# Date 2008-01-16 Time 05:58:11 PST -0800 (1200491891.39 s)
#phil __OFF__

Command line arguments: "../952.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2033
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 952

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.8686, 86.822, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01116
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   2.0112

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 2.01116
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.3028 [2122/2149]  1910   212  10.0%
  bin  2:  4.3028 -  3.4283 [2035/2051]  1831   204  10.0%
  bin  3:  3.4283 -  2.9988 [2018/2037]  1815   203  10.1%
  bin  4:  2.9988 -  2.7264 [1995/2025]  1799   196   9.8%
  bin  5:  2.7264 -  2.5319 [1978/1997]  1778   200  10.1%
  bin  6:  2.5319 -  2.3832 [1968/2004]  1776   192   9.8%
  bin  7:  2.3832 -  2.2643 [1972/2005]  1769   203  10.3%
  bin  8:  2.2643 -  2.1660 [1946/1978]  1750   196  10.1%
  bin  9:  2.1660 -  2.0829 [1950/1980]  1758   192   9.8%
  bin 10:  2.0829 -  2.0112 [1605/2010]  1444   161  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 7
        2.26 -     2.92: 1444
        2.92 -     3.58: 4394
        3.58 -     4.24: 9013
        4.24 -     4.90: 12965
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.598 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.959 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.959 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.968 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27818 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_952/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.8686 86.82195 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: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4000   r_free= 0.3848   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.203379                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7988 0.99   1376  154 0.3233 0.3378       6.449      6.4192|
|  2:  4.7988 -  3.8293 0.99   1332  145 0.3325 0.3439      6.7014       6.713|
|  3:  3.8293 -  3.3512 0.99   1301  147 0.3595 0.3266      6.5653      6.4891|
|  4:  3.3512 -  3.0476 0.99   1293  144 0.3891 0.3576      6.4473      6.3488|
|  5:  3.0476 -  2.8307 0.99   1285  139 0.4181 0.3875      6.3002      6.2869|
|  6:  2.8307 -  2.6647 0.99   1279  145 0.4286 0.4085      6.2174      6.1191|
|  7:  2.6647 -  2.5319 0.99   1267  141 0.4277 0.3782      6.1678       6.047|
|  8:  2.5319 -  2.4222 0.98   1277  140 0.4420 0.4083      6.1268      6.1266|
|  9:  2.4222 -  2.3293 0.98   1273  144 0.4449 0.4584       6.058      6.1298|
| 10:  2.3293 -  2.2492 0.98   1235  133 0.4532 0.4120      6.0615       5.963|
| 11:  2.2492 -  2.1790 1.00   1272  148 0.4428 0.4175      5.9938      6.0029|
| 12:  2.1790 -  2.1169 0.97   1252  129 0.4617 0.4623      5.9486      6.0014|
| 13:  2.1169 -  2.0613 0.98   1242  142 0.4550 0.4438      5.8444      5.8195|
| 14:  2.0613 -  2.0112 0.74    946  108 0.4331 0.4561      5.7856      5.7593|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7988  1376   154  0.74  30.45   0.84     0.77      56959.51|
|  2:  4.7988 -  3.8293  1332   145  0.78  27.72   0.93     0.85      69955.63|
|  3:  3.8293 -  3.3512  1301   147  0.73  33.01   0.93     0.86      71556.51|
|  4:  3.3512 -  3.0476  1293   144  0.68  37.01   0.92     0.82      62637.63|
|  5:  3.0476 -  2.8307  1285   139  0.61  42.84   0.92     0.78      51810.53|
|  6:  2.8307 -  2.6647  1279   145  0.61  43.62   0.92     0.76      43762.05|
|  7:  2.6647 -  2.5319  1267   141  0.59  44.61   0.95     0.76      39886.42|
|  8:  2.5319 -  2.4222  1277   140  0.57  46.32   0.94     0.75      38897.01|
|  9:  2.4222 -  2.3293  1273   144  0.55  48.12   0.93     0.74      37461.94|
| 10:  2.3293 -  2.2492  1235   133  0.54  48.64   0.96     0.74      35297.37|
| 11:  2.2492 -  2.1790  1272   148  0.54  49.24   0.96     0.74      33410.77|
| 12:  2.1790 -  2.1169  1252   129  0.51  51.37   0.96     0.73      32457.12|
| 13:  2.1169 -  2.0613  1242   142  0.48  53.87   0.94     0.68      29434.70|
| 14:  2.0613 -  2.0112   946   108  0.47  54.26   0.96     0.63      24365.48|
|alpha:            min =        0.63 max =            0.86 mean =         0.76|
|beta:             min =    24365.48 max =        71556.51 mean =     45514.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.26|
|phase err.(test): min =        0.00 max =           89.51 mean =        43.38|
|-----------------------------------------------------------------------------|

============================== 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 = 8.800172              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.565   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.250263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.119   (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 |  1.598 -  1.928:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.928 -  2.258:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.258 -  2.588:       20 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.588 -  2.919:     1424 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.919 -  3.249:     1864 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.249 -  3.579:     2530 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.579 -  3.909:     4625 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.909 -  4.240:     4388 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.240 -  4.570:     5910 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.570 -  4.900:     7055 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.598 |       0.180 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    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: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4000   r_free= 0.3848   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.203379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3884   r_free= 0.3740   ksol= 0.30   Bsol= 50.00   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,5.00,-1.26,0.00,-0.00,-0.00); trace/3= 0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.187980                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.992314              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.373   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.637069              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.024   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3884      final r-factor (work) = 0.2683          |
| start r-factor (free) = 0.3740      final r-factor (free) = 0.2928          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8953 = 7.99 * 0.50 * 6.1886 + 1.00 * 0.1648                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0069 = 7.99 * 0.50 * 5.9790 + 1.00 * 0.1138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2683      final r-factor (work) = 0.2485          |
| start r-factor (free) = 0.2928      final r-factor (free) = 0.2973          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8155 = 0.64 * 1.00 * 5.9790 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7784 = 0.64 * 1.00 * 5.8304 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.83  16.45    None  None   None       |
|    all(noH): 2823   0      0.00    104.83  16.45    None  None   None       |
|    Sol.    : 438    0      3.15    66.38   37.28    None  None   None       |
|    Mac.    : 2385   0      0.00    104.83  12.62    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 -  10.483: 1111   |   5:    52.415 -  62.898:   61        |
|      1:    10.483 -  20.966: 1061   |   6:    62.898 -  73.381:    2        |
|      2:    20.966 -  31.449:  287   |   7:    73.381 -  83.864:    0        |
|      3:    31.449 -  41.932:  174   |   8:    83.864 -  94.347:    0        |
|      4:    41.932 -  52.415:  126   |   9:    94.347 - 104.830:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2485 r_free = 0.2973             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2482 r_free = 0.2965             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2482   r_free= 0.2965   ksol= 0.30   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,5.00,-1.26,0.00,-0.00,-0.00); trace/3= 0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.832100                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2465   r_free= 0.2940   ksol= 0.33   Bsol= 71.35   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.55,-0.70,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.827568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.007292              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.716  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.743305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.890   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2465      final r-factor (work) = 0.1819          |
