# Date 2008-01-16 Time 06:17:23 PST -0800 (1200493043.54 s)
#phil __OFF__

Command line arguments: "../1083.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32355
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1083

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 48.1033, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00131
Completeness in resolution range: 0.950369
Completeness with d_max=infinity: 0.947427

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0013

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00131
Completeness in resolution range: 0.950369
Completeness with d_max=infinity: 0.947427

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2823 [2169/2197]  1953   216  10.0%
  bin  2:  4.2823 -  3.4117 [2066/2089]  1859   207  10.0%
  bin  3:  3.4117 -  2.9842 [2051/2073]  1843   208  10.1%
  bin  4:  2.9842 -  2.7131 [2042/2061]  1845   197   9.6%
  bin  5:  2.7131 -  2.5196 [2023/2052]  1814   209  10.3%
  bin  6:  2.5196 -  2.3716 [2000/2041]  1804   196   9.8%
  bin  7:  2.3716 -  2.2532 [1983/2018]  1782   201  10.1%
  bin  8:  2.2532 -  2.1554 [2007/2045]  1810   197   9.8%
  bin  9:  2.1554 -  2.0727 [1995/2027]  1797   198   9.9%
  bin 10:  2.0727 -  2.0013 [1253/2009]  1123   130  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.37 -     2.07: 5
        2.07 -     2.78: 554
        2.78 -     3.49: 4418
        3.49 -     4.19: 9177
        4.19 -     4.90: 13653
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.366 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.624 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.711 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.788 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27802 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_1083/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 48.10325 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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4357   r_free= 0.4146   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.254006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7763 0.99   1403  154 0.3556 0.3804      6.5268      6.5047|
|  2:  4.7763 -  3.8109 0.99   1363  150 0.3826 0.3924      6.8233      6.7897|
|  3:  3.8109 -  3.3350 0.99   1317  154 0.4091 0.3559      6.6475       6.557|
|  4:  3.3350 -  3.0328 0.99   1327  141 0.4291 0.4035      6.4972      6.4252|
|  5:  3.0328 -  2.8169 0.99   1301  148 0.4552 0.4425      6.3482      6.3973|
|  6:  2.8169 -  2.6517 0.98   1292  146 0.4671 0.4214      6.2528      6.1261|
|  7:  2.6517 -  2.5196 0.99   1311  144 0.4720 0.4086      6.2207      6.1483|
|  8:  2.5196 -  2.4103 0.99   1286  144 0.4764 0.4432      6.1365      6.1479|
|  9:  2.4103 -  2.3179 0.98   1300  140 0.4812 0.4652      6.0995      6.0722|
| 10:  2.3179 -  2.2382 0.98   1268  140 0.4582 0.4243      6.0632      6.0137|
| 11:  2.2382 -  2.1684 0.98   1284  147 0.4920 0.4373      6.0459      5.9988|
| 12:  2.1684 -  2.1066 0.99   1279  138 0.4745 0.4707      5.9441      5.9803|
| 13:  2.1066 -  2.0512 0.97   1262  138 0.4636 0.4471      5.8421      5.8264|
| 14:  2.0512 -  2.0013 0.49    637   75 0.4565 0.4348      5.7839      5.7089|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7763  1403   154  0.71  33.71   0.82     0.75      69942.66|
|  2:  4.7763 -  3.8109  1363   150  0.74  31.78   0.90     0.81      88041.51|
|  3:  3.8109 -  3.3350  1317   154  0.66  38.66   0.90     0.81      92307.84|
|  4:  3.3350 -  3.0328  1327   141  0.59  44.40   0.90     0.76      82014.85|
|  5:  3.0328 -  2.8169  1301   148  0.53  49.80   0.89     0.71      66052.94|
|  6:  2.8169 -  2.6517  1292   146  0.53  49.31   0.89     0.70      52474.03|
|  7:  2.6517 -  2.5196  1311   144  0.55  48.16   0.91     0.71      45561.44|
|  8:  2.5196 -  2.4103  1286   144  0.52  50.73   0.92     0.71      43095.03|
|  9:  2.4103 -  2.3179  1300   140  0.51  51.02   0.91     0.70      41194.69|
| 10:  2.3179 -  2.2382  1268   140  0.51  51.46   0.95     0.70      38184.52|
| 11:  2.2382 -  2.1684  1284   147  0.51  51.84   0.93     0.71      35647.42|
| 12:  2.1684 -  2.1066  1279   138  0.49  53.37   0.95     0.71      33834.27|
| 13:  2.1066 -  2.0512  1262   138  0.45  56.02   0.93     0.66      30092.27|
| 14:  2.0512 -  2.0013   637    75  0.44  56.95   0.95     0.59      25117.92|
|alpha:            min =        0.59 max =            0.81 mean =         0.72|
|beta:             min =    25117.92 max =        92307.84 mean =     54589.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.12|
|phase err.(test): min =        0.00 max =           89.88 mean =        47.04|
|-----------------------------------------------------------------------------|

============================== 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 = 6.310131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.778   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.574927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.906   (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 |  1.366 -  1.719:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.719 -  2.073:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.073 -  2.426:        8 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.426 -  2.780:      546 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.780 -  3.133:     2121 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.133 -  3.486:     2297 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.486 -  3.840:     4420 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.840 -  4.193:     4757 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.193 -  4.547:     6145 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.547 -  4.900:     7508 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| 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  1.366 |       0.267 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4357   r_free= 0.4146   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.254006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4250   r_free= 0.4041   ksol= 0.29   Bsol= 36.61   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,5.17,-2.25,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.245086                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.618964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.436   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.787756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.797   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4250      final r-factor (work) = 0.3557          |
| start r-factor (free) = 0.4041      final r-factor (free) = 0.3795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7077 = 5.62 * 0.50 * 6.2420 + 1.00 * 0.1708                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3238 = 5.62 * 0.50 * 6.1298 + 1.00 * 0.1021                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3557      final r-factor (work) = 0.3302          |
| start r-factor (free) = 0.3795      final r-factor (free) = 0.3838          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8349 = 0.79 * 1.00 * 6.1298 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8246 = 0.79 * 1.00 * 6.0760 + 1.00 * 0.0382                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.13   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    75.13   17.20    None  None   None       |
|    Sol.    : 438    0      0.00    69.77   35.58    None  None   None       |
|    Mac.    : 2385   0      0.00    75.13   13.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.513:  648   |   5:    37.563 -  45.076:  104        |
|      1:     7.513 -  15.025:  863   |   6:    45.076 -  52.588:   81        |
|      2:    15.025 -  22.538:  608   |   7:    52.588 -  60.101:   48        |
|      3:    22.538 -  30.050:  288   |   8:    60.101 -  67.613:   10        |
|      4:    30.050 -  37.563:  171   |   9:    67.613 -  75.126:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3302 r_free = 0.3838             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3297 r_free = 0.3829             target_work(ml) = 6.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3297   r_free= 0.3829   ksol= 0.29   Bsol= 36.61   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,5.17,-2.25,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.077121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3295   r_free= 0.3824   ksol= 0.29   Bsol= 36.61   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,3.08,-0.95,0.00,-0.00,-0.00); trace/3= 0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.079268                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.529671              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.706  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.941397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.370   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3295      final r-factor (work) = 0.2679          |
