# Date 2008-01-16 Time 05:47:59 PST -0800 (1200491279.24 s)
#phil __OFF__

Command line arguments: "../885.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15130
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 885

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.98276
Completeness in resolution range: 0.961518
Completeness with d_max=infinity: 0.9586

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9828

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.98276
Completeness in resolution range: 0.961518
Completeness with d_max=infinity: 0.9586

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1032 -  4.2431 [2137/2162]  1924   213  10.0%
  bin  2:  4.2431 -  3.3803 [2050/2070]  1845   205  10.0%
  bin  3:  3.3803 -  2.9566 [2041/2060]  1836   205  10.0%
  bin  4:  2.9566 -  2.6880 [2007/2037]  1808   199   9.9%
  bin  5:  2.6880 -  2.4962 [2010/2029]  1813   197   9.8%
  bin  6:  2.4962 -  2.3496 [1982/2007]  1776   206  10.4%
  bin  7:  2.3496 -  2.2324 [1973/2001]  1775   198  10.0%
  bin  8:  2.2324 -  2.1355 [1972/2008]  1777   195   9.9%
  bin  9:  2.1355 -  2.0535 [1974/2016]  1779   195   9.9%
  bin 10:  2.0535 -  1.9828 [1443/1983]  1297   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2187
        3.04 -     3.66: 4688
        3.66 -     4.28: 9068
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.274 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28247 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_885/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 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: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3034   r_free= 0.2999   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.997329                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.2795 0.2704      6.3282      6.2708|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.2396 0.2330      6.3841      6.3052|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.2490 0.2346      6.2429      6.3396|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.2774 0.3037      6.1768      6.2074|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.3133 0.2729      6.0613      6.0004|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.3035 0.3125      5.9602      5.9151|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.3209 0.2977      5.9609      5.9613|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.3301 0.3284      5.9225       5.924|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.3254 0.3333      5.8663      5.8459|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.3428 0.3281      5.8609      5.7993|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.3511 0.3801      5.8344      5.9019|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.3541 0.3349       5.798      5.7889|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.3608 0.3768       5.685      5.6501|
| 14:  2.0322 -  1.9828 0.62    787   90 0.3812 0.3752      5.7045      5.6427|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.81  24.43   0.86     0.83      37941.06|
|  2:  4.7328 -  3.7759  1337   150  0.86  20.13   0.98     0.93      39031.12|
|  3:  3.7759 -  3.3043  1316   141  0.83  23.78   1.01     0.98      38431.78|
|  4:  3.3043 -  3.0048  1305   152  0.81  26.10   1.00     0.96      33971.15|
|  5:  3.0048 -  2.7908  1294   143  0.76  30.22   0.99     0.94      28661.42|
|  6:  2.7908 -  2.6272  1298   138  0.76  30.27   1.00     0.93      23833.17|
|  7:  2.6272 -  2.4962  1286   140  0.75  31.03   1.02     0.93      22464.59|
|  8:  2.4962 -  2.3880  1269   148  0.75  31.75   1.02     0.94      20794.31|
|  9:  2.3880 -  2.2964  1256   145  0.75  31.91   1.04     0.95      19956.13|
| 10:  2.2964 -  2.2174  1294   138  0.73  33.13   1.05     0.96      18715.81|
| 11:  2.2174 -  2.1483  1268   138  0.71  35.20   1.06     0.96      19280.87|
| 12:  2.1483 -  2.0870  1248   142  0.71  35.45   1.05     0.94      18200.55|
| 13:  2.0870 -  2.0322  1282   139  0.66  38.95   1.05     0.92      16278.39|
| 14:  2.0322 -  1.9828   787    90  0.71  35.55   1.04     0.92      12884.78|
|alpha:            min =        0.83 max =            0.98 mean =         0.94|
|beta:             min =    12884.78 max =        39031.12 mean =     25557.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.97 mean =        30.32|
|phase err.(test): min =        0.00 max =           89.75 mean =        29.98|
|-----------------------------------------------------------------------------|

============================== 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 = 3.775789              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.023   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.638760              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.814   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1988 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1861 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2827 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4660 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4408 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5627 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6665 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3034   r_free= 0.2999   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.997329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2895   r_free= 0.2878   ksol= 0.33   Bsol= 50.44   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.01,-1.70,0.00,-0.00,-0.00); trace/3= -1.01                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.974849                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.403863              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.266   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.317867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.696   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2895      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.2878      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3485 = 3.40 * 0.50 * 5.9858 + 1.00 * 0.1611                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7086 = 3.40 * 0.50 * 5.6682 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1682      final r-factor (work) = 0.1531          |
| start r-factor (free) = 0.1902      final r-factor (free) = 0.1968          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8078 = 0.32 * 1.00 * 5.6682 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7207 = 0.32 * 1.00 * 5.3862 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    71.75   17.02    None  None   None       |
|    all(noH): 2823   0      1.62    71.75   17.02    None  None   None       |
|    Sol.    : 438    0      6.21    71.75   38.95    None  None   None       |
|    Mac.    : 2385   0      1.62    68.46   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.616 -   8.629:  645   |   5:    36.685 -  43.699:  107        |
|      1:     8.629 -  15.643: 1235   |   6:    43.699 -  50.712:   85        |
|      2:    15.643 -  22.657:  395   |   7:    50.712 -  57.726:   60        |
|      3:    22.657 -  29.671:  129   |   8:    57.726 -  64.740:   38        |
