# Date 2008-01-16 Time 04:44:31 PST -0800 (1200487471.37 s)
#phil __OFF__

Command line arguments: "../444.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11496
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 444

-------------------------------------------------------------------------------
  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: (69.5475, 47.3993, 85.9581, 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: 3.26, 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: (69.5475, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8642 1.98058
Completeness in resolution range: 0.963267
Completeness with d_max=infinity: 0.960245

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8642
                             d_min =   1.9806

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: (69.5475, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8642 1.98058
Completeness in resolution range: 0.963267
Completeness with d_max=infinity: 0.960245

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8647 -  4.2372 [2136/2164]  1922   214  10.0%
  bin  2:  4.2372 -  3.3761 [2042/2061]  1839   203   9.9%
  bin  3:  3.3761 -  2.9532 [2035/2055]  1831   204  10.0%
  bin  4:  2.9532 -  2.6849 [2006/2031]  1809   197   9.8%
  bin  5:  2.6849 -  2.4934 [1999/2019]  1794   205  10.3%
  bin  6:  2.4934 -  2.3470 [1970/2016]  1777   193   9.8%
  bin  7:  2.3470 -  2.2299 [1972/2004]  1774   198  10.0%
  bin  8:  2.2299 -  2.1331 [1963/1999]  1763   200  10.2%
  bin  9:  2.1331 -  2.0512 [1948/1978]  1751   197  10.1%
  bin 10:  2.0512 -  1.9806 [1518/2009]  1370   148   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2197
        3.04 -     3.66: 4705
        3.66 -     4.28: 9035
        4.28 -     4.90: 12415
  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
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.925 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.038 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.074 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.157 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28368 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_444/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 69.5475 47.3993 85.95805 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3092   r_free= 0.3030   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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: 6.003821                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1389  154 0.2762 0.2855      6.3299      6.3352|
|  2:  4.7255 -  3.7710 0.99   1329  150 0.2411 0.2205       6.373      6.3335|
|  3:  3.7710 -  3.3002 0.99   1314  149 0.2616 0.2505      6.2817      6.3037|
|  4:  3.3002 -  3.0012 0.99   1303  133 0.2802 0.2744      6.1652      6.0798|
|  5:  3.0012 -  2.7876 0.99   1286  148 0.3113 0.2634      6.0591      5.9676|
|  6:  2.7876 -  2.6242 0.98   1282  143 0.3242 0.3314       5.994      5.9006|
|  7:  2.6242 -  2.4934 0.99   1292  146 0.3281 0.2785      5.9784      5.8102|
|  8:  2.4934 -  2.3853 0.98   1275  137 0.3352 0.3711       5.925      6.0327|
|  9:  2.3853 -  2.2938 0.98   1271  146 0.3499 0.3458      5.8877      5.8858|
| 10:  2.2938 -  2.2150 0.97   1245  136 0.3514 0.3691      5.8895       5.854|
| 11:  2.2150 -  2.1459 0.99   1276  144 0.3507 0.3565      5.8095      5.8916|
| 12:  2.1459 -  2.0847 0.98   1275  141 0.3637 0.3684      5.7905      5.8253|
| 13:  2.0847 -  2.0300 0.97   1256  134 0.3776 0.3571      5.7299      5.6636|
| 14:  2.0300 -  1.9806 0.67    837   98 0.3641 0.3628      5.6573      5.5773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8647 -  4.7255  1389   154  0.78  27.01   0.87     0.79      45169.70|
|  2:  4.7255 -  3.7710  1329   150  0.85  21.03   0.99     0.92      41530.11|
|  3:  3.7710 -  3.3002  1314   149  0.84  22.92   1.00     0.97      36254.31|
|  4:  3.3002 -  3.0012  1303   133  0.82  24.52   1.00     0.97      30351.88|
|  5:  3.0012 -  2.7876  1286   148  0.78  28.30   1.00     0.96      24946.20|
|  6:  2.7876 -  2.6242  1282   143  0.77  29.54   1.01     0.95      21907.14|
|  7:  2.6242 -  2.4934  1292   146  0.78  28.80   1.01     0.96      20202.18|
|  8:  2.4934 -  2.3853  1275   137  0.75  31.23   1.03     0.95      20827.48|
|  9:  2.3853 -  2.2938  1271   146  0.72  34.16   1.03     0.94      20780.17|
| 10:  2.2938 -  2.2150  1245   136  0.71  35.25   1.05     0.92      20646.91|
| 11:  2.2150 -  2.1459  1276   144  0.70  35.91   1.05     0.96      19832.96|
| 12:  2.1459 -  2.0847  1275   141  0.70  36.14   1.06     0.97      18271.15|
| 13:  2.0847 -  2.0300  1256   134  0.70  36.35   1.04     0.96      15882.32|
| 14:  2.0300 -  1.9806   837    98  0.71  35.09   1.04     0.92      12756.35|
|alpha:            min =        0.79 max =            0.97 mean =         0.94|
|beta:             min =    12756.35 max =        45169.70 mean =     25484.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.93 mean =        30.24|