| start r-factor (free) = 0.2940      final r-factor (free) = 0.2142          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7934 = 4.01 * 0.50 * 5.8292 + 1.00 * 0.1138                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4897 = 4.01 * 0.50 * 5.7003 + 1.00 * 0.0684                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1819      final r-factor (work) = 0.1638          |
| start r-factor (free) = 0.2142      final r-factor (free) = 0.2064          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2695 = 0.74 * 1.00 * 5.7003 + 1.00 * 0.0325                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0889 = 0.74 * 1.00 * 5.4830 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.60   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    99.60   17.73    None  None   None       |
|    Sol.    : 438    0      3.97    99.60   43.47    None  None   None       |
|    Mac.    : 2385   0      0.00    98.04   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:     0.000 -   9.960: 1126   |   5:    49.800 -  59.760:   85        |
|      1:     9.960 -  19.920: 1012   |   6:    59.760 -  69.720:   71        |
|      2:    19.920 -  29.880:  239   |   7:    69.720 -  79.680:   35        |
|      3:    29.880 -  39.840:  140   |   8:    79.680 -  89.640:   18        |
|      4:    39.840 -  49.800:   92   |   9:    89.640 -  99.600:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1638 r_free = 0.2064             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1636 r_free = 0.2062             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1636   r_free= 0.2062   ksol= 0.33   Bsol= 71.35   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,1.55,-0.70,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.466368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1632   r_free= 0.2064   ksol= 0.33   Bsol= 78.47   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,0.07,-0.55,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.464333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.877243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.122  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383526              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1632      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.2064      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9558 = 2.88 * 0.50 * 5.4826 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7971 = 2.88 * 0.50 * 5.3725 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1786      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0738 = 0.38 * 1.00 * 5.3725 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0338 = 0.38 * 1.00 * 5.2732 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.35   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    99.35   17.02    None  None   None       |
|    Sol.    : 438    0      0.67    99.27   42.43    None  None   None       |
|    Mac.    : 2385   0      0.00    99.35   12.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.935: 1205   |   5:    49.673 -  59.607:   88        |
|      1:     9.935 -  19.869:  996   |   6:    59.607 -  69.542:   69        |
|      2:    19.869 -  29.804:  198   |   7:    69.542 -  79.476:   25        |
|      3:    29.804 -  39.738:  124   |   8:    79.476 -  89.411:   14        |
|      4:    39.738 -  49.673:  100   |   9:    89.411 -  99.345:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1705             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1704             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1704   ksol= 0.33   Bsol= 78.47   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,0.07,-0.55,0.00,-0.00,-0.00); trace/3= -0.73                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1703   ksol= 0.33   Bsol= 72.74   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.42,-0.21,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249311                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.568179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.627501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.412  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2034 = 1.57 * 0.50 * 5.2740 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1612 = 1.57 * 0.50 * 5.2363 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1672      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2970 = 0.63 * 1.00 * 5.2363 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2863 = 0.63 * 1.00 * 5.2186 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.21  16.70    None  None   None       |
|    all(noH): 2823   0      0.00    104.21  16.70    None  None   None       |
|    Sol.    : 438    0      0.00    102.95  41.95    None  None   None       |
|    Mac.    : 2385   0      0.00    104.21  12.07    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 -  10.421: 1341   |   5:    52.107 -  62.529:   92        |
|      1:    10.421 -  20.843:  899   |   6:    62.529 -  72.950:   42        |
|      2:    20.843 -  31.264:  189   |   7:    72.950 -  83.371:   24        |
|      3:    31.264 -  41.686:  121   |   8:    83.371 -  93.793:    7        |
|      4:    41.686 -  52.107:  103   |   9:    93.793 - 104.214:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1678             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1677             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1677   ksol= 0.33   Bsol= 72.74   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.42,-0.21,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220247                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1676   ksol= 0.33   Bsol= 70.67   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-0.56,-0.12,-0.00,-0.00,-0.00); trace/3= -0.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220125                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.951384              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.926  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308775              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.344  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1467 = 1.95 * 0.50 * 5.2180 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1375 = 1.95 * 0.50 * 5.2005 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6173 = 0.31 * 1.00 * 5.2005 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6130 = 0.31 * 1.00 * 5.1910 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.91  16.10    None  None   None       |
|    all(noH): 2823   0      0.00    101.91  16.10    None  None   None       |
|    Sol.    : 438    0      1.58    99.19   39.97    None  None   None       |
|    Mac.    : 2385   0      0.00    101.91  11.71    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 -  10.191: 1350   |   5:    50.955 -  61.146:   84        |
|      1:    10.191 -  20.382:  891   |   6:    61.146 -  71.337:   40        |
|      2:    20.382 -  30.573:  200   |   7:    71.337 -  81.527:   18        |
|      3:    30.573 -  40.764:  121   |   8:    81.527 -  91.718:    4        |
|      4:    40.764 -  50.955:  109   |   9:    91.718 - 101.909:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1637             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1637             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1637   ksol= 0.33   Bsol= 70.67   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-0.56,-0.12,-0.00,-0.00,-0.00); trace/3= -0.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.187753                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7988 0.99   1376  154 0.1005 0.1304      5.3975      5.5406|
|  2:  4.7988 -  3.8293 0.99   1332  145 0.0869 0.1069      5.4411      5.6194|
|  3:  3.8293 -  3.3512 0.99   1301  147 0.1055 0.1480      5.4754      5.8484|
|  4:  3.3512 -  3.0476 0.99   1293  144 0.1273 0.1660      5.4985      5.6466|