| start r-factor (free) = 0.3824      final r-factor (free) = 0.3126          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9833 = 7.53 * 0.50 * 6.0776 + 1.00 * 0.1021                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6378 = 7.53 * 0.50 * 5.9837 + 1.00 * 0.1100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2679      final r-factor (work) = 0.2481          |
| start r-factor (free) = 0.3126      final r-factor (free) = 0.3113          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6588 = 0.94 * 1.00 * 5.9837 + 1.00 * 0.0257                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5270 = 0.94 * 1.00 * 5.8531 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.72   18.17    None  None   None       |
|    all(noH): 2823   0      0.00    97.72   18.17    None  None   None       |
|    Sol.    : 438    0      0.00    93.84   39.47    None  None   None       |
|    Mac.    : 2385   0      0.00    97.72   14.26    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 -   9.772: 1028   |   5:    48.861 -  58.633:   83        |
|      1:     9.772 -  19.544:  885   |   6:    58.633 -  68.405:   48        |
|      2:    19.544 -  29.316:  385   |   7:    68.405 -  78.177:   28        |
|      3:    29.316 -  39.089:  214   |   8:    78.177 -  87.949:   13        |
|      4:    39.089 -  48.861:  132   |   9:    87.949 -  97.721:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2481 r_free = 0.3113             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2479 r_free = 0.3110             target_work(ml) = 5.852         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2479   r_free= 0.3110   ksol= 0.29   Bsol= 36.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,3.08,-0.95,0.00,-0.00,-0.00); trace/3= 0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.851787                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2476   r_free= 0.3091   ksol= 0.32   Bsol= 61.84   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,1.95,-0.05,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.851681                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.509897              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.221  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.278235              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2476      final r-factor (work) = 0.1950          |
| start r-factor (free) = 0.3091      final r-factor (free) = 0.2467          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1660 = 6.51 * 0.50 * 5.8545 + 1.00 * 0.1100                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8081 = 6.51 * 0.50 * 5.7542 + 1.00 * 0.0785                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1950      final r-factor (work) = 0.1793          |
| start r-factor (free) = 0.2467      final r-factor (free) = 0.2249          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6181 = 0.28 * 1.00 * 5.7542 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5647 = 0.28 * 1.00 * 5.5866 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.18   17.11    None  None   None       |
|    all(noH): 2823   0      0.00    95.18   17.11    None  None   None       |
|    Sol.    : 438    0      3.61    95.18   40.04    None  None   None       |
|    Mac.    : 2385   0      0.00    94.64   12.90    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 -   9.518: 1122   |   5:    47.590 -  57.108:   85        |
|      1:     9.518 -  19.036:  953   |   6:    57.108 -  66.626:   51        |
|      2:    19.036 -  28.554:  271   |   7:    66.626 -  76.144:   21        |
|      3:    28.554 -  38.072:  148   |   8:    76.144 -  85.662:   12        |
|      4:    38.072 -  47.590:  155   |   9:    85.662 -  95.180:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1793 r_free = 0.2249             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1792 r_free = 0.2249             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1792   r_free= 0.2249   ksol= 0.32   Bsol= 61.84   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,1.95,-0.05,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.546580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1791   r_free= 0.2240   ksol= 0.32   Bsol= 70.26   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,0.36,-0.48,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.546225                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.583522              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.631  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.773826              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.583  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1791      final r-factor (work) = 0.1505          |
| start r-factor (free) = 0.2240      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2998 = 2.58 * 0.50 * 5.5901 + 1.00 * 0.0787                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1275 = 2.58 * 0.50 * 5.4669 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1505      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2407 = 0.77 * 1.00 * 5.4669 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1581 = 0.77 * 1.00 * 5.3569 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    104.65  17.27    None  None   None       |
|    all(noH): 2823   0      0.52    104.65  17.27    None  None   None       |
|    Sol.    : 438    0      4.40    103.55  43.50    None  None   None       |
|    Mac.    : 2385   0      0.52    104.65  12.45    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:     0.523 -  10.935: 1407   |   5:    52.585 -  62.997:   94        |
|      1:    10.935 -  21.348:  808   |   6:    62.997 -  73.409:   54        |
|      2:    21.348 -  31.760:  195   |   7:    73.409 -  83.822:   26        |
|      3:    31.760 -  42.172:  128   |   8:    83.822 -  94.234:    9        |
|      4:    42.172 -  52.585:   99   |   9:    94.234 - 104.646:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1413 r_free = 0.1879             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1413 r_free = 0.1879             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1413   r_free= 0.1879   ksol= 0.32   Bsol= 70.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,0.36,-0.48,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.345014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1881   ksol= 0.33   Bsol= 75.84   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.18,-0.37,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.345621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.086011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.313  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.705203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.050  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1881      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6533 = 2.09 * 0.50 * 5.3574 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5967 = 2.09 * 0.50 * 5.3062 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7547 = 0.71 * 1.00 * 5.3062 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7307 = 0.71 * 1.00 * 5.2722 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.39  16.93    None  None   None       |
|    all(noH): 2823   0      0.00    110.39  16.93    None  None   None       |
|    Sol.    : 438    0      4.64    110.39  43.28    None  None   None       |
|    Mac.    : 2385   0      0.00    108.21  12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.039: 1450   |   5:    55.193 -  66.232:   77        |
|      1:    11.039 -  22.077:  816   |   6:    66.232 -  77.271:   42        |
|      2:    22.077 -  33.116:  172   |   7:    77.271 -  88.310:   22        |
|      3:    33.116 -  44.155:  121   |   8:    88.310 -  99.348:    7        |
|      4:    44.155 -  55.193:  113   |   9:    99.348 - 110.387:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1275 r_free = 0.1780             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1274 r_free = 0.1780             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1780   ksol= 0.33   Bsol= 75.84   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.18,-0.37,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.266172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7763 0.99   1403  154 0.1015 0.1328      5.4137      5.5707|
|  2:  4.7763 -  3.8109 0.99   1363  150 0.0880 0.1113      5.4631      5.6638|