|phase err.(test): min =        0.00 max =           89.84 mean =        30.22|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.000770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.309   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.563311              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.557   (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:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 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:     1998 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2832 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4641 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4394 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5661 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6754 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.198 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3092   r_free= 0.3030   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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: 6.003821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2961   r_free= 0.2876   ksol= 0.31   Bsol= 35.90   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,0.65,-1.33,0.00,-0.00,-0.00); trace/3= -0.95                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.978977                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.695905              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.278   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.412   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2961      final r-factor (work) = 0.1656          |
| start r-factor (free) = 0.2876      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2451 = 3.70 * 0.50 * 5.9967 + 1.00 * 0.1634                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5219 = 3.70 * 0.50 * 5.6578 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1656      final r-factor (work) = 0.1500          |
| start r-factor (free) = 0.1829      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7721 = 0.31 * 1.00 * 5.6578 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6814 = 0.31 * 1.00 * 5.3601 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.76   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    73.76   16.96    None  None   None       |
|    Sol.    : 438    0      6.73    68.09   38.12    None  None   None       |
|    Mac.    : 2385   0      0.00    73.76   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.376:  385   |   5:    36.878 -  44.253:  124        |
|      1:     7.376 -  14.751: 1411   |   6:    44.253 -  51.629:   98        |
|      2:    14.751 -  22.127:  448   |   7:    51.629 -  59.005:   65        |
|      3:    22.127 -  29.502:  154   |   8:    59.005 -  66.380:   24        |
|      4:    29.502 -  36.878:  107   |   9:    66.380 -  73.756:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1500 r_free = 0.1862             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1497 r_free = 0.1860             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1497   r_free= 0.1860   ksol= 0.31   Bsol= 35.90   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,0.65,-1.33,0.00,-0.00,-0.00); trace/3= -0.95                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.369724                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1484   r_free= 0.1849   ksol= 0.31   Bsol= 44.25   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-1.44,-1.73,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.366027                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.255788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.369  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.122479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.461  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1286 = 2.26 * 0.50 * 5.3746 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0001 = 2.26 * 0.50 * 5.2690 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6535 = 0.12 * 1.00 * 5.2690 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6403 = 0.12 * 1.00 * 5.1744 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.44    75.05   16.47    None  None   None       |
|    all(noH): 2823   0      2.44    75.05   16.47    None  None   None       |
|    Sol.    : 438    0      5.63    64.32   36.54    None  None   None       |
|    Mac.    : 2385   0      2.44    75.05   12.78    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:     2.439 -   9.700:  918   |   5:    38.743 -  46.004:  116        |
|      1:     9.700 -  16.960: 1106   |   6:    46.004 -  53.265:   86        |
|      2:    16.960 -  24.221:  300   |   7:    53.265 -  60.526:   34        |
|      3:    24.221 -  31.482:  127   |   8:    60.526 -  67.787:   12        |
|      4:    31.482 -  38.743:  122   |   9:    67.787 -  75.047:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1537             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1536             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1536   ksol= 0.31   Bsol= 44.25   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-1.44,-1.73,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158733                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1531   ksol= 0.32   Bsol= 45.40   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.76,-1.46,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159279                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.615741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.636  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.585  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1511          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8257 = 2.62 * 0.50 * 5.1752 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7713 = 2.62 * 0.50 * 5.1257 + 1.00 * 0.0675                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1511      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1895 = 0.43 * 1.00 * 5.1257 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1820 = 0.43 * 1.00 * 5.1048 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    80.07   16.61    None  None   None       |