|  5:  3.0476 -  2.8307 0.99   1285  139 0.1442 0.1821      5.4005      5.5723|
|  6:  2.8307 -  2.6647 0.99   1279  145 0.1336 0.2030      5.2933      5.5369|
|  7:  2.6647 -  2.5319 0.99   1267  141 0.1309 0.1763      5.2146      5.4088|
|  8:  2.5319 -  2.4222 0.98   1277  140 0.1250 0.1793      5.1401      5.3997|
|  9:  2.4222 -  2.3293 0.98   1273  144 0.1238 0.1875      5.0737      5.3734|
| 10:  2.3293 -  2.2492 0.98   1235  133 0.1211 0.1852      5.0343      5.2229|
| 11:  2.2492 -  2.1790 1.00   1272  148 0.1223 0.1810      4.9785      5.2916|
| 12:  2.1790 -  2.1169 0.97   1252  129 0.1187 0.1815      4.9398      5.2249|
| 13:  2.1169 -  2.0613 0.98   1242  142 0.1214 0.1747      4.8409      5.0752|
| 14:  2.0613 -  2.0112 0.74    946  108 0.1132 0.1865      4.7211      5.0223|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7988  1376   154  0.94   9.39   0.96     0.93       7550.10|
|  2:  4.7988 -  3.8293  1332   145  0.95   8.01   0.99     0.98       8943.06|
|  3:  3.8293 -  3.3512  1301   147  0.93  11.18   1.01     1.00      10391.99|
|  4:  3.3512 -  3.0476  1293   144  0.91  14.23   0.99     0.97      11031.53|
|  5:  3.0476 -  2.8307  1285   139  0.89  17.05   0.99     0.97       9441.16|
|  6:  2.8307 -  2.6647  1279   145  0.89  17.04   0.98     0.95       8079.19|
|  7:  2.6647 -  2.5319  1267   141  0.90  16.43   0.98     0.96       6861.54|
|  8:  2.5319 -  2.4222  1277   140  0.90  16.19   0.97     0.94       6082.68|
|  9:  2.4222 -  2.3293  1273   144  0.90  16.30   0.98     0.93       5328.57|
| 10:  2.3293 -  2.2492  1235   133  0.90  16.51   0.98     0.93       4961.73|
| 11:  2.2492 -  2.1790  1272   148  0.89  16.81   0.97     0.93       4568.33|
| 12:  2.1790 -  2.1169  1252   129  0.91  15.98   0.98     0.97       4396.58|
| 13:  2.1169 -  2.0613  1242   142  0.90  16.62   0.97     0.95       3659.70|
| 14:  2.0613 -  2.0112   946   108  0.91  15.60   0.94     0.90       2786.88|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     2786.88 max =        11031.53 mean =      6830.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.73|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1636   ksol= 0.32   Bsol= 67.12   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.45,0.11,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.187794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1636   ksol= 0.32   Bsol= 67.12   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.45,0.11,-0.00,0.00,0.00); trace/3= -0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.187794                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.7988 0.99   1376  154 0.1003 0.1307      5.3971      5.5407|
|  2:  4.7988 -  3.8293 0.99   1332  145 0.0867 0.1065      5.4396      5.6166|
|  3:  3.8293 -  3.3512 0.99   1301  147 0.1055 0.1480      5.4747      5.8491|
|  4:  3.3512 -  3.0476 0.99   1293  144 0.1274 0.1661      5.4991      5.6468|
|  5:  3.0476 -  2.8307 0.99   1285  139 0.1444 0.1821      5.4013       5.573|
|  6:  2.8307 -  2.6647 0.99   1279  145 0.1336 0.2028      5.2936      5.5365|
|  7:  2.6647 -  2.5319 0.99   1267  141 0.1310 0.1764       5.215      5.4095|
|  8:  2.5319 -  2.4222 0.98   1277  140 0.1251 0.1794      5.1405         5.4|
|  9:  2.4222 -  2.3293 0.98   1273  144 0.1237 0.1873       5.074      5.3735|
| 10:  2.3293 -  2.2492 0.98   1235  133 0.1211 0.1855      5.0348      5.2245|
| 11:  2.2492 -  2.1790 1.00   1272  148 0.1224 0.1809      4.9787      5.2915|
| 12:  2.1790 -  2.1169 0.97   1252  129 0.1187 0.1816      4.9398      5.2256|
| 13:  2.1169 -  2.0613 0.98   1242  142 0.1215 0.1748      4.8408      5.0753|
| 14:  2.0613 -  2.0112 0.74    946  108 0.1132 0.1863      4.7208      5.0214|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.7988  1376   154  0.94   9.40   0.96     0.94       7552.61|
|  2:  4.7988 -  3.8293  1332   145  0.95   8.00   1.00     0.98       8921.45|
|  3:  3.8293 -  3.3512  1301   147  0.94  11.15   1.01     1.00      10366.81|
|  4:  3.3512 -  3.0476  1293   144  0.91  14.23   1.00     0.97      11039.51|
|  5:  3.0476 -  2.8307  1285   139  0.89  17.05   0.99     0.97       9446.25|
|  6:  2.8307 -  2.6647  1279   145  0.89  17.05   0.98     0.96       8081.82|
|  7:  2.6647 -  2.5319  1267   141  0.90  16.43   0.99     0.96       6863.79|
|  8:  2.5319 -  2.4222  1277   140  0.90  16.20   0.98     0.95       6088.91|
|  9:  2.4222 -  2.3293  1273   144  0.90  16.31   0.99     0.94       5334.82|
| 10:  2.3293 -  2.2492  1235   133  0.90  16.52   0.99     0.94       4968.15|
| 11:  2.2492 -  2.1790  1272   148  0.89  16.81   0.98     0.94       4572.12|
| 12:  2.1790 -  2.1169  1252   129  0.91  15.98   0.99     0.98       4399.75|
| 13:  2.1169 -  2.0613  1242   142  0.90  16.62   0.98     0.96       3657.73|
| 14:  2.0613 -  2.0112   946   108  0.91  15.58   0.95     0.91       2781.68|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2781.68 max =        11039.51 mean =      6829.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.76 mean =        14.73|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.308)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.91  16.10    None  None   None       |
|    all(noH): 2823   0      0.00    101.91  16.10    None  None   None       |
|    Sol.    : 438    0      1.59    99.19   39.98    None  None   None       |
|    Mac.    : 2385   0      0.00    101.91  11.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.194: 1350   |   5:    50.958 -  61.149:   84        |
|      1:    10.194 -  20.385:  891   |   6:    61.149 -  71.339:   40        |
|      2:    20.385 -  30.576:  200   |   7:    71.339 -  81.530:   18        |
|      3:    30.576 -  40.767:  121   |   8:    81.530 -  91.721:    4        |
|      4:    40.767 -  50.958:  109   |   9:    91.721 - 101.912:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.460 - 4.816
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 330
   mapped sites are within: 0.712 - 4.816

peak=    5.957 closest distance to " O   HOH Z 111 " =    2.249
peak=    5.762 closest distance to " O   HOH Z 210 " =    1.215
peak=    5.600 closest distance to " CB  GLN A 223 " =    1.394
peak=    5.170 closest distance to " CB  SER A  63 " =    1.260
peak=    4.982 closest distance to " CG  PRO A  54 " =    1.334
peak=    4.837 closest distance to " O   HOH Z 232 " =    2.317
peak=    4.806 closest distance to " CB  GLN A 183 " =    1.256
peak=    4.721 closest distance to " CG  PRO A 198 " =    1.224
peak=    4.691 closest distance to " CB  ARG A 190 " =    1.727
peak=    4.690 closest distance to " O   PRO A 198 " =    1.557
peak=    4.550 closest distance to " CG  PRO A 213 " =    1.222
peak=    4.502 closest distance to " CB  PRO A  54 " =    0.898
peak=    4.501 closest distance to " O   HOH Z 134 " =    1.642
peak=    4.494 closest distance to " CB  ARG A 275 " =    0.886
peak=    4.430 closest distance to " O   HOH Z 433 " =    1.554
peak=    4.410 closest distance to " O   HOH Z 298 " =    2.039
peak=    4.380 closest distance to " CZ  PHE A 218 " =    1.127
peak=    4.367 closest distance to " O   HOH Z 369 " =    2.056
peak=    4.344 closest distance to " O   HOH Z 234 " =    3.878
peak=    4.343 closest distance to " NH2 ARG A 156 " =    1.207
peak=    4.341 closest distance to " CA  TYR A  30 " =    0.906
peak=    4.328 closest distance to " CB  GLU A 128 " =    1.107
peak=    4.322 closest distance to " O   HOH Z  15 " =    2.087
peak=    4.305 closest distance to " O   HOH Z 402 " =    1.581
peak=    4.302 closest distance to " O   HOH Z  40 " =    1.889
peak=    4.257 closest distance to " CA  ALA A  51 " =    0.982
peak=    4.243 closest distance to " O   HOH Z  44 " =    2.230
peak=    4.198 closest distance to " O   HOH Z 133 " =    2.530
peak=    4.198 closest distance to " O   HOH Z  43 " =    1.973
peak=    4.190 closest distance to " CB  TYR A 169 " =    0.796
peak=    4.189 closest distance to " CD  ARG A 269 " =    0.943
peak=    4.161 closest distance to " CB  GLU A 277 " =    3.775
peak=    4.157 closest distance to " CB  GLU A 152 " =    1.158
peak=    4.153 closest distance to " O   HOH Z 423 " =    1.861
peak=    4.142 closest distance to " O   HOH Z 265 " =    2.123
peak=    4.130 closest distance to " CB  ARG A  79 " =    1.374
peak=    4.123 closest distance to " O   HOH Z 189 " =    2.596
peak=    4.116 closest distance to " O   HOH Z 403 " =    1.714
peak=    4.083 closest distance to " CB  VAL A 202 " =    1.519
