# Date 2008-01-16 Time 05:40:25 PST -0800 (1200490825.79 s)
#phil __OFF__

Command line arguments: "../830.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25263
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 830

-------------------------------------------------------------------------------
  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: (70.6012, 47.8686, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, 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: (70.6012, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00122
Completeness in resolution range: 0.963836
Completeness with d_max=infinity: 0.96081

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   2.0012

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: (70.6012, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 2.00122
Completeness in resolution range: 0.963836
Completeness with d_max=infinity: 0.96081

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.2815 [2132/2160]  1920   212   9.9%
  bin  2:  4.2815 -  3.4114 [2041/2060]  1836   205  10.0%
  bin  3:  3.4114 -  2.9840 [2030/2050]  1828   202  10.0%
  bin  4:  2.9840 -  2.7129 [2000/2025]  1802   198   9.9%
  bin  5:  2.7129 -  2.5194 [1992/2011]  1790   202  10.1%
  bin  6:  2.5194 -  2.3715 [1980/2025]  1786   194   9.8%
  bin  7:  2.3715 -  2.2531 [1974/2008]  1772   202  10.2%
  bin  8:  2.2531 -  2.1553 [1958/1993]  1759   199  10.2%
  bin  9:  2.1553 -  2.0726 [1956/1984]  1764   192   9.8%
  bin 10:  2.0726 -  2.0012 [1526/2008]  1373   153  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/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:
        1.76 -     2.39: 10
        2.39 -     3.02: 1993
        3.02 -     3.64: 4562
        3.64 -     4.27: 8971
        4.27 -     4.90: 12422
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.760 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 206 " - " O   HOH Z 342 "  1.893 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.999 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.031 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27953 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_830/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/model_refine_001.geo

CPU time processing inputs: 9.49


============================ 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 = 70.60125 47.8686 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3753   r_free= 0.3598   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.177454                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7751 0.99   1382  155 0.3154 0.3319      6.4349      6.4249|
|  2:  4.7751 -  3.8104 0.99   1338  145 0.3113 0.3285       6.663      6.6571|
|  3:  3.8104 -  3.3347 0.99   1307  150 0.3359 0.3038       6.534      6.4663|
|  4:  3.3347 -  3.0325 0.99   1303  141 0.3577 0.3134      6.4037      6.2802|
|  5:  3.0325 -  2.8167 0.99   1285  142 0.3870 0.3520      6.2755      6.2579|
|  6:  2.8167 -  2.6516 0.98   1288  143 0.3986 0.3689      6.1849       6.046|
|  7:  2.6516 -  2.5194 0.99   1273  143 0.4044 0.3481      6.1542      5.9961|
|  8:  2.5194 -  2.4102 0.98   1274  138 0.4138 0.4043      6.0964      6.1304|
|  9:  2.4102 -  2.3178 0.98   1283  145 0.4189 0.4235      6.0318      6.0893|
| 10:  2.3178 -  2.2380 0.97   1236  139 0.4254 0.3965      6.0457      5.9714|
| 11:  2.2380 -  2.1683 0.99   1273  144 0.4145 0.3622      5.9684       5.929|
| 12:  2.1683 -  2.1065 0.98   1275  133 0.4188 0.4498      5.9161      5.9993|
| 13:  2.1065 -  2.0512 0.97   1239  143 0.4268 0.3828      5.8204      5.7675|
| 14:  2.0512 -  2.0012 0.68    874   98 0.3991 0.4368      5.7455      5.7549|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7751  1382   155  0.74  30.28   0.85     0.77      56342.50|
|  2:  4.7751 -  3.8104  1338   145  0.80  26.56   0.94     0.86      64498.76|
|  3:  3.8104 -  3.3347  1307   150  0.75  30.93   0.95     0.89      64059.01|
|  4:  3.3347 -  3.0325  1303   141  0.72  33.84   0.94     0.86      53889.90|
|  5:  3.0325 -  2.8167  1285   142  0.66  38.72   0.94     0.83      44773.98|
|  6:  2.8167 -  2.6516  1288   143  0.65  39.76   0.94     0.81      37087.87|
|  7:  2.6516 -  2.5194  1273   143  0.64  40.54   0.96     0.81      34702.27|
|  8:  2.5194 -  2.4102  1274   138  0.61  43.00   0.96     0.80      34478.08|
|  9:  2.4102 -  2.3178  1283   145  0.58  45.53   0.95     0.79      34060.19|
| 10:  2.3178 -  2.2380  1236   139  0.59  44.99   0.98     0.79      31664.89|
| 11:  2.2380 -  2.1683  1273   144  0.59  45.09   0.99     0.82      29434.94|
| 12:  2.1683 -  2.1065  1275   133  0.58  45.96   1.00     0.81      27859.51|
| 13:  2.1065 -  2.0512  1239   143  0.55  48.45   0.96     0.77      25246.13|
| 14:  2.0512 -  2.0012   874    98  0.54  48.99   1.00     0.71      20985.14|
|alpha:            min =        0.71 max =            0.89 mean =         0.81|
|beta:             min =    20985.14 max =        64498.76 mean =     40667.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           89.97 mean =        39.83|
|phase err.(test): min =        0.00 max =           89.94 mean =        39.97|
|-----------------------------------------------------------------------------|