|  3:  3.8109 -  3.3350 0.99   1317  154 0.1152 0.1696      5.5515      5.9165|
|  4:  3.3350 -  3.0328 0.99   1327  141 0.1411 0.1839      5.5772      5.7453|
|  5:  3.0328 -  2.8169 0.99   1301  148 0.1553 0.1963      5.4846      5.6594|
|  6:  2.8169 -  2.6517 0.98   1292  146 0.1488 0.2217      5.3712      5.5811|
|  7:  2.6517 -  2.5196 0.99   1311  144 0.1464 0.1971      5.3049      5.5709|
|  8:  2.5196 -  2.4103 0.99   1286  144 0.1404 0.1909      5.2116      5.4013|
|  9:  2.4103 -  2.3179 0.98   1300  140 0.1403 0.2113      5.1811       5.439|
| 10:  2.3179 -  2.2382 0.98   1268  140 0.1360 0.2012      5.1097      5.3439|
| 11:  2.2382 -  2.1684 0.98   1284  147 0.1314 0.1939      5.0548      5.3421|
| 12:  2.1684 -  2.1066 0.99   1279  138 0.1258 0.1811      4.9831      5.2125|
| 13:  2.1066 -  2.0512 0.97   1262  138 0.1351 0.2053      4.9188      5.1849|
| 14:  2.0512 -  2.0013 0.49    637   75 0.1285 0.2109      4.8211      5.0852|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7763  1403   154  0.94   9.56   0.96     0.93       7595.11|
|  2:  4.7763 -  3.8109  1363   150  0.95   8.62   1.00     0.98       9732.17|
|  3:  3.8109 -  3.3350  1317   154  0.92  12.66   1.02     1.01      12287.91|
|  4:  3.3350 -  3.0328  1327   141  0.90  16.40   1.00     0.97      13229.80|
|  5:  3.0328 -  2.8169  1301   148  0.87  19.32   1.00     0.97      11762.95|
|  6:  2.8169 -  2.6517  1292   146  0.88  18.92   0.98     0.95       9552.28|
|  7:  2.6517 -  2.5196  1311   144  0.88  18.26   0.98     0.94       8189.98|
|  8:  2.5196 -  2.4103  1286   144  0.88  18.54   0.98     0.95       7232.37|
|  9:  2.4103 -  2.3179  1300   140  0.88  18.31   0.98     0.93       6586.48|
| 10:  2.3179 -  2.2382  1268   140  0.88  18.58   0.97     0.93       5885.34|
| 11:  2.2382 -  2.1684  1284   147  0.88  18.56   0.97     0.92       5391.01|
| 12:  2.1684 -  2.1066  1279   138  0.90  17.27   0.98     0.96       4920.73|
| 13:  2.1066 -  2.0512  1262   138  0.88  19.09   0.97     0.96       4378.62|
| 14:  2.0512 -  2.0013   637    75  0.88  18.25   0.95     0.90       3512.88|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     3512.88 max =        13229.80 mean =      8074.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.45|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1780   ksol= 0.33   Bsol= 73.06   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,-0.14,-0.03,-0.00,-0.00,-0.00); trace/3= -0.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.266265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1780   ksol= 0.33   Bsol= 73.06   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,-0.14,-0.03,-0.00,-0.00,-0.00); trace/3= -0.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.266265                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7763 0.99   1403  154 0.1015 0.1331      5.4143      5.5714|
|  2:  4.7763 -  3.8109 0.99   1363  150 0.0880 0.1112       5.463       5.662|
|  3:  3.8109 -  3.3350 0.99   1317  154 0.1153 0.1696      5.5514      5.9171|
|  4:  3.3350 -  3.0328 0.99   1327  141 0.1410 0.1840      5.5778      5.7457|
|  5:  3.0328 -  2.8169 0.99   1301  148 0.1554 0.1965      5.4848      5.6598|
|  6:  2.8169 -  2.6517 0.98   1292  146 0.1487 0.2213      5.3709      5.5794|
|  7:  2.6517 -  2.5196 0.99   1311  144 0.1465 0.1976      5.3047      5.5709|
|  8:  2.5196 -  2.4103 0.99   1286  144 0.1403 0.1910      5.2117      5.4009|
|  9:  2.4103 -  2.3179 0.98   1300  140 0.1401 0.2114      5.1811      5.4395|
| 10:  2.3179 -  2.2382 0.98   1268  140 0.1360 0.2015      5.1103      5.3447|
| 11:  2.2382 -  2.1684 0.98   1284  147 0.1314 0.1941      5.0545      5.3422|
| 12:  2.1684 -  2.1066 0.99   1279  138 0.1257 0.1818      4.9832      5.2151|
| 13:  2.1066 -  2.0512 0.97   1262  138 0.1352 0.2047      4.9189       5.184|
| 14:  2.0512 -  2.0013 0.49    637   75 0.1285 0.2103       4.821      5.0832|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7763  1403   154  0.94   9.57   0.96     0.93       7610.43|
|  2:  4.7763 -  3.8109  1363   150  0.95   8.62   1.00     0.99       9727.21|
|  3:  3.8109 -  3.3350  1317   154  0.92  12.65   1.02     1.01      12274.21|
|  4:  3.3350 -  3.0328  1327   141  0.90  16.41   1.01     0.97      13242.07|
|  5:  3.0328 -  2.8169  1301   148  0.87  19.31   1.00     0.98      11748.17|
|  6:  2.8169 -  2.6517  1292   146  0.88  18.90   0.99     0.95       9541.02|
|  7:  2.6517 -  2.5196  1311   144  0.88  18.25   0.99     0.95       8183.07|
|  8:  2.5196 -  2.4103  1286   144  0.88  18.55   0.99     0.96       7240.86|
|  9:  2.4103 -  2.3179  1300   140  0.88  18.31   0.99     0.94       6591.55|
| 10:  2.3179 -  2.2382  1268   140  0.88  18.60   0.98     0.94       5892.47|
| 11:  2.2382 -  2.1684  1284   147  0.88  18.56   0.98     0.93       5391.70|
| 12:  2.1684 -  2.1066  1279   138  0.90  17.29   0.99     0.97       4927.39|
| 13:  2.1066 -  2.0512  1262   138  0.88  19.09   0.98     0.98       4375.57|
| 14:  2.0512 -  2.0013   637    75  0.88  18.25   0.96     0.91       3506.14|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3506.14 max =        13242.07 mean =      8074.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.45|
|phase err.(test): min =        0.00 max =           89.96 mean =        15.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.358)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.39  16.93    None  None   None       |
|    all(noH): 2823   0      0.00    110.39  16.93    None  None   None       |
|    Sol.    : 438    0      4.64    110.39  43.28    None  None   None       |
|    Mac.    : 2385   0      0.00    108.21  12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.042: 1450   |   5:    55.196 -  66.235:   77        |
|      1:    11.042 -  22.080:  816   |   6:    66.235 -  77.274:   42        |
|      2:    22.080 -  33.119:  172   |   7:    77.274 -  88.312:   22        |
|      3:    33.119 -  44.158:  121   |   8:    88.312 -  99.351:    7        |
|      4:    44.158 -  55.196:  113   |   9:    99.351 - 110.390:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 4.776
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 338
   mapped sites are within: 0.721 - 4.776

peak=   10.187 closest distance to " O  BHOH Z  74 " =    1.013
peak=    5.672 closest distance to " O   HOH Z 111 " =    2.163
peak=    5.520 closest distance to " O   HOH Z 210 " =    1.379
peak=    5.257 closest distance to " CB  SER A  63 " =    1.284
peak=    5.155 closest distance to " CB  GLN A 223 " =    1.374
peak=    5.040 closest distance to " O   HOH Z 400 " =    0.939
peak=    4.971 closest distance to " CG  PRO A 213 " =    1.283
peak=    4.882 closest distance to " CG  PRO A  54 " =    1.339
peak=    4.852 closest distance to " CG  PRO A 198 " =    1.257
peak=    4.810 closest distance to " O   HOH Z 232 " =    2.343
peak=    4.796 closest distance to " O   HOH Z 433 " =    1.831
peak=    4.711 closest distance to " CA  TYR A  30 " =    0.988
peak=    4.627 closest distance to " O   HOH Z 134 " =    1.992
peak=    4.622 closest distance to " O   HOH Z  41 " =    1.026
peak=    4.598 closest distance to " O   PRO A 198 " =    1.557
peak=    4.497 closest distance to " O   HOH Z 133 " =    2.232
peak=    4.469 closest distance to " CA  ALA A  51 " =    0.986
peak=    4.441 closest distance to " O   HOH Z 209 " =    2.344
peak=    4.428 closest distance to " CB  ARG A 275 " =    0.851
peak=    4.419 closest distance to " CG  PRO A 280 " =    0.867
peak=    4.391 closest distance to " CB  PRO A  54 " =    0.889
peak=    4.386 closest distance to " CB  LEU A 228 " =    1.147
peak=    4.378 closest distance to " CB  ARG A 190 " =    1.758
peak=    4.368 closest distance to " CB  GLN A 183 " =    1.266
peak=    4.367 closest distance to " CB  GLU A 128 " =    1.111
peak=    4.355 closest distance to " O   HOH Z  15 " =    2.114
peak=    4.316 closest distance to " CD  ARG A 269 " =    0.903
peak=    4.273 closest distance to " O   HOH Z 234 " =    3.719
peak=    4.222 closest distance to " CB  TRP A 266 " =    1.004
peak=    4.198 closest distance to " CB  TRP A 179 " =    1.432
peak=    4.189 closest distance to " O   HOH Z 425 " =    1.550
peak=    4.189 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.188 closest distance to " O   HOH Z  47 " =    1.545
peak=    4.185 closest distance to " O   HOH Z  49 " =    0.984
peak=    4.162 closest distance to " CG2BVAL A  41 " =    0.938
peak=    4.159 closest distance to " O   HOH Z 369 " =    2.063
peak=    4.152 closest distance to " O   THR A 251 " =    1.304
peak=    4.144 closest distance to " O   HOH Z 412 " =    3.363
peak=    4.135 closest distance to " O   HOH Z 357 " =    2.197
peak=    4.116 closest distance to " O   HOH Z  80 " =    2.121
