417 closest distance to " OD1 ASP A 171 " =    1.675
peak=   -3.416 closest distance to " OG BSER A 134 " =    1.790
peak=   -3.410 closest distance to " O   HOH Z 247 " =    0.888
peak=   -3.409 closest distance to " O   HOH Z 384 " =    2.906
peak=   -3.408 closest distance to " O   HOH Z 313 " =    1.685
peak=   -3.398 closest distance to " CD  GLU A 277 " =    1.194
peak=   -3.396 closest distance to " ND2 ASN A 187 " =    1.358
peak=   -3.393 closest distance to " CA  ASP A  27 " =    2.486
peak=   -3.392 closest distance to " C   HIS A 108 " =    1.179
peak=   -3.389 closest distance to " OD1 ASN A 148 " =    1.417
peak=   -3.380 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.375 closest distance to " N   SER A 212 " =    1.973
peak=   -3.367 closest distance to " NE2 GLN A 278 " =    1.757
peak=   -3.363 closest distance to " O   HOH Z 108 " =    1.311
peak=   -3.358 closest distance to " CG2 ILE A 151 " =    2.605
peak=   -3.354 closest distance to " O   HOH Z 174 " =    2.661
peak=   -3.354 closest distance to " ND2BASN A 224 " =    1.692
peak=   -3.352 closest distance to " O   GLY A  17 " =    1.175
peak=   -3.347 closest distance to " O   HOH Z 412 " =    4.499
peak=   -3.346 closest distance to " CE  LYS A  76 " =    2.706
peak=   -3.339 closest distance to " CG  LEU A 167 " =    0.886
peak=   -3.336 closest distance to " CD  PRO A 213 " =    2.022
peak=   -3.332 closest distance to " O   HOH Z 426 " =    1.591
peak=   -3.327 closest distance to " O   HOH Z 147 " =    1.605
peak=   -3.327 closest distance to " SG BCYS A 201 " =    2.050
peak=   -3.325 closest distance to " O   PRO A 198 " =    1.382
peak=   -3.317 closest distance to " O   HOH Z 241 " =    1.241
peak=   -3.316 closest distance to " CB  ASP A 286 " =    2.086
peak=   -3.312 closest distance to " CE1 PHE A  59 " =    2.097
peak=   -3.307 closest distance to " O   PHE A 218 " =    1.435
peak=   -3.305 closest distance to " C   ASN A 285 " =    2.403
peak=   -3.304 closest distance to " O   HOH Z 337 " =    1.288
peak=   -3.298 closest distance to " CE  MET A 105 " =    2.515
peak=   -3.298 closest distance to " O   GLN A 240 " =    2.158
peak=   -3.296 closest distance to " OE1 GLN A  77 " =    0.907
peak=   -3.294 closest distance to " O   HOH Z 139 " =    0.956
peak=   -3.292 closest distance to " CB  PHE A 192 " =    1.883
peak=   -3.291 closest distance to " O   HOH Z 372 " =    2.500
peak=   -3.289 closest distance to " CG2 ILE A  20 " =    3.012
peak=   -3.286 closest distance to " O   HOH Z 282 " =    0.801
peak=   -3.284 closest distance to " O   HOH Z   1 " =    1.372
peak=   -3.283 closest distance to " O   HOH Z 177 " =    1.932
peak=   -3.283 closest distance to " CG  LEU A  83 " =    1.968
peak=   -3.283 closest distance to " CA  GLY A 203 " =    2.466
peak=   -3.280 closest distance to " CE2 PHE A 218 " =    2.493
peak=   -3.280 closest distance to " CD2 TYR A 293 " =    2.125
peak=   -3.277 closest distance to " O   HOH Z  60 " =    1.133
peak=   -3.277 closest distance to " NH2 ARG A  79 " =    2.075
peak=   -3.275 closest distance to " CB  GLN A  11 " =    1.712
peak=   -3.273 closest distance to " C   MET A 188 " =    1.601
peak=   -3.269 closest distance to " O   HOH Z 252 " =    3.911
peak=   -3.268 closest distance to " O   ALA A  34 " =    2.542
peak=   -3.260 closest distance to " CZ  PHE A  16 " =    2.292
peak=   -3.259 closest distance to " O   HOH Z  86 " =    2.739
peak=   -3.258 closest distance to " O   VAL A 125 " =    2.334
peak=   -3.256 closest distance to " CD2 HIS A 207 " =    2.315