============================== 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 = 4.227449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.564   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.027520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.757   (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 |  1.760 -  2.074:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.074 -  2.388:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.388 -  2.702:      108 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.702 -  3.016:     1885 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.016 -  3.330:     1856 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.330 -  3.644:     2706 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.644 -  3.958:     4627 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.958 -  4.272:     4344 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.272 -  4.586:     5639 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.586 -  4.900:     6783 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| 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  1.760 |       0.179 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3753   r_free= 0.3598   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.177454                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3597   r_free= 0.3442   ksol= 0.30   Bsol= 43.08   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,5.47,-1.84,0.00,-0.00,-0.00); trace/3= 0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.156492                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.908175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.361   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.535083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3597      final r-factor (work) = 0.2817          |
| start r-factor (free) = 0.3442      final r-factor (free) = 0.3050          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1977 = 3.91 * 0.50 * 6.1582 + 1.00 * 0.1641                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7773 = 3.91 * 0.50 * 5.9756 + 1.00 * 0.1003                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2817      final r-factor (work) = 0.2584          |
| start r-factor (free) = 0.3050      final r-factor (free) = 0.3144          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2035 = 0.54 * 1.00 * 5.9756 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1568 = 0.54 * 1.00 * 5.8782 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.39   16.91    None  None   None       |
|    all(noH): 2823   0      0.00    85.39   16.91    None  None   None       |
|    Sol.    : 438    0      1.36    85.39   35.98    None  None   None       |
|    Mac.    : 2385   0      0.00    71.23   13.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.539:  823   |   5:    42.695 -  51.234:   92        |
|      1:     8.539 -  17.078: 1033   |   6:    51.234 -  59.773:   67        |
|      2:    17.078 -  25.617:  435   |   7:    59.773 -  68.312:   25        |
|      3:    25.617 -  34.156:  202   |   8:    68.312 -  76.851:   10        |
|      4:    34.156 -  42.695:  135   |   9:    76.851 -  85.389:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2584 r_free = 0.3144             target_work(ml) = 5.885         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2582 r_free = 0.3142             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2582   r_free= 0.3142   ksol= 0.30   Bsol= 43.08   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,5.47,-1.84,0.00,-0.00,-0.00); trace/3= 0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.883981                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2565   r_free= 0.3119   ksol= 0.32   Bsol= 62.22   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,2.12,-0.87,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.880524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.023083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.733   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.443856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.659  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2565      final r-factor (work) = 0.1922          |
| start r-factor (free) = 0.3119      final r-factor (free) = 0.2318          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9215 = 4.02 * 0.50 * 5.8767 + 1.00 * 0.1003                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6571 = 4.02 * 0.50 * 5.7585 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1922      final r-factor (work) = 0.1758          |
| start r-factor (free) = 0.2318      final r-factor (free) = 0.2185          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5674 = 0.44 * 1.00 * 5.7585 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4753 = 0.44 * 1.00 * 5.5524 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.83   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    85.83   17.01    None  None   None       |
|    Sol.    : 438    0      3.85    85.83   39.35    None  None   None       |
|    Mac.    : 2385   0      0.00    79.93   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.583:  877   |   5:    42.915 -  51.498:  108        |
|      1:     8.583 -  17.166: 1103   |   6:    51.498 -  60.081:   76        |
|      2:    17.166 -  25.749:  321   |   7:    60.081 -  68.664:   35        |
|      3:    25.749 -  34.332:  165   |   8:    68.664 -  77.248:   20        |
|      4:    34.332 -  42.915:  115   |   9:    77.248 -  85.831:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1758 r_free = 0.2185             target_work(ml) = 5.532         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1756 r_free = 0.2185             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1756   r_free= 0.2185   ksol= 0.32   Bsol= 62.22   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,2.12,-0.87,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.530927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1751   r_free= 0.2176   ksol= 0.32   Bsol= 66.97   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,0.34,-0.62,0.00,-0.00,-0.00); trace/3= -0.68                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.528936                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.636840              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.750  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.048793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.849  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1751      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2176      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1694 = 3.64 * 0.50 * 5.5520 + 1.00 * 0.0735                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9156 = 3.64 * 0.50 * 5.4143 + 1.00 * 0.0703                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6893 = 1.05 * 1.00 * 5.4143 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5395 = 1.05 * 1.00 * 5.2705 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.99   16.95    None  None   None       |
|    all(noH): 2823   0      0.00    94.99   16.95    None  None   None       |
|    Sol.    : 438    0      4.37    92.70   41.95    None  None   None       |
|    Mac.    : 2385   0      0.00    94.99   12.36    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 -   9.499: 1108   |   5:    47.495 -  56.994:  102        |
|      1:     9.499 -  18.998: 1059   |   6:    56.994 -  66.492:   70        |
|      2:    18.998 -  28.497:  200   |   7:    66.492 -  75.991:   36        |
|      3:    28.497 -  37.996:  136   |   8:    75.991 -  85.490:   11        |
|      4:    37.996 -  47.495:   97   |   9:    85.490 -  94.989:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1711             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1268 r_free = 0.1711             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1711   ksol= 0.32   Bsol= 66.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,0.34,-0.62,0.00,-0.00,-0.00); trace/3= -0.68                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.246006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1711   ksol= 0.33   Bsol= 69.38   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.36,-0.44,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.247629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.581953              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.781  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.564  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5118 = 3.58 * 0.50 * 5.2717 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4039 = 3.58 * 0.50 * 5.2082 + 1.00 * 0.0762                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4419 = 0.66 * 1.00 * 5.2082 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4198 = 0.66 * 1.00 * 5.1753 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.65   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    97.65   16.59    None  None   None       |