peak=    4.107 closest distance to " CG1 ILE A  33 " =    1.270
peak=    4.097 closest distance to " NH2 ARG A 156 " =    1.191
peak=    4.072 closest distance to " CA  ALA A 160 " =    1.023
peak=    4.068 closest distance to " O   HOH Z  97 " =    2.000
peak=    4.042 closest distance to " O   HOH Z 214 " =    1.547
peak=    4.042 closest distance to " O   HOH Z 418 " =    1.913
peak=    4.015 closest distance to " O   HOH Z  95 " =    1.950
peak=    4.004 closest distance to " CZ  PHE A 218 " =    1.125
peak=    3.988 closest distance to " OD1 ASN A 301 " =    1.217
peak=    3.971 closest distance to " O   HOH Z  67 " =    2.091
peak=    3.970 closest distance to " O   HOH Z  78 " =    2.226
peak=    3.949 closest distance to " CD  ARG A  66 " =    2.806
peak=    3.948 closest distance to " O   HOH Z 196 " =    2.029
peak=    3.945 closest distance to " O   HOH Z 394 " =    1.676
peak=    3.943 closest distance to " CG2 VAL A  78 " =    0.962
peak=    3.939 closest distance to " O   HOH Z  20 " =    1.882
peak=    3.934 closest distance to " O   HOH Z   7 " =    1.066
peak=    3.921 closest distance to " O   HOH Z 176 " =    2.066
peak=    3.916 closest distance to " CA  ALA A  21 " =    1.488
peak=    3.914 closest distance to " O   HOH Z  40 " =    1.918
peak=    3.913 closest distance to " CB  TYR A 169 " =    0.811
peak=    3.909 closest distance to " O   HOH Z 404 " =    1.619
peak=    3.908 closest distance to " CB  SER A 141 " =    1.046
peak=    3.908 closest distance to " O   HOH Z 118 " =    1.524
peak=    3.907 closest distance to " OE1 GLN A  11 " =    2.100
peak=    3.904 closest distance to " O   HOH Z 120 " =    1.047
peak=    3.902 closest distance to " O   HOH Z 298 " =    2.024
peak=    3.893 closest distance to " NE2 HIS A 115 " =    1.124
peak=    3.882 closest distance to " CA  ARG A 195 " =    1.121
peak=    3.880 closest distance to " O   HOH Z 227 " =    1.831
peak=    3.880 closest distance to " CB  SER A  62 " =    0.841
peak=    3.872 closest distance to " CB  VAL A 202 " =    1.505
peak=    3.866 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.854 closest distance to " O   HOH Z  88 " =    1.728
peak=    3.816 closest distance to " O   HOH Z 403 " =    1.870
peak=    3.815 closest distance to " O   HOH Z 193 " =    1.981
peak=    3.813 closest distance to " O   HOH Z 271 " =    2.518
peak=    3.811 closest distance to " O   HOH Z 426 " =    1.362
peak=    3.808 closest distance to " CD2 LEU A 297 " =    1.121
peak=    3.806 closest distance to " O   HOH Z 265 " =    1.995
peak=    3.801 closest distance to " CD1 LEU A 300 " =    1.225
peak=    3.799 closest distance to " O   HOH Z 423 " =    1.800
peak=    3.788 closest distance to " CA  GLY A 196 " =    1.023
peak=    3.771 closest distance to " CB  MET A 105 " =    1.137
peak=    3.770 closest distance to " CB  PRO A  54 " =    1.334
peak=    3.766 closest distance to " O   HOH Z 406 " =    1.583
peak=    3.765 closest distance to " O   HOH Z 432 " =    1.821
peak=    3.759 closest distance to " CA  ASP A 191 " =    0.892
peak=    3.748 closest distance to " O   HOH Z 352 " =    1.913
peak=    3.745 closest distance to " O   HOH Z 415 " =    1.157
peak=    3.744 closest distance to " CB  ASP A 140 " =    0.847
peak=    3.742 closest distance to " O   HOH Z 377 " =    1.391
peak=    3.736 closest distance to " O   HOH Z 301 " =    1.523
peak=    3.727 closest distance to " O   HOH Z 327 " =    1.775
peak=    3.726 closest distance to " N   SER A 164 " =    1.069
peak=    3.711 closest distance to " CA  LEU A  83 " =    1.417
peak=    3.700 closest distance to " O   HOH Z 132 " =    2.702
peak=    3.698 closest distance to " C   ILE A 106 " =    1.815
peak=    3.695 closest distance to " O   HOH Z 431 " =    1.198
peak=    3.692 closest distance to " CG1 ILE A 120 " =    1.003
peak=    3.689 closest distance to " CD  ARG A 159 " =    0.832
peak=    3.684 closest distance to " CG2 ILE A 151 " =    0.906
peak=    3.680 closest distance to " CD2 TRP A 179 " =    1.361
peak=    3.679 closest distance to " CG1 VAL A 153 " =    1.029
peak=    3.676 closest distance to " CA  ILE A 106 " =    0.804
peak=    3.661 closest distance to " O   HOH Z 247 " =    1.518
peak=    3.652 closest distance to " O   HOH Z 343 " =    2.465
peak=    3.646 closest distance to " O   HOH Z 316 " =    2.996
peak=    3.639 closest distance to " O   HOH Z 128 " =    2.273
peak=    3.639 closest distance to " CD  LYS A 166 " =    1.450
peak=    3.634 closest distance to " O   HOH Z  30 " =    1.923
peak=    3.625 closest distance to " O  BHOH Z 338 " =    0.895
peak=    3.616 closest distance to " N   ILE A  33 " =    0.998
peak=    3.616 closest distance to " O   HOH Z 189 " =    2.474
peak=    3.611 closest distance to " N   ASN A  39 " =    1.290
peak=    3.611 closest distance to " CB  PRO A 198 " =    0.925
peak=    3.610 closest distance to " O   HOH Z 374 " =    2.668
peak=    3.608 closest distance to " O   HOH Z 201 " =    2.841
peak=    3.603 closest distance to " CB  GLU A 152 " =    1.158
peak=    3.595 closest distance to " CB  GLN A 194 " =    1.045
peak=    3.585 closest distance to " NE2 GLN A  11 " =    1.028
peak=    3.583 closest distance to " O   HOH Z 174 " =    1.261
peak=    3.576 closest distance to " CG  PRO A 243 " =    1.189
peak=    3.573 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.573 closest distance to " ND2 ASN A 301 " =    1.068
peak=    3.571 closest distance to " O   ALA A 165 " =    1.413
peak=    3.571 closest distance to " O   HOH Z 437 " =    1.585
peak=    3.568 closest distance to " CA  VAL A  41 " =    0.870
peak=    3.566 closest distance to " O   HOH Z 389 " =    2.001
peak=    3.564 closest distance to " OH  TYR A 169 " =    0.920
peak=    3.562 closest distance to " O   HOH Z 362 " =    3.288
peak=    3.554 closest distance to " C   VAL A 265 " =    1.143
peak=    3.554 closest distance to " CG2 VAL A 197 " =    1.243
peak=    3.543 closest distance to " CA  THR A 294 " =    1.754
peak=    3.541 closest distance to " O   HOH Z  22 " =    2.614
peak=    3.536 closest distance to " CB  GLU A 277 " =    3.900
peak=    3.535 closest distance to " CG AARG A 275 " =    1.207
peak=    3.532 closest distance to " O   HOH Z 126 " =    2.333
peak=    3.531 closest distance to " O   HOH Z 368 " =    1.971
peak=    3.531 closest distance to " CA  ASP A 124 " =    0.851
peak=    3.530 closest distance to " CZ3 TRP A 266 " =    1.047
peak=    3.528 closest distance to " CB  ASN A 285 " =    0.799
peak=    3.525 closest distance to " CB  ALA A  34 " =    0.721
peak=    3.523 closest distance to " O   HOH Z  54 " =    1.184
peak=    3.522 closest distance to " CG2 ILE A  20 " =    1.331
peak=    3.515 closest distance to " O   HOH Z 284 " =    2.973
peak=    3.512 closest distance to " CA  SER A  12 " =    1.584
peak=    3.511 closest distance to " CZ3 TRP A  85 " =    0.945
peak=    3.511 closest distance to " CD2 LEU A 255 " =    1.563
peak=    3.511 closest distance to " C   GLY A  80 " =    1.068
peak=    3.511 closest distance to " CB  ASN A 142 " =    1.146
peak=    3.508 closest distance to " CA  THR A 221 " =    1.636
peak=    3.508 closest distance to " O   GLY A  91 " =    1.121
peak=    3.502 closest distance to " O   HOH Z 124 " =    2.122
peak=    3.501 closest distance to " O   HOH Z 214 " =    2.366
peak=    3.500 closest distance to " OD1 ASN A  69 " =    2.482
peak=    3.496 closest distance to " O   HOH Z  63 " =    1.546
peak=    3.495 closest distance to " O   HOH Z 245 " =    1.316
peak=    3.493 closest distance to " O   HOH Z 301 " =    2.121
peak=    3.492 closest distance to " CD  ARG A 195 " =    1.073
peak=    3.489 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.483 closest distance to " O   SER A  87 " =    2.321
peak=    3.479 closest distance to " CB  GLN A  88 " =    1.206
peak=    3.477 closest distance to " CA  SER A  87 " =    0.977
peak=    3.468 closest distance to " CB  ARG A  79 " =    1.400
peak=    3.464 closest distance to " CG  GLN A  77 " =    0.804
peak=    3.464 closest distance to " O   HOH Z 423 " =    3.352
peak=    3.461 closest distance to " CB  MET A  40 " =    0.743
peak=    3.460 closest distance to " O   HOH Z 185 " =    1.779
peak=    3.457 closest distance to " O   HOH Z  44 " =    1.769
peak=    3.454 closest distance to " OD1 ASN A 217 " =    1.617
peak=    3.453 closest distance to " O   GLN A  11 " =    0.985
peak=    3.448 closest distance to " O   HOH Z 405 " =    4.339
peak=    3.445 closest distance to " CG  GLU A  37 " =    0.983
peak=    3.444 closest distance to " O   HOH Z 422 " =    0.950
peak=    3.444 closest distance to " ND1 HIS A  81 " =    1.541
peak=    3.443 closest distance to " NZ  LYS A 117 " =    3.031