peak=   -3.253 closest distance to " CZ  PHE A 130 " =    2.560
peak=   -3.251 closest distance to " O   HOH Z 191 " =    3.253
peak=   -3.250 closest distance to " C   LEU A 143 " =    1.348
peak=   -3.248 closest distance to " O   HOH Z 219 " =    4.407
peak=   -3.248 closest distance to " N   ASP A 270 " =    1.397
peak=   -3.241 closest distance to " OH  TYR A 247 " =    2.182
peak=   -3.236 closest distance to " O   ALA A 180 " =    1.089
peak=   -3.232 closest distance to " C   LEU A 222 " =    0.753
peak=   -3.232 closest distance to " O   HOH Z  63 " =    2.131
peak=   -3.231 closest distance to " O   HOH Z  51 " =    1.012
peak=   -3.231 closest distance to " OXT GLY A 302 " =    3.319
peak=   -3.231 closest distance to " O   HOH Z 145 " =    1.310
peak=   -3.229 closest distance to " CB  CYS A 254 " =    2.173
peak=   -3.229 closest distance to " O   ALA A   7 " =    1.547
peak=   -3.222 closest distance to " CB  PRO A 163 " =    2.579
peak=   -3.219 closest distance to " CD  LYS A 289 " =    2.329
peak=   -3.211 closest distance to " CE3 TRP A 274 " =    2.469
peak=   -3.208 closest distance to " CZ BARG A 275 " =    1.877
peak=   -3.203 closest distance to " NE2 GLN A 194 " =    1.858
peak=   -3.202 closest distance to " CB  ASP A 132 " =    2.344
peak=   -3.197 closest distance to " N   LYS A 166 " =    1.844
peak=   -3.196 closest distance to " CZ  PHE A 155 " =    1.149
peak=   -3.196 closest distance to " CG  ARG A 269 " =    2.564
peak=   -3.195 closest distance to " O   ARG A 145 " =    1.495
peak=   -3.193 closest distance to " O   HOH Z 232 " =    1.774
peak=   -3.190 closest distance to " CB  ASN A  39 " =    2.237
peak=   -3.188 closest distance to " CG  GLN A 240 " =    2.427
peak=   -3.187 closest distance to " CA  ASP A 298 " =    1.134
peak=   -3.187 closest distance to " O   SER A 135 " =    1.436
peak=   -3.180 closest distance to " O   HOH Z 171 " =    1.462
peak=   -3.179 closest distance to " CB  PHE A 130 " =    1.238
peak=   -3.174 closest distance to " NH2 ARG A  79 " =    1.585
peak=   -3.174 closest distance to " CB  ASP A 200 " =    2.636
peak=   -3.170 closest distance to " O   HOH Z 118 " =    1.715
peak=   -3.169 closest distance to " C   ALA A 114 " =    2.313
peak=   -3.168 closest distance to " O   GLY A 211 " =    1.193
peak=   -3.158 closest distance to " O   HOH Z 409 " =    5.980
peak=   -3.158 closest distance to " CB  ALA A 129 " =    2.415
peak=   -3.157 closest distance to " CG2 THR A  18 " =    2.779
peak=   -3.154 closest distance to " CG1 VAL A 197 " =    2.313
peak=   -3.149 closest distance to " NE2 GLN A  58 " =    3.097
peak=   -3.144 closest distance to " CD1 TRP A 179 " =    0.887
peak=   -3.142 closest distance to " O   ASP A 272 " =    2.406
peak=   -3.142 closest distance to " O   LYS A 181 " =    2.888
peak=   -3.139 closest distance to " CH2 TRP A 177 " =    2.379
peak=   -3.138 closest distance to " CD2 PHE A 192 " =    2.077
peak=   -3.130 closest distance to " O   HOH Z 406 " =    2.344
peak=   -3.130 closest distance to " CB  ALA A  10 " =    2.249
peak=   -3.123 closest distance to " O   HOH Z 184 " =    1.850
peak=   -3.120 closest distance to " O   GLU A 152 " =    1.388
peak=   -3.113 closest distance to " CD1 LEU A  83 " =    2.901
peak=   -3.113 closest distance to " N   ALA A 226 " =    2.145
peak=   -3.100 closest distance to " O   HOH Z 134 " =    3.712
peak=   -3.098 closest distance to " O   HOH Z 429 " =    1.949
peak=   -3.094 closest distance to " CA  SER A  62 " =    2.626
peak=   -3.093 closest distance to " O   HOH Z   9 " =    1.149
peak=   -3.085 closest distance to " O   HOH Z  65 " =    0.781