|    Sol.    : 438    0      1.76    93.62   41.29    None  None   None       |
|    Mac.    : 2385   0      0.00    97.65   12.05    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 -   9.765: 1215   |   5:    48.826 -  58.591:   95        |
|      1:     9.765 -  19.531:  989   |   6:    58.591 -  68.357:   61        |
|      2:    19.531 -  29.296:  196   |   7:    68.357 -  78.122:   26        |
|      3:    29.296 -  39.061:  120   |   8:    78.122 -  87.887:    9        |
|      4:    39.061 -  48.826:  108   |   9:    87.887 -  97.652:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1621             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1621             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1621   ksol= 0.33   Bsol= 69.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-0.36,-0.44,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.169353                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1620   ksol= 0.32   Bsol= 65.75   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.45,-0.22,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.169221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.392629              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.281  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.755981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.567  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2676 = 2.39 * 0.50 * 5.1754 + 1.00 * 0.0762                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2493 = 2.39 * 0.50 * 5.1704 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9198 = 0.76 * 1.00 * 5.1704 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9163 = 0.76 * 1.00 * 5.1657 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   16.29    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   16.29    None  None   None       |
|    Sol.    : 438    0      2.01    93.79   40.79    None  None   None       |
|    Mac.    : 2385   0      0.00    99.31   11.79    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 -   9.931: 1307   |   5:    49.655 -  59.586:  100        |
|      1:     9.931 -  19.862:  911   |   6:    59.586 -  69.517:   50        |
|      2:    19.862 -  29.793:  201   |   7:    69.517 -  79.448:   23        |
|      3:    29.793 -  39.724:  116   |   8:    79.448 -  89.379:    7        |
|      4:    39.724 -  49.655:  104   |   9:    89.379 -  99.310:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1616             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1617             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1617   ksol= 0.32   Bsol= 65.75   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,-0.45,-0.22,-0.00,-0.00,-0.00); trace/3= -0.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166856                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7751 0.99   1382  155 0.0995 0.1294      5.3862      5.5357|
|  2:  4.7751 -  3.8104 0.99   1338  145 0.0843 0.1060      5.4167      5.6015|
|  3:  3.8104 -  3.3347 0.99   1307  150 0.1022 0.1451      5.4513      5.8414|
|  4:  3.3347 -  3.0325 0.99   1303  141 0.1243 0.1657      5.4721      5.6398|
|  5:  3.0325 -  2.8167 0.99   1285  142 0.1358 0.1792       5.364      5.5412|
|  6:  2.8167 -  2.6516 0.98   1288  143 0.1287 0.2032      5.2619      5.5049|
|  7:  2.6516 -  2.5194 0.99   1273  143 0.1272 0.1704      5.1924      5.3711|
|  8:  2.5194 -  2.4102 0.98   1274  138 0.1199 0.1784      5.1155      5.3957|
|  9:  2.4102 -  2.3178 0.98   1283  145 0.1198 0.1881      5.0528      5.3753|
| 10:  2.3178 -  2.2380 0.97   1236  139 0.1163 0.1817      5.0115      5.2236|
| 11:  2.2380 -  2.1683 0.99   1273  144 0.1203 0.1844      4.9691      5.2931|
| 12:  2.1683 -  2.1065 0.98   1275  133 0.1128 0.1766      4.9124      5.2037|
| 13:  2.1065 -  2.0512 0.97   1239  143 0.1166 0.1761      4.8205      5.0825|
| 14:  2.0512 -  2.0012 0.68    874   98 0.1081 0.1742      4.7023       4.967|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7751  1382   155  0.94   9.26   0.96     0.94       7319.93|
|  2:  4.7751 -  3.8104  1338   145  0.95   7.94   1.00     0.98       8671.64|
|  3:  3.8104 -  3.3347  1307   150  0.94  10.90   1.02     1.01       9988.06|
|  4:  3.3347 -  3.0325  1303   141  0.92  14.06   1.00     0.98      10613.85|
|  5:  3.0325 -  2.8167  1285   142  0.90  16.49   0.99     0.97       8958.63|
|  6:  2.8167 -  2.6516  1288   143  0.89  16.77   0.98     0.95       7764.60|
|  7:  2.6516 -  2.5194  1273   143  0.90  16.20   0.98     0.96       6635.46|
|  8:  2.5194 -  2.4102  1274   138  0.90  15.81   0.98     0.95       5916.13|
|  9:  2.4102 -  2.3178  1283   145  0.90  16.44   0.98     0.94       5244.58|
| 10:  2.3178 -  2.2380  1236   139  0.90  16.35   0.98     0.94       4911.30|
| 11:  2.2380 -  2.1683  1273   144  0.90  16.76   0.98     0.93       4530.67|
| 12:  2.1683 -  2.1065  1275   133  0.91  15.66   0.98     0.97       4255.90|
| 13:  2.1065 -  2.0512  1239   143  0.90  16.59   0.97     0.96       3608.79|
| 14:  2.0512 -  2.0012   874    98  0.91  15.54   0.95     0.91       2768.62|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2768.62 max =        10613.85 mean =      6635.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.54|
|phase err.(test): min =        0.00 max =           88.81 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1616   ksol= 0.32   Bsol= 65.46   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.37,0.00,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1616   ksol= 0.32   Bsol= 65.46   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.37,0.00,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166945                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.7751 0.99   1382  155 0.0995 0.1296      5.3866       5.537|
|  2:  4.7751 -  3.8104 0.99   1338  145 0.0844 0.1061      5.4175      5.6018|
|  3:  3.8104 -  3.3347 0.99   1307  150 0.1022 0.1452      5.4518       5.842|
|  4:  3.3347 -  3.0325 0.99   1303  141 0.1243 0.1659      5.4722        5.64|
|  5:  3.0325 -  2.8167 0.99   1285  142 0.1358 0.1793      5.3637      5.5412|
|  6:  2.8167 -  2.6516 0.98   1288  143 0.1287 0.2028      5.2615      5.5035|
|  7:  2.6516 -  2.5194 0.99   1273  143 0.1272 0.1706      5.1921      5.3714|
|  8:  2.5194 -  2.4102 0.98   1274  138 0.1199 0.1783      5.1157      5.3956|
|  9:  2.4102 -  2.3178 0.98   1283  145 0.1197 0.1878      5.0529      5.3753|
| 10:  2.3178 -  2.2380 0.97   1236  139 0.1163 0.1819      5.0118      5.2249|
| 11:  2.2380 -  2.1683 0.99   1273  144 0.1203 0.1843      4.9691      5.2927|
| 12:  2.1683 -  2.1065 0.98   1275  133 0.1127 0.1768      4.9123      5.2046|
| 13:  2.1065 -  2.0512 0.97   1239  143 0.1166 0.1763      4.8205      5.0824|
| 14:  2.0512 -  2.0012 0.68    874   98 0.1081 0.1739      4.7019      4.9657|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0489 -  4.7751  1382   155  0.94   9.28   0.97     0.94       7335.40|
|  2:  4.7751 -  3.8104  1338   145  0.95   7.97   1.00     0.99       8685.78|
|  3:  3.8104 -  3.3347  1307   150  0.94  10.91   1.02     1.02      10001.66|
|  4:  3.3347 -  3.0325  1303   141  0.92  14.07   1.01     0.98      10618.25|
|  5:  3.0325 -  2.8167  1285   142  0.90  16.48   1.00     0.97       8948.47|
|  6:  2.8167 -  2.6516  1288   143  0.90  16.75   0.99     0.96       7754.82|
|  7:  2.6516 -  2.5194  1273   143  0.90  16.19   0.99     0.96       6630.64|
|  8:  2.5194 -  2.4102  1274   138  0.90  15.82   0.99     0.95       5919.21|
|  9:  2.4102 -  2.3178  1283   145  0.90  16.45   0.99     0.94       5249.84|
| 10:  2.3178 -  2.2380  1236   139  0.90  16.36   0.99     0.95       4915.11|
| 11:  2.2380 -  2.1683  1273   144  0.90  16.76   0.99     0.94       4533.48|
| 12:  2.1683 -  2.1065  1275   133  0.91  15.66   0.99     0.98       4258.52|
| 13:  2.1065 -  2.0512  1239   143  0.90  16.59   0.98     0.97       3606.70|
| 14:  2.0512 -  2.0012   874    98  0.91  15.52   0.96     0.92       2762.94|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2762.94 max =        10618.25 mean =      6638.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.54|
|phase err.(test): min =        0.00 max =           88.80 mean =        13.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.31   16.30    None  None   None       |
|    all(noH): 2823   0      0.00    99.31   16.30    None  None   None       |
|    Sol.    : 438    0      2.02    93.79   40.80    None  None   None       |
|    Mac.    : 2385   0      0.00    99.31   11.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.934: 1307   |   5:    49.658 -  59.589:  100        |
|      1:     9.934 -  19.865:  911   |   6:    59.589 -  69.520:   50        |
|      2:    19.865 -  29.796:  201   |   7:    69.520 -  79.451:   23        |
|      3:    29.796 -  39.727:  116   |   8:    79.451 -  89.382:    7        |
|      4:    39.727 -  49.658:  104   |   9:    89.382 -  99.313:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.594 - 4.777
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 320
   mapped sites are within: 0.738 - 4.777