peak=    3.443 closest distance to " O   HOH Z 346 " =    1.622
peak=    3.443 closest distance to " O   HOH Z 358 " =    1.409
peak=    3.436 closest distance to " O   HOH Z 435 " =    3.056
peak=    3.434 closest distance to " CB  ARG A 190 " =    1.129
peak=    3.432 closest distance to " CB  ASN A 187 " =    1.153
peak=    3.429 closest distance to " O   ALA A 158 " =    1.231
peak=    3.428 closest distance to " OE1 GLN A  58 " =    3.366
peak=    3.424 closest distance to " CB  PRO A 243 " =    1.142
peak=    3.419 closest distance to " CB  PHE A 283 " =    0.931
peak=    3.419 closest distance to " CG2 THR A  42 " =    0.939
peak=    3.416 closest distance to " CB  ALA A 256 " =    1.433
peak=    3.414 closest distance to " CB  SER A  26 " =    0.803
peak=    3.414 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.413 closest distance to " CB  ALA A 100 " =    1.558
peak=    3.412 closest distance to " CA  GLN A 223 " =    0.857
peak=    3.411 closest distance to " O   HOH Z 402 " =    1.652
peak=    3.411 closest distance to " CA  TRP A 274 " =    0.976
peak=    3.411 closest distance to " CA  GLN A  88 " =    1.331
peak=    3.409 closest distance to " O   HOH Z 395 " =    1.419
peak=    3.409 closest distance to " O   HOH Z  40 " =    2.180
peak=    3.408 closest distance to " CD1 LEU A 222 " =    0.810
peak=    3.406 closest distance to " O   HOH Z 174 " =    1.844
peak=    3.405 closest distance to " CA  GLU A 152 " =    0.919
peak=    3.402 closest distance to " O   HOH Z 336 " =    1.642
peak=    3.399 closest distance to " CB  TYR A 116 " =    1.250
peak=    3.396 closest distance to " N   TYR A 116 " =    1.699
peak=    3.394 closest distance to " O   ARG A 275 " =    0.786
peak=    3.394 closest distance to " CB  ASP A 124 " =    0.863
peak=    3.392 closest distance to " CB  GLU A 277 " =    0.764
peak=    3.389 closest distance to " CB  GLU A 175 " =    1.375
peak=    3.381 closest distance to " O   HOH Z 134 " =    2.245
peak=    3.377 closest distance to " CA  ALA A 295 " =    1.108
peak=    3.374 closest distance to " O   HOH Z 373 " =    1.634
peak=    3.373 closest distance to " NH1 ARG A 269 " =    0.730
peak=    3.372 closest distance to " O   HOH Z 154 " =    1.269
peak=    3.370 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.367 closest distance to " CA  ARG A 102 " =    1.251
peak=    3.361 closest distance to " CD BLYS A 290 " =    0.991
peak=    3.358 closest distance to " O   HOH Z  48 " =    1.982
peak=    3.356 closest distance to " CA  GLN A  11 " =    1.305
peak=    3.355 closest distance to " N   TYR A  15 " =    0.867
peak=    3.353 closest distance to " NH2AARG A 190 " =    1.420
peak=    3.352 closest distance to " O   ASN A  74 " =    1.559
peak=    3.351 closest distance to " O   HOH Z 281 " =    4.776
peak=    3.349 closest distance to " CA  ASN A 176 " =    1.303
peak=    3.349 closest distance to " CB  ILE A 199 " =    1.099
peak=    3.348 closest distance to " O   HOH Z 150 " =    1.819
peak=    3.345 closest distance to " CB  GLN A 103 " =    0.994
peak=    3.342 closest distance to " O   HOH Z 344 " =    3.191
peak=    3.338 closest distance to " O   HOH Z  49 " =    2.069
peak=    3.336 closest distance to " CA  ASN A 215 " =    1.209
peak=    3.335 closest distance to " OG BSER A 164 " =    2.252
peak=    3.335 closest distance to " OG  SER A  97 " =    3.503
peak=    3.333 closest distance to " O   HOH Z 368 " =    4.409
peak=    3.325 closest distance to " CE3 TRP A  85 " =    1.148
peak=    3.325 closest distance to " O   HOH Z  11 " =    1.379
peak=    3.324 closest distance to " NZ  LYS A 166 " =    3.234
peak=    3.321 closest distance to " CA  LYS A  48 " =    1.394
peak=    3.320 closest distance to " CA  GLY A  98 " =    1.093
peak=    3.317 closest distance to " CA  ASP A 162 " =    1.244
peak=    3.315 closest distance to " CA  GLN A  73 " =    1.398
peak=    3.312 closest distance to " CB  GLU A  46 " =    1.017
peak=    3.310 closest distance to " NH2BARG A 145 " =    2.005
peak=    3.308 closest distance to " CB  ARG A 269 " =    0.860
peak=    3.307 closest distance to " CB  LEU A  83 " =    0.794
peak=    3.305 closest distance to " O   HOH Z  57 " =    1.749
peak=    3.304 closest distance to " OG  SER A 245 " =    1.635
peak=    3.303 closest distance to " CA  LYS A 117 " =    1.355
peak=    3.302 closest distance to " CA  GLU A  46 " =    0.822
peak=    3.301 closest distance to " OG1 THR A 157 " =    1.192
peak=    3.301 closest distance to " O   HOH Z 155 " =    3.228
peak=    3.297 closest distance to " O   HOH Z 104 " =    2.803
peak=    3.293 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.289 closest distance to " CB  ALA A 248 " =    1.169
peak=    3.284 closest distance to " O   HOH Z 371 " =    3.336
peak=    3.283 closest distance to " CG2 THR A 220 " =    0.756
peak=    3.277 closest distance to " CA  ARG A 139 " =    1.530
peak=    3.276 closest distance to " CG2 THR A  29 " =    1.506
peak=    3.270 closest distance to " CG2 VAL A 257 " =    0.924
peak=    3.268 closest distance to " O   HOH Z 325 " =    4.029
peak=    3.266 closest distance to " NH2BARG A 102 " =    1.091
peak=    3.263 closest distance to " NH1AARG A 145 " =    1.086
peak=    3.259 closest distance to " CE3 TRP A 274 " =    3.680
peak=    3.256 closest distance to " O   HOH Z 258 " =    2.185
peak=    3.256 closest distance to " O   HOH Z 380 " =    1.715
peak=    3.254 closest distance to " O   HOH Z  50 " =    3.637
peak=    3.251 closest distance to " O   HOH Z 417 " =    3.062
peak=    3.251 closest distance to " O   HOH Z 279 " =    2.254
peak=    3.250 closest distance to " OD2 ASP A 200 " =    1.349
peak=    3.249 closest distance to " NE2 GLN A 278 " =    2.569
peak=    3.246 closest distance to " CB  ARG A  79 " =    0.926
peak=    3.241 closest distance to " O   HOH Z 139 " =    4.673
peak=    3.237 closest distance to " CB  MET A  47 " =    0.960
peak=    3.233 closest distance to " O   HOH Z 223 " =    1.000
peak=    3.232 closest distance to " O   HOH Z  48 " =    1.576
peak=    3.232 closest distance to " CA  ARG A 156 " =    1.029
peak=    3.230 closest distance to " CD1 LEU A   5 " =    1.284
peak=    3.227 closest distance to " O   HOH Z 193 " =    1.727
peak=    3.225 closest distance to " O   HOH Z 365 " =    2.987
peak=    3.223 closest distance to " O   HOH Z  88 " =    3.681
peak=    3.221 closest distance to " O   HOH Z 327 " =    2.429
peak=    3.220 closest distance to " CA  VAL A 125 " =    1.266
peak=    3.219 closest distance to " CA  ASP A 132 " =    1.216
peak=    3.216 closest distance to " O   HOH Z 383 " =    2.187
peak=    3.214 closest distance to " OG1 THR A 294 " =    2.481
peak=    3.211 closest distance to " OH  TYR A  30 " =    1.396
peak=    3.209 closest distance to " CA  ALA A 291 " =    0.850
peak=    3.208 closest distance to " O   HOH Z  21 " =    1.813
peak=    3.206 closest distance to " O   HOH Z  71 " =    2.313
peak=    3.205 closest distance to " OG  SER A  62 " =    3.059
peak=    3.201 closest distance to " O   SER A  26 " =    1.631
peak=    3.200 closest distance to " CA  TYR A 116 " =    1.432
peak=    3.199 closest distance to " O   HOH Z  78 " =    1.800
peak=    3.195 closest distance to " CE1 TYR A 186 " =    1.341
peak=    3.195 closest distance to " CD  ARG A  24 " =    1.468
peak=    3.191 closest distance to " O   HOH Z 433 " =    1.907
peak=    3.190 closest distance to " O   SER A 276 " =    1.296
peak=    3.188 closest distance to " CA  GLY A 229 " =    0.860
peak=    3.187 closest distance to " O   HOH Z 428 " =    1.059
peak=    3.185 closest distance to " CA  ASN A 217 " =    1.340
peak=    3.184 closest distance to " O   HOH Z  49 " =    1.462
peak=    3.182 closest distance to " CD1 TRP A 266 " =    1.195
peak=    3.179 closest distance to " CE1 HIS A 108 " =    1.088
peak=    3.178 closest distance to " O   LYS A 290 " =    1.843
peak=    3.178 closest distance to " N   LYS A 166 " =    0.915
peak=    3.177 closest distance to " O   HOH Z 146 " =    1.555
peak=    3.177 closest distance to " O   HOH Z 234 " =    1.853
peak=    3.174 closest distance to " O   HOH Z 294 " =    1.659
peak=    3.171 closest distance to " CA  MET A 105 " =    1.231
peak=    3.167 closest distance to " O   ASP A 200 " =    1.472
peak=    3.165 closest distance to " O   HOH Z 145 " =    2.140
peak=    3.158 closest distance to " O   HOH Z 261 " =    1.893
peak=    3.157 closest distance to " NH1 ARG A  14 " =    1.327
peak=    3.156 closest distance to " CB  SER A 210 " =    0.954
peak=    3.151 closest distance to " O   HOH Z 109 " =    2.025
peak=    3.142 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.140 closest distance to " O   HOH Z   6 " =    1.111
peak=    3.137 closest distance to " CB  SER A   3 " =    1.373