peak=    4.081 closest distance to " CD  LYS A 166 " =    1.311
peak=    4.078 closest distance to " CB  TRP A 266 " =    0.994
peak=    4.059 closest distance to " CB  LEU A 228 " =    1.085
peak=    4.053 closest distance to " O   HOH Z 412 " =    3.635
peak=    4.048 closest distance to " CG1 ILE A  33 " =    1.216
peak=    4.025 closest distance to " O   HOH Z 368 " =    2.162
peak=    3.987 closest distance to " O   HOH Z 271 " =    2.844
peak=    3.949 closest distance to " O   HOH Z  20 " =    1.664
peak=    3.945 closest distance to " CA  ASP A 191 " =    0.839
peak=    3.935 closest distance to " ND2 ASN A 249 " =    2.090
peak=    3.930 closest distance to " CB  ASP A 140 " =    0.876
peak=    3.927 closest distance to " CA  PRO A  54 " =    1.363
peak=    3.925 closest distance to " O   HOH Z  80 " =    1.800
peak=    3.921 closest distance to " O   HOH Z  97 " =    2.045
peak=    3.909 closest distance to " O   HOH Z 383 " =    2.187
peak=    3.902 closest distance to " CG2BVAL A  41 " =    0.944
peak=    3.901 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.895 closest distance to " CG  ARG A  66 " =    2.621
peak=    3.891 closest distance to " O   THR A 251 " =    1.213
peak=    3.872 closest distance to " O   HOH Z  68 " =    2.007
peak=    3.872 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.866 closest distance to " O   HOH Z 128 " =    2.173
peak=    3.866 closest distance to " CG  PRO A 243 " =    1.148
peak=    3.861 closest distance to " O   HOH Z 285 " =    3.051
peak=    3.849 closest distance to " O   HOH Z  63 " =    1.893
peak=    3.842 closest distance to " CG2 THR A 221 " =    1.020
peak=    3.836 closest distance to " O   HOH Z 418 " =    1.584
peak=    3.834 closest distance to " O   ALA A 165 " =    1.340
peak=    3.830 closest distance to " ND2 ASN A 187 " =    1.484
peak=    3.826 closest distance to " CA  ARG A 195 " =    1.178
peak=    3.817 closest distance to " O   HOH Z 214 " =    2.563
peak=    3.811 closest distance to " N   ASN A  39 " =    1.291
peak=    3.804 closest distance to " O   HOH Z 126 " =    1.578
peak=    3.800 closest distance to " O   HOH Z  21 " =    1.837
peak=    3.799 closest distance to " CA  ALA A  21 " =    1.319
peak=    3.799 closest distance to " CB  ASN A 148 " =    1.369
peak=    3.797 closest distance to " O   HOH Z 425 " =    1.372
peak=    3.787 closest distance to " CB  MET A  40 " =    0.838
peak=    3.779 closest distance to " O   HOH Z 352 " =    1.879
peak=    3.778 closest distance to " CB  ASP A 124 " =    0.712
peak=    3.770 closest distance to " C   ILE A 106 " =    1.864
peak=    3.770 closest distance to " O   SER A  87 " =    2.283
peak=    3.765 closest distance to " CD2 TRP A 179 " =    1.307
peak=    3.760 closest distance to " CD1 LEU A 300 " =    1.181
peak=    3.758 closest distance to " CB  SER A   3 " =    1.403
peak=    3.755 closest distance to " CB  SER A 141 " =    1.047
peak=    3.739 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.739 closest distance to " CA  ARG A  36 " =    1.131
peak=    3.738 closest distance to " O   HOH Z 346 " =    1.461
peak=    3.734 closest distance to " CD2 LEU A 297 " =    0.955
peak=    3.722 closest distance to " O   HOH Z 236 " =    1.975
peak=    3.711 closest distance to " O   HOH Z 406 " =    1.647
peak=    3.705 closest distance to " O   HOH Z 374 " =    2.874
peak=    3.699 closest distance to " O   HOH Z 126 " =    2.079
peak=    3.690 closest distance to " CA  GLU A 152 " =    0.909
peak=    3.680 closest distance to " CA  ALA A 160 " =    0.917
peak=    3.661 closest distance to " O   ASN A  74 " =    1.616
peak=    3.657 closest distance to " O   HOH Z 362 " =    3.473
peak=    3.652 closest distance to " CB  TRP A 179 " =    1.475
peak=    3.643 closest distance to " CG1 VAL A 153 " =    1.040
peak=    3.640 closest distance to " CA  ILE A 106 " =    0.818
peak=    3.632 closest distance to " OD1 ASN A 217 " =    1.718
peak=    3.631 closest distance to " O   HOH Z  19 " =    1.839
peak=    3.629 closest distance to " O   HOH Z 280 " =    2.985
peak=    3.613 closest distance to " O   HOH Z  59 " =    2.478
peak=    3.613 closest distance to " O   HOH Z 303 " =    2.327
peak=    3.612 closest distance to " CD1 LEU A  96 " =    0.730
peak=    3.611 closest distance to " OE1 GLN A  11 " =    2.003
peak=    3.597 closest distance to " O   HOH Z 279 " =    2.212
peak=    3.590 closest distance to " O   HOH Z  30 " =    1.317
peak=    3.590 closest distance to " O   HOH Z 421 " =    1.744
peak=    3.579 closest distance to " O   HOH Z 132 " =    2.846
peak=    3.575 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.575 closest distance to " CA  GLY A 241 " =    0.845
peak=    3.574 closest distance to " CZ  PHE A 192 " =    0.890
peak=    3.573 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.571 closest distance to " CA  SER A  87 " =    1.062
peak=    3.569 closest distance to " OD2 ASP A 298 " =    3.903
peak=    3.563 closest distance to " O   HOH Z 109 " =    2.482
peak=    3.559 closest distance to " O   ALA A 158 " =    1.233
peak=    3.558 closest distance to " NZ  LYS A 117 " =    3.181
peak=    3.555 closest distance to " O   HOH Z 247 " =    1.488
peak=    3.555 closest distance to " O   HOH Z 196 " =    1.201
peak=    3.550 closest distance to " CB  ALA A 291 " =    1.288
peak=    3.550 closest distance to " O   HOH Z 403 " =    1.443
peak=    3.549 closest distance to " O   HOH Z  44 " =    1.805
peak=    3.549 closest distance to " CB  VAL A 265 " =    1.261
peak=    3.548 closest distance to " CA  ASP A 162 " =    1.183
peak=    3.543 closest distance to " O   HOH Z 316 " =    3.104
peak=    3.542 closest distance to " CG  GLU A  37 " =    0.905
peak=    3.542 closest distance to " CB  ASN A 187 " =    1.111
peak=    3.531 closest distance to " O   HOH Z 163 " =    1.666
peak=    3.526 closest distance to " O   HOH Z 391 " =    2.996
peak=    3.525 closest distance to " N   CYS A 260 " =    0.859
peak=    3.524 closest distance to " O   HOH Z 197 " =    1.901
peak=    3.521 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.518 closest distance to " O   HOH Z 437 " =    1.430
peak=    3.516 closest distance to " O   HOH Z 344 " =    3.220
peak=    3.515 closest distance to " CB  LEU A  83 " =    0.829
peak=    3.515 closest distance to " N   ILE A  33 " =    1.043
peak=    3.502 closest distance to " CB  GLU A  46 " =    1.012
peak=    3.497 closest distance to " O   HOH Z  49 " =    0.873
peak=    3.497 closest distance to " O   HOH Z 135 " =    1.980
peak=    3.493 closest distance to " O   HOH Z 281 " =    4.803
peak=    3.493 closest distance to " O   HOH Z 193 " =    1.979
peak=    3.491 closest distance to " O   HOH Z 180 " =    2.191
peak=    3.487 closest distance to " CG AARG A 275 " =    1.140
peak=    3.487 closest distance to " O   HOH Z 357 " =    2.105
peak=    3.487 closest distance to " CB  SER A  62 " =    0.835
peak=    3.480 closest distance to " O   HOH Z 291 " =    1.505
peak=    3.478 closest distance to " O   HOH Z 426 " =    1.521
peak=    3.476 closest distance to " CA  ASN A 217 " =    1.315
peak=    3.475 closest distance to " NE2 GLN A  77 " =    3.370
peak=    3.465 closest distance to " CA  THR A 221 " =    0.880
peak=    3.464 closest distance to " CB  ASN A 142 " =    1.148
peak=    3.463 closest distance to " CZ3 TRP A 266 " =    1.071
peak=    3.453 closest distance to " CD  ARG A 159 " =    0.831
peak=    3.452 closest distance to " CB  ALA A  71 " =    1.306
peak=    3.450 closest distance to " O   HOH Z 130 " =    2.214
peak=    3.449 closest distance to " CB  PRO A 198 " =    1.027
peak=    3.442 closest distance to " CZ  PHE A  38 " =    1.266
peak=    3.438 closest distance to " CE1 TYR A 186 " =    1.231
peak=    3.435 closest distance to " CB  TYR A 116 " =    1.091
peak=    3.434 closest distance to " CG2 ILE A 120 " =    0.991
peak=    3.433 closest distance to " O   HOH Z 125 " =    3.782
peak=    3.432 closest distance to " O   HOH Z 294 " =    1.516
peak=    3.430 closest distance to " O   HOH Z 102 " =    1.289
peak=    3.426 closest distance to " O   THR A 220 " =    1.139
peak=    3.422 closest distance to " O   HOH Z  88 " =    1.707
peak=    3.421 closest distance to " CB  PHE A 204 " =    0.855
peak=    3.416 closest distance to " O   HOH Z 158 " =    2.962
peak=    3.415 closest distance to " N   ASN A 127 " =    1.232
peak=    3.409 closest distance to " O   HOH Z 427 " =    3.145