peak=    6.073 closest distance to " O   HOH Z 111 " =    2.401
peak=    5.757 closest distance to " O   HOH Z 210 " =    1.072
peak=    5.655 closest distance to " CB  GLN A 223 " =    1.381
peak=    5.183 closest distance to " CG  PRO A  54 " =    1.352
peak=    5.128 closest distance to " CB  SER A  63 " =    1.207
peak=    4.903 closest distance to " C   PRO A 198 " =    1.543
peak=    4.744 closest distance to " CA  TYR A  30 " =    0.926
peak=    4.744 closest distance to " O   HOH Z 232 " =    2.341
peak=    4.709 closest distance to " CB  ARG A 190 " =    1.733
peak=    4.706 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.671 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.623 closest distance to " CB  PRO A  54 " =    0.905
peak=    4.603 closest distance to " CG  PRO A  90 " =    1.131
peak=    4.593 closest distance to " CB  GLN A 183 " =    1.300
peak=    4.447 closest distance to " CG  PRO A 198 " =    1.224
peak=    4.440 closest distance to " O   HOH Z 134 " =    1.611
peak=    4.405 closest distance to " O   HOH Z 234 " =    3.821
peak=    4.403 closest distance to " CG  PRO A 280 " =    0.762
peak=    4.386 closest distance to " O   HOH Z  44 " =    2.341
peak=    4.373 closest distance to " CB  GLU A 128 " =    1.137
peak=    4.341 closest distance to " O   HOH Z  15 " =    2.196
peak=    4.318 closest distance to " CB  ARG A  79 " =    1.373
peak=    4.318 closest distance to " O   HOH Z  43 " =    2.042
peak=    4.283 closest distance to " O   HOH Z 298 " =    1.911
peak=    4.271 closest distance to " O   HOH Z  40 " =    1.955
peak=    4.271 closest distance to " CZ  PHE A 218 " =    1.127
peak=    4.259 closest distance to " O   HOH Z 369 " =    2.351
peak=    4.255 closest distance to " CG  PRO A 243 " =    1.135
peak=    4.248 closest distance to " O   HOH Z 403 " =    1.725
peak=    4.229 closest distance to " O   HOH Z 189 " =    2.473
peak=    4.172 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.172 closest distance to " O   HOH Z 402 " =    1.530
peak=    4.162 closest distance to " CB  GLU A 277 " =    3.725
peak=    4.139 closest distance to " CA  ALA A  21 " =    1.339
peak=    4.138 closest distance to " CB  TYR A 169 " =    0.824
peak=    4.120 closest distance to " CD  ARG A 269 " =    0.993
peak=    4.118 closest distance to " O   HOH Z  80 " =    1.759
peak=    4.094 closest distance to " O   HOH Z 423 " =    1.893
peak=    4.080 closest distance to " NH2 ARG A 156 " =    1.178
peak=    4.071 closest distance to " O   HOH Z 412 " =    3.604
peak=    4.062 closest distance to " CG1 ILE A  33 " =    1.217
peak=    4.054 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.045 closest distance to " O   HOH Z 133 " =    2.591
peak=    4.041 closest distance to " CA  ALA A  51 " =    0.947
peak=    4.005 closest distance to " O   HOH Z  20 " =    1.622
peak=    3.995 closest distance to " O   HOH Z  97 " =    2.019
peak=    3.987 closest distance to " O   HOH Z  67 " =    2.068
peak=    3.959 closest distance to " ND2 ASN A 249 " =    2.064
peak=    3.937 closest distance to " C   ILE A 106 " =    1.873
peak=    3.931 closest distance to " NZ  LYS A 117 " =    3.183
peak=    3.927 closest distance to " O   SER A  87 " =    2.266
peak=    3.923 closest distance to " O   HOH Z 108 " =    2.876
peak=    3.921 closest distance to " CA  ARG A 195 " =    1.178
peak=    3.916 closest distance to " O   HOH Z  63 " =    1.883
peak=    3.912 closest distance to " CG  ARG A  66 " =    2.597
peak=    3.907 closest distance to " O   HOH Z  21 " =    1.806
peak=    3.906 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.905 closest distance to " O   HOH Z 265 " =    2.105
peak=    3.895 closest distance to " OD1 ASN A  69 " =    2.555
peak=    3.884 closest distance to " NE2 GLN A  11 " =    0.984
peak=    3.874 closest distance to " CA  ARG A  36 " =    1.139
peak=    3.862 closest distance to " O   HOH Z 284 " =    2.989
peak=    3.860 closest distance to " O   HOH Z 374 " =    2.779
peak=    3.858 closest distance to " O   HOH Z 180 " =    2.263
peak=    3.856 closest distance to " CB  VAL A 202 " =    1.519
peak=    3.853 closest distance to " O   HOH Z  44 " =    1.904
peak=    3.849 closest distance to " O   HOH Z  78 " =    1.691
peak=    3.845 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.845 closest distance to " CD2 TRP A 179 " =    1.311
peak=    3.843 closest distance to " O   HOH Z 383 " =    2.183
peak=    3.830 closest distance to " CB  SER A   3 " =    1.337
peak=    3.821 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.819 closest distance to " CA  ASN A 176 " =    1.717
peak=    3.813 closest distance to " O   HOH Z 352 " =    1.886
peak=    3.810 closest distance to " NH2BARG A 145 " =    2.156
peak=    3.809 closest distance to " CB  TRP A 266 " =    0.974
peak=    3.806 closest distance to " CB  TRP A 179 " =    1.467
peak=    3.806 closest distance to " O   ASN A  74 " =    1.609
peak=    3.804 closest distance to " O   HOH Z 421 " =    1.772
peak=    3.803 closest distance to " O   HOH Z  59 " =    2.408
peak=    3.801 closest distance to " CB  ASP A 140 " =    0.892
peak=    3.800 closest distance to " O   HOH Z 368 " =    2.160
peak=    3.780 closest distance to " O   HOH Z 303 " =    2.214
peak=    3.777 closest distance to " O   HOH Z 418 " =    1.482
peak=    3.777 closest distance to " CB  ASN A 148 " =    1.418
peak=    3.764 closest distance to " CD2 LEU A 297 " =    0.902
peak=    3.751 closest distance to " O   HOH Z 357 " =    2.085
peak=    3.747 closest distance to " CD1 LEU A 300 " =    1.166
peak=    3.740 closest distance to " O   HOH Z 433 " =    1.391
peak=    3.729 closest distance to " O   HOH Z 287 " =    1.943
peak=    3.727 closest distance to " CA  ALA A 160 " =    0.892
peak=    3.714 closest distance to " O   ALA A 165 " =    1.338
peak=    3.709 closest distance to " O   HOH Z 147 " =    1.809
peak=    3.702 closest distance to " CG2 THR A 221 " =    1.080
peak=    3.701 closest distance to " O   THR A 251 " =    1.182
peak=    3.700 closest distance to " O   HOH Z 126 " =    1.558
peak=    3.696 closest distance to " O   HOH Z 279 " =    2.226
peak=    3.683 closest distance to " O   HOH Z 344 " =    3.211
peak=    3.681 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.679 closest distance to " O   HOH Z 291 " =    1.497
peak=    3.678 closest distance to " O   HOH Z 362 " =    3.601
peak=    3.667 closest distance to " O   HOH Z 132 " =    2.779
peak=    3.662 closest distance to " CE  LYS A  76 " =    0.813
peak=    3.654 closest distance to " CB  SER A 141 " =    1.007
peak=    3.654 closest distance to " CG2BVAL A  41 " =    0.831
peak=    3.652 closest distance to " CB  ALA A 291 " =    1.307
peak=    3.649 closest distance to " CG2 VAL A  78 " =    1.012
peak=    3.644 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.644 closest distance to " O   HOH Z 426 " =    1.532
peak=    3.640 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.636 closest distance to " CA  ALA A 295 " =    1.122
peak=    3.635 closest distance to " NE2 GLN A  77 " =    3.387
peak=    3.635 closest distance to " O   HOH Z 258 " =    2.166
peak=    3.632 closest distance to " O   HOH Z 214 " =    2.581
peak=    3.631 closest distance to " O   HOH Z 126 " =    2.034
peak=    3.627 closest distance to " OG BSER A 164 " =    2.417
peak=    3.624 closest distance to " O   HOH Z 346 " =    1.575
peak=    3.615 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.613 closest distance to " O   HOH Z 345 " =    1.621
peak=    3.608 closest distance to " O   HOH Z 158 " =    3.031
peak=    3.607 closest distance to " O   HOH Z 193 " =    1.883
peak=    3.604 closest distance to " O   HOH Z 316 " =    3.031
peak=    3.599 closest distance to " ND2 ASN A 187 " =    1.513
peak=    3.590 closest distance to " N   ASN A  39 " =    1.348
peak=    3.588 closest distance to " CB  MET A  40 " =    0.898
peak=    3.583 closest distance to " CA  ASP A 191 " =    0.865
peak=    3.578 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.576 closest distance to " CD1 ILE A 106 " =    0.920
peak=    3.573 closest distance to " CZ  PHE A  38 " =    1.285
peak=    3.571 closest distance to " NZ  LYS A 166 " =    3.092
peak=    3.571 closest distance to " O   HOH Z  19 " =    1.701
peak=    3.566 closest distance to " N   CYS A 260 " =    0.816
peak=    3.565 closest distance to " O   HOH Z  35 " =    2.410
peak=    3.563 closest distance to " O   HOH Z 371 " =    3.270
peak=    3.558 closest distance to " O   HOH Z 435 " =    2.989
peak=    3.546 closest distance to " CB  SER A  62 " =    0.802
peak=    3.543 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.528 closest distance to " O   HOH Z 250 " =    1.476
peak=    3.525 closest distance to " O   HOH Z 427 " =    3.056
peak=    3.523 closest distance to " CA  ASN A 215 " =    1.113
peak=    3.521 closest distance to " O   HOH Z 130 " =    2.278
peak=    3.520 closest distance to " O   HOH Z 163 " =    1.599
peak=    3.513 closest distance to " O   HOH Z 425 " =    1.299
peak=    3.511 closest distance to " CE1 TYR A 186 " =    1.306
peak=    3.505 closest distance to " CA  THR A 221 " =    0.928
peak=    3.499 closest distance to " CG2 VAL A 257 " =    0.849
peak=    3.499 closest distance to " OG BSER A 134 " =    2.912
peak=    3.497 closest distance to " OD2 ASP A 298 " =    3.900
peak=    3.486 closest distance to " O   HOH Z 142 " =    1.537
peak=    3.480 closest distance to " O   TRP A 274 " =    1.878
peak=    3.478 closest distance to " CZ  PHE A 192 " =    0.946
peak=    3.472 closest distance to " O   HOH Z 250 " =    1.638
peak=    3.463 closest distance to " CG  GLN A  58 " =    2.642
peak=    3.461 closest distance to " O   THR A 220 " =    1.178
peak=    3.458 closest distance to " O   HOH Z 247 " =    1.409
peak=    3.457 closest distance to " O   HOH Z 173 " =    2.278
peak=    3.450 closest distance to " CB  ASN A 285 " =    0.908
peak=    3.447 closest distance to " O   HOH Z 272 " =    1.919