peak=    3.137 closest distance to " CB  VAL A 265 " =    1.301
peak=    3.135 closest distance to " NZ  LYS A 117 " =    1.746
peak=    3.131 closest distance to " CA  GLY A 241 " =    0.766
peak=    3.127 closest distance to " O   GLY A  57 " =    2.668
peak=    3.127 closest distance to " CB  PHE A  16 " =    1.309
peak=    3.120 closest distance to " O   HOH Z 141 " =    1.677
peak=    3.119 closest distance to " CG2 ILE A 120 " =    0.912
peak=    3.114 closest distance to " CB  ALA A  71 " =    1.272
peak=    3.107 closest distance to " O   HOH Z 156 " =    2.669
peak=    3.106 closest distance to " CB  ALA A 137 " =    1.143
peak=    3.106 closest distance to " CB  SER A 216 " =    0.847
peak=    3.106 closest distance to " O   HOH Z   2 " =    1.609
peak=    3.096 closest distance to " O   HOH Z  78 " =    1.110
peak=    3.094 closest distance to " O   HOH Z 303 " =    2.335
peak=    3.076 closest distance to " CB  ARG A 156 " =    0.992
peak=    3.066 closest distance to " CG  LYS A  76 " =    1.146
peak=    3.065 closest distance to " CA  ALA A 100 " =    1.237
peak=    3.064 closest distance to " CB  SER A  28 " =    1.126
peak=    3.044 closest distance to " O   HOH Z 409 " =    3.009

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.782 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 227 from: 227
   mapped sites are within: 0.782 - 5.875

peak=   -4.581 closest distance to " O   HOH Z 166 " =    1.643
peak=   -4.546 closest distance to " O   HOH Z 411 " =    5.046
peak=   -4.332 closest distance to " CD  GLN A 223 " =    1.486
peak=   -4.320 closest distance to " CD1 PHE A  59 " =    1.922
peak=   -4.125 closest distance to " O   HOH Z 150 " =    0.964
peak=   -4.124 closest distance to " C   ASN A 285 " =    2.444
peak=   -4.086 closest distance to " N   ARG A 275 " =    1.012
peak=   -4.086 closest distance to " CA  GLY A 203 " =    2.356
peak=   -4.033 closest distance to " NH2 ARG A  66 " =    1.531
peak=   -4.014 closest distance to " CG  PRO A 243 " =    1.557
peak=   -3.994 closest distance to " O   HOH Z 407 " =    0.785
peak=   -3.994 closest distance to " CD2 LEU A 237 " =    2.647
peak=   -3.984 closest distance to " CD  PRO A 213 " =    2.326
peak=   -3.982 closest distance to " CB  SER A 146 " =    2.197
peak=   -3.977 closest distance to " O   PRO A 198 " =    1.381
peak=   -3.969 closest distance to " O   VAL A  67 " =    2.932
peak=   -3.969 closest distance to " O   HOH Z 155 " =    1.512
peak=   -3.957 closest distance to " OG  SER A  97 " =    2.236
peak=   -3.951 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.948 closest distance to " O   HOH Z  19 " =    2.211
peak=   -3.939 closest distance to " CD  GLN A  58 " =    1.168
peak=   -3.930 closest distance to " CB  GLU A 277 " =    1.254
peak=   -3.930 closest distance to " O   HOH Z 243 " =    2.271
peak=   -3.920 closest distance to " CB  ALA A  10 " =    2.031
peak=   -3.917 closest distance to " CD1 LEU A 167 " =    2.156
peak=   -3.899 closest distance to " OD1 ASN A 148 " =    1.522
peak=   -3.878 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.857 closest distance to " ND2 ASN A  45 " =    1.807
peak=   -3.851 closest distance to " O   HOH Z 369 " =    2.421
peak=   -3.850 closest distance to " O   HOH Z 348 " =    2.285
peak=   -3.838 closest distance to " CD  ARG A 156 " =    2.155
peak=   -3.827 closest distance to " C   THR A 279 " =    1.087
peak=   -3.826 closest distance to " O   HOH Z 308 " =    1.513
peak=   -3.800 closest distance to " CG2 ILE A  49 " =    2.669
peak=   -3.798 closest distance to " O   HOH Z 117 " =    4.507
peak=   -3.798 closest distance to " O   HOH Z 109 " =    3.538
peak=   -3.790 closest distance to " CD1 PHE A 130 " =    2.305
peak=   -3.783 closest distance to " O   HOH Z  37 " =    1.889
peak=   -3.781 closest distance to " CD  GLN A  88 " =    0.888
peak=   -3.776 closest distance to " N   ALA A  43 " =    2.736
peak=   -3.774 closest distance to " N   ASP A 272 " =    1.229
peak=   -3.763 closest distance to " OXT GLY A 302 " =    3.095
peak=   -3.762 closest distance to " O   HOH Z 166 " =    2.392
peak=   -3.759 closest distance to " O   HOH Z  58 " =    0.915
peak=   -3.754 closest distance to " C   SER A 206 " =    1.483
peak=   -3.753 closest distance to " C   HIS A 108 " =    1.125
peak=   -3.723 closest distance to " CB  ALA A  43 " =    2.643
peak=   -3.719 closest distance to " OD1 ASP A 191 " =    1.515
peak=   -3.711 closest distance to " O   HOH Z  52 " =    1.907
peak=   -3.700 closest distance to " O   HOH Z 207 " =    1.349
peak=   -3.685 closest distance to " NE2 GLN A  94 " =    1.686
peak=   -3.685 closest distance to " O   HOH Z   7 " =    1.053
peak=   -3.681 closest distance to " CA  SER A 164 " =    2.231
peak=   -3.674 closest distance to " OE1 GLN A  88 " =    0.968
peak=   -3.674 closest distance to " O   HOH Z 388 " =    1.907
peak=   -3.652 closest distance to " CD2 PHE A  61 " =    1.980
peak=   -3.646 closest distance to " O   PHE A 218 " =    1.376
peak=   -3.642 closest distance to " O   ALA A   7 " =    1.583
peak=   -3.633 closest distance to " CA  GLY A 241 " =    2.295
peak=   -3.626 closest distance to " O   HOH Z  38 " =    1.282
peak=   -3.626 closest distance to " O   VAL A  67 " =    3.023
peak=   -3.622 closest distance to " CB  PRO A 243 " =    2.771
peak=   -3.619 closest distance to " O   HOH Z   5 " =    1.535
peak=   -3.612 closest distance to " O   HOH Z 418 " =    1.342
peak=   -3.605 closest distance to " OD2 ASP A 171 " =    1.925
peak=   -3.602 closest distance to " CG  ARG A 269 " =    2.409
peak=   -3.595 closest distance to " O   VAL A 174 " =    1.998
peak=   -3.593 closest distance to " O   HOH Z 290 " =    1.094
peak=   -3.590 closest distance to " O   HOH Z  71 " =    1.692
peak=   -3.583 closest distance to " CB  ALA A 291 " =    2.450
peak=   -3.582 closest distance to " O   ALA A   1 " =    2.059
peak=   -3.571 closest distance to " O   HOH Z 377 " =    0.848
peak=   -3.562 closest distance to " OH  TYR A 169 " =    0.984
peak=   -3.561 closest distance to " CD2 PHE A  59 " =    2.438
peak=   -3.560 closest distance to " O   HOH Z 234 " =    4.289
peak=   -3.554 closest distance to " CD  GLU A 236 " =    1.101
peak=   -3.545 closest distance to " CD  ARG A  14 " =    3.415
peak=   -3.544 closest distance to " CA  PRO A 198 " =    1.199
peak=   -3.541 closest distance to " O   HOH Z   6 " =    1.499
peak=   -3.516 closest distance to " O   HOH Z 422 " =    1.158
peak=   -3.512 closest distance to " O   HOH Z 351 " =    1.599
peak=   -3.510 closest distance to " CG2 THR A 221 " =    2.325
peak=   -3.509 closest distance to " O   HOH Z 275 " =    1.609
peak=   -3.505 closest distance to " O   HOH Z 185 " =    2.259
peak=   -3.494 closest distance to " NE2 GLN A 223 " =    1.099
peak=   -3.492 closest distance to " O   HOH Z  43 " =    1.232
peak=   -3.490 closest distance to " O   HOH Z 200 " =    1.384
peak=   -3.483 closest distance to " O   HOH Z 150 " =    1.735
peak=   -3.472 closest distance to " O   ALA A 256 " =    1.709
peak=   -3.472 closest distance to " CG  MET A 105 " =    0.981
peak=   -3.466 closest distance to " OE2 GLU A  53 " =    1.078
peak=   -3.455 closest distance to " C   ALA A 158 " =    1.317
peak=   -3.455 closest distance to " OG  SER A  87 " =    1.726
peak=   -3.453 closest distance to " CA  VAL A 197 " =    0.991
peak=   -3.450 closest distance to " O   HOH Z 331 " =    1.144
peak=   -3.447 closest distance to " CE2 PHE A  61 " =    2.615
peak=   -3.441 closest distance to " O   HOH Z 165 " =    1.952
peak=   -3.436 closest distance to " N   GLN A  58 " =    1.423
peak=   -3.432 closest distance to " O   HOH Z 111 " =    1.355
peak=   -3.426 closest distance to " O   ILE A 109 " =    2.694
peak=   -3.422 closest distance to " O   HOH Z 109 " =    3.292
peak=   -3.421 closest distance to " CD2 TRP A 274 " =    2.351
peak=   -3.414 closest distance to " O   HOH Z 184 " =    1.386
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.404 closest distance to " O   HOH Z  90 " =    3.615
peak=   -3.398 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.397 closest distance to " SG  CYS A 168 " =    1.016
peak=   -3.391 closest distance to " CD2 LEU A 167 " =    1.834
peak=   -3.386 closest distance to " O   HOH Z 292 " =    4.554
peak=   -3.385 closest distance to " O   THR A  18 " =    1.683
peak=   -3.385 closest distance to " O   HOH Z 407 " =    1.798
peak=   -3.380 closest distance to " N   SER A 134 " =    1.219
peak=   -3.379 closest distance to " ND2 ASN A  60 " =    1.485
peak=   -3.375 closest distance to " CB  ALA A   9 " =    2.707
peak=   -3.374 closest distance to " CD1 LEU A  25 " =    2.530
peak=   -3.373 closest distance to " O   HOH Z 326 " =    4.914