peak=    3.408 closest distance to " O   HOH Z 174 " =    2.322
peak=    3.399 closest distance to " CB  MET A  47 " =    0.963
peak=    3.397 closest distance to " CD1 ILE A 106 " =    0.900
peak=    3.395 closest distance to " CE  LYS A  76 " =    0.818
peak=    3.394 closest distance to " OG BSER A 164 " =    2.429
peak=    3.393 closest distance to " N   GLY A  98 " =    1.145
peak=    3.391 closest distance to " CB  ILE A 120 " =    1.293
peak=    3.386 closest distance to " CA  GLU A  46 " =    0.828
peak=    3.382 closest distance to " O   HOH Z 141 " =    1.621
peak=    3.380 closest distance to " O   HOH Z 176 " =    1.633
peak=    3.379 closest distance to " O   HOH Z   1 " =    2.851
peak=    3.377 closest distance to " NE2 GLN A  11 " =    1.107
peak=    3.373 closest distance to " CG2 THR A 220 " =    0.743
peak=    3.371 closest distance to " CA  LYS A 117 " =    1.238
peak=    3.369 closest distance to " O   HOH Z 245 " =    1.364
peak=    3.367 closest distance to " O   HOH Z  66 " =    2.125
peak=    3.364 closest distance to " O   HOH Z 258 " =    2.165
peak=    3.364 closest distance to " NE2 HIS A 115 " =    1.056
peak=    3.358 closest distance to " CB  GLN A 103 " =    0.881
peak=    3.358 closest distance to " CG2 ILE A  20 " =    1.415
peak=    3.358 closest distance to " OG  SER A 245 " =    1.674
peak=    3.356 closest distance to " O   HOH Z  78 " =    1.644
peak=    3.354 closest distance to " CG2AVAL A  72 " =    1.959
peak=    3.353 closest distance to " N   ASN A 252 " =    1.182
peak=    3.353 closest distance to " O   HOH Z  48 " =    1.953
peak=    3.351 closest distance to " O   HOH Z  88 " =    3.523
peak=    3.347 closest distance to " CA  ASP A 124 " =    0.787
peak=    3.344 closest distance to " CB  ALA A 248 " =    1.282
peak=    3.341 closest distance to " O   HOH Z 345 " =    1.720
peak=    3.341 closest distance to " CA  VAL A  41 " =    0.880
peak=    3.339 closest distance to " O   ASP A 124 " =    1.298
peak=    3.335 closest distance to " NZ  LYS A  48 " =    1.279
peak=    3.333 closest distance to " O   HOH Z 336 " =    1.750
peak=    3.333 closest distance to " O   HOH Z 371 " =    3.016
peak=    3.330 closest distance to " O   HOH Z 193 " =    1.684
peak=    3.330 closest distance to " C   TYR A 214 " =    1.488
peak=    3.329 closest distance to " OE1 GLU A   2 " =    1.945
peak=    3.327 closest distance to " O   HOH Z 250 " =    1.472
peak=    3.322 closest distance to " NE1 TRP A 274 " =    0.806
peak=    3.320 closest distance to " O   HOH Z 173 " =    2.278
peak=    3.316 closest distance to " CB  ALA A 100 " =    1.352
peak=    3.314 closest distance to " CD  ARG A  66 " =    2.506
peak=    3.313 closest distance to " CD  ARG A 195 " =    0.983
peak=    3.312 closest distance to " O   HOH Z 128 " =    2.195
peak=    3.306 closest distance to " NH1AARG A 145 " =    1.326
peak=    3.306 closest distance to " CD BLYS A 290 " =    1.049
peak=    3.305 closest distance to " CG  ARG A 219 " =    1.209
peak=    3.304 closest distance to " CG1 VAL A 174 " =    1.220
peak=    3.299 closest distance to " CG  LEU A 167 " =    1.127
peak=    3.298 closest distance to " O  BHOH Z 338 " =    2.200
peak=    3.296 closest distance to " CA  GLN A  88 " =    1.326
peak=    3.291 closest distance to " O   HOH Z 199 " =    1.651
peak=    3.288 closest distance to " CA  VAL A 125 " =    1.223
peak=    3.288 closest distance to " OH  TYR A  30 " =    1.233
peak=    3.287 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.279 closest distance to " CB  ASN A 148 " =    1.977
peak=    3.277 closest distance to " NZ  LYS A 117 " =    1.626
peak=    3.277 closest distance to " CB  MET A 105 " =    1.019
peak=    3.275 closest distance to " OG BSER A 134 " =    2.825
peak=    3.274 closest distance to " CA  ALA A  84 " =    1.249
peak=    3.273 closest distance to " O   HOH Z 353 " =    2.807
peak=    3.272 closest distance to " ND1 HIS A  81 " =    1.634
peak=    3.263 closest distance to " O   HOH Z 305 " =    3.866
peak=    3.261 closest distance to " CA  LEU A  83 " =    1.408
peak=    3.259 closest distance to " CG2 VAL A 197 " =    1.132
peak=    3.252 closest distance to " CA  ALA A 233 " =    1.664
peak=    3.251 closest distance to " O   HOH Z 367 " =    2.297
peak=    3.248 closest distance to " CG  GLN A  58 " =    2.671
peak=    3.247 closest distance to " O   HOH Z 128 " =    1.810
peak=    3.244 closest distance to " N   ASP A 132 " =    1.130
peak=    3.243 closest distance to " O   TRP A 274 " =    1.826
peak=    3.242 closest distance to " O   HOH Z 394 " =    1.675
peak=    3.242 closest distance to " CA  MET A 105 " =    1.039
peak=    3.239 closest distance to " CB  PRO A  90 " =    1.215
peak=    3.238 closest distance to " CZ3 TRP A  85 " =    0.962
peak=    3.236 closest distance to " O   HOH Z 185 " =    1.754
peak=    3.230 closest distance to " NH1 ARG A  14 " =    1.125
peak=    3.230 closest distance to " CA  ASN A 215 " =    1.138
peak=    3.229 closest distance to " O   HOH Z 387 " =    2.751
peak=    3.229 closest distance to " O   HOH Z 250 " =    1.526
peak=    3.228 closest distance to " CG2 VAL A 257 " =    0.896
peak=    3.227 closest distance to " CD2 LEU A 255 " =    1.478
peak=    3.227 closest distance to " CB  ALA A 104 " =    0.739
peak=    3.226 closest distance to " CA  LEU A 282 " =    1.031
peak=    3.223 closest distance to " O   HOH Z 148 " =    3.292
peak=    3.220 closest distance to " CA  ALA A 100 " =    1.031
peak=    3.219 closest distance to " O   HOH Z 164 " =    3.510
peak=    3.219 closest distance to " O   HOH Z 295 " =    1.503
peak=    3.217 closest distance to " O   HOH Z 156 " =    2.620
peak=    3.216 closest distance to " O   TYR A 116 " =    1.335
peak=    3.207 closest distance to " CB  ALA A   9 " =    1.606
peak=    3.205 closest distance to " O   HOH Z 139 " =    4.816
peak=    3.204 closest distance to " O   HOH Z 332 " =    1.567
peak=    3.204 closest distance to " O   HOH Z 248 " =    1.862
peak=    3.202 closest distance to " O   HOH Z 411 " =    1.740
peak=    3.199 closest distance to " O   HOH Z 417 " =    3.134
peak=    3.198 closest distance to " CG  MET A 185 " =    1.166
peak=    3.197 closest distance to " N   THR A  52 " =    1.078
peak=    3.197 closest distance to " O   HOH Z 432 " =    1.801
peak=    3.195 closest distance to " O   HOH Z 386 " =    2.304
peak=    3.195 closest distance to " O   HOH Z 325 " =    2.175
peak=    3.195 closest distance to " N   VAL A 126 " =    1.581
peak=    3.194 closest distance to " CA  THR A 221 " =    1.498
peak=    3.193 closest distance to " CB  ASP A 298 " =    1.222
peak=    3.193 closest distance to " CG2 THR A  29 " =    1.387
peak=    3.192 closest distance to " NH1 ARG A 269 " =    0.737
peak=    3.184 closest distance to " O   HOH Z 299 " =    4.610
peak=    3.182 closest distance to " CB  ALA A 242 " =    0.850
peak=    3.180 closest distance to " O   HOH Z 272 " =    1.937
peak=    3.180 closest distance to " CB  ASN A 285 " =    0.882
peak=    3.179 closest distance to " CB  GLN A  89 " =    1.110
peak=    3.174 closest distance to " OH  TYR A 116 " =    1.219
peak=    3.172 closest distance to " CD  PRO A  54 " =    1.084
peak=    3.172 closest distance to " CA  GLN A 223 " =    0.867
peak=    3.171 closest distance to " O   HOH Z 234 " =    1.915
peak=    3.166 closest distance to " CB  PHE A 283 " =    0.789
peak=    3.166 closest distance to " O   HOH Z 116 " =    1.742
peak=    3.163 closest distance to " O   HOH Z 150 " =    1.570
peak=    3.161 closest distance to " OG  SER A  62 " =    2.987
peak=    3.157 closest distance to " CA  MET A 188 " =    1.033
peak=    3.157 closest distance to " CG2 ILE A 106 " =    0.977
peak=    3.156 closest distance to " O   HOH Z  97 " =    2.359
peak=    3.156 closest distance to " O   HOH Z 365 " =    2.883
peak=    3.153 closest distance to " CB  PRO A 243 " =    1.305
peak=    3.144 closest distance to " CB  LEU A 300 " =    1.016
peak=    3.139 closest distance to " O   HOH Z 422 " =    2.498
peak=    3.137 closest distance to " O   HOH Z 171 " =    3.907
peak=    3.134 closest distance to " CA  GLY A 196 " =    0.996
peak=    3.133 closest distance to " CG1 ILE A  49 " =    1.572
peak=    3.133 closest distance to " CB  THR A 157 " =    1.141
peak=    3.131 closest distance to " O   VAL A  72 " =    3.198
peak=    3.128 closest distance to " CA  ASP A 140 " =    1.296
peak=    3.126 closest distance to " O   HOH Z 145 " =    2.475