|      4:    29.671 -  36.685:  112   |   9:    64.740 -  71.754:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1531 r_free = 0.1968             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1528 r_free = 0.1969             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1528   r_free= 0.1969   ksol= 0.33   Bsol= 50.44   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.01,-1.70,0.00,-0.00,-0.00); trace/3= -1.01                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.401287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1519   r_free= 0.1951   ksol= 0.33   Bsol= 57.05   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.14,-1.77,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.396996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.004216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.768  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.126339              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.648  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1519      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1951      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1708 = 3.00 * 0.50 * 5.3985 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0131 = 3.00 * 0.50 * 5.2947 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6775 = 0.13 * 1.00 * 5.2947 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6622 = 0.13 * 1.00 * 5.1904 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    70.67   16.61    None  None   None       |
|    all(noH): 2823   0      2.07    70.67   16.61    None  None   None       |
|    Sol.    : 438    0      6.23    70.67   37.02    None  None   None       |
|    Mac.    : 2385   0      2.07    69.44   12.86    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:     2.074 -   8.934:  669   |   5:    36.373 -  43.233:  104        |
|      1:     8.934 -  15.794: 1261   |   6:    43.233 -  50.092:   81        |
|      2:    15.794 -  22.653:  366   |   7:    50.092 -  56.952:   61        |
|      3:    22.653 -  29.513:  124   |   8:    56.952 -  63.812:   22        |
|      4:    29.513 -  36.373:  124   |   9:    63.812 -  70.672:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1573             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1574             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1574   ksol= 0.33   Bsol= 57.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.14,-1.77,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1565   ksol= 0.33   Bsol= 57.05   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.59,-1.56,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163158                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.435495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.918  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.432927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.091  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9738 = 3.44 * 0.50 * 5.1893 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8910 = 3.44 * 0.50 * 5.1321 + 1.00 * 0.0753                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2283 = 0.43 * 1.00 * 5.1321 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2191 = 0.43 * 1.00 * 5.1075 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    77.36   16.88    None  None   None       |
|    all(noH): 2823   0      1.29    77.36   16.88    None  None   None       |
|    Sol.    : 438    0      6.28    74.90   38.66    None  None   None       |
|    Mac.    : 2385   0      1.29    77.36   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.290 -   8.897:  727   |   5:    39.323 -  46.929:  114        |
|      1:     8.897 -  16.503: 1256   |   6:    46.929 -  54.536:   84        |
|      2:    16.503 -  24.110:  333   |   7:    54.536 -  62.142:   52        |
|      3:    24.110 -  31.716:  129   |   8:    62.142 -  69.749:   20        |
|      4:    31.716 -  39.323:  101   |   9:    69.749 -  77.355:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1526             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1526             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1526   ksol= 0.33   Bsol= 57.05   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.59,-1.56,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106863                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1526   ksol= 0.33   Bsol= 57.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.55,-1.34,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106783                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.594555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.923  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.335  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7016 = 2.59 * 0.50 * 5.1079 + 1.00 * 0.0753                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6940 = 2.59 * 0.50 * 5.1091 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2884 = 0.45 * 1.00 * 5.1091 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2893 = 0.45 * 1.00 * 5.1102 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    80.78   16.79    None  None   None       |
|    all(noH): 2823   0      0.99    80.78   16.79    None  None   None       |
|    Sol.    : 438    0      6.60    76.76   38.74    None  None   None       |
|    Mac.    : 2385   0      0.99    80.78   12.76    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:     0.987 -   8.967:  791   |   5:    40.885 -  48.864:  100        |
|      1:     8.967 -  16.946: 1234   |   6:    48.864 -  56.844:   83        |
|      2:    16.946 -  24.926:  305   |   7:    56.844 -  64.823:   42        |
|      3:    24.926 -  32.905:  134   |   8:    64.823 -  72.803:   15        |
|      4:    32.905 -  40.885:  113   |   9:    72.803 -  80.782:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1536             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1536             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1536   ksol= 0.33   Bsol= 57.05   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.55,-1.34,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112299                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1536   ksol= 0.33   Bsol= 57.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.42,-1.16,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112142                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.833319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.168  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.183830              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.051  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3061 = 2.83 * 0.50 * 5.1107 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3058 = 2.83 * 0.50 * 5.1076 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1055      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9473 = 0.18 * 1.00 * 5.1076 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9472 = 0.18 * 1.00 * 5.1130 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    79.35   16.34    None  None   None       |
|    all(noH): 2823   0      1.51    79.35   16.34    None  None   None       |
|    Sol.    : 438    0      6.49    77.01   37.10    None  None   None       |
|    Mac.    : 2385   0      1.51    79.35   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.507 -   9.291:  894   |   5:    40.428 -  48.212:   97        |
|      1:     9.291 -  17.075: 1165   |   6:    48.212 -  55.996:   79        |
|      2:    17.075 -  24.859:  285   |   7:    55.996 -  63.781:   27        |
|      3:    24.859 -  32.644:  133   |   8:    63.781 -  71.565:   12        |
|      4:    32.644 -  40.428:  126   |   9:    71.565 -  79.349:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1544             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1062 r_free = 0.1543             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1543   ksol= 0.33   Bsol= 57.05   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.42,-1.16,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111240                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.0975 0.1268      5.3736      5.5282|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.0838 0.1152      5.4331      5.6428|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.1028 0.1491      5.4547      5.8689|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.1150 0.1576      5.4283      5.5605|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.1281 0.1722      5.3059      5.5536|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.1136 0.1795      5.1763      5.4299|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.1214 0.1569      5.1405      5.3354|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.1056 0.1660      4.9951      5.3002|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.1072 0.1732      4.9789       5.261|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.1051 0.1708      4.9063      5.2265|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.1066 0.1738      4.9059      5.2455|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.1027 0.1571      4.8388      5.0975|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.1064 0.1750      4.7431        5.06|