peak=    3.446 closest distance to " OE1 GLU A   2 " =    2.024
peak=    3.437 closest distance to " CA  SER A  87 " =    1.053
peak=    3.432 closest distance to " CA  ASP A 162 " =    1.172
peak=    3.431 closest distance to " CD BLYS A 290 " =    1.008
peak=    3.430 closest distance to " CB  GLU A  46 " =    1.009
peak=    3.426 closest distance to " O   HOH Z  49 " =    1.880
peak=    3.422 closest distance to " C   SER A  32 " =    1.075
peak=    3.405 closest distance to " O   HOH Z 295 " =    1.504
peak=    3.404 closest distance to " CB  VAL A 265 " =    1.211
peak=    3.401 closest distance to " CA  VAL A  41 " =    0.886
peak=    3.400 closest distance to " O   HOH Z 294 " =    1.538
peak=    3.398 closest distance to " CG1 VAL A 153 " =    1.032
peak=    3.395 closest distance to " O   HOH Z 109 " =    2.599
peak=    3.389 closest distance to " O   HOH Z  30 " =    1.221
peak=    3.382 closest distance to " O   HOH Z 156 " =    2.631
peak=    3.381 closest distance to " NZ  LYS A  48 " =    1.212
peak=    3.380 closest distance to " OE1 GLN A  11 " =    1.969
peak=    3.379 closest distance to " CZ3 TRP A 266 " =    1.067
peak=    3.376 closest distance to " O   HOH Z  48 " =    1.886
peak=    3.375 closest distance to " O   HOH Z  66 " =    2.108
peak=    3.371 closest distance to " O   HOH Z 419 " =    1.639
peak=    3.370 closest distance to " CD  PRO A  54 " =    1.059
peak=    3.370 closest distance to " CB  GLN A 103 " =    0.909
peak=    3.370 closest distance to " CA  GLU A 152 " =    0.865
peak=    3.370 closest distance to " O   ALA A 158 " =    1.216
peak=    3.369 closest distance to " CG1BVAL A  72 " =    1.798
peak=    3.369 closest distance to " O  BHOH Z  74 " =    1.222
peak=    3.366 closest distance to " CB  ALA A  71 " =    1.287
peak=    3.365 closest distance to " CA  ASP A 124 " =    0.738
peak=    3.360 closest distance to " CA  GLN A  88 " =    1.310
peak=    3.357 closest distance to " OD2 ASP A 286 " =    2.889
peak=    3.357 closest distance to " CB  SER A  28 " =    1.083
peak=    3.356 closest distance to " CB  TYR A 116 " =    1.032
peak=    3.353 closest distance to " OH  TYR A 116 " =    1.165
peak=    3.352 closest distance to " O   HOH Z 145 " =    2.412
peak=    3.347 closest distance to " O   HOH Z  88 " =    3.545
peak=    3.344 closest distance to " CB  SER A 273 " =    0.859
peak=    3.343 closest distance to " O   HOH Z 282 " =    2.077
peak=    3.340 closest distance to " O   HOH Z 411 " =    1.725
peak=    3.340 closest distance to " NH1AARG A 145 " =    1.251
peak=    3.338 closest distance to " CB  ASN A 148 " =    1.969
peak=    3.335 closest distance to " O   HOH Z 327 " =    1.667
peak=    3.332 closest distance to " O   HOH Z 299 " =    4.529
peak=    3.330 closest distance to " O   HOH Z 416 " =    2.994
peak=    3.329 closest distance to " CA  ASP A 140 " =    1.203
peak=    3.325 closest distance to " O   HOH Z 185 " =    1.726
peak=    3.325 closest distance to " CB  ALA A 248 " =    1.297
peak=    3.322 closest distance to " CG  GLU A  37 " =    0.874
peak=    3.319 closest distance to " O   HOH Z 336 " =    1.676
peak=    3.318 closest distance to " CB  ILE A 120 " =    1.285
peak=    3.314 closest distance to " CB  LEU A  83 " =    0.839
peak=    3.312 closest distance to " CD  ARG A 159 " =    0.843
peak=    3.309 closest distance to " CB  GLN A  89 " =    1.242
peak=    3.305 closest distance to " NE2 HIS A 115 " =    0.989
peak=    3.304 closest distance to " CG2 ILE A 120 " =    0.964
peak=    3.295 closest distance to " O   HOH Z 281 " =    4.777
peak=    3.294 closest distance to " CB  ARG A 139 " =    0.870
peak=    3.293 closest distance to " O   HOH Z 125 " =    3.808
peak=    3.291 closest distance to " CD  ARG A  66 " =    2.529
peak=    3.290 closest distance to " O   HOH Z 325 " =    2.153
peak=    3.289 closest distance to " CB  TYR A 169 " =    0.842
peak=    3.282 closest distance to " CA  VAL A 125 " =    1.282
peak=    3.282 closest distance to " CA  ASN A 217 " =    1.289
peak=    3.280 closest distance to " CB  ASN A 187 " =    1.186
peak=    3.278 closest distance to " O   HOH Z 261 " =    1.783
peak=    3.277 closest distance to " O   HOH Z 227 " =    1.682
peak=    3.275 closest distance to " O   HOH Z 139 " =    4.761
peak=    3.272 closest distance to " CA  ALA A  84 " =    1.296
peak=    3.270 closest distance to " CE1 HIS A 108 " =    1.128
peak=    3.264 closest distance to " ND1 HIS A  81 " =    1.632
peak=    3.263 closest distance to " CA  LEU A  83 " =    1.387
peak=    3.262 closest distance to " OG1 THR A 294 " =    2.464
peak=    3.262 closest distance to " CA  THR A 221 " =    1.422
peak=    3.258 closest distance to " CG2 THR A  29 " =    1.390
peak=    3.257 closest distance to " CB  PRO A 198 " =    1.083
peak=    3.253 closest distance to " CG  ARG A 219 " =    1.202
peak=    3.249 closest distance to " O   HOH Z 365 " =    2.896
peak=    3.248 closest distance to " CG AARG A 275 " =    1.153
peak=    3.244 closest distance to " CG  GLN A  11 " =    1.348
peak=    3.242 closest distance to " CA  ALA A 291 " =    0.858
peak=    3.240 closest distance to " CG  LEU A 167 " =    1.118
peak=    3.239 closest distance to " N   ASP A 132 " =    1.191
peak=    3.237 closest distance to " CG2 THR A 220 " =    0.772
peak=    3.237 closest distance to " O   HOH Z 403 " =    1.400
peak=    3.236 closest distance to " O   HOH Z 183 " =    1.517
peak=    3.232 closest distance to " O   HOH Z 423 " =    3.371
peak=    3.231 closest distance to " OG  SER A 245 " =    1.622
peak=    3.230 closest distance to " O   HOH Z  97 " =    2.514
peak=    3.228 closest distance to " O   HOH Z 128 " =    2.214
peak=    3.224 closest distance to " ND2 ASN A 249 " =    0.924
peak=    3.224 closest distance to " O   HOH Z 386 " =    2.283
peak=    3.220 closest distance to " CB  ASN A 215 " =    1.206
peak=    3.219 closest distance to " CB  TYR A 247 " =    0.950
peak=    3.218 closest distance to " C   TYR A 214 " =    1.530
peak=    3.217 closest distance to " O   HOH Z 437 " =    1.460
peak=    3.216 closest distance to " CB  MET A  47 " =    0.984
peak=    3.216 closest distance to " CB  ARG A 269 " =    0.788
peak=    3.215 closest distance to " O   HOH Z   1 " =    2.697
peak=    3.214 closest distance to " O   HOH Z 305 " =    3.747
peak=    3.212 closest distance to " O   HOH Z 393 " =    3.317
peak=    3.211 closest distance to " CG  MET A 185 " =    1.157
peak=    3.210 closest distance to " CB  HIS A 108 " =    0.812
peak=    3.208 closest distance to " CB  ASN A 142 " =    1.181
peak=    3.208 closest distance to " O   HOH Z 359 " =    1.450
peak=    3.207 closest distance to " O   HOH Z 417 " =    3.097
peak=    3.207 closest distance to " CA  ALA A 100 " =    1.098
peak=    3.203 closest distance to " CA  MET A 188 " =    1.025
peak=    3.199 closest distance to " O   HOH Z 197 " =    1.993
peak=    3.197 closest distance to " CA  THR A 264 " =    0.868
peak=    3.196 closest distance to " CA  ILE A 106 " =    0.828
peak=    3.193 closest distance to " O   HOH Z 261 " =    1.649
peak=    3.190 closest distance to " O   HOH Z 387 " =    2.633
peak=    3.183 closest distance to " O   GLY A  57 " =    2.700
peak=    3.182 closest distance to " CB  THR A 157 " =    1.110
peak=    3.181 closest distance to " CG2 ILE A  20 " =    1.280
peak=    3.181 closest distance to " O   HOH Z 171 " =    3.913
peak=    3.179 closest distance to " O   HOH Z 327 " =    2.366
peak=    3.175 closest distance to " CB  MET A 105 " =    1.044
peak=    3.172 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.172 closest distance to " CG2 ILE A 106 " =    0.927
peak=    3.167 closest distance to " NH1 ARG A  14 " =    1.213
peak=    3.167 closest distance to " N   GLY A  98 " =    1.186
peak=    3.166 closest distance to " CZ3 TRP A  85 " =    0.972
peak=    3.165 closest distance to " NH2AARG A 275 " =    3.473
peak=    3.162 closest distance to " O   HOH Z  54 " =    1.617
peak=    3.161 closest distance to " O   HOH Z 196 " =    1.126
peak=    3.159 closest distance to " CB  SER A 212 " =    1.029
peak=    3.158 closest distance to " CB  ALA A 100 " =    1.321
peak=    3.152 closest distance to " N   ASN A 127 " =    1.255
peak=    3.147 closest distance to " O   HOH Z 353 " =    2.834
peak=    3.147 closest distance to " O   HOH Z 148 " =    3.291
peak=    3.146 closest distance to " O   HOH Z 128 " =    1.756
peak=    3.143 closest distance to " O   HOH Z 383 " =    1.619
peak=    3.142 closest distance to " CA  ALA A 233 " =    1.683
peak=    3.135 closest distance to " CZ2 TRP A 179 " =    1.812
peak=    3.131 closest distance to " CB  PHE A 204 " =    0.955
peak=    3.129 closest distance to " O   HOH Z 150 " =    1.526
peak=    3.128 closest distance to " O   VAL A  72 " =    3.204
peak=    3.126 closest distance to " ND2 ASN A 301 " =    1.607
peak=    3.123 closest distance to " CB  ASP A 298 " =    1.246
peak=    3.114 closest distance to " CD1AILE A 234 " =    0.885
peak=    3.106 closest distance to " CB  PRO A 243 " =    1.271
peak=    3.099 closest distance to " CA  GLN A 223 " =    0.824
peak=    3.094 closest distance to " CG  MET A 185 " =    1.099
peak=    3.091 closest distance to " CA  ALA A 248 " =    1.208
peak=    3.091 closest distance to " O   HOH Z 248 " =    1.819
peak=    3.087 closest distance to " O   ALA A 242 " =    1.198
peak=    3.087 closest distance to " O   HOH Z 394 " =    1.656
peak=    3.085 closest distance to " NZ  LYS A 117 " =    2.357
peak=    3.062 closest distance to " C   GLY A  80 " =    1.030
peak=    3.058 closest distance to " O   HOH Z 251 " =    1.540
peak=    3.052 closest distance to " NE1 TRP A 266 " =    1.349
peak=    3.040 closest distance to " O   THR A 251 " =    1.915
peak=    3.039 closest distance to " CA  ALA A 299 " =    0.985
peak=    3.032 closest distance to " O   HOH Z 271 " =    2.137
peak=    3.029 closest distance to " O   HOH Z  90 " =    3.382