peak=    3.118 closest distance to " O   HOH Z 251 " =    1.645
peak=    3.112 closest distance to " O   HOH Z 261 " =    1.775
peak=    3.112 closest distance to " CB  ASN A 215 " =    1.166
peak=    3.108 closest distance to " CB  SER A  28 " =    1.087
peak=    3.105 closest distance to " N   TYR A  15 " =    0.741
peak=    3.101 closest distance to " CZ2 TRP A 179 " =    1.817
peak=    3.099 closest distance to " O   HOH Z  88 " =    2.863
peak=    3.097 closest distance to " NZ ALYS A 290 " =    1.021
peak=    3.088 closest distance to " CG  GLN A  11 " =    1.234
peak=    3.085 closest distance to " NH2AARG A 275 " =    3.424
peak=    3.084 closest distance to " CG ALYS A 290 " =    1.149
peak=    3.082 closest distance to " N   ARG A 190 " =    0.977
peak=    3.082 closest distance to " N   ARG A 156 " =    1.483
peak=    3.071 closest distance to " CB  ALA A  43 " =    0.891
peak=    3.065 closest distance to " O   HOH Z 409 " =    2.950
peak=    3.054 closest distance to " NE2 GLN A  58 " =    4.140
peak=    3.048 closest distance to " CA  LYS A  48 " =    1.318
peak=    3.038 closest distance to " OD2 ASP A 298 " =    3.624
peak=    3.004 closest distance to " OD2 ASP A 200 " =    1.259

                           ----------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: 0.700 - 5.903
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.700 - 5.903

peak=   -4.617 closest distance to " O   HOH Z 266 " =    5.140
peak=   -4.302 closest distance to " CD  ARG A 156 " =    2.080
peak=   -4.289 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -4.268 closest distance to " O   HOH Z 166 " =    1.663
peak=   -4.241 closest distance to " O   HOH Z   5 " =    1.576
peak=   -4.225 closest distance to " CD  GLN A  58 " =    0.997
peak=   -4.216 closest distance to " CD  GLN A 223 " =    1.336
peak=   -4.207 closest distance to " CG1 VAL A 250 " =    2.704
peak=   -4.160 closest distance to " O   HOH Z 196 " =    2.432
peak=   -4.131 closest distance to " N   ALA A  43 " =    2.696
peak=   -4.081 closest distance to " O   GLY A 136 " =    2.371
peak=   -4.077 closest distance to " OD1 ASN A 148 " =    1.510
peak=   -4.054 closest distance to " O   HOH Z 290 " =    1.088
peak=   -4.044 closest distance to " CB  PRO A 243 " =    2.724
peak=   -4.041 closest distance to " OG  SER A  97 " =    2.238
peak=   -4.037 closest distance to " O   HOH Z 283 " =    2.279
peak=   -4.027 closest distance to " O   HOH Z 377 " =    1.079
peak=   -4.016 closest distance to " O   VAL A  67 " =    2.620
peak=   -4.011 closest distance to " OXT GLY A 302 " =    2.978
peak=   -4.008 closest distance to " CE2 TYR A  30 " =    2.707
peak=   -3.976 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.924 closest distance to " CD1 LEU A 101 " =    2.527
peak=   -3.923 closest distance to " C   HIS A 108 " =    1.116
peak=   -3.902 closest distance to " C   ASN A 285 " =    2.452
peak=   -3.892 closest distance to " O   HOH Z 394 " =    1.593
peak=   -3.881 closest distance to " CD1 PHE A  59 " =    1.945
peak=   -3.873 closest distance to " O   HOH Z  13 " =    1.746
peak=   -3.866 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.850 closest distance to " CD  ARG A  14 " =    3.433
peak=   -3.824 closest distance to " C   SER A 206 " =    1.492
peak=   -3.806 closest distance to " O   HOH Z 185 " =    2.545
peak=   -3.802 closest distance to " ND2 ASN A  45 " =    1.925
peak=   -3.795 closest distance to " CB  ALA A  10 " =    2.139
peak=   -3.791 closest distance to " O   PRO A 163 " =    2.182
peak=   -3.791 closest distance to " CB  ALA A 161 " =    2.683
peak=   -3.780 closest distance to " CH2 TRP A 179 " =    1.195
peak=   -3.775 closest distance to " O   HOH Z 210 " =    0.790
peak=   -3.735 closest distance to " CE2 PHE A  61 " =    2.580
peak=   -3.728 closest distance to " O   HOH Z  71 " =    1.678
peak=   -3.727 closest distance to " O   HOH Z 150 " =    1.936
peak=   -3.709 closest distance to " NH2 ARG A  66 " =    1.754
peak=   -3.701 closest distance to " CD1 LEU A  25 " =    2.498
peak=   -3.687 closest distance to " CB  PHE A 208 " =    2.332
peak=   -3.684 closest distance to " O   ALA A  10 " =    1.748
peak=   -3.669 closest distance to " NE2 GLN A 103 " =    1.821
peak=   -3.628 closest distance to " O   HOH Z 150 " =    1.092
peak=   -3.625 closest distance to " CB  ASP A 132 " =    2.385
peak=   -3.625 closest distance to " CG2 ILE A 263 " =    2.359
peak=   -3.609 closest distance to " CG  ASP A 231 " =    0.858
peak=   -3.604 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.604 closest distance to " O   HOH Z  52 " =    1.690
peak=   -3.592 closest distance to " ND2 ASN A  45 " =    1.097
peak=   -3.586 closest distance to " CA  GLY A 133 " =    2.368
peak=   -3.586 closest distance to " O   HOH Z 292 " =    4.611
peak=   -3.569 closest distance to " O   HOH Z 264 " =    1.826
peak=   -3.566 closest distance to " CD  PRO A 213 " =    2.247
peak=   -3.565 closest distance to " O   HOH Z  19 " =    2.151
peak=   -3.556 closest distance to " O   HOH Z 351 " =    1.612
peak=   -3.555 closest distance to " O   HOH Z 234 " =    4.442
peak=   -3.554 closest distance to " O   HOH Z 252 " =    4.008
peak=   -3.552 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.543 closest distance to " ND2 ASN A 187 " =    1.703
peak=   -3.528 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.502 closest distance to " OD1 ASP A 191 " =    1.577
peak=   -3.502 closest distance to " CH2 TRP A 177 " =    2.096
peak=   -3.497 closest distance to " CA  GLY A 241 " =    2.353
peak=   -3.494 closest distance to " CB  ALA A   9 " =    2.678
peak=   -3.493 closest distance to " O   ALA A  34 " =    2.521
peak=   -3.493 closest distance to " CG  ARG A 269 " =    2.325
peak=   -3.490 closest distance to " O   HOH Z 197 " =    1.999
peak=   -3.490 closest distance to " NH2 ARG A 159 " =    2.342
peak=   -3.490 closest distance to " O   HOH Z 298 " =    2.647
peak=   -3.489 closest distance to " O   SER A 276 " =    1.700
peak=   -3.486 closest distance to " O   HOH Z 377 " =    2.122
peak=   -3.480 closest distance to " O   HOH Z   6 " =    1.487
peak=   -3.477 closest distance to " O   HOH Z 301 " =    2.431
peak=   -3.464 closest distance to " O   HOH Z 165 " =    1.898
peak=   -3.463 closest distance to " ND2 ASN A 249 " =    2.463
peak=   -3.459 closest distance to " CB  ALA A 291 " =    2.392
peak=   -3.456 closest distance to " O   HOH Z 353 " =    2.309
peak=   -3.456 closest distance to " O   HOH Z 166 " =    1.922
peak=   -3.454 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.448 closest distance to " NE2 GLN A 194 " =    1.921
peak=   -3.447 closest distance to " O   SER A 210 " =    1.934
peak=   -3.436 closest distance to " O   HOH Z 407 " =    3.664
peak=   -3.430 closest distance to " CE3 TRP A 150 " =    2.069
peak=   -3.415 closest distance to " O   HOH Z 106 " =    2.055
peak=   -3.415 closest distance to " CE BMET A  47 " =    1.989
peak=   -3.415 closest distance to " O   HOH Z 150 " =    2.014
peak=   -3.404 closest distance to " O   HOH Z  49 " =    1.246
peak=   -3.404 closest distance to " O   SER A 271 " =    2.099
peak=   -3.402 closest distance to " CB  ALA A  43 " =    2.602
peak=   -3.401 closest distance to " CD1 ILE A 151 " =    2.390
peak=   -3.401 closest distance to " O   HOH Z 128 " =    2.536
peak=   -3.396 closest distance to " CZ  PHE A  38 " =    1.903
peak=   -3.392 closest distance to " CG1 VAL A  78 " =    2.777
peak=   -3.389 closest distance to " CD2 PHE A  61 " =    2.007
peak=   -3.387 closest distance to " O   HOH Z 368 " =    1.838
peak=   -3.387 closest distance to " O   VAL A  67 " =    2.987
peak=   -3.378 closest distance to " OG BSER A 210 " =    2.184
peak=   -3.378 closest distance to " O   HOH Z 275 " =    1.556
peak=   -3.376 closest distance to " C   ALA A 158 " =    1.364
peak=   -3.374 closest distance to " O   HOH Z 177 " =    1.774
peak=   -3.369 closest distance to " CD1 TRP A 179 " =    0.999
peak=   -3.363 closest distance to " O   HOH Z 200 " =    1.331
peak=   -3.361 closest distance to " N   SER A 276 " =    1.532
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    1.922
peak=   -3.354 closest distance to " O   HOH Z 236 " =    1.523
peak=   -3.353 closest distance to " NH2AARG A 275 " =    5.396
peak=   -3.352 closest distance to " O   VAL A 189 " =    2.652
peak=   -3.347 closest distance to " NH2 ARG A  79 " =    1.596
peak=   -3.342 closest distance to " O   HOH Z 426 " =    1.693