| 14:  2.0322 -  1.9828 0.62    787   90 0.1001 0.1607      4.6238      4.8566|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.94   9.05   0.98     0.95       7110.26|
|  2:  4.7328 -  3.7759  1337   150  0.95   7.89   1.01     1.00       9165.21|
|  3:  3.7759 -  3.3043  1316   141  0.94  11.07   1.02     1.01      10089.33|
|  4:  3.3043 -  3.0048  1305   152  0.92  13.54   1.00     0.98      10095.66|
|  5:  3.0048 -  2.7908  1294   143  0.90  15.68   0.99     0.96       8168.55|
|  6:  2.7908 -  2.6272  1298   138  0.90  15.71   0.98     0.96       6830.32|
|  7:  2.6272 -  2.4962  1286   140  0.91  15.09   0.99     0.95       5926.81|
|  8:  2.4962 -  2.3880  1269   148  0.92  14.15   0.99     0.97       4681.19|
|  9:  2.3880 -  2.2964  1256   145  0.92  14.36   1.00     0.97       4524.50|
| 10:  2.2964 -  2.2174  1294   138  0.91  14.74   1.00     0.97       4027.99|
| 11:  2.2174 -  2.1483  1268   138  0.90  15.68   0.98     0.94       4083.08|
| 12:  2.1483 -  2.0870  1248   142  0.92  14.38   1.00     1.00       3762.13|
| 13:  2.0870 -  2.0322  1282   139  0.91  15.65   0.99     0.98       3106.62|
| 14:  2.0322 -  1.9828   787    90  0.93  13.37   0.97     0.94       2347.96|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2347.96 max =        10095.66 mean =      6136.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1544   ksol= 0.33   Bsol= 57.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.28,-0.97,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111290                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1544   ksol= 0.33   Bsol= 57.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.28,-0.97,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.0975 0.1269      5.3741      5.5289|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.0838 0.1151      5.4333      5.6426|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.1028 0.1491      5.4547      5.8688|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.1150 0.1576      5.4282      5.5605|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.1281 0.1722      5.3059      5.5536|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.1136 0.1794      5.1763      5.4295|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.1214 0.1570      5.1405      5.3356|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.1056 0.1660      4.9951         5.3|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.1072 0.1731       4.979      5.2607|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.1051 0.1709      4.9064      5.2272|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.1066 0.1738      4.9061      5.2458|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.1027 0.1572      4.8389      5.0978|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.1064 0.1750       4.743      5.0598|
| 14:  2.0322 -  1.9828 0.62    787   90 0.1001 0.1606      4.6233      4.8558|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.94   9.06   0.98     0.95       7117.85|
|  2:  4.7328 -  3.7759  1337   150  0.95   7.89   1.01     1.00       9170.09|
|  3:  3.7759 -  3.3043  1316   141  0.94  11.06   1.02     1.01      10088.13|
|  4:  3.3043 -  3.0048  1305   152  0.92  13.54   1.00     0.98      10094.80|
|  5:  3.0048 -  2.7908  1294   143  0.90  15.68   0.99     0.96       8165.74|
|  6:  2.7908 -  2.6272  1298   138  0.90  15.71   0.99     0.96       6829.45|
|  7:  2.6272 -  2.4962  1286   140  0.91  15.09   0.99     0.96       5925.74|
|  8:  2.4962 -  2.3880  1269   148  0.92  14.15   0.99     0.97       4680.66|
|  9:  2.3880 -  2.2964  1256   145  0.92  14.36   1.00     0.97       4523.84|
| 10:  2.2964 -  2.2174  1294   138  0.91  14.74   1.00     0.98       4030.30|
| 11:  2.2174 -  2.1483  1268   138  0.90  15.69   0.99     0.95       4085.77|
| 12:  2.1483 -  2.0870  1248   142  0.92  14.38   1.01     1.00       3764.66|
| 13:  2.0870 -  2.0322  1282   139  0.91  15.64   1.00     0.99       3105.51|
| 14:  2.0322 -  1.9828   787    90  0.93  13.36   0.98     0.95       2345.10|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2345.10 max =        10094.80 mean =      6137.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.96 mean =        13.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.45    79.30   16.29    None  None   None       |
|    all(noH): 2823   0      1.45    79.30   16.29    None  None   None       |
|    Sol.    : 438    0      6.44    76.96   37.04    None  None   None       |
|    Mac.    : 2385   0      1.45    79.30   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.453 -   9.237:  894   |   5:    40.374 -  48.158:   97        |
|      1:     9.237 -  17.022: 1165   |   6:    48.158 -  55.943:   79        |
|      2:    17.022 -  24.806:  285   |   7:    55.943 -  63.727:   27        |
|      3:    24.806 -  32.590:  133   |   8:    63.727 -  71.511:   12        |
|      4:    32.590 -  40.374:  126   |   9:    71.511 -  79.295:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 4.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 291
   mapped sites are within: 0.749 - 4.691

peak=    5.715 closest distance to " NH2 ARG A  56 " =    2.149
peak=    5.686 closest distance to " NE2 GLN A  11 " =    1.206
peak=    5.384 closest distance to " CG  PRO A  54 " =    1.285
peak=    5.373 closest distance to " O   HOH Z 232 " =    2.366
peak=    5.303 closest distance to " O   HOH Z 126 " =    1.894
peak=    4.940 closest distance to " CB  GLN A 223 " =    1.430
peak=    4.892 closest distance to " CB  SER A  63 " =    1.209
peak=    4.869 closest distance to " O   HOH Z 144 " =    1.725
peak=    4.835 closest distance to " CB  GLN A 183 " =    1.178
peak=    4.705 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.694 closest distance to " C   PRO A 198 " =    1.463
peak=    4.635 closest distance to " CB  ARG A  79 " =    1.359
peak=    4.595 closest distance to " O   HOH Z 369 " =    2.082
peak=    4.574 closest distance to " O   HOH Z 236 " =    2.059
peak=    4.527 closest distance to " O   HOH Z  15 " =    2.253
peak=    4.523 closest distance to " O   HOH Z 298 " =    1.929
peak=    4.493 closest distance to " CB  GLU A 152 " =    1.219
peak=    4.466 closest distance to " O   HOH Z 303 " =    2.088
peak=    4.456 closest distance to " CB  ASN A 148 " =    1.477
peak=    4.448 closest distance to " CB  PRO A  54 " =    0.937
peak=    4.398 closest distance to " ND2 ASN A 187 " =    1.483
peak=    4.357 closest distance to " O   HOH Z  78 " =    1.721
peak=    4.355 closest distance to " O   HOH Z 193 " =    1.911
peak=    4.306 closest distance to " CB  ASN A 187 " =    1.273
peak=    4.293 closest distance to " O   HOH Z 234 " =    3.722
peak=    4.274 closest distance to " CB  ARG A 190 " =    1.536
peak=    4.260 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.248 closest distance to " O   HOH Z 158 " =    3.042
peak=    4.240 closest distance to " OD1 ASN A  69 " =    2.655
peak=    4.220 closest distance to " CA  TYR A  30 " =    0.948
peak=    4.213 closest distance to " CA  ASN A 215 " =    1.152
peak=    4.206 closest distance to " O   HOH Z 427 " =    2.910
peak=    4.196 closest distance to " O   HOH Z 250 " =    1.518
peak=    4.156 closest distance to " O   HOH Z  61 " =    1.633