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.853 - 5.984
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 215
   mapped sites are within: 0.853 - 5.984

peak=   -4.720 closest distance to " O   HOH Z 266 " =    4.961
peak=   -4.301 closest distance to " CB  PRO A 243 " =    2.711
peak=   -4.272 closest distance to " CD  ARG A 156 " =    2.067
peak=   -4.271 closest distance to " O   HOH Z   5 " =    1.595
peak=   -4.213 closest distance to " CD1 LEU A 101 " =    2.511
peak=   -4.208 closest distance to " CD  GLN A 223 " =    1.323
peak=   -4.185 closest distance to " OXT GLY A 302 " =    2.936
peak=   -4.125 closest distance to " C   HIS A 108 " =    1.111
peak=   -4.098 closest distance to " CG1 VAL A 250 " =    2.691
peak=   -4.076 closest distance to " O   VAL A  67 " =    2.689
peak=   -4.068 closest distance to " O   HOH Z 166 " =    1.769
peak=   -4.067 closest distance to " O   HOH Z 196 " =    2.253
peak=   -4.028 closest distance to " N   ALA A  43 " =    2.666
peak=   -4.026 closest distance to " CD  GLN A  58 " =    1.069
peak=   -4.022 closest distance to " O   HOH Z  13 " =    1.702
peak=   -4.013 closest distance to " OG  SER A  97 " =    2.227
peak=   -3.992 closest distance to " O   PRO A 198 " =    1.325
peak=   -3.941 closest distance to " CB  ASP A 132 " =    2.405
peak=   -3.941 closest distance to " CG1 VAL A 112 " =    2.577
peak=   -3.924 closest distance to " ND2 ASN A  45 " =    1.747
peak=   -3.922 closest distance to " O   HOH Z 283 " =    2.232
peak=   -3.917 closest distance to " O   PRO A 163 " =    2.190
peak=   -3.913 closest distance to " CB  ALA A 161 " =    2.656
peak=   -3.885 closest distance to " O   HOH Z 292 " =    4.608
peak=   -3.881 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.865 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.826 closest distance to " O   HOH Z 231 " =    2.376
peak=   -3.815 closest distance to " CD  ARG A  14 " =    3.420
peak=   -3.807 closest distance to " O   HOH Z 348 " =    2.276
peak=   -3.797 closest distance to " CD1 PHE A  59 " =    1.922
peak=   -3.763 closest distance to " OE1 GLN A 223 " =    2.171
peak=   -3.761 closest distance to " O   HOH Z  52 " =    1.599
peak=   -3.760 closest distance to " O   HOH Z 377 " =    2.044
peak=   -3.759 closest distance to " CE2 TYR A  30 " =    2.684
peak=   -3.752 closest distance to " O   HOH Z 185 " =    2.468
peak=   -3.746 closest distance to " ND2 ASN A  45 " =    1.074
peak=   -3.741 closest distance to " O   HOH Z 166 " =    1.892
peak=   -3.740 closest distance to " CH2 TRP A 179 " =    1.230
peak=   -3.736 closest distance to " C   SER A 206 " =    1.530
peak=   -3.718 closest distance to " NH2 ARG A  66 " =    1.761
peak=   -3.713 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.708 closest distance to " O   HOH Z 165 " =    1.986
peak=   -3.700 closest distance to " CG  ASP A 231 " =    0.868
peak=   -3.691 closest distance to " O   HOH Z 353 " =    2.306
peak=   -3.679 closest distance to " CG2 ILE A 263 " =    2.319
peak=   -3.675 closest distance to " O   SER A 210 " =    1.868
peak=   -3.670 closest distance to " O   ALA A  10 " =    1.721
peak=   -3.643 closest distance to " O   HOH Z 372 " =    2.484
peak=   -3.639 closest distance to " O   HOH Z 407 " =    3.514
peak=   -3.616 closest distance to " O   VAL A  67 " =    2.824
peak=   -3.614 closest distance to " C   LEU A 143 " =    1.145
peak=   -3.612 closest distance to " CE BMET A  47 " =    2.182
peak=   -3.611 closest distance to " CD  ARG A 139 " =    1.573
peak=   -3.603 closest distance to " O   HOH Z 377 " =    1.328
peak=   -3.602 closest distance to " C   ASN A 285 " =    2.419
peak=   -3.596 closest distance to " O   HOH Z  71 " =    1.756
peak=   -3.576 closest distance to " CA  SER A 276 " =    1.512
peak=   -3.575 closest distance to " O   HOH Z 290 " =    1.121
peak=   -3.573 closest distance to " O   HOH Z   6 " =    1.526
peak=   -3.570 closest distance to " CB  ALA A 291 " =    2.402
peak=   -3.562 closest distance to " O   HOH Z 252 " =    4.027
peak=   -3.559 closest distance to " CG  GLU A  53 " =    1.459
peak=   -3.558 closest distance to " O   ALA A   1 " =    1.974
peak=   -3.557 closest distance to " NE1 TRP A 266 " =    2.375
peak=   -3.556 closest distance to " CB  ALA A  10 " =    2.137
peak=   -3.548 closest distance to " CZ  TYR A 169 " =    1.824
peak=   -3.535 closest distance to " OD1 ASN A 148 " =    1.526
peak=   -3.534 closest distance to " ND2 ASN A 187 " =    1.658
peak=   -3.527 closest distance to " CG1 VAL A  78 " =    2.657
peak=   -3.527 closest distance to " O   HOH Z 234 " =    4.357
peak=   -3.521 closest distance to " CE3 TRP A 150 " =    2.104
peak=   -3.520 closest distance to " O   HOH Z 150 " =    1.930
peak=   -3.511 closest distance to " O   HOH Z 150 " =    2.243
peak=   -3.498 closest distance to " O   ALA A  34 " =    2.469
peak=   -3.497 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.496 closest distance to " CG  PRO A 243 " =    1.804
peak=   -3.495 closest distance to " O   HOH Z  19 " =    2.203
peak=   -3.494 closest distance to " CB  ALA A 248 " =    2.067
peak=   -3.493 closest distance to " N   THR A  52 " =    1.696
peak=   -3.491 closest distance to " CE2 PHE A  61 " =    2.589
peak=   -3.475 closest distance to " CG2 VAL A 189 " =    2.232
peak=   -3.470 closest distance to " O   HOH Z 128 " =    2.565
peak=   -3.467 closest distance to " NH2 ARG A 159 " =    2.394
peak=   -3.458 closest distance to " OG BSER A 210 " =    2.115
peak=   -3.454 closest distance to " OD1 ASP A 191 " =    1.622
peak=   -3.444 closest distance to " O   HOH Z 426 " =    1.720
peak=   -3.439 closest distance to " CG  ARG A 219 " =    2.522
peak=   -3.435 closest distance to " OD1 ASN A 187 " =    1.654
peak=   -3.432 closest distance to " OG  SER A  62 " =    1.663
peak=   -3.432 closest distance to " O   HOH Z 393 " =    1.547
peak=   -3.425 closest distance to " CD  PRO A 213 " =    2.183
peak=   -3.424 closest distance to " CD2 LEU A 300 " =    2.994
peak=   -3.424 closest distance to " O   HOH Z  90 " =    1.921
peak=   -3.421 closest distance to " O   HOH Z 311 " =    3.635
peak=   -3.420 closest distance to " CA  GLY A 133 " =    2.352
peak=   -3.416 closest distance to " CB  TRP A  85 " =    2.421
peak=   -3.416 closest distance to " ND2 ASN A 249 " =    2.224
peak=   -3.412 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.408 closest distance to " OG BSER A 210 " =    1.432
peak=   -3.408 closest distance to " NE2 GLN A 103 " =    1.813
peak=   -3.405 closest distance to " CD2 TYR A 293 " =    1.944
peak=   -3.403 closest distance to " C   ASN A 187 " =    1.951
peak=   -3.401 closest distance to " O   HOH Z 210 " =    0.919
peak=   -3.398 closest distance to " O   ALA A 160 " =    1.594
peak=   -3.396 closest distance to " O   HOH Z 351 " =    1.551
peak=   -3.394 closest distance to " CG2 ILE A  49 " =    2.713