peak=   -3.372 closest distance to " CG  GLU A  53 " =    1.296
peak=   -3.371 closest distance to " O   HOH Z 423 " =    2.328
peak=   -3.369 closest distance to " NH2 ARG A  66 " =    1.354
peak=   -3.369 closest distance to " CG1 VAL A 189 " =    2.599
peak=   -3.366 closest distance to " CH2 TRP A 177 " =    1.974
peak=   -3.366 closest distance to " OG BSER A 210 " =    1.176
peak=   -3.363 closest distance to " CB  PRO A 213 " =    1.745
peak=   -3.358 closest distance to " O   HOH Z  91 " =    2.164
peak=   -3.355 closest distance to " O   HOH Z 252 " =    4.196
peak=   -3.350 closest distance to " CH2 TRP A 179 " =    1.220
peak=   -3.350 closest distance to " OE1 GLN A 223 " =    2.277
peak=   -3.350 closest distance to " O   ARG A  79 " =    1.093
peak=   -3.348 closest distance to " O   HOH Z 120 " =    1.071
peak=   -3.347 closest distance to " O   HOH Z 128 " =    4.260
peak=   -3.344 closest distance to " O   HOH Z 251 " =    1.995
peak=   -3.344 closest distance to " CB  PRO A 280 " =    2.319
peak=   -3.339 closest distance to " CA  SER A 276 " =    1.408
peak=   -3.331 closest distance to " O   TYR A  15 " =    1.618
peak=   -3.320 closest distance to " CG  PRO A 198 " =    2.322
peak=   -3.317 closest distance to " O   TRP A  92 " =    1.951
peak=   -3.304 closest distance to " O   HOH Z  41 " =    2.254
peak=   -3.302 closest distance to " O   HOH Z 151 " =    1.522
peak=   -3.295 closest distance to " CG  PRO A 163 " =    1.687
peak=   -3.293 closest distance to " O   HOH Z 137 " =    1.374
peak=   -3.292 closest distance to " C   GLY A  17 " =    1.259
peak=   -3.288 closest distance to " O   HOH Z 313 " =    1.358
peak=   -3.288 closest distance to " O   HOH Z 426 " =    1.977
peak=   -3.287 closest distance to " O   HOH Z  37 " =    1.541
peak=   -3.286 closest distance to " CD2 PHE A 225 " =    1.307
peak=   -3.286 closest distance to " CE  MET A  93 " =    1.924
peak=   -3.286 closest distance to " O   HOH Z 414 " =    1.818
peak=   -3.285 closest distance to " O   HOH Z 251 " =    5.123
peak=   -3.281 closest distance to " O   HOH Z  49 " =    1.050
peak=   -3.280 closest distance to " O   HOH Z  93 " =    2.087
peak=   -3.275 closest distance to " O   GLY A 118 " =    2.172
peak=   -3.275 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.272 closest distance to " O   ASP A 171 " =    1.049
peak=   -3.259 closest distance to " CA  ASN A 127 " =    1.061
peak=   -3.258 closest distance to " CE2 PHE A  38 " =    1.992
peak=   -3.258 closest distance to " O   HOH Z   7 " =    1.736
peak=   -3.255 closest distance to " O   GLN A  11 " =    1.074
peak=   -3.252 closest distance to " OG1 THR A  82 " =    1.715
peak=   -3.246 closest distance to " O   HOH Z 400 " =    1.261
peak=   -3.244 closest distance to " O   HOH Z 113 " =    2.078
peak=   -3.238 closest distance to " O   HOH Z 114 " =    3.763
peak=   -3.232 closest distance to " NE1 TRP A 177 " =    2.076
peak=   -3.226 closest distance to " CG  MET A  93 " =    2.508
peak=   -3.223 closest distance to " OG BSER A 210 " =    2.181
peak=   -3.221 closest distance to " O   SER A 135 " =    1.764
peak=   -3.220 closest distance to " OD1 ASN A 173 " =    1.496
peak=   -3.217 closest distance to " C   GLN A 240 " =    2.454
peak=   -3.216 closest distance to " CG2BVAL A  41 " =    1.320
peak=   -3.216 closest distance to " OG  SER A  26 " =    1.506
peak=   -3.212 closest distance to " O   HOH Z 189 " =    1.854
peak=   -3.209 closest distance to " O   HOH Z 422 " =    1.444
peak=   -3.206 closest distance to " NH2 ARG A 159 " =    2.441
peak=   -3.204 closest distance to " O   HOH Z 174 " =    1.636
peak=   -3.204 closest distance to " O   HOH Z 380 " =    4.416
peak=   -3.202 closest distance to " O   HOH Z 236 " =    1.806
peak=   -3.201 closest distance to " O   HOH Z 417 " =    2.987
peak=   -3.200 closest distance to " O   HOH Z 283 " =    2.177
peak=   -3.200 closest distance to " O   HOH Z 111 " =    2.040
peak=   -3.199 closest distance to " O   HOH Z 392 " =    1.366
peak=   -3.193 closest distance to " CG  LEU A  83 " =    2.227
peak=   -3.188 closest distance to " O   HOH Z 156 " =    3.703
peak=   -3.188 closest distance to " O   HOH Z 134 " =    2.052
peak=   -3.187 closest distance to " O   LEU A 101 " =    2.290
peak=   -3.187 closest distance to " ND2 ASN A  45 " =    1.097
peak=   -3.185 closest distance to " O   HOH Z 280 " =    2.259
peak=   -3.177 closest distance to " CB  PHE A  16 " =    2.483
peak=   -3.176 closest distance to " CA  GLY A 241 " =    3.293
peak=   -3.174 closest distance to " CE3 TRP A 274 " =    2.519
peak=   -3.172 closest distance to " OG1 THR A  82 " =    1.312
peak=   -3.171 closest distance to " O   HOH Z 323 " =    1.358
peak=   -3.168 closest distance to " ND2BASN A 224 " =    2.056
peak=   -3.166 closest distance to " O   HOH Z 325 " =    1.954
peak=   -3.164 closest distance to " CD2 PHE A 192 " =    2.170
peak=   -3.160 closest distance to " CD2 TYR A 293 " =    1.814
peak=   -3.160 closest distance to " O   HOH Z 128 " =    2.474
peak=   -3.159 closest distance to " N   ILE A 120 " =    1.048
peak=   -3.158 closest distance to " CB  ASP A 162 " =    2.587
peak=   -3.157 closest distance to " O   HOH Z 222 " =    1.340
peak=   -3.155 closest distance to " OD1 ASN A  39 " =    2.346
peak=   -3.155 closest distance to " O   HOH Z 318 " =    1.383
peak=   -3.154 closest distance to " CD2 HIS A 115 " =    1.083
peak=   -3.151 closest distance to " O   HOH Z 400 " =    0.814
peak=   -3.144 closest distance to " CG  TRP A 266 " =    1.980
peak=   -3.141 closest distance to " O   HOH Z 423 " =    1.463
peak=   -3.133 closest distance to " O   HOH Z 259 " =    2.163
peak=   -3.127 closest distance to " OG BSER A 164 " =    5.017
peak=   -3.123 closest distance to " O   HOH Z 403 " =    1.001
peak=   -3.121 closest distance to " O   GLY A 196 " =    1.253
peak=   -3.121 closest distance to " O   HOH Z 166 " =    2.060
peak=   -3.111 closest distance to " CD  ARG A 139 " =    1.545
peak=   -3.109 closest distance to " OD2 ASP A 298 " =    1.069
peak=   -3.105 closest distance to " O   ALA A  34 " =    2.606
peak=   -3.102 closest distance to " CG2 VAL A 189 " =    2.259
peak=   -3.100 closest distance to " OE1 GLN A  88 " =    1.315
peak=   -3.097 closest distance to " OD2 ASP A 171 " =    2.399
peak=   -3.096 closest distance to " O   HOH Z  48 " =    0.782
peak=   -3.092 closest distance to " O   HOH Z 430 " =    5.875
peak=   -3.091 closest distance to " O   HOH Z 350 " =    1.207
peak=   -3.087 closest distance to " NZ  LYS A 119 " =    1.968
peak=   -3.083 closest distance to " OE1 GLN A  88 " =    1.009
peak=   -3.067 closest distance to " O   HOH Z 146 " =    1.330
peak=   -3.064 closest distance to " O   HOH Z  11 " =    1.645
peak=   -3.060 closest distance to " OG1 THR A  29 " =    1.801
peak=   -3.050 closest distance to " O   HOH Z 118 " =    1.461
peak=   -3.048 closest distance to " CD  GLN A  58 " =    1.242
peak=   -3.030 closest distance to " O   ARG A  56 " =    1.904
peak=   -3.027 closest distance to " C   GLU A  46 " =    0.918

================= 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    :  0.4357 0.4146   6.254006e+00   6.217000e+00
   1_bss:  0.4250 0.4041   6.245086e+00   6.204517e+00
   1_xyz:  0.3557 0.3795   6.120484e+00   6.158994e+00
   1_adp:  0.3302 0.3838   6.078522e+00   6.162393e+00
   1_occ:  0.3297 0.3829   6.077121e+00   6.161665e+00
   2_bss:  0.3295 0.3824   6.079268e+00   6.162674e+00
   2_xyz:  0.2679 0.3126   5.892600e+00   6.016722e+00
   2_adp:  0.2481 0.3113   5.852427e+00   6.013689e+00
   2_occ:  0.2479 0.3110   5.851787e+00   6.013421e+00
   3_bss:  0.2476 0.3091   5.851681e+00   6.012662e+00
   3_xyz:  0.1950 0.2467   5.624784e+00   5.808802e+00
   3_adp:  0.1793 0.2249   5.547170e+00   5.727219e+00
   3_occ:  0.1792 0.2249   5.546580e+00   5.726556e+00
   4_bss:  0.1791 0.2240   5.546225e+00   5.724087e+00
   4_xyz:  0.1505 0.1908   5.387189e+00   5.578944e+00
   4_adp:  0.1413 0.1879   5.345309e+00   5.554529e+00
   4_occ:  0.1413 0.1879   5.345014e+00   5.554333e+00
   5_bss:  0.1415 0.1881   5.345621e+00   5.555062e+00
   5_xyz:  0.1300 0.1796   5.280640e+00   5.510492e+00
   5_adp:  0.1275 0.1780   5.266161e+00   5.498727e+00
   5_occ:  0.1274 0.1780   5.266172e+00   5.498849e+00
   5_bss:  0.1274 0.1780   5.266265e+00   5.498866e+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:  0.286  36.615  -1.517   5.166  -2.248   0.000  -0.000  -0.000
   1_xyz:  0.286  36.615  -1.517   5.166  -2.248   0.000  -0.000  -0.000
   1_adp:  0.286  36.615  -1.517   5.166  -2.248   0.000  -0.000  -0.000
   1_occ:  0.286  36.615  -1.517   5.166  -2.248   0.000  -0.000  -0.000
   2_bss:  0.286  36.615  -1.464   3.081  -0.953   0.000  -0.000  -0.000