peak=    4.148 closest distance to " CB  VAL A 265 " =    1.320
peak=    4.063 closest distance to " CD  ARG A 159 " =    0.749
peak=    4.047 closest distance to " CG2 VAL A 257 " =    0.973
peak=    4.045 closest distance to " O   HOH Z 272 " =    1.820
peak=    4.023 closest distance to " O   HOH Z   1 " =    1.972
peak=    4.003 closest distance to " O   HOH Z 346 " =    1.614
peak=    3.992 closest distance to " O   HOH Z 189 " =    2.190
peak=    3.990 closest distance to " O   HOH Z 386 " =    3.166
peak=    3.987 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.984 closest distance to " O   HOH Z  40 " =    1.960
peak=    3.966 closest distance to " O   HOH Z 261 " =    2.093
peak=    3.951 closest distance to " O   HOH Z 132 " =    2.469
peak=    3.944 closest distance to " O   HOH Z 214 " =    2.025
peak=    3.941 closest distance to " O   HOH Z 368 " =    2.042
peak=    3.936 closest distance to " O   HOH Z 217 " =    3.261
peak=    3.913 closest distance to " O   HOH Z 133 " =    2.385
peak=    3.910 closest distance to " CB  SER A 212 " =    1.147
peak=    3.901 closest distance to " O   HOH Z  21 " =    1.754
peak=    3.881 closest distance to " CD  ARG A  66 " =    2.263
peak=    3.877 closest distance to " O   HOH Z  63 " =    2.049
peak=    3.864 closest distance to " O   HOH Z   9 " =    2.027
peak=    3.864 closest distance to " O   HOH Z 193 " =    1.698
peak=    3.846 closest distance to " CB  GLU A 128 " =    0.944
peak=    3.833 closest distance to " CZ  PHE A 218 " =    1.028
peak=    3.830 closest distance to " O   HOH Z  78 " =    2.114
peak=    3.817 closest distance to " CD2 TRP A 179 " =    1.301
peak=    3.811 closest distance to " O   HOH Z 133 " =    1.656
peak=    3.810 closest distance to " O   HOH Z 213 " =    1.860
peak=    3.808 closest distance to " O   HOH Z 389 " =    1.978
peak=    3.796 closest distance to " O   HOH Z 403 " =    1.682
peak=    3.795 closest distance to " ND1 HIS A  86 " =    1.685
peak=    3.795 closest distance to " CB  TRP A 266 " =    0.981
peak=    3.788 closest distance to " O   HOH Z 209 " =    2.326
peak=    3.780 closest distance to " CG  PRO A 243 " =    1.091
peak=    3.776 closest distance to " O   HOH Z 419 " =    2.044
peak=    3.772 closest distance to " OD2 ASP A 286 " =    2.869
peak=    3.768 closest distance to " O   HOH Z  61 " =    1.500
peak=    3.763 closest distance to " CB  GLN A  88 " =    1.246
peak=    3.749 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.739 closest distance to " O   HOH Z  54 " =    2.517
peak=    3.734 closest distance to " O   HOH Z  10 " =    1.868
peak=    3.734 closest distance to " CA  ALA A 233 " =    1.126
peak=    3.716 closest distance to " O   HOH Z 219 " =    2.082
peak=    3.715 closest distance to " CA  THR A 264 " =    0.881
peak=    3.714 closest distance to " CB  ALA A  34 " =    1.053
peak=    3.711 closest distance to " O   HOH Z 180 " =    2.106
peak=    3.705 closest distance to " NH1AARG A 145 " =    1.230
peak=    3.704 closest distance to " O   HOH Z 371 " =    2.894
peak=    3.702 closest distance to " CB  ASN A 142 " =    0.960
peak=    3.688 closest distance to " CB  SER A   3 " =    1.360
peak=    3.684 closest distance to " O   SER A  87 " =    2.196
peak=    3.681 closest distance to " O   HOH Z 248 " =    1.637
peak=    3.671 closest distance to " CG  LEU A 167 " =    1.272
peak=    3.668 closest distance to " CA  THR A 221 " =    1.009
peak=    3.667 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.667 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.661 closest distance to " NH2BARG A 145 " =    2.184
peak=    3.658 closest distance to " CB  TYR A 169 " =    0.763
peak=    3.654 closest distance to " O   HOH Z 344 " =    3.150
peak=    3.648 closest distance to " O   HOH Z 426 " =    1.634
peak=    3.646 closest distance to " O   HOH Z 327 " =    1.712
peak=    3.645 closest distance to " CA  ALA A  21 " =    1.188
peak=    3.640 closest distance to " O   HOH Z 305 " =    3.610
peak=    3.638 closest distance to " O   HOH Z 316 " =    3.054
peak=    3.637 closest distance to " O   HOH Z 245 " =    1.320
peak=    3.635 closest distance to " CB  GLU A 277 " =    3.561
peak=    3.635 closest distance to " CG2 THR A 221 " =    1.047
peak=    3.629 closest distance to " O   HOH Z 203 " =    1.819
peak=    3.614 closest distance to " CA  SER A  87 " =    0.971
peak=    3.602 closest distance to " O   HOH Z 371 " =    1.836
peak=    3.590 closest distance to " CB  SER A 216 " =    0.800
peak=    3.579 closest distance to " O   HOH Z  66 " =    2.173
peak=    3.572 closest distance to " CB  ARG A 139 " =    0.979
peak=    3.571 closest distance to " O   HOH Z 193 " =    2.009
peak=    3.570 closest distance to " N   PHE A 130 " =    1.250
peak=    3.570 closest distance to " O   HOH Z 406 " =    1.624
peak=    3.569 closest distance to " CD2 LEU A 255 " =    1.569
peak=    3.568 closest distance to " O   HOH Z 291 " =    1.594
peak=    3.557 closest distance to " CB  MET A  40 " =    0.842
peak=    3.557 closest distance to " CG  PRO A 198 " =    1.229
peak=    3.556 closest distance to " O   HOH Z 425 " =    2.085
peak=    3.555 closest distance to " O   HOH Z 261 " =    2.297
peak=    3.554 closest distance to " O   HOH Z 280 " =    3.013
peak=    3.554 closest distance to " NE2 HIS A 207 " =    1.415
peak=    3.551 closest distance to " O   HOH Z 368 " =    3.593
peak=    3.547 closest distance to " OD1BASN A 224 " =    2.336
peak=    3.546 closest distance to " O   HOH Z 128 " =    2.251
peak=    3.544 closest distance to " O   HOH Z 172 " =    3.080
peak=    3.537 closest distance to " CB  ALA A   1 " =    4.691
peak=    3.534 closest distance to " O   HOH Z 188 " =    2.104
peak=    3.532 closest distance to " O   HOH Z 207 " =    1.810
peak=    3.523 closest distance to " CB  VAL A 202 " =    1.587
peak=    3.510 closest distance to " O   HOH Z 175 " =    2.144
peak=    3.491 closest distance to " O   HOH Z 147 " =    1.811
peak=    3.483 closest distance to " O   HOH Z 302 " =    1.965
peak=    3.480 closest distance to " CB  ASN A 224 " =    1.022
peak=    3.469 closest distance to " O   HOH Z 329 " =    3.808
peak=    3.463 closest distance to " O   HOH Z 411 " =    1.782
peak=    3.462 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.462 closest distance to " O   HOH Z 353 " =    2.714
peak=    3.460 closest distance to " O   HOH Z 273 " =    2.731
peak=    3.446 closest distance to " O   HOH Z 234 " =    1.709
peak=    3.444 closest distance to " O   ASN A 209 " =    1.262
peak=    3.437 closest distance to " O   HOH Z 313 " =    1.898
peak=    3.433 closest distance to " O   HOH Z 166 " =    3.824
peak=    3.432 closest distance to " CB  ASN A 110 " =    1.100
peak=    3.430 closest distance to " O   HOH Z  88 " =    3.183
peak=    3.425 closest distance to " CD1 LEU A 300 " =    1.203
peak=    3.415 closest distance to " O   HOH Z  93 " =    2.597
peak=    3.412 closest distance to " O   HOH Z 213 " =    2.542
peak=    3.411 closest distance to " CA  MET A  40 " =    1.140
peak=    3.408 closest distance to " O   HOH Z 345 " =    1.758
peak=    3.406 closest distance to " O   MET A 105 " =    1.776
peak=    3.406 closest distance to " CB  TRP A 179 " =    1.441
peak=    3.403 closest distance to " N   ARG A 156 " =    1.324
peak=    3.402 closest distance to " NH2AARG A 275 " =    3.633
peak=    3.396 closest distance to " CD BLYS A 290 " =    1.174
peak=    3.394 closest distance to " O   HOH Z 391 " =    2.858
peak=    3.382 closest distance to " OG BSER A 164 " =    2.316
peak=    3.368 closest distance to " O   HOH Z 325 " =    3.915
peak=    3.366 closest distance to " CD  ARG A 219 " =    1.158
peak=    3.366 closest distance to " CB  TYR A 116 " =    0.807
peak=    3.364 closest distance to " CD1 ILE A 106 " =    0.784
peak=    3.363 closest distance to " CB  GLU A  46 " =    1.084