peak=   -3.341 closest distance to " C   THR A 279 " =    1.104
peak=   -3.341 closest distance to " CG  PRO A 243 " =    1.788
peak=   -3.340 closest distance to " OG BSER A 210 " =    1.425
peak=   -3.335 closest distance to " CB  SER A 146 " =    2.212
peak=   -3.335 closest distance to " O   HOH Z 111 " =    1.962
peak=   -3.328 closest distance to " O   HOH Z 372 " =    2.560
peak=   -3.327 closest distance to " CG2BVAL A  41 " =    1.561
peak=   -3.326 closest distance to " CD  GLN A  58 " =    0.932
peak=   -3.324 closest distance to " CB  PHE A 192 " =    1.969
peak=   -3.323 closest distance to " NE1 TRP A 266 " =    2.362
peak=   -3.321 closest distance to " CG1AVAL A 121 " =    1.583
peak=   -3.318 closest distance to " CD2 PHE A 225 " =    1.280
peak=   -3.314 closest distance to " O   HOH Z 114 " =    3.718
peak=   -3.313 closest distance to " CG  GLU A  53 " =    1.486
peak=   -3.306 closest distance to " O   HOH Z 111 " =    1.479
peak=   -3.303 closest distance to " OG  SER A  62 " =    1.668
peak=   -3.298 closest distance to " CD2 LEU A 167 " =    1.834
peak=   -3.298 closest distance to " CG2 ILE A  49 " =    2.742
peak=   -3.294 closest distance to " O   HOH Z 136 " =    2.115
peak=   -3.294 closest distance to " O   HOH Z 311 " =    3.785
peak=   -3.291 closest distance to " CG2 VAL A 189 " =    2.168
peak=   -3.290 closest distance to " OD1 ASN A 187 " =    1.639
peak=   -3.287 closest distance to " CB  PHE A  16 " =    2.602
peak=   -3.286 closest distance to " O   HOH Z 117 " =    4.502
peak=   -3.286 closest distance to " C   LEU A 143 " =    1.176
peak=   -3.276 closest distance to " O   ALA A   1 " =    1.941
peak=   -3.267 closest distance to " OH  TYR A 169 " =    0.974
peak=   -3.266 closest distance to " CB  ALA A 291 " =    2.204
peak=   -3.265 closest distance to " O   HOH Z  78 " =    1.831
peak=   -3.263 closest distance to " O   PHE A 218 " =    1.483
peak=   -3.262 closest distance to " O   HOH Z 149 " =    1.973
peak=   -3.260 closest distance to " CD2 PHE A  59 " =    2.538
peak=   -3.259 closest distance to " CD  LYS A 289 " =    2.446
peak=   -3.255 closest distance to " O   HOH Z 414 " =    1.639
peak=   -3.253 closest distance to " CG  GLU A 277 " =    1.181
peak=   -3.253 closest distance to " O   HOH Z  38 " =    1.350
peak=   -3.251 closest distance to " O   HOH Z  90 " =    1.823
peak=   -3.248 closest distance to " CA  GLY A 241 " =    3.194
peak=   -3.247 closest distance to " O   HOH Z 393 " =    1.580
peak=   -3.247 closest distance to " O   HOH Z 396 " =    1.869
peak=   -3.236 closest distance to " CE  MET A  93 " =    1.427
peak=   -3.233 closest distance to " C   ILE A 234 " =    1.251
peak=   -3.233 closest distance to " OG BSER A 134 " =    1.287
peak=   -3.232 closest distance to " CZ  TYR A 169 " =    1.801
peak=   -3.232 closest distance to " O   HOH Z 283 " =    5.903
peak=   -3.230 closest distance to " CD1 ILE A 263 " =    1.993
peak=   -3.228 closest distance to " NE2 GLN A  88 " =    1.031
peak=   -3.226 closest distance to " C   ASN A 187 " =    1.937
peak=   -3.225 closest distance to " O   HOH Z  37 " =    1.897
peak=   -3.225 closest distance to " O   HOH Z 350 " =    2.001
peak=   -3.224 closest distance to " O   GLY A 196 " =    1.119
peak=   -3.221 closest distance to " CD1 LEU A 228 " =    2.411
peak=   -3.219 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.212 closest distance to " C   ARG A  79 " =    2.639
peak=   -3.211 closest distance to " N   SER A   3 " =    2.144
peak=   -3.208 closest distance to " O   HOH Z  11 " =    1.860
peak=   -3.207 closest distance to " ND2 ASN A  60 " =    1.843
peak=   -3.206 closest distance to " CB  GLN A  11 " =    1.682
peak=   -3.206 closest distance to " O   HOH Z 371 " =    1.665
peak=   -3.205 closest distance to " O   ALA A  34 " =    2.144
peak=   -3.199 closest distance to " CG1 VAL A 112 " =    2.752
peak=   -3.190 closest distance to " O   HOH Z 171 " =    2.155
peak=   -3.186 closest distance to " CA  VAL A 197 " =    1.020
peak=   -3.184 closest distance to " O   GLY A 118 " =    2.216
peak=   -3.182 closest distance to " CG  PRO A 163 " =    2.326
peak=   -3.178 closest distance to " O   HOH Z 313 " =    1.365
peak=   -3.171 closest distance to " O   HOH Z  88 " =    2.517
peak=   -3.169 closest distance to " O   ASP A  27 " =    2.185
peak=   -3.168 closest distance to " CG1 VAL A 125 " =    2.064
peak=   -3.167 closest distance to " OE2 GLU A 152 " =    2.348
peak=   -3.166 closest distance to " O   ALA A 160 " =    1.563
peak=   -3.163 closest distance to " O   HOH Z  77 " =    1.972
peak=   -3.155 closest distance to " N   GLN A  58 " =    1.582
peak=   -3.146 closest distance to " NH2 ARG A  66 " =    4.046
peak=   -3.138 closest distance to " O   HOH Z 189 " =    1.757
peak=   -3.132 closest distance to " CG1 VAL A 112 " =    2.894
peak=   -3.130 closest distance to " CB  PRO A 163 " =    2.652
peak=   -3.125 closest distance to " OG1 THR A  82 " =    1.415
peak=   -3.124 closest distance to " CB  TRP A  85 " =    2.451
peak=   -3.123 closest distance to " O   GLY A 211 " =    1.377
peak=   -3.123 closest distance to " O   ASN A 301 " =    1.300
peak=   -3.120 closest distance to " CE3 TRP A 274 " =    2.517
peak=   -3.117 closest distance to " O   HOH Z 422 " =    1.402
peak=   -3.115 closest distance to " O   HOH Z 378 " =    1.391
peak=   -3.114 closest distance to " O   HOH Z 384 " =    1.996
peak=   -3.112 closest distance to " O   HOH Z 193 " =    2.421
peak=   -3.104 closest distance to " O   HOH Z  30 " =    0.700
peak=   -3.104 closest distance to " O   HOH Z 191 " =    5.713
peak=   -3.100 closest distance to " NE2 GLN A  58 " =    2.731
peak=   -3.089 closest distance to " O   HOH Z 259 " =    1.996
peak=   -3.085 closest distance to " O   HOH Z 423 " =    2.324
peak=   -3.083 closest distance to " O   HOH Z 357 " =    2.076
peak=   -3.078 closest distance to " N   TYR A  68 " =    2.947
peak=   -3.076 closest distance to " N   ASP A 171 " =    2.434
peak=   -3.075 closest distance to " CA  SER A  62 " =    2.506
peak=   -3.074 closest distance to " O   HOH Z 193 " =    1.849
peak=   -3.074 closest distance to " OG BSER A 134 " =    1.968
peak=   -3.069 closest distance to " O   HOH Z 240 " =    3.736
peak=   -3.069 closest distance to " O   HOH Z 326 " =    4.963
peak=   -3.065 closest distance to " CG  TRP A 266 " =    1.826
peak=   -3.055 closest distance to " C   GLU A  46 " =    0.974
peak=   -3.055 closest distance to " O   ASP A 171 " =    1.083

================= 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    :  0.4000 0.3848   6.203379e+00   6.170660e+00
   1_bss:  0.3884 0.3740   6.187980e+00   6.151154e+00
   1_xyz:  0.2683 0.2928   5.882102e+00   5.954485e+00
   1_adp:  0.2485 0.2973   5.833118e+00   5.962723e+00
   1_occ:  0.2482 0.2965   5.832100e+00   5.962193e+00
   2_bss:  0.2465 0.2940   5.827568e+00   5.957942e+00
   2_xyz:  0.1819 0.2142   5.539407e+00   5.685200e+00
   2_adp:  0.1638 0.2064   5.467144e+00   5.650708e+00
   2_occ:  0.1636 0.2062   5.466368e+00   5.650108e+00
   3_bss:  0.1632 0.2064   5.464333e+00   5.647826e+00
   3_xyz:  0.1337 0.1786   5.294443e+00   5.512256e+00
   3_adp:  0.1278 0.1705   5.248977e+00   5.467670e+00
   3_occ:  0.1276 0.1704   5.248151e+00   5.466828e+00
   4_bss:  0.1280 0.1703   5.249311e+00   5.466377e+00
   4_xyz:  0.1241 0.1672   5.224852e+00   5.444346e+00
   4_adp:  0.1227 0.1678   5.220752e+00   5.445804e+00
   4_occ:  0.1226 0.1677   5.220247e+00   5.445707e+00
   5_bss:  0.1226 0.1676   5.220125e+00   5.445726e+00
   5_xyz:  0.1174 0.1654   5.191126e+00   5.430664e+00
   5_adp:  0.1174 0.1637   5.187638e+00   5.423421e+00
   5_occ:  0.1174 0.1637   5.187753e+00   5.423980e+00
   5_bss:  0.1173 0.1636   5.187794e+00   5.424048e+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:  0.300  50.000  -2.264   4.997  -1.255   0.000  -0.000  -0.000
   1_xyz:  0.300  50.000  -2.264   4.997  -1.255   0.000  -0.000  -0.000
   1_adp:  0.300  50.000  -2.264   4.997  -1.255   0.000  -0.000  -0.000
   1_occ:  0.300  50.000  -2.264   4.997  -1.255   0.000  -0.000  -0.000
   2_bss:  0.330  71.346  -1.814   1.551  -0.699   0.000  -0.000  -0.000
   2_xyz:  0.330  71.346  -1.814   1.551  -0.699   0.000  -0.000  -0.000
   2_adp:  0.330  71.346  -1.814   1.551  -0.699   0.000  -0.000  -0.000
   2_occ:  0.330  71.346  -1.814   1.551  -0.699   0.000  -0.000  -0.000