peak=   -3.389 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.366
peak=   -3.381 closest distance to " CB  PHE A 192 " =    1.923
peak=   -3.380 closest distance to " C   ALA A 158 " =    1.380
peak=   -3.376 closest distance to " O   HOH Z 198 " =    2.252
peak=   -3.374 closest distance to " C   THR A 279 " =    1.103
peak=   -3.368 closest distance to " OD2 ASP A 171 " =    1.888
peak=   -3.364 closest distance to " O   HOH Z 171 " =    2.107
peak=   -3.362 closest distance to " CD2 PHE A 225 " =    1.296
peak=   -3.362 closest distance to " CB  ALA A  43 " =    2.574
peak=   -3.361 closest distance to " O   HOH Z 422 " =    1.592
peak=   -3.355 closest distance to " CD  GLN A  58 " =    0.988
peak=   -3.349 closest distance to " NH2 ARG A  79 " =    2.064
peak=   -3.348 closest distance to " CD  LYS A 289 " =    2.418
peak=   -3.341 closest distance to " CA  GLY A 203 " =    2.259
peak=   -3.328 closest distance to " O   HOH Z 368 " =    1.863
peak=   -3.326 closest distance to " O   HOH Z 236 " =    1.613
peak=   -3.325 closest distance to " CE  MET A  93 " =    1.328
peak=   -3.321 closest distance to " O   HOH Z 283 " =    5.984
peak=   -3.316 closest distance to " O   HOH Z 111 " =    1.417
peak=   -3.314 closest distance to " CD1 LEU A 167 " =    2.134
peak=   -3.308 closest distance to " OG BSER A 134 " =    1.915
peak=   -3.307 closest distance to " O   HOH Z 414 " =    1.667
peak=   -3.307 closest distance to " NE2 GLN A 194 " =    1.874
peak=   -3.305 closest distance to " O   HOH Z 102 " =    1.496
peak=   -3.302 closest distance to " N   ALA A 226 " =    2.084
peak=   -3.295 closest distance to " NE2 GLN A  88 " =    1.022
peak=   -3.293 closest distance to " O   HOH Z  11 " =    1.883
peak=   -3.293 closest distance to " NE2 GLN A  88 " =    1.802
peak=   -3.292 closest distance to " CB  ALA A   9 " =    2.595
peak=   -3.290 closest distance to " O   HOH Z 123 " =    2.371
peak=   -3.290 closest distance to " O   HOH Z 136 " =    1.995
peak=   -3.287 closest distance to " O   HOH Z 150 " =    1.213
peak=   -3.285 closest distance to " O   HOH Z 177 " =    1.796
peak=   -3.283 closest distance to " O   HOH Z  78 " =    1.810
peak=   -3.282 closest distance to " O   HOH Z 145 " =    2.099
peak=   -3.274 closest distance to " O   HOH Z 106 " =    2.024
peak=   -3.274 closest distance to " NH2 ARG A  79 " =    1.648
peak=   -3.274 closest distance to " O   TRP A  92 " =    1.921
peak=   -3.274 closest distance to " O   HOH Z 114 " =    3.750
peak=   -3.271 closest distance to " ND2 ASN A  60 " =    1.832
peak=   -3.267 closest distance to " OD2 ASP A 171 " =    2.298
peak=   -3.266 closest distance to " CA  GLY A  98 " =    2.221
peak=   -3.262 closest distance to " ND2 ASN A  69 " =    1.615
peak=   -3.261 closest distance to " CZ  PHE A  59 " =    1.908
peak=   -3.259 closest distance to " CD1 ILE A 151 " =    2.372
peak=   -3.258 closest distance to " O   HOH Z 264 " =    1.780
peak=   -3.258 closest distance to " CD2 PHE A  59 " =    2.530
peak=   -3.255 closest distance to " CB  ASP A 286 " =    1.972
peak=   -3.252 closest distance to " CZ  PHE A  38 " =    1.947
peak=   -3.251 closest distance to " CB  PHE A  16 " =    2.577
peak=   -3.250 closest distance to " O   HOH Z 275 " =    1.548
peak=   -3.246 closest distance to " N   GLN A  58 " =    1.538
peak=   -3.244 closest distance to " CD1 ILE A 263 " =    1.974
peak=   -3.244 closest distance to " N   ALA A 248 " =    1.739
peak=   -3.240 closest distance to " CH2 TRP A 177 " =    2.013
peak=   -3.226 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.221 closest distance to " NH1 ARG A 195 " =    2.655
peak=   -3.217 closest distance to " OE2 GLU A 152 " =    2.360
peak=   -3.210 closest distance to " O   HOH Z 275 " =    1.844
peak=   -3.209 closest distance to " O   HOH Z 423 " =    2.359
peak=   -3.209 closest distance to " CZ3 TRP A 274 " =    2.501
peak=   -3.207 closest distance to " O   HOH Z 191 " =    5.678
peak=   -3.203 closest distance to " O   ASN A 187 " =    1.606
peak=   -3.203 closest distance to " N   TYR A  68 " =    2.873
peak=   -3.202 closest distance to " O   GLY A 196 " =    1.127
peak=   -3.200 closest distance to " CD  ARG A 195 " =    5.121
peak=   -3.197 closest distance to " NH2AARG A 275 " =    5.351
peak=   -3.196 closest distance to " CD1 LEU A 228 " =    2.349
peak=   -3.195 closest distance to " O   ALA A  34 " =    2.096
peak=   -3.193 closest distance to " O   HOH Z 396 " =    1.886
peak=   -3.190 closest distance to " NH2 ARG A  66 " =    3.930
peak=   -3.190 closest distance to " CA  VAL A 197 " =    1.041
peak=   -3.186 closest distance to " O   HOH Z 389 " =    1.778
peak=   -3.183 closest distance to " O   HOH Z 232 " =    1.614
peak=   -3.180 closest distance to " OH  TYR A 169 " =    1.030
peak=   -3.179 closest distance to " O   HOH Z  37 " =    1.829
peak=   -3.162 closest distance to " O   HOH Z 392 " =    1.442
peak=   -3.161 closest distance to " NE2 GLN A  58 " =    2.724
peak=   -3.159 closest distance to " O   HOH Z  77 " =    1.962
peak=   -3.159 closest distance to " CA  SER A  62 " =    2.478
peak=   -3.151 closest distance to " O   HOH Z 200 " =    1.423
peak=   -3.151 closest distance to " O   VAL A 125 " =    2.200
peak=   -3.150 closest distance to " CD1 TRP A 179 " =    1.087
peak=   -3.150 closest distance to " O   HOH Z 366 " =    1.909
peak=   -3.150 closest distance to " O   HOH Z  30 " =    0.924
peak=   -3.142 closest distance to " CD2 PHE A  61 " =    2.046
peak=   -3.136 closest distance to " ND2 ASN A  60 " =    1.510
peak=   -3.133 closest distance to " C   ARG A  79 " =    2.628
peak=   -3.129 closest distance to " O   SER A   3 " =    1.243
peak=   -3.125 closest distance to " O   HOH Z 298 " =    2.739
peak=   -3.124 closest distance to " O   HOH Z 117 " =    4.505
peak=   -3.121 closest distance to " OE2 GLU A   2 " =    1.623
peak=   -3.117 closest distance to " O   SER A  95 " =    1.727
peak=   -3.116 closest distance to " CG1 VAL A 112 " =    2.917
peak=   -3.115 closest distance to " O   HOH Z  91 " =    2.133
peak=   -3.109 closest distance to " CH2 TRP A 150 " =    1.102
peak=   -3.106 closest distance to " CG1 VAL A 112 " =    2.917
peak=   -3.103 closest distance to " CG  MET A 105 " =    0.901
peak=   -3.098 closest distance to " O   ARG A  24 " =    2.162
peak=   -3.096 closest distance to " O   HOH Z 174 " =    2.174
peak=   -3.091 closest distance to " OD1 ASN A  39 " =    2.260
peak=   -3.089 closest distance to " O   HOH Z 350 " =    2.098
peak=   -3.087 closest distance to " OH  TYR A 247 " =    1.818
peak=   -3.072 closest distance to " CG2BVAL A  41 " =    1.604
peak=   -3.069 closest distance to " OD2 ASP A  50 " =    2.181
peak=   -3.064 closest distance to " O   GLY A 118 " =    2.276
peak=   -3.060 closest distance to " SD  MET A 188 " =    2.397
peak=   -3.028 closest distance to " CB  ALA A 131 " =    2.002