peak=    3.360 closest distance to " OG  SER A  22 " =    2.778
peak=    3.360 closest distance to " CA  ALA A 158 " =    1.157
peak=    3.360 closest distance to " N   ASN A 127 " =    1.305
peak=    3.359 closest distance to " CD2 LEU A 297 " =    0.849
peak=    3.357 closest distance to " CA  ALA A 291 " =    0.891
peak=    3.356 closest distance to " O   HOH Z  96 " =    2.075
peak=    3.355 closest distance to " CA  ALA A  51 " =    0.892
peak=    3.353 closest distance to " CB  ALA A 248 " =    0.914
peak=    3.351 closest distance to " CB  THR A 157 " =    1.114
peak=    3.350 closest distance to " CB  ARG A 138 " =    1.042
peak=    3.350 closest distance to " CG2 ILE A 120 " =    1.285
peak=    3.350 closest distance to " CG2AVAL A  72 " =    1.605
peak=    3.349 closest distance to " CD1 ILE A 263 " =    1.353
peak=    3.348 closest distance to " CA  ALA A  84 " =    1.458
peak=    3.347 closest distance to " CB  SER A  62 " =    1.192
peak=    3.341 closest distance to " O   HOH Z 407 " =    2.309
peak=    3.341 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.338 closest distance to " CB  LEU A 143 " =    1.110
peak=    3.337 closest distance to " O   HOH Z  85 " =    2.290
peak=    3.335 closest distance to " O   HOH Z 386 " =    3.034
peak=    3.333 closest distance to " CB  ILE A 120 " =    1.228
peak=    3.332 closest distance to " CZ  ARG A  14 " =    2.046
peak=    3.328 closest distance to " CG  MET A 113 " =    1.269
peak=    3.327 closest distance to " CG  LYS A  76 " =    0.939
peak=    3.314 closest distance to " CD  ARG A 269 " =    0.925
peak=    3.310 closest distance to " O   HOH Z   3 " =    1.911
peak=    3.309 closest distance to " O   HOH Z   1 " =    1.711
peak=    3.306 closest distance to " O   HOH Z 423 " =    2.774
peak=    3.305 closest distance to " O   HOH Z 411 " =    3.870
peak=    3.304 closest distance to " O   HOH Z 148 " =    3.345
peak=    3.300 closest distance to " O   HOH Z 345 " =    3.531
peak=    3.300 closest distance to " O   HOH Z 281 " =    4.034
peak=    3.297 closest distance to " O   HOH Z 199 " =    1.628
peak=    3.294 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.291 closest distance to " O   HOH Z 423 " =    1.800
peak=    3.290 closest distance to " O   HOH Z 435 " =    1.878
peak=    3.289 closest distance to " CD  LYS A 166 " =    1.242
peak=    3.289 closest distance to " O   HOH Z  44 " =    2.985
peak=    3.288 closest distance to " O   HOH Z 437 " =    1.483
peak=    3.283 closest distance to " CE1 TYR A 186 " =    1.302
peak=    3.282 closest distance to " O   HOH Z 359 " =    4.161
peak=    3.277 closest distance to " CB  GLN A 278 " =    0.815
peak=    3.276 closest distance to " O   HOH Z 295 " =    1.559
peak=    3.275 closest distance to " O   HOH Z 433 " =    1.800
peak=    3.274 closest distance to " O   HOH Z 271 " =    2.421
peak=    3.270 closest distance to " O   HOH Z 218 " =    4.447
peak=    3.268 closest distance to " CG AARG A 275 " =    1.201
peak=    3.268 closest distance to " CG1 VAL A 153 " =    0.860
peak=    3.267 closest distance to " O   HOH Z 227 " =    2.110
peak=    3.263 closest distance to " CB  THR A 235 " =    1.077
peak=    3.261 closest distance to " CA  ARG A 195 " =    1.236
peak=    3.258 closest distance to " O   HOH Z  53 " =    2.581
peak=    3.253 closest distance to " OE1 GLN A  11 " =    2.169
peak=    3.247 closest distance to " O   HOH Z 128 " =    2.170
peak=    3.247 closest distance to " O   HOH Z 152 " =    1.800
peak=    3.245 closest distance to " O   HOH Z 381 " =    1.666
peak=    3.243 closest distance to " O   HOH Z 402 " =    1.436
peak=    3.234 closest distance to " O   HOH Z  64 " =    2.227
peak=    3.233 closest distance to " CA  GLY A 267 " =    1.119
peak=    3.231 closest distance to " O   HOH Z 185 " =    1.828
peak=    3.231 closest distance to " CA  LYS A 117 " =    1.195
peak=    3.223 closest distance to " CG  GLN A  89 " =    1.528
peak=    3.220 closest distance to " O   HOH Z 116 " =    1.761
peak=    3.219 closest distance to " O   HOH Z  66 " =    2.140
peak=    3.218 closest distance to " O  BHOH Z 338 " =    2.395
peak=    3.216 closest distance to " O   HOH Z 409 " =    2.586
peak=    3.215 closest distance to " CE BLYS A 290 " =    1.191
peak=    3.215 closest distance to " O   HOH Z 286 " =    2.224
peak=    3.214 closest distance to " O   HOH Z 285 " =    2.721
peak=    3.209 closest distance to " O   HOH Z 163 " =    1.824
peak=    3.204 closest distance to " CD  PRO A 243 " =    1.570
peak=    3.201 closest distance to " CB  MET A  47 " =    1.042
peak=    3.197 closest distance to " CB  HIS A 108 " =    0.760
peak=    3.196 closest distance to " OG BSER A 134 " =    2.853
peak=    3.193 closest distance to " O   HOH Z 319 " =    2.266
peak=    3.189 closest distance to " N   SER A 146 " =    1.706
peak=    3.189 closest distance to " CB  TRP A 150 " =    1.328
peak=    3.187 closest distance to " CB  VAL A 126 " =    1.009
peak=    3.186 closest distance to " OD1 ASN A 217 " =    1.693
peak=    3.181 closest distance to " CA  ALA A 154 " =    0.945
peak=    3.180 closest distance to " O   HOH Z  59 " =    1.869
peak=    3.178 closest distance to " O   HOH Z 294 " =    1.470
peak=    3.175 closest distance to " CA  ASN A 217 " =    1.236
peak=    3.175 closest distance to " CD2 HIS A  81 " =    1.169
peak=    3.173 closest distance to " CB  PRO A  90 " =    1.222
peak=    3.173 closest distance to " O   HOH Z  43 " =    2.221
peak=    3.170 closest distance to " ND1 HIS A  81 " =    1.651
peak=    3.167 closest distance to " N   ASN A  39 " =    1.238
peak=    3.165 closest distance to " N   SER A 135 " =    1.271
peak=    3.165 closest distance to " CA  TYR A 116 " =    1.316
peak=    3.161 closest distance to " O   HOH Z 144 " =    1.851
peak=    3.160 closest distance to " O   HOH Z 332 " =    1.512
peak=    3.157 closest distance to " CZ2 TRP A 179 " =    1.700
peak=    3.155 closest distance to " CA  LYS A 290 " =    1.340
peak=    3.153 closest distance to " OG  SER A  97 " =    3.603
peak=    3.147 closest distance to " CG  GLN A 240 " =    3.569
peak=    3.146 closest distance to " CB  LEU A 255 " =    0.784
peak=    3.145 closest distance to " CG  ARG A 159 " =    0.852
peak=    3.141 closest distance to " O   HOH Z 358 " =    3.734
peak=    3.141 closest distance to " CB  SER A  26 " =    1.609
peak=    3.139 closest distance to " O   HOH Z  49 " =    2.741
peak=    3.131 closest distance to " O   HOH Z  59 " =    1.877
peak=    3.129 closest distance to " O   HOH Z 298 " =    2.418
peak=    3.129 closest distance to " O   HOH Z 109 " =    2.590
peak=    3.127 closest distance to " O   HOH Z 153 " =    1.597
peak=    3.126 closest distance to " N   CYS A 260 " =    0.837
peak=    3.124 closest distance to " O   HOH Z  88 " =    3.846
peak=    3.121 closest distance to " NH1 ARG A 138 " =    1.153
peak=    3.119 closest distance to " CG BARG A 102 " =    1.848
peak=    3.119 closest distance to " CA  ILE A 234 " =    0.930
peak=    3.117 closest distance to " OG  SER A  62 " =    2.948
peak=    3.111 closest distance to " CG  MET A 185 " =    1.161
peak=    3.105 closest distance to " OG  SER A 206 " =    1.245
peak=    3.104 closest distance to " CB  ALA A 291 " =    1.359
peak=    3.102 closest distance to " CB  THR A 294 " =    1.688
peak=    3.099 closest distance to " O   HOH Z 422 " =    2.641
peak=    3.095 closest distance to " O   HOH Z 336 " =    1.928
peak=    3.089 closest distance to " CB  ASP A 171 " =    1.122
peak=    3.085 closest distance to " CA  MET A 105 " =    0.932
peak=    3.072 closest distance to " O   HOH Z  49 " =    2.148
peak=    3.072 closest distance to " O   PRO A  90 " =    1.353
peak=    3.071 closest distance to " OG  SER A  62 " =    3.037
peak=    3.069 closest distance to " O   HOH Z 365 " =    2.916
peak=    3.068 closest distance to " NH1BARG A 145 " =    1.220
peak=    3.062 closest distance to " CA  ARG A  36 " =    1.023