   3_bss:  0.331  78.474  -1.724   0.073  -0.546   0.000  -0.000  -0.000
   3_xyz:  0.331  78.474  -1.724   0.073  -0.546   0.000  -0.000  -0.000
   3_adp:  0.331  78.474  -1.724   0.073  -0.546   0.000  -0.000  -0.000
   3_occ:  0.331  78.474  -1.724   0.073  -0.546   0.000  -0.000  -0.000
   4_bss:  0.330  72.742  -1.475  -0.418  -0.207  -0.000  -0.000  -0.000
   4_xyz:  0.330  72.742  -1.475  -0.418  -0.207  -0.000  -0.000  -0.000
   4_adp:  0.330  72.742  -1.475  -0.418  -0.207  -0.000  -0.000  -0.000
   4_occ:  0.330  72.742  -1.475  -0.418  -0.207  -0.000  -0.000  -0.000
   5_bss:  0.325  70.667  -1.394  -0.556  -0.120  -0.000  -0.000  -0.000
   5_xyz:  0.325  70.667  -1.394  -0.556  -0.120  -0.000  -0.000  -0.000
   5_adp:  0.325  70.667  -1.394  -0.556  -0.120  -0.000  -0.000  -0.000
   5_occ:  0.325  70.667  -1.394  -0.556  -0.120  -0.000  -0.000  -0.000
   5_bss:  0.322  67.120  -1.156  -0.453   0.114  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.269 0.6056  0.7616    45511.508
   1_bss:  42.526 0.6130  0.7831    42623.467
   1_xyz:  31.026 0.7470  0.9212    23639.016
   1_adp:  31.378 0.7426  0.8994    24059.034
   1_occ:  31.378 0.7425  0.8990    24004.428
   2_bss:  30.940 0.7475  0.8842    23623.736
   2_xyz:  21.292 0.8485  0.9660    11852.099
   2_adp:  20.091 0.8607  0.9625    10967.253
   2_occ:  20.069 0.8609  0.9625    10952.515
   3_bss:  19.953 0.8621  0.9503    10866.356
   3_xyz:  16.779 0.8911  0.9670     8061.567
   3_adp:  15.664 0.9013  0.9617     7437.135
   3_occ:  15.640 0.9016  0.9616     7426.432
   4_bss:  15.641 0.9015  0.9633     7432.015
   4_xyz:  15.131 0.9060  0.9659     7095.248
   4_adp:  15.136 0.9061  0.9566     7135.256
   4_occ:  15.131 0.9062  0.9564     7132.897
   5_bss:  15.130 0.9062  0.9569     7133.101
   5_xyz:  14.832 0.9084  0.9589     6899.199
   5_adp:  14.662 0.9100  0.9513     6822.928
   5_occ:  14.670 0.9099  0.9512     6829.802
   5_bss:  14.671 0.9099  0.9578     6829.244
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6478e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6478e-01
   1_xyz:   1.497  0.013  0.092 15.644  0.006  4.118   1.1377e-01
   1_adp:   1.497  0.013  0.092 15.644  0.006  4.118   1.1377e-01
   1_occ:   1.497  0.013  0.092 15.644  0.006  4.118   1.1377e-01
   2_bss:   1.497  0.013  0.092 15.644  0.006  4.118   1.1377e-01
   2_xyz:   1.115  0.008  0.076 14.753  0.005  4.139   6.8420e-02
   2_adp:   1.115  0.008  0.076 14.753  0.005  4.139   6.8420e-02
   2_occ:   1.115  0.008  0.076 14.753  0.005  4.139   6.8420e-02
   3_bss:   1.115  0.008  0.076 14.753  0.005  4.139   6.8420e-02
   3_xyz:   1.069  0.009  0.076 14.869  0.004  4.117   6.8140e-02
   3_adp:   1.069  0.009  0.076 14.869  0.004  4.117   6.8140e-02
   3_occ:   1.069  0.009  0.076 14.869  0.004  4.117   6.8140e-02
   4_bss:   1.069  0.009  0.076 14.869  0.004  4.117   6.8140e-02
   4_xyz:   0.957  0.007  0.072 14.659  0.003  4.121   5.5518e-02
   4_adp:   0.957  0.007  0.072 14.659  0.003  4.121   5.5518e-02
   4_occ:   0.957  0.007  0.072 14.659  0.003  4.121   5.5518e-02
   5_bss:   0.957  0.007  0.072 14.659  0.003  4.121   5.5518e-02
   5_xyz:   1.031  0.009  0.078 14.757  0.003  4.125   6.3398e-02
   5_adp:   1.031  0.009  0.078 14.757  0.003  4.125   6.3398e-02
   5_occ:   1.031  0.009  0.078 14.757  0.003  4.125   6.3398e-02
   5_bss:   1.031  0.009  0.078 14.757  0.003  4.125   6.3398e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.598   2.4428e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.598   2.4428e-01
   1_xyz:  10.541  0.089  0.389 85.965  0.044  2.077   9.8045e-02
   1_adp:  10.541  0.089  0.389 85.965  0.044  2.077   9.8045e-02
   1_occ:  10.541  0.089  0.389 85.965  0.044  2.077   9.8045e-02
   2_bss:  10.541  0.089  0.389 85.965  0.044  2.077   9.8045e-02
   2_xyz:   7.752  0.043  0.220 83.495  0.050  2.266   5.5616e-02
   2_adp:   7.752  0.043  0.220 83.495  0.050  2.266   5.5616e-02
   2_occ:   7.752  0.043  0.220 83.495  0.050  2.266   5.5616e-02
   3_bss:   7.752  0.043  0.220 83.495  0.050  2.266   5.5616e-02
   3_xyz:   7.559  0.051  0.241 80.670  0.040  2.300   5.4296e-02
   3_adp:   7.559  0.051  0.241 80.670  0.040  2.300   5.4296e-02
   3_occ:   7.559  0.051  0.241 80.670  0.040  2.300   5.4296e-02
   4_bss:   7.559  0.051  0.241 80.670  0.040  2.300   5.4296e-02
   4_xyz:   7.594  0.040  0.220 81.899  0.041  2.387   3.4286e-02
   4_adp:   7.594  0.040  0.220 81.899  0.041  2.387   3.4286e-02
   4_occ:   7.594  0.040  0.220 81.899  0.041  2.387   3.4286e-02
   5_bss:   7.594  0.040  0.220 81.899  0.041  2.387   3.4286e-02
   5_xyz:   7.876  0.042  0.248 81.071  0.038  2.338   3.9379e-02
   5_adp:   7.876  0.042  0.248 81.071  0.038  2.338   3.9379e-02
   5_occ:   7.876  0.042  0.248 81.071  0.038  2.338   3.9379e-02
   5_bss:   7.876  0.042  0.248 81.071  0.038  2.338   3.9379e-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: 104.83   0.00  16.45 104.83   0.00  12.62  66.38   3.15  37.28
   1_occ: 104.83   0.00  16.45 104.83   0.00  12.62  66.38   3.15  37.28
   2_bss: 104.83   0.00  16.45 104.83   0.00  12.62  66.38   3.15  37.28
   2_xyz: 104.83   0.00  16.45 104.83   0.00  12.62  66.38   3.15  37.28
   2_adp:  99.60   0.00  17.73  98.04   0.00  13.01  99.60   3.97  43.47
   2_occ:  99.60   0.00  17.73  98.04   0.00  13.01  99.60   3.97  43.47
   3_bss:  99.60   0.00  17.73  98.04   0.00  13.01  99.60   3.97  43.47
   3_xyz:  99.60   0.00  17.73  98.04   0.00  13.01  99.60   3.97  43.47
   3_adp:  99.35   0.00  17.02  99.35   0.00  12.35  99.27   0.67  42.43
   3_occ:  99.35   0.00  17.02  99.35   0.00  12.35  99.27   0.67  42.43
   4_bss:  99.35   0.00  17.02  99.35   0.00  12.35  99.27   0.67  42.43
   4_xyz:  99.35   0.00  17.02  99.35   0.00  12.35  99.27   0.67  42.43
   4_adp: 104.21   0.00  16.70 104.21   0.00  12.07 102.95   0.00  41.95
   4_occ: 104.21   0.00  16.70 104.21   0.00  12.07 102.95   0.00  41.95
   5_bss: 104.21   0.00  16.70 104.21   0.00  12.07 102.95   0.00  41.95
   5_xyz: 104.21   0.00  16.70 104.21   0.00  12.07 102.95   0.00  41.95
   5_adp: 101.91   0.00  16.10 101.91   0.00  11.71  99.19   1.58  39.97
   5_occ: 101.91   0.00  16.10 101.91   0.00  11.71  99.19   1.58  39.97
   5_bss: 101.91   0.00  16.10 101.91   0.00  11.71  99.19   1.59  39.98
------------------------------------------------------------------------
 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:    1.447    0.035    0.416
   1_adp:    1.447    0.035    0.416
   1_occ:    1.447    0.035    0.416
   2_bss:    1.447    0.035    0.416
   2_xyz:    1.193    0.044    0.515
   2_adp:    1.193    0.044    0.515
   2_occ:    1.193    0.044    0.515
   3_bss:    1.193    0.044    0.515
   3_xyz:    1.300    0.041    0.609
   3_adp:    1.300    0.041    0.609
   3_occ:    1.300    0.041    0.609
   4_bss:    1.300    0.041    0.609
   4_xyz:    1.290    0.037    0.623
   4_adp:    1.290    0.037    0.623
   4_occ:    1.290    0.037    0.623
   5_bss:    1.290    0.037    0.623
   5_xyz:    1.288    0.061    0.644
   5_adp:    1.288    0.061    0.644
   5_occ:    1.288    0.061    0.644
   5_bss:    1.288    0.061    0.644
------------------------------------------------------------------------

CPU time actual refinement: 324.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/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_952/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_952/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.05 
  Macro-tasks:
    bulk solvent and scale       = 42.09  
    individual site refinement   = 130.71 
    weights calculation          = 29.13  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 208.56 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 101.14 
    alpha_beta                      = 8.29   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 109.94 
    fmodel                         = 6.83   
    r_factors                      = 0.26   
    phase_errors                   = 10.68  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 240.39 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.638 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    627 calls, 100.87 s
gradients_fft:          572 calls,  96.82 s

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

# Date 2008-01-16 Time 06:03:47 PST -0800 (1200492227.85 s)
Start R-work = 0.4000, R-free = 0.3848 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.3884, R-free = 0.3740
Final R-work = 0.1173, R-free = 0.1636