   2_xyz:  0.286  36.615  -1.464   3.081  -0.953   0.000  -0.000  -0.000
   2_adp:  0.286  36.615  -1.464   3.081  -0.953   0.000  -0.000  -0.000
   2_occ:  0.286  36.615  -1.464   3.081  -0.953   0.000  -0.000  -0.000
   3_bss:  0.316  61.840  -0.699   1.949  -0.054   0.000  -0.000  -0.000
   3_xyz:  0.316  61.840  -0.699   1.949  -0.054   0.000  -0.000  -0.000
   3_adp:  0.316  61.840  -0.699   1.949  -0.054   0.000  -0.000  -0.000
   3_occ:  0.316  61.840  -0.699   1.949  -0.054   0.000  -0.000  -0.000
   4_bss:  0.324  70.261  -1.320   0.357  -0.483   0.000  -0.000  -0.000
   4_xyz:  0.324  70.261  -1.320   0.357  -0.483   0.000  -0.000  -0.000
   4_adp:  0.324  70.261  -1.320   0.357  -0.483   0.000  -0.000  -0.000
   4_occ:  0.324  70.261  -1.320   0.357  -0.483   0.000  -0.000  -0.000
   5_bss:  0.330  75.843  -1.322  -0.176  -0.373  -0.000  -0.000  -0.000
   5_xyz:  0.330  75.843  -1.322  -0.176  -0.373  -0.000  -0.000  -0.000
   5_adp:  0.330  75.843  -1.322  -0.176  -0.373  -0.000  -0.000  -0.000
   5_occ:  0.330  75.843  -1.322  -0.176  -0.373  -0.000  -0.000  -0.000
   5_bss:  0.327  73.055  -1.026  -0.142  -0.034  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.109 0.5591  0.7206    54593.304
   1_bss:  46.336 0.5671  0.7410    51399.280
   1_xyz:  43.357 0.6025  0.7774    43923.805
   1_adp:  43.785 0.5968  0.7652    44163.749
   1_occ:  43.724 0.5975  0.7652    44046.547
   2_bss:  43.602 0.5991  0.7637    43988.476
   2_xyz:  34.226 0.7091  0.8819    27608.062
   2_adp:  33.740 0.7149  0.8684    27221.615
   2_occ:  33.707 0.7152  0.8681    27169.612
   3_bss:  33.531 0.7174  0.8780    26981.715
   3_xyz:  25.143 0.8094  0.9624    16038.346
   3_adp:  22.322 0.8392  0.9722    13501.753
   3_occ:  22.305 0.8394  0.9724    13485.116
   4_bss:  22.203 0.8403  0.9444    13368.755
   4_xyz:  18.406 0.8766  0.9627     9463.446
   4_adp:  17.716 0.8832  0.9568     9027.072
   4_occ:  17.714 0.8832  0.9568     9025.403
   5_bss:  17.699 0.8833  0.9525     9021.247
   5_xyz:  16.668 0.8926  0.9585     8230.701
   5_adp:  16.375 0.8953  0.9511     8073.410
   5_occ:  16.379 0.8952  0.9510     8074.744
   5_bss:  16.381 0.8952  0.9587     8074.610
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7085e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7085e-01
   1_xyz:   1.398  0.010  0.087 15.540  0.005  4.115   1.0207e-01
   1_adp:   1.398  0.010  0.087 15.540  0.005  4.115   1.0207e-01
   1_occ:   1.398  0.010  0.087 15.540  0.005  4.115   1.0207e-01
   2_bss:   1.398  0.010  0.087 15.540  0.005  4.115   1.0207e-01
   2_xyz:   1.441  0.011  0.094 15.448  0.006  4.114   1.1000e-01
   2_adp:   1.441  0.011  0.094 15.448  0.006  4.114   1.1000e-01
   2_occ:   1.441  0.011  0.094 15.448  0.006  4.114   1.1000e-01
   3_bss:   1.441  0.011  0.094 15.448  0.006  4.114   1.1000e-01
   3_xyz:   1.145  0.010  0.078 15.160  0.005  4.130   7.8490e-02
   3_adp:   1.145  0.010  0.078 15.160  0.005  4.130   7.8490e-02
   3_occ:   1.145  0.010  0.078 15.160  0.005  4.130   7.8490e-02
   4_bss:   1.145  0.010  0.078 15.160  0.005  4.130   7.8490e-02
   4_xyz:   1.063  0.008  0.076 14.562  0.004  4.126   6.5547e-02
   4_adp:   1.063  0.008  0.076 14.562  0.004  4.126   6.5547e-02
   4_occ:   1.063  0.008  0.076 14.562  0.004  4.126   6.5547e-02
   5_bss:   1.063  0.008  0.076 14.562  0.004  4.126   6.5547e-02
   5_xyz:   1.031  0.008  0.074 14.604  0.003  4.133   6.2243e-02
   5_adp:   1.031  0.008  0.074 14.604  0.003  4.133   6.2243e-02
   5_occ:   1.031  0.008  0.074 14.604  0.003  4.133   6.2243e-02
   5_bss:   1.031  0.008  0.074 14.604  0.003  4.133   6.2243e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.366   2.4481e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.366   2.4481e-01
   1_xyz:  10.171  0.079  0.348 86.678  0.033  2.023   7.1743e-02
   1_adp:  10.171  0.079  0.348 86.678  0.033  2.023   7.1743e-02
   1_occ:  10.171  0.079  0.348 86.678  0.033  2.023   7.1743e-02
   2_bss:  10.171  0.079  0.348 86.678  0.033  2.023   7.1743e-02
   2_xyz:   7.797  0.066  0.280 85.532  0.024  2.166   8.1438e-02
   2_adp:   7.797  0.066  0.280 85.532  0.024  2.166   8.1438e-02
   2_occ:   7.797  0.066  0.280 85.532  0.024  2.166   8.1438e-02
   3_bss:   7.797  0.066  0.280 85.532  0.024  2.166   8.1438e-02
   3_xyz:   8.275  0.067  0.242 82.146  0.053  2.162   6.8652e-02
   3_adp:   8.275  0.067  0.242 82.146  0.053  2.162   6.8652e-02
   3_occ:   8.275  0.067  0.242 82.146  0.053  2.162   6.8652e-02
   4_bss:   8.275  0.067  0.242 82.146  0.053  2.162   6.8652e-02
   4_xyz:   7.810  0.052  0.265 82.485  0.048  2.265   6.7661e-02
   4_adp:   7.810  0.052  0.265 82.485  0.048  2.265   6.7661e-02
   4_occ:   7.810  0.052  0.265 82.485  0.048  2.265   6.7661e-02
   5_bss:   7.810  0.052  0.265 82.485  0.048  2.265   6.7661e-02
   5_xyz:   7.800  0.051  0.239 83.374  0.035  2.281   4.0336e-02
   5_adp:   7.800  0.051  0.239 83.374  0.035  2.281   4.0336e-02
   5_occ:   7.800  0.051  0.239 83.374  0.035  2.281   4.0336e-02
   5_bss:   7.800  0.051  0.239 83.374  0.035  2.281   4.0336e-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:  75.13   0.00  17.20  75.13   0.00  13.83  69.77   0.00  35.58
   1_occ:  75.13   0.00  17.20  75.13   0.00  13.83  69.77   0.00  35.58
   2_bss:  75.13   0.00  17.20  75.13   0.00  13.83  69.77   0.00  35.58
   2_xyz:  75.13   0.00  17.20  75.13   0.00  13.83  69.77   0.00  35.58
   2_adp:  97.72   0.00  18.17  97.72   0.00  14.26  93.84   0.00  39.47
   2_occ:  97.72   0.00  18.17  97.72   0.00  14.26  93.84   0.00  39.47
   3_bss:  97.72   0.00  18.17  97.72   0.00  14.26  93.84   0.00  39.47
   3_xyz:  97.72   0.00  18.17  97.72   0.00  14.26  93.84   0.00  39.47
   3_adp:  95.18   0.00  17.11  94.64   0.00  12.90  95.18   3.61  40.04
   3_occ:  95.18   0.00  17.11  94.64   0.00  12.90  95.18   3.61  40.04
   4_bss:  95.18   0.00  17.11  94.64   0.00  12.90  95.18   3.61  40.04
   4_xyz:  95.18   0.00  17.11  94.64   0.00  12.90  95.18   3.61  40.04
   4_adp: 104.65   0.52  17.27 104.65   0.52  12.45 103.55   4.40  43.50
   4_occ: 104.65   0.52  17.27 104.65   0.52  12.45 103.55   4.40  43.50
   5_bss: 104.65   0.52  17.27 104.65   0.52  12.45 103.55   4.40  43.50
   5_xyz: 104.65   0.52  17.27 104.65   0.52  12.45 103.55   4.40  43.50
   5_adp: 110.39   0.00  16.93 108.21   0.00  12.09 110.39   4.64  43.28
   5_occ: 110.39   0.00  16.93 108.21   0.00  12.09 110.39   4.64  43.28
   5_bss: 110.39   0.00  16.93 108.21   0.00  12.09 110.39   4.64  43.28
------------------------------------------------------------------------
 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:    1.727    0.015    0.284
   1_adp:    1.727    0.015    0.284
   1_occ:    1.727    0.015    0.284
   2_bss:    1.727    0.015    0.284
   2_xyz:    1.403    0.054    0.521
   2_adp:    1.403    0.054    0.521
   2_occ:    1.403    0.054    0.521
   3_bss:    1.403    0.054    0.521
   3_xyz:    1.678    0.064    0.688
   3_adp:    1.678    0.064    0.688
   3_occ:    1.678    0.064    0.688
   4_bss:    1.678    0.064    0.688
   4_xyz:    1.634    0.076    0.748
   4_adp:    1.634    0.076    0.748
   4_occ:    1.634    0.076    0.748
   5_bss:    1.634    0.076    0.748
   5_xyz:    1.639    0.099    0.786
   5_adp:    1.639    0.099    0.786
   5_occ:    1.639    0.099    0.786
   5_bss:    1.639    0.099    0.786
------------------------------------------------------------------------

CPU time actual refinement: 325.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/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_1083/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1083/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.34 
  Macro-tasks:
    bulk solvent and scale       = 41.76  
    individual site refinement   = 130.43 
    weights calculation          = 29.45  
    collect and process          = 6.48   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 208.22 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 102.03 
    alpha_beta                      = 8.49   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 109.98 
    fmodel                         = 6.94   
    r_factors                      = 0.18   
    phase_errors                   = 10.77  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 242.11 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    622 calls, 101.75 s
gradients_fft:          567 calls,  97.45 s

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

# Date 2008-01-16 Time 06:23:02 PST -0800 (1200493382.16 s)
Start R-work = 0.4357, R-free = 0.4146 (no bulk solvent and anisotropic scale)
Final R-work = 0.1438, R-free = 0.1925 (no bulk solvent and anisotropic scale)

Start R-work = 0.4250, R-free = 0.4041
Final R-work = 0.1274, R-free = 0.1780