peak=    3.061 closest distance to " CA  ALA A 299 " =    0.867

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 5.348
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.714 - 5.348

peak=   -4.836 closest distance to " CB  PRO A 243 " =    2.627
peak=   -4.563 closest distance to " O   HOH Z 266 " =    4.965
peak=   -4.450 closest distance to " CD  ARG A 156 " =    2.058
peak=   -4.315 closest distance to " O   HOH Z 435 " =    2.800
peak=   -4.279 closest distance to " CG  GLN A 223 " =    1.916
peak=   -4.233 closest distance to " O   HOH Z 290 " =    1.273
peak=   -4.203 closest distance to " O   VAL A  67 " =    2.648
peak=   -4.201 closest distance to " O   HOH Z 389 " =    1.943
peak=   -4.182 closest distance to " CB  PRO A 280 " =    2.156
peak=   -4.166 closest distance to " OG BSER A 134 " =    1.242
peak=   -4.140 closest distance to " SG  CYS A 254 " =    3.488
peak=   -4.025 closest distance to " CZ3 TRP A 179 " =    1.116
peak=   -4.014 closest distance to " CG1 VAL A 112 " =    2.849
peak=   -3.969 closest distance to " C   HIS A 108 " =    1.189
peak=   -3.953 closest distance to " ND2 ASN A  45 " =    1.801
peak=   -3.895 closest distance to " N   ALA A  43 " =    2.590
peak=   -3.892 closest distance to " CD  GLN A  58 " =    0.976
peak=   -3.892 closest distance to " O   HOH Z 313 " =    1.901
peak=   -3.868 closest distance to " O   HOH Z 198 " =    1.311
peak=   -3.860 closest distance to " O   HOH Z 372 " =    2.482
peak=   -3.858 closest distance to " CD1 ILE A 263 " =    3.118
peak=   -3.856 closest distance to " O   HOH Z 351 " =    1.418
peak=   -3.847 closest distance to " CD  ARG A 139 " =    1.650
peak=   -3.838 closest distance to " O   HOH Z 231 " =    2.272
peak=   -3.827 closest distance to " CA  VAL A  67 " =    2.817
peak=   -3.820 closest distance to " CB  ALA A 291 " =    2.159
peak=   -3.809 closest distance to " O   HOH Z  38 " =    1.501
peak=   -3.809 closest distance to " O   PRO A 198 " =    1.265
peak=   -3.787 closest distance to " O   HOH Z 185 " =    2.233
peak=   -3.755 closest distance to " O   HOH Z 114 " =    3.056
peak=   -3.754 closest distance to " CD1 PHE A  59 " =    1.859
peak=   -3.752 closest distance to " OD1 ASP A 171 " =    1.644
peak=   -3.752 closest distance to " O   HOH Z 198 " =    2.115
peak=   -3.741 closest distance to " CZ  TYR A 169 " =    1.592
peak=   -3.739 closest distance to " O   HOH Z  43 " =    1.665
peak=   -3.727 closest distance to " O   HOH Z  10 " =    1.476
peak=   -3.722 closest distance to " CE  MET A 105 " =    2.292
peak=   -3.713 closest distance to " O   VAL A 189 " =    2.565
peak=   -3.709 closest distance to " CB  ALA A  43 " =    2.492
peak=   -3.695 closest distance to " O   HOH Z 407 " =    3.175
peak=   -3.686 closest distance to " CD2 PHE A 192 " =    2.033
peak=   -3.669 closest distance to " NH2AARG A 275 " =    5.348
peak=   -3.655 closest distance to " O   HOH Z 211 " =    1.645
peak=   -3.630 closest distance to " CB  PRO A 163 " =    2.520
peak=   -3.630 closest distance to " CD2 LEU A 237 " =    2.799
peak=   -3.601 closest distance to " CB  ALA A 161 " =    2.588
peak=   -3.601 closest distance to " O   HOH Z 359 " =    3.344
peak=   -3.598 closest distance to " O   HOH Z  73 " =    2.174
peak=   -3.590 closest distance to " CE2 TYR A  30 " =    2.756
peak=   -3.587 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.584 closest distance to " CG  PHE A 283 " =    2.684
peak=   -3.583 closest distance to " O   HOH Z 377 " =    0.736
peak=   -3.578 closest distance to " CZ BARG A 275 " =    1.760
peak=   -3.576 closest distance to " CE2 PHE A 218 " =    2.433
peak=   -3.573 closest distance to " OG BSER A 134 " =    1.685
peak=   -3.569 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.563 closest distance to " O   HOH Z  52 " =    1.189
peak=   -3.558 closest distance to " CZ  PHE A  59 " =    1.537
peak=   -3.553 closest distance to " O   ARG A 145 " =    1.495
peak=   -3.540 closest distance to " CA  GLY A  98 " =    1.879
peak=   -3.534 closest distance to " O   HOH Z 395 " =    5.194
peak=   -3.522 closest distance to " C   ASN A 285 " =    2.397
peak=   -3.512 closest distance to " C   LEU A 222 " =    0.714
peak=   -3.501 closest distance to " CB  TRP A  85 " =    2.488
peak=   -3.498 closest distance to " CD2 TYR A 247 " =    2.528
peak=   -3.494 closest distance to " C   ALA A 158 " =    1.456
peak=   -3.494 closest distance to " CB  ALA A 291 " =    2.212
peak=   -3.491 closest distance to " CG1 VAL A 197 " =    2.170
peak=   -3.488 closest distance to " CB  ASN A  39 " =    2.223
peak=   -3.482 closest distance to " O   HOH Z 394 " =    1.383
peak=   -3.480 closest distance to " CA  GLY A 203 " =    2.263
peak=   -3.477 closest distance to " OD1 ASN A 148 " =    1.551
peak=   -3.469 closest distance to " O   HOH Z 126 " =    1.879
peak=   -3.467 closest distance to " CD1 LEU A 297 " =    2.434
peak=   -3.464 closest distance to " CG2 ILE A 263 " =    2.265
peak=   -3.462 closest distance to " O   HOH Z 353 " =    2.166
peak=   -3.458 closest distance to " O   HOH Z  60 " =    2.371
peak=   -3.456 closest distance to " CG  ASP A 231 " =    0.740
peak=   -3.454 closest distance to " N   THR A 157 " =    1.529
peak=   -3.451 closest distance to " O   GLY A 211 " =    1.364
peak=   -3.450 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.448 closest distance to " OXT GLY A 302 " =    2.867
peak=   -3.446 closest distance to " O   HOH Z 193 " =    2.026
peak=   -3.442 closest distance to " CD1 LEU A 228 " =    2.309
peak=   -3.441 closest distance to " CB  CYS A 254 " =    2.276
peak=   -3.432 closest distance to " O   PRO A 163 " =    2.015
peak=   -3.426 closest distance to " CB  PHE A 208 " =    2.237
peak=   -3.411 closest distance to " CB  TYR A  15 " =    2.192
peak=   -3.399 closest distance to " O   HOH Z  11 " =    1.794
peak=   -3.396 closest distance to " O   HOH Z 311 " =    3.676
peak=   -3.394 closest distance to " CE3 TRP A 274 " =    1.080
peak=   -3.390 closest distance to " CD1 LEU A 101 " =    2.339
peak=   -3.390 closest distance to " CA  GLY A 133 " =    2.047
peak=   -3.387 closest distance to " O   HOH Z 426 " =    1.577
peak=   -3.379 closest distance to " O   GLN A 240 " =    2.127
peak=   -3.379 closest distance to " CA  GLY A 241 " =    2.281
peak=   -3.374 closest distance to " O   SER A 135 " =    1.432
peak=   -3.370 closest distance to " CB  ALA A 248 " =    2.056
peak=   -3.364 closest distance to " CG1 VAL A 250 " =    2.690
peak=   -3.360 closest distance to " CE BMET A  47 " =    1.906
peak=   -3.344 closest distance to " CB  ALA A 248 " =    2.474
peak=   -3.339 closest distance to " CD2 LEU A 300 " =    2.800
peak=   -3.338 closest distance to " ND2 ASN A 187 " =    1.435
peak=   -3.326 closest distance to " O   HOH Z 176 " =    0.797
peak=   -3.325 closest distance to " CE3 TRP A 274 " =    2.393
peak=   -3.324 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.319 closest distance to " SD  MET A 188 " =    2.224
peak=   -3.318 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.315 closest distance to " O   GLN A 240 " =    2.337
peak=   -3.313 closest distance to " O   HOH Z 111 " =    1.340
peak=   -3.312 closest distance to " CG  GLU A 152 " =    0.783
peak=   -3.308 closest distance to " NH2 ARG A  79 " =    1.937
peak=   -3.308 closest distance to " CD2 PHE A 225 " =    1.147
peak=   -3.305 closest distance to " O   PHE A 218 " =    1.629
peak=   -3.295 closest distance to " SG ACYS A 201 " =    1.875
peak=   -3.293 closest distance to " CB  CYS A 201 " =    2.547
peak=   -3.292 closest distance to " O   HOH Z 371 " =    1.395
peak=   -3.291 closest distance to " NE2 GLN A 278 " =    1.637
peak=   -3.290 closest distance to " O   HOH Z 174 " =    2.567
peak=   -3.290 closest distance to " N   THR A 235 " =    1.308
peak=   -3.284 closest distance to " CD2 PHE A  61 " =    2.007
peak=   -3.282 closest distance to " CB  ALA A 131 " =    2.057