peak=   -3.084 closest distance to " CD1 TRP A  70 " =    1.064
peak=   -3.084 closest distance to " O   ALA A  84 " =    1.792
peak=   -3.071 closest distance to " CB  ALA A 248 " =    2.439
peak=   -3.069 closest distance to " CD  GLU A 152 " =    0.762

================= 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    :  0.4501 0.4462   6.259004e+00   6.240274e+00
   1_bss:  0.4418 0.4421   6.253136e+00   6.233375e+00
   1_xyz:  0.2779 0.3105   5.901664e+00   5.981180e+00
   1_adp:  0.2495 0.3234   5.850395e+00   6.015216e+00
   1_occ:  0.2490 0.3235   5.850329e+00   6.015861e+00
   2_bss:  0.2469 0.3228   5.851805e+00   6.016796e+00
   2_xyz:  0.1938 0.2539   5.624809e+00   5.817884e+00
   2_adp:  0.1813 0.2358   5.563429e+00   5.751305e+00
   2_occ:  0.1812 0.2356   5.562923e+00   5.751022e+00
   3_bss:  0.1812 0.2354   5.562397e+00   5.750190e+00
   3_xyz:  0.1422 0.1900   5.348946e+00   5.562981e+00
   3_adp:  0.1334 0.1804   5.295303e+00   5.514018e+00
   3_occ:  0.1333 0.1805   5.295523e+00   5.514956e+00
   4_bss:  0.1335 0.1803   5.293891e+00   5.512052e+00
   4_xyz:  0.1212 0.1680   5.211353e+00   5.445244e+00
   4_adp:  0.1193 0.1652   5.197177e+00   5.430896e+00
   4_occ:  0.1192 0.1652   5.197047e+00   5.430978e+00
   5_bss:  0.1191 0.1651   5.196895e+00   5.430805e+00
   5_xyz:  0.1172 0.1640   5.190067e+00   5.427725e+00
   5_adp:  0.1184 0.1634   5.195856e+00   5.429136e+00
   5_occ:  0.1183 0.1633   5.195569e+00   5.428853e+00
   5_bss:  0.1183 0.1633   5.195757e+00   5.428977e+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:  0.348  80.000  -0.854   0.488   3.175   0.000   0.000   0.000
   1_xyz:  0.348  80.000  -0.854   0.488   3.175   0.000   0.000   0.000
   1_adp:  0.348  80.000  -0.854   0.488   3.175   0.000   0.000   0.000
   1_occ:  0.348  80.000  -0.854   0.488   3.175   0.000   0.000   0.000
   2_bss:  0.357  91.394  -1.673  -1.526   0.787  -0.000   0.000   0.000
   2_xyz:  0.357  91.394  -1.673  -1.526   0.787  -0.000   0.000   0.000
   2_adp:  0.357  91.394  -1.673  -1.526   0.787  -0.000   0.000   0.000
   2_occ:  0.357  91.394  -1.673  -1.526   0.787  -0.000   0.000   0.000
   3_bss:  0.339  80.000  -1.856  -2.002   0.049  -0.000   0.000   0.000
   3_xyz:  0.339  80.000  -1.856  -2.002   0.049  -0.000   0.000   0.000
   3_adp:  0.339  80.000  -1.856  -2.002   0.049  -0.000   0.000   0.000
   3_occ:  0.339  80.000  -1.856  -2.002   0.049  -0.000   0.000   0.000
   4_bss:  0.330  72.029  -2.216  -2.527  -0.526  -0.000  -0.000  -0.000
   4_xyz:  0.330  72.029  -2.216  -2.527  -0.526  -0.000  -0.000  -0.000
   4_adp:  0.330  72.029  -2.216  -2.527  -0.526  -0.000  -0.000  -0.000
   4_occ:  0.330  72.029  -2.216  -2.527  -0.526  -0.000  -0.000  -0.000
   5_bss:  0.320  63.332  -2.209  -2.616  -0.607  -0.000  -0.000  -0.000
   5_xyz:  0.320  63.332  -2.209  -2.616  -0.607  -0.000  -0.000  -0.000
   5_adp:  0.320  63.332  -2.209  -2.616  -0.607  -0.000  -0.000  -0.000
   5_occ:  0.320  63.332  -2.209  -2.616  -0.607  -0.000  -0.000  -0.000
   5_bss:  0.314  56.326  -2.208  -2.626  -0.574  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.267 0.4790  0.6364    60981.392
   1_bss:  52.678 0.4853  0.6718    59464.578
   1_xyz:  31.344 0.7439  0.9576    25076.574
   1_adp:  33.458 0.7185  0.9332    27614.470
   1_occ:  33.516 0.7177  0.9317    27638.866
   2_bss:  33.473 0.7185  0.8798    27775.515
   2_xyz:  25.275 0.8071  0.9577    16249.684
   2_adp:  22.790 0.8340  0.9685    14054.363
   2_occ:  22.789 0.8339  0.9682    14036.471
   3_bss:  22.763 0.8341  0.9525    14015.780