================= 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    :  0.3753 0.3598   6.177454e+00   6.139168e+00
   1_bss:  0.3597 0.3442   6.156492e+00   6.114203e+00
   1_xyz:  0.2817 0.3050   5.935165e+00   5.999230e+00
   1_adp:  0.2584 0.3144   5.884711e+00   6.014709e+00
   1_occ:  0.2582 0.3142   5.883981e+00   6.014960e+00
   2_bss:  0.2565 0.3119   5.880524e+00   6.012164e+00
   2_xyz:  0.1922 0.2318   5.597222e+00   5.753413e+00
   2_adp:  0.1758 0.2185   5.531673e+00   5.704560e+00
   2_occ:  0.1756 0.2185   5.530927e+00   5.703846e+00
   3_bss:  0.1751 0.2176   5.528936e+00   5.700199e+00
   3_xyz:  0.1367 0.1795   5.306676e+00   5.518372e+00
   3_adp:  0.1269 0.1711   5.246401e+00   5.471759e+00
   3_occ:  0.1268 0.1711   5.246006e+00   5.471269e+00
   4_bss:  0.1272 0.1711   5.247629e+00   5.471458e+00
   4_xyz:  0.1160 0.1634   5.182121e+00   5.425972e+00
   4_adp:  0.1141 0.1621   5.169433e+00   5.414542e+00
   4_occ:  0.1141 0.1621   5.169353e+00   5.414785e+00
   5_bss:  0.1140 0.1620   5.169221e+00   5.414777e+00
   5_xyz:  0.1140 0.1615   5.168507e+00   5.412077e+00
   5_adp:  0.1136 0.1616   5.166920e+00   5.411646e+00
   5_occ:  0.1136 0.1617   5.166856e+00   5.411819e+00
   5_bss:  0.1135 0.1616   5.166945e+00   5.411974e+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:  0.299  43.082  -3.079   5.470  -1.840   0.000  -0.000  -0.000
   1_xyz:  0.299  43.082  -3.079   5.470  -1.840   0.000  -0.000  -0.000
   1_adp:  0.299  43.082  -3.079   5.470  -1.840   0.000  -0.000  -0.000
   1_occ:  0.299  43.082  -3.079   5.470  -1.840   0.000  -0.000  -0.000
   2_bss:  0.320  62.219  -2.029   2.116  -0.875   0.000  -0.000  -0.000
   2_xyz:  0.320  62.219  -2.029   2.116  -0.875   0.000  -0.000  -0.000
   2_adp:  0.320  62.219  -2.029   2.116  -0.875   0.000  -0.000  -0.000
   2_occ:  0.320  62.219  -2.029   2.116  -0.875   0.000  -0.000  -0.000
   3_bss:  0.324  66.971  -1.762   0.336  -0.623   0.000  -0.000  -0.000
   3_xyz:  0.324  66.971  -1.762   0.336  -0.623   0.000  -0.000  -0.000
   3_adp:  0.324  66.971  -1.762   0.336  -0.623   0.000  -0.000  -0.000
   3_occ:  0.324  66.971  -1.762   0.336  -0.623   0.000  -0.000  -0.000
   4_bss:  0.328  69.378  -1.661  -0.359  -0.439  -0.000  -0.000  -0.000
   4_xyz:  0.328  69.378  -1.661  -0.359  -0.439  -0.000  -0.000  -0.000
   4_adp:  0.328  69.378  -1.661  -0.359  -0.439  -0.000  -0.000  -0.000
   4_occ:  0.328  69.378  -1.661  -0.359  -0.439  -0.000  -0.000  -0.000
   5_bss:  0.324  65.749  -1.442  -0.447  -0.219  -0.000  -0.000  -0.000
   5_xyz:  0.324  65.749  -1.442  -0.447  -0.219  -0.000  -0.000  -0.000
   5_adp:  0.324  65.749  -1.442  -0.447  -0.219  -0.000  -0.000  -0.000
   5_occ:  0.324  65.749  -1.442  -0.447  -0.219  -0.000  -0.000  -0.000
   5_bss:  0.322  65.464  -1.225  -0.372   0.004  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  39.840 0.6477  0.8111    40665.074
   1_bss:  38.932 0.6567  0.8229    37252.233
   1_xyz:  32.997 0.7250  0.8903    26731.332
   1_adp:  33.830 0.7148  0.8638    27722.345
   1_occ:  33.858 0.7144  0.8633    27731.929
   2_bss:  33.341 0.7206  0.8630    27322.170
   2_xyz:  23.315 0.8278  0.9596    13800.936
   2_adp:  21.576 0.8461  0.9609    12379.261
   2_occ:  21.556 0.8464  0.9609    12363.470
   3_bss:  21.404 0.8479  0.9495    12244.732
   3_xyz:  16.949 0.8895  0.9745     8126.953
   3_adp:  15.792 0.9000  0.9685     7445.437
   3_occ:  15.782 0.9001  0.9685     7439.614
   4_bss:  15.790 0.9001  0.9645     7460.265
   4_xyz:  14.871 0.9077  0.9693     6811.934
   4_adp:  14.594 0.9102  0.9626     6699.537
   4_occ:  14.595 0.9102  0.9625     6700.076
   5_bss:  14.595 0.9102  0.9668     6698.104
   5_xyz:  14.494 0.9111  0.9663     6621.214
   5_adp:  14.480 0.9113  0.9571     6633.110
   5_occ:  14.480 0.9113  0.9571     6634.707
   5_bss:  14.485 0.9113  0.9631     6637.360
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6407e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6407e-01
   1_xyz:   1.393  0.011  0.087 15.386  0.005  4.115   1.0032e-01
   1_adp:   1.393  0.011  0.087 15.386  0.005  4.115   1.0032e-01
   1_occ:   1.393  0.011  0.087 15.386  0.005  4.115   1.0032e-01
   2_bss:   1.393  0.011  0.087 15.386  0.005  4.115   1.0032e-01
   2_xyz:   1.191  0.008  0.082 14.381  0.006  4.132   7.3512e-02
   2_adp:   1.191  0.008  0.082 14.381  0.006  4.132   7.3512e-02
   2_occ:   1.191  0.008  0.082 14.381  0.006  4.132   7.3512e-02
   3_bss:   1.191  0.008  0.082 14.381  0.006  4.132   7.3512e-02
   3_xyz:   1.089  0.009  0.075 14.624  0.004  4.116   7.0256e-02
   3_adp:   1.089  0.009  0.075 14.624  0.004  4.116   7.0256e-02
   3_occ:   1.089  0.009  0.075 14.624  0.004  4.116   7.0256e-02
   4_bss:   1.089  0.009  0.075 14.624  0.004  4.116   7.0256e-02
   4_xyz:   1.143  0.010  0.082 14.710  0.004  4.124   7.6211e-02
   4_adp:   1.143  0.010  0.082 14.710  0.004  4.124   7.6211e-02
   4_occ:   1.143  0.010  0.082 14.710  0.004  4.124   7.6211e-02
   5_bss:   1.143  0.010  0.082 14.710  0.004  4.124   7.6211e-02
   5_xyz:   1.040  0.009  0.077 14.440  0.004  4.125   6.3911e-02
   5_adp:   1.040  0.009  0.077 14.440  0.004  4.125   6.3911e-02
   5_occ:   1.040  0.009  0.077 14.440  0.004  4.125   6.3911e-02
   5_bss:   1.040  0.009  0.077 14.440  0.004  4.125   6.3911e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.760   2.4331e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.760   2.4331e-01
   1_xyz:  10.722  0.082  0.484 86.716  0.038  2.080   1.0982e-01
   1_adp:  10.722  0.082  0.484 86.716  0.038  2.080   1.0982e-01
   1_occ:  10.722  0.082  0.484 86.716  0.038  2.080   1.0982e-01
   2_bss:  10.722  0.082  0.484 86.716  0.038  2.080   1.0982e-01
   2_xyz:   8.020  0.045  0.244 84.720  0.053  2.285   7.3199e-02
   2_adp:   8.020  0.045  0.244 84.720  0.053  2.285   7.3199e-02
   2_occ:   8.020  0.045  0.244 84.720  0.053  2.285   7.3199e-02
   3_bss:   8.020  0.045  0.244 84.720  0.053  2.285   7.3199e-02
   3_xyz:   7.977  0.064  0.241 81.621  0.030  2.306   6.8484e-02
   3_adp:   7.977  0.064  0.241 81.621  0.030  2.306   6.8484e-02
   3_occ:   7.977  0.064  0.241 81.621  0.030  2.306   6.8484e-02
   4_bss:   7.977  0.064  0.241 81.621  0.030  2.306   6.8484e-02
   4_xyz:   8.112  0.057  0.281 82.023  0.037  2.307   6.1251e-02
   4_adp:   8.112  0.057  0.281 82.023  0.037  2.307   6.1251e-02
   4_occ:   8.112  0.057  0.281 82.023  0.037  2.307   6.1251e-02
   5_bss:   8.112  0.057  0.281 82.023  0.037  2.307   6.1251e-02
   5_xyz:   7.796  0.044  0.256 80.822  0.033  2.376   4.4649e-02
   5_adp:   7.796  0.044  0.256 80.822  0.033  2.376   4.4649e-02
   5_occ:   7.796  0.044  0.256 80.822  0.033  2.376   4.4649e-02
   5_bss:   7.796  0.044  0.256 80.822  0.033  2.376   4.4649e-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:  85.39   0.00  16.91  71.23   0.00  13.40  85.39   1.36  35.98
   1_occ:  85.39   0.00  16.91  71.23   0.00  13.40  85.39   1.36  35.98
   2_bss:  85.39   0.00  16.91  71.23   0.00  13.40  85.39   1.36  35.98
   2_xyz:  85.39   0.00  16.91  71.23   0.00  13.40  85.39   1.36  35.98
   2_adp:  85.83   0.00  17.01  79.93   0.00  12.91  85.83   3.85  39.35
   2_occ:  85.83   0.00  17.01  79.93   0.00  12.91  85.83   3.85  39.35
   3_bss:  85.83   0.00  17.01  79.93   0.00  12.91  85.83   3.85  39.35
   3_xyz:  85.83   0.00  17.01  79.93   0.00  12.91  85.83   3.85  39.35
   3_adp:  94.99   0.00  16.95  94.99   0.00  12.36  92.70   4.37  41.95
   3_occ:  94.99   0.00  16.95  94.99   0.00  12.36  92.70   4.37  41.95
   4_bss:  94.99   0.00  16.95  94.99   0.00  12.36  92.70   4.37  41.95
   4_xyz:  94.99   0.00  16.95  94.99   0.00  12.36  92.70   4.37  41.95
   4_adp:  97.65   0.00  16.59  97.65   0.00  12.05  93.62   1.76  41.29
   4_occ:  97.65   0.00  16.59  97.65   0.00  12.05  93.62   1.76  41.29
   5_bss:  97.65   0.00  16.59  97.65   0.00  12.05  93.62   1.76  41.29
   5_xyz:  97.65   0.00  16.59  97.65   0.00  12.05  93.62   1.76  41.29
   5_adp:  99.31   0.00  16.29  99.31   0.00  11.79  93.79   2.01  40.79
   5_occ:  99.31   0.00  16.29  99.31   0.00  11.79  93.79   2.01  40.79
   5_bss:  99.31   0.00  16.30  99.31   0.00  11.80  93.79   2.02  40.80
------------------------------------------------------------------------
 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:    1.793    0.012    0.308
   1_adp:    1.793    0.012    0.308
   1_occ:    1.793    0.012    0.308
   2_bss:    1.793    0.012    0.308
   2_xyz:    1.204    0.013    0.453
   2_adp:    1.204    0.013    0.453
   2_occ:    1.204    0.013    0.453
   3_bss:    1.204    0.013    0.453
   3_xyz:    1.259    0.059    0.571
   3_adp:    1.259    0.059    0.571
   3_occ:    1.259    0.059    0.571
   4_bss:    1.259    0.059    0.571
   4_xyz:    1.265    0.015    0.598
   4_adp:    1.265    0.015    0.598
   4_occ:    1.265    0.015    0.598
   5_bss:    1.265    0.015    0.598
   5_xyz:    1.239    0.077    0.611
   5_adp:    1.239    0.077    0.611
   5_occ:    1.239    0.077    0.611
   5_bss:    1.239    0.077    0.611
------------------------------------------------------------------------

CPU time actual refinement: 331.46


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/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_830/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_830/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.31 
  Macro-tasks:
    bulk solvent and scale       = 39.00  
    individual site refinement   = 140.16 
    weights calculation          = 28.78  
    collect and process          = 6.44   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.48 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 105.59 
    alpha_beta                      = 8.25   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 115.71 
    fmodel                         = 6.15   
    r_factors                      = 0.19   
    phase_errors                   = 10.67  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 249.87 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.661 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    648 calls, 105.23 s
gradients_fft:          593 calls, 101.49 s

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

# Date 2008-01-16 Time 05:46:09 PST -0800 (1200491169.59 s)
Start R-work = 0.3753, R-free = 0.3598 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.3597, R-free = 0.3442
Final R-work = 0.1135, R-free = 0.1616