peak=   -3.281 closest distance to " CG2 THR A 178 " =    2.249
peak=   -3.281 closest distance to " O   HOH Z 317 " =    1.538
peak=   -3.280 closest distance to " O   HOH Z 256 " =    1.545
peak=   -3.275 closest distance to " CB  ASP A 286 " =    2.087
peak=   -3.273 closest distance to " C   LEU A 143 " =    1.237
peak=   -3.271 closest distance to " O   HOH Z 266 " =    4.780
peak=   -3.267 closest distance to " CG  GLU A 277 " =    1.233
peak=   -3.266 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.265 closest distance to " N   SER A 212 " =    2.063
peak=   -3.264 closest distance to " O   HOH Z 111 " =    1.820
peak=   -3.263 closest distance to " O   HOH Z 253 " =    3.902
peak=   -3.262 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.262 closest distance to " OG  SER A  87 " =    1.358
peak=   -3.259 closest distance to " CD  GLN A  88 " =    0.794
peak=   -3.257 closest distance to " C   MET A 188 " =    1.369
peak=   -3.255 closest distance to " O   HOH Z 298 " =    1.246
peak=   -3.252 closest distance to " NH1 ARG A 195 " =    2.569
peak=   -3.252 closest distance to " OD2 ASP A 171 " =    2.173
peak=   -3.251 closest distance to " CG  ARG A 269 " =    2.363
peak=   -3.246 closest distance to " CB  ASP A 132 " =    2.261
peak=   -3.246 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.243 closest distance to " CA  GLY A 241 " =    3.109
peak=   -3.240 closest distance to " O   HOH Z 295 " =    1.511
peak=   -3.240 closest distance to " O   ALA A 292 " =    2.081
peak=   -3.239 closest distance to " O   HOH Z 348 " =    1.866
peak=   -3.234 closest distance to " O   HOH Z  98 " =    2.290
peak=   -3.226 closest distance to " NE2 GLN A 103 " =    1.578
peak=   -3.224 closest distance to " N   MET A 105 " =    2.577
peak=   -3.222 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.222 closest distance to " O   HOH Z 196 " =    2.163
peak=   -3.221 closest distance to " O   HOH Z 385 " =    2.098
peak=   -3.216 closest distance to " O   HOH Z  51 " =    1.232
peak=   -3.212 closest distance to " O   HOH Z 244 " =    1.978
peak=   -3.211 closest distance to " CG  GLU A 152 " =    1.171
peak=   -3.210 closest distance to " C   GLN A  58 " =    1.975
peak=   -3.208 closest distance to " NE  ARG A  36 " =    1.918
peak=   -3.205 closest distance to " NE2 GLN A 194 " =    1.717
peak=   -3.204 closest distance to " O   SER A  95 " =    1.504
peak=   -3.203 closest distance to " NH2 ARG A  79 " =    1.641
peak=   -3.202 closest distance to " OE1 GLN A 223 " =    1.947
peak=   -3.199 closest distance to " O   TRP A  70 " =    1.500
peak=   -3.198 closest distance to " O   SER A  22 " =    2.412
peak=   -3.196 closest distance to " O   VAL A 189 " =    1.529
peak=   -3.195 closest distance to " OD1AASN A 224 " =    1.784
peak=   -3.189 closest distance to " OD1 ASP A 191 " =    1.814
peak=   -3.183 closest distance to " O   HOH Z  93 " =    2.434
peak=   -3.178 closest distance to " O   HOH Z  13 " =    1.518
peak=   -3.174 closest distance to " CA  SER A 135 " =    1.377
peak=   -3.169 closest distance to " O   HOH Z  63 " =    1.656
peak=   -3.168 closest distance to " O   GLY A  17 " =    1.214
peak=   -3.167 closest distance to " O   HOH Z 298 " =    2.567
peak=   -3.164 closest distance to " O   HOH Z 114 " =    1.640
peak=   -3.161 closest distance to " CA  TRP A 274 " =    1.401
peak=   -3.157 closest distance to " CD1 ILE A 199 " =    2.577
peak=   -3.153 closest distance to " CE  LYS A  76 " =    2.748
peak=   -3.152 closest distance to " ND2 ASN A  60 " =    1.345
peak=   -3.151 closest distance to " O   HOH Z   6 " =    1.429
peak=   -3.151 closest distance to " N   PHE A  59 " =    2.041
peak=   -3.151 closest distance to " OD1 ASN A 187 " =    1.633
peak=   -3.150 closest distance to " CG  PRO A 163 " =    2.609
peak=   -3.150 closest distance to " O   HOH Z 282 " =    1.119
peak=   -3.149 closest distance to " O   LYS A 289 " =    3.081
peak=   -3.148 closest distance to " CG1 VAL A 230 " =    2.049
peak=   -3.148 closest distance to " O   ALA A 161 " =    1.639
peak=   -3.144 closest distance to " O   HOH Z 241 " =    1.329
peak=   -3.142 closest distance to " OD2 ASP A  50 " =    1.736
peak=   -3.139 closest distance to " O   HOH Z 281 " =    4.930
peak=   -3.133 closest distance to " CH2 TRP A 177 " =    2.088
peak=   -3.133 closest distance to " O   HOH Z 168 " =    1.826
peak=   -3.130 closest distance to " O   HOH Z 134 " =    2.985
peak=   -3.129 closest distance to " O   HOH Z 323 " =    1.296
peak=   -3.115 closest distance to " O   HOH Z 290 " =    0.960
peak=   -3.109 closest distance to " CE3 TRP A 123 " =    1.231
peak=   -3.103 closest distance to " O   HOH Z 128 " =    2.613
peak=   -3.101 closest distance to " O   HOH Z 310 " =    1.856
peak=   -3.101 closest distance to " CG1 VAL A 125 " =    1.980
peak=   -3.097 closest distance to " O   HOH Z  89 " =    2.972
peak=   -3.094 closest distance to " OH  TYR A 172 " =    1.731
peak=   -3.092 closest distance to " N   ASP A 171 " =    2.303
peak=   -3.084 closest distance to " NH2 ARG A  24 " =    1.815
peak=   -3.082 closest distance to " O   HOH Z 123 " =    2.461
peak=   -3.080 closest distance to " C   GLY A  13 " =    1.003
peak=   -3.079 closest distance to " CA  GLY A 241 " =    2.822
peak=   -3.070 closest distance to " CB  LEU A  83 " =    2.382
peak=   -3.051 closest distance to " OE1 GLN A  88 " =    1.266
peak=   -3.032 closest distance to " CB  CYS A 201 " =    2.309
peak=   -3.028 closest distance to " O   HOH Z 263 " =    3.189

================= 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    :  0.3034 0.2999   5.997329e+00   5.981867e+00
   1_bss:  0.2895 0.2878   5.974849e+00   5.955688e+00
   1_xyz:  0.1682 0.1902   5.455533e+00   5.556789e+00
   1_adp:  0.1531 0.1968   5.402639e+00   5.593081e+00
   1_occ:  0.1528 0.1969   5.401287e+00   5.592128e+00
   2_bss:  0.1519 0.1951   5.396996e+00   5.584663e+00
   2_xyz:  0.1200 0.1651   5.200336e+00   5.432692e+00
   2_adp:  0.1169 0.1573   5.165627e+00   5.389212e+00
   2_occ:  0.1167 0.1574   5.165236e+00   5.389565e+00
   3_bss:  0.1168 0.1565   5.163158e+00   5.385895e+00
   3_xyz:  0.1088 0.1532   5.118415e+00   5.364553e+00
   3_adp:  0.1065 0.1526   5.106877e+00   5.360900e+00
   3_occ:  0.1065 0.1526   5.106863e+00   5.361050e+00
   4_bss:  0.1064 0.1526   5.106783e+00   5.360945e+00
   4_xyz:  0.1070 0.1532   5.112506e+00   5.367352e+00
   4_adp:  0.1067 0.1536   5.112318e+00   5.369709e+00
   4_occ:  0.1067 0.1536   5.112299e+00   5.369787e+00
   5_bss:  0.1066 0.1536   5.112142e+00   5.369611e+00
   5_xyz:  0.1055 0.1548   5.110013e+00   5.374212e+00
   5_adp:  0.1063 0.1544   5.111296e+00   5.371629e+00
   5_occ:  0.1062 0.1543   5.111240e+00   5.371701e+00
   5_bss:  0.1062 0.1544   5.111290e+00   5.371718e+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:  0.334  50.441  -1.354   0.013  -1.701   0.000  -0.000  -0.000
   1_xyz:  0.334  50.441  -1.354   0.013  -1.701   0.000  -0.000  -0.000
   1_adp:  0.334  50.441  -1.354   0.013  -1.701   0.000  -0.000  -0.000
   1_occ:  0.334  50.441  -1.354   0.013  -1.701   0.000  -0.000  -0.000
   2_bss:  0.332  57.052  -2.331  -2.144  -1.765  -0.000  -0.000  -0.000
   2_xyz:  0.332  57.052  -2.331  -2.144  -1.765  -0.000  -0.000  -0.000
   2_adp:  0.332  57.052  -2.331  -2.144  -1.765  -0.000  -0.000  -0.000
   2_occ:  0.332  57.052  -2.331  -2.144  -1.765  -0.000  -0.000  -0.000
   3_bss:  0.333  57.052  -2.511  -2.591  -1.555  -0.000  -0.000  -0.000
   3_xyz:  0.333  57.052  -2.511  -2.591  -1.555  -0.000  -0.000  -0.000
   3_adp:  0.333  57.052  -2.511  -2.591  -1.555  -0.000  -0.000  -0.000
   3_occ:  0.333  57.052  -2.511  -2.591  -1.555  -0.000  -0.000  -0.000
   4_bss:  0.333  57.052  -2.369  -2.553  -1.345  -0.000  -0.000  -0.000
   4_xyz:  0.333  57.052  -2.369  -2.553  -1.345  -0.000  -0.000  -0.000
   4_adp:  0.333  57.052  -2.369  -2.553  -1.345  -0.000  -0.000  -0.000