   3_xyz:  18.035 0.8795  0.9833     9184.535
   3_adp:  16.796 0.8913  0.9844     8344.446
   3_occ:  16.818 0.8911  0.9842     8360.752
   4_bss:  16.763 0.8915  0.9680     8288.365
   4_xyz:  15.139 0.9054  0.9749     7063.291
   4_adp:  14.778 0.9088  0.9727     6892.379
   4_occ:  14.780 0.9087  0.9726     6891.050
   5_bss:  14.782 0.9087  0.9707     6886.656
   5_xyz:  14.699 0.9096  0.9710     6868.210
   5_adp:  14.674 0.9100  0.9693     6914.563
   5_occ:  14.672 0.9100  0.9692     6909.967
   5_bss:  14.677 0.9100  0.9679     6908.919
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6554e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6554e-01
   1_xyz:   1.511  0.013  0.101 16.259  0.007  4.113   1.2905e-01
   1_adp:   1.511  0.013  0.101 16.259  0.007  4.113   1.2905e-01
   1_occ:   1.511  0.013  0.101 16.259  0.007  4.113   1.2905e-01
   2_bss:   1.511  0.013  0.101 16.259  0.007  4.113   1.2905e-01
   2_xyz:   1.010  0.006  0.075 14.445  0.004  4.126   5.6991e-02
   2_adp:   1.010  0.006  0.075 14.445  0.004  4.126   5.6991e-02
   2_occ:   1.010  0.006  0.075 14.445  0.004  4.126   5.6991e-02
   3_bss:   1.010  0.006  0.075 14.445  0.004  4.126   5.6991e-02
   3_xyz:   1.024  0.007  0.075 14.691  0.003  4.125   6.0793e-02
   3_adp:   1.024  0.007  0.075 14.691  0.003  4.125   6.0793e-02
   3_occ:   1.024  0.007  0.075 14.691  0.003  4.125   6.0793e-02
   4_bss:   1.024  0.007  0.075 14.691  0.003  4.125   6.0793e-02
   4_xyz:   1.043  0.009  0.078 14.614  0.004  4.115   6.5132e-02
   4_adp:   1.043  0.009  0.078 14.614  0.004  4.115   6.5132e-02
   4_occ:   1.043  0.009  0.078 14.614  0.004  4.115   6.5132e-02
   5_bss:   1.043  0.009  0.078 14.614  0.004  4.115   6.5132e-02
   5_xyz:   0.997  0.008  0.075 14.470  0.004  4.117   6.0053e-02
   5_adp:   0.997  0.008  0.075 14.470  0.004  4.117   6.0053e-02
   5_occ:   0.997  0.008  0.075 14.470  0.004  4.117   6.0053e-02
   5_bss:   0.997  0.008  0.075 14.470  0.004  4.117   6.0053e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4253e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4253e-01
   1_xyz:   9.471  0.092  0.328 81.933  0.056  2.047   1.1316e-01
   1_adp:   9.471  0.092  0.328 81.933  0.056  2.047   1.1316e-01
   1_occ:   9.471  0.092  0.328 81.933  0.056  2.047   1.1316e-01
   2_bss:   9.471  0.092  0.328 81.933  0.056  2.047   1.1316e-01
   2_xyz:   6.770  0.038  0.289 80.051  0.046  2.375   4.6853e-02
   2_adp:   6.770  0.038  0.289 80.051  0.046  2.375   4.6853e-02
   2_occ:   6.770  0.038  0.289 80.051  0.046  2.375   4.6853e-02
   3_bss:   6.770  0.038  0.289 80.051  0.046  2.375   4.6853e-02
   3_xyz:   8.354  0.039  0.237 81.746  0.034  2.348   6.2554e-02
   3_adp:   8.354  0.039  0.237 81.746  0.034  2.348   6.2554e-02
   3_occ:   8.354  0.039  0.237 81.746  0.034  2.348   6.2554e-02
   4_bss:   8.354  0.039  0.237 81.746  0.034  2.348   6.2554e-02
   4_xyz:   7.805  0.051  0.249 82.237  0.038  2.339   5.7620e-02
   4_adp:   7.805  0.051  0.249 82.237  0.038  2.339   5.7620e-02
   4_occ:   7.805  0.051  0.249 82.237  0.038  2.339   5.7620e-02
   5_bss:   7.805  0.051  0.249 82.237  0.038  2.339   5.7620e-02
   5_xyz:   7.875  0.043  0.227 83.510  0.036  2.366   4.0005e-02
   5_adp:   7.875  0.043  0.227 83.510  0.036  2.366   4.0005e-02
   5_occ:   7.875  0.043  0.227 83.510  0.036  2.366   4.0005e-02
   5_bss:   7.875  0.043  0.227 83.510  0.036  2.366   4.0005e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 109.98   0.00  18.87  85.25   0.00  13.99 109.98   1.48  45.45
   1_occ: 109.98   0.00  18.87  85.25   0.00  13.99 109.98   1.48  45.45
   2_bss: 109.98   0.00  18.87  85.25   0.00  13.99 109.98   1.48  45.45
   2_xyz: 109.98   0.00  18.87  85.25   0.00  13.99 109.98   1.48  45.45
   2_adp: 105.09   0.00  18.23  84.87   0.00  13.42 105.09   4.64  44.44
   2_occ: 105.09   0.00  18.23  84.87   0.00  13.42 105.09   4.64  44.44
   3_bss: 105.09   0.00  18.23  84.87   0.00  13.42 105.09   4.64  44.44
   3_xyz: 105.09   0.00  18.23  84.87   0.00  13.42 105.09   4.64  44.44
   3_adp:  98.58   0.29  17.80  85.73   0.29  13.01  98.58   5.71  43.90
   3_occ:  98.58   0.29  17.80  85.73   0.29  13.01  98.58   5.71  43.90
   4_bss:  98.58   0.29  17.80  85.73   0.29  13.01  98.58   5.71  43.90
   4_xyz:  98.58   0.29  17.80  85.73   0.29  13.01  98.58   5.71  43.90
   4_adp:  92.99   0.57  17.46  87.45   0.57  12.91  92.99   5.00  42.24
   4_occ:  92.99   0.57  17.46  87.45   0.57  12.91  92.99   5.00  42.24
   5_bss:  92.99   0.57  17.46  87.45   0.57  12.91  92.99   5.00  42.24
   5_xyz:  92.99   0.57  17.46  87.45   0.57  12.91  92.99   5.00  42.24
   5_adp:  85.08   1.22  16.82  85.08   1.22  12.73  84.38   6.02  39.07
   5_occ:  85.08   1.22  16.82  85.08   1.22  12.73  84.38   6.02  39.07
   5_bss:  85.03   1.17  16.78  85.03   1.17  12.69  84.34   5.98  39.03
------------------------------------------------------------------------
 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:    1.412    0.031    0.481
   1_adp:    1.412    0.031    0.481
   1_occ:    1.412    0.031    0.481
   2_bss:    1.412    0.031    0.481
   2_xyz:    1.324    0.039    0.541
   2_adp:    1.324    0.039    0.541
   2_occ:    1.324    0.039    0.541
   3_bss:    1.324    0.039    0.541
   3_xyz:    1.317    0.042    0.654
   3_adp:    1.317    0.042    0.654
   3_occ:    1.317    0.042    0.654
   4_bss:    1.317    0.042    0.654
   4_xyz:    1.459    0.065    0.670
   4_adp:    1.459    0.065    0.670
   4_occ:    1.459    0.065    0.670
   5_bss:    1.459    0.065    0.670
   5_xyz:    1.560    0.077    0.685
   5_adp:    1.560    0.077    0.685
   5_occ:    1.560    0.077    0.685
   5_bss:    1.560    0.077    0.685
------------------------------------------------------------------------

CPU time actual refinement: 363.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/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_999/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_999/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 363.39 
  Macro-tasks:
    bulk solvent and scale       = 58.77  
    individual site refinement   = 140.24 
    weights calculation          = 31.08  
    collect and process          = 6.67   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 236.85 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 114.19 
    alpha_beta                      = 8.56   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.05 
    fmodel                         = 9.10   
    r_factors                      = 0.26   
    phase_errors                   = 11.62  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 262.85 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.153 micro seconds
Total CPU time: 6.28 minutes
from_scatterers_fft:    630 calls, 113.74 s
gradients_fft:          575 calls, 105.11 s

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

# Date 2008-01-16 Time 06:11:28 PST -0800 (1200492688.32 s)
Start R-work = 0.4501, R-free = 0.4462 (no bulk solvent and anisotropic scale)
Final R-work = 0.1419, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4418, R-free = 0.4421
Final R-work = 0.1183, R-free = 0.1633