   4_occ:  0.333  57.052  -2.369  -2.553  -1.345  -0.000  -0.000  -0.000
   5_bss:  0.327  57.052  -2.204  -2.420  -1.157  -0.000  -0.000  -0.000
   5_xyz:  0.327  57.052  -2.204  -2.420  -1.157  -0.000  -0.000  -0.000
   5_adp:  0.327  57.052  -2.204  -2.420  -1.157  -0.000  -0.000  -0.000
   5_occ:  0.327  57.052  -2.204  -2.420  -1.157  -0.000  -0.000  -0.000
   5_bss:  0.327  56.998  -2.050  -2.282  -0.971  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.287 0.7586  0.9361    25558.171
   1_bss:  29.237 0.7682  0.9159    22920.873
   1_xyz:  17.479 0.8866  1.0035     9176.048
   1_adp:  18.417 0.8774  0.9984     9791.547
   1_occ:  18.402 0.8775  0.9981     9759.535
   2_bss:  18.191 0.8794  0.9631     9605.949
   2_xyz:  14.974 0.9066  0.9795     6901.822
   2_adp:  14.018 0.9147  0.9810     6388.188
   2_occ:  14.025 0.9147  0.9808     6386.559
   3_bss:  13.963 0.9151  0.9761     6310.673
   3_xyz:  13.435 0.9195  0.9770     6049.589
   3_adp:  13.379 0.9200  0.9719     5976.314
   3_occ:  13.384 0.9199  0.9718     5977.378
   4_bss:  13.384 0.9199  0.9765     5977.420
   4_xyz:  13.469 0.9194  0.9759     6071.744
   4_adp:  13.507 0.9191  0.9701     6083.481
   4_occ:  13.508 0.9191  0.9700     6083.572
   5_bss:  13.506 0.9191  0.9756     6079.406
   5_xyz:  13.574 0.9187  0.9753     6152.631
   5_adp:  13.500 0.9193  0.9705     6138.666
   5_occ:  13.504 0.9192  0.9704     6136.388
   5_bss:  13.505 0.9192  0.9741     6137.103
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6115e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6115e-01
   1_xyz:   1.005  0.008  0.071 15.254  0.005  4.113   6.1701e-02
   1_adp:   1.005  0.008  0.071 15.254  0.005  4.113   6.1701e-02
   1_occ:   1.005  0.008  0.071 15.254  0.005  4.113   6.1701e-02
   2_bss:   1.005  0.008  0.071 15.254  0.005  4.113   6.1701e-02
   2_xyz:   0.986  0.007  0.076 15.134  0.004  4.120   5.9853e-02
   2_adp:   0.986  0.007  0.076 15.134  0.004  4.120   5.9853e-02
   2_occ:   0.986  0.007  0.076 15.134  0.004  4.120   5.9853e-02
   3_bss:   0.986  0.007  0.076 15.134  0.004  4.120   5.9853e-02
   3_xyz:   1.090  0.010  0.084 15.369  0.004  4.112   7.5318e-02
   3_adp:   1.090  0.010  0.084 15.369  0.004  4.112   7.5318e-02
   3_occ:   1.090  0.010  0.084 15.369  0.004  4.112   7.5318e-02
   4_bss:   1.090  0.010  0.084 15.369  0.004  4.112   7.5318e-02
   4_xyz:   1.021  0.008  0.079 15.185  0.004  4.112   6.6004e-02
   4_adp:   1.021  0.008  0.079 15.185  0.004  4.112   6.6004e-02
   4_occ:   1.021  0.008  0.079 15.185  0.004  4.112   6.6004e-02
   5_bss:   1.021  0.008  0.079 15.185  0.004  4.112   6.6004e-02
   5_xyz:   1.059  0.009  0.081 15.254  0.004  4.113   7.0060e-02
   5_adp:   1.059  0.009  0.081 15.254  0.004  4.113   7.0060e-02
   5_occ:   1.059  0.009  0.081 15.254  0.004  4.113   7.0060e-02
   5_bss:   1.059  0.009  0.081 15.254  0.004  4.113   7.0060e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4116e-01
   1_xyz:   8.512  0.047  0.269 84.891  0.044  2.302   5.7722e-02
   1_adp:   8.512  0.047  0.269 84.891  0.044  2.302   5.7722e-02
   1_occ:   8.512  0.047  0.269 84.891  0.044  2.302   5.7722e-02
   2_bss:   8.512  0.047  0.269 84.891  0.044  2.302   5.7722e-02
   2_xyz:   7.368  0.043  0.223 83.419  0.030  2.329   4.4602e-02
   2_adp:   7.368  0.043  0.223 83.419  0.030  2.329   4.4602e-02
   2_occ:   7.368  0.043  0.223 83.419  0.030  2.329   4.4602e-02
   3_bss:   7.368  0.043  0.223 83.419  0.030  2.329   4.4602e-02
   3_xyz:   7.344  0.050  0.272 84.929  0.038  2.210   7.0378e-02
   3_adp:   7.344  0.050  0.272 84.929  0.038  2.210   7.0378e-02
   3_occ:   7.344  0.050  0.272 84.929  0.038  2.210   7.0378e-02
   4_bss:   7.344  0.050  0.272 84.929  0.038  2.210   7.0378e-02
   4_xyz:   7.139  0.046  0.250 84.473  0.037  2.335   5.3136e-02
   4_adp:   7.139  0.046  0.250 84.473  0.037  2.335   5.3136e-02
   4_occ:   7.139  0.046  0.250 84.473  0.037  2.335   5.3136e-02
   5_bss:   7.139  0.046  0.250 84.473  0.037  2.335   5.3136e-02
   5_xyz:   7.146  0.046  0.256 84.475  0.039  2.243   5.4806e-02
   5_adp:   7.146  0.046  0.256 84.475  0.039  2.243   5.4806e-02
   5_occ:   7.146  0.046  0.256 84.475  0.039  2.243   5.4806e-02
   5_bss:   7.146  0.046  0.256 84.475  0.039  2.243   5.4806e-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:  71.75   1.62  17.02  68.46   1.62  12.99  71.75   6.21  38.95
   1_occ:  71.75   1.62  17.02  68.46   1.62  12.99  71.75   6.21  38.95
   2_bss:  71.75   1.62  17.02  68.46   1.62  12.99  71.75   6.21  38.95
   2_xyz:  71.75   1.62  17.02  68.46   1.62  12.99  71.75   6.21  38.95
   2_adp:  70.67   2.07  16.61  69.44   2.07  12.86  70.67   6.23  37.02
   2_occ:  70.67   2.07  16.61  69.44   2.07  12.86  70.67   6.23  37.02
   3_bss:  70.67   2.07  16.61  69.44   2.07  12.86  70.67   6.23  37.02
   3_xyz:  70.67   2.07  16.61  69.44   2.07  12.86  70.67   6.23  37.02
   3_adp:  77.36   1.29  16.88  77.36   1.29  12.88  74.90   6.28  38.66
   3_occ:  77.36   1.29  16.88  77.36   1.29  12.88  74.90   6.28  38.66
   4_bss:  77.36   1.29  16.88  77.36   1.29  12.88  74.90   6.28  38.66
   4_xyz:  77.36   1.29  16.88  77.36   1.29  12.88  74.90   6.28  38.66
   4_adp:  80.78   0.99  16.79  80.78   0.99  12.76  76.76   6.60  38.74
   4_occ:  80.78   0.99  16.79  80.78   0.99  12.76  76.76   6.60  38.74
   5_bss:  80.78   0.99  16.79  80.78   0.99  12.76  76.76   6.60  38.74
   5_xyz:  80.78   0.99  16.79  80.78   0.99  12.76  76.76   6.60  38.74
   5_adp:  79.35   1.51  16.34  79.35   1.51  12.53  77.01   6.49  37.10
   5_occ:  79.35   1.51  16.34  79.35   1.51  12.53  77.01   6.49  37.10
   5_bss:  79.30   1.45  16.29  79.30   1.45  12.48  76.96   6.44  37.04
------------------------------------------------------------------------
 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:    0.954    0.019    0.286
   1_adp:    0.954    0.019    0.286
   1_occ:    0.954    0.019    0.286
   2_bss:    0.954    0.019    0.286
   2_xyz:    0.732    0.020    0.341
   2_adp:    0.732    0.020    0.341
   2_occ:    0.732    0.020    0.341
   3_bss:    0.732    0.020    0.341
   3_xyz:    0.889    0.027    0.365
   3_adp:    0.889    0.027    0.365
   3_occ:    0.889    0.027    0.365
   4_bss:    0.889    0.027    0.365
   4_xyz:    1.026    0.021    0.371
   4_adp:    1.026    0.021    0.371
   4_occ:    1.026    0.021    0.371
   5_bss:    1.026    0.021    0.371
   5_xyz:    1.160    0.014    0.378
   5_adp:    1.160    0.014    0.378
   5_occ:    1.160    0.014    0.378
   5_bss:    1.160    0.014    0.378
------------------------------------------------------------------------

CPU time actual refinement: 322.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/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_885/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_885/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.63 
  Macro-tasks:
    bulk solvent and scale       = 36.35  
    individual site refinement   = 132.59 
    weights calculation          = 28.53  
    collect and process          = 6.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 204.12 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 102.68 
    alpha_beta                      = 8.12   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.45 
    fmodel                         = 6.69   
    r_factors                      = 0.18   
    phase_errors                   = 11.31  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 244.06 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.539 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    666 calls, 102.35 s
gradients_fft:          611 calls,  98.68 s

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

# Date 2008-01-16 Time 05:53:34 PST -0800 (1200491614.82 s)
Start R-work = 0.3034, R-free = 0.2999 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.2895, R-free = 0.2878
Final R-work = 0.1062, R-free = 0.1544