|    all(noH): 2823   0      1.52    80.07   16.61    None  None   None       |
|    Sol.    : 438    0      5.85    66.47   37.89    None  None   None       |
|    Mac.    : 2385   0      1.52    80.07   12.70    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:     1.525 -   9.379:  879   |   5:    40.798 -  48.652:  120        |
|      1:     9.379 -  17.234: 1171   |   6:    48.652 -  56.507:   90        |
|      2:    17.234 -  25.089:  285   |   7:    56.507 -  64.361:   33        |
|      3:    25.089 -  32.943:  127   |   8:    64.361 -  72.216:    7        |
|      4:    32.943 -  40.798:  108   |   9:    72.216 -  80.070:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1515             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1074 r_free = 0.1516             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1516   ksol= 0.32   Bsol= 45.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.76,-1.46,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.108581                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1516   ksol= 0.32   Bsol= 45.54   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.76,-1.28,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.486924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.696  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.962937              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.824  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4155 = 2.49 * 0.50 * 5.1051 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4141 = 2.49 * 0.50 * 5.1068 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0321 = 1.96 * 1.00 * 5.1068 + 1.00 * 0.0079                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0302 = 1.96 * 1.00 * 5.1049 + 1.00 * 0.0095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.41    91.47   16.82    None  None   None       |
|    all(noH): 2823   0      0.41    91.47   16.82    None  None   None       |
|    Sol.    : 438    0      5.57    76.15   39.39    None  None   None       |
|    Mac.    : 2385   0      0.41    91.47   12.67    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:     0.411 -   9.517:  987   |   5:    45.941 -  55.047:  100        |
|      1:     9.517 -  18.623: 1154   |   6:    55.047 -  64.153:   67        |
|      2:    18.623 -  27.729:  229   |   7:    64.153 -  73.259:   20        |
|      3:    27.729 -  36.835:  137   |   8:    73.259 -  82.365:    4        |
|      4:    36.835 -  45.941:  121   |   9:    82.365 -  91.471:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1062 r_free = 0.1539             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1062 r_free = 0.1539             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1539   ksol= 0.32   Bsol= 45.54   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.76,-1.28,-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: 5.111702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1539   ksol= 0.32   Bsol= 47.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.54,-1.02,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.436331              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.591  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.118692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.665  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1060      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7311 = 1.44 * 0.50 * 5.1062 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7314 = 1.44 * 0.50 * 5.1238 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8651 = 2.12 * 1.00 * 5.1238 + 1.00 * 0.0095                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8750 = 2.12 * 1.00 * 5.1283 + 1.00 * 0.0099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.49   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    92.49   16.66    None  None   None       |
|    Sol.    : 438    0      5.18    77.40   39.35    None  None   None       |
|    Mac.    : 2385   0      0.00    92.49   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.249:  963   |   5:    46.243 -  55.491:   94        |
|      1:     9.249 -  18.497: 1177   |   6:    55.491 -  64.740:   66        |
|      2:    18.497 -  27.746:  233   |   7:    64.740 -  73.988:   20        |
|      3:    27.746 -  36.994:  136   |   8:    73.988 -  83.237:    4        |
|      4:    36.994 -  46.243:  126   |   9:    83.237 -  92.485:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1560             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1560             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1560   ksol= 0.32   Bsol= 47.23   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-1.54,-1.02,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1389  154 0.0981 0.1270      5.3774      5.5132|
|  2:  4.7255 -  3.7710 0.99   1329  150 0.0840 0.1075      5.4234      5.6097|
|  3:  3.7710 -  3.3002 0.99   1314  149 0.1022 0.1487      5.4505      5.8444|
|  4:  3.3002 -  3.0012 0.99   1303  133 0.1173 0.1545      5.4328      5.6084|
|  5:  3.0012 -  2.7876 0.99   1286  148 0.1255 0.1637      5.3031      5.4954|
|  6:  2.7876 -  2.6242 0.98   1282  143 0.1206 0.1913      5.2029      5.4524|
|  7:  2.6242 -  2.4934 0.99   1292  146 0.1178 0.1621      5.1303      5.3249|
|  8:  2.4934 -  2.3853 0.98   1275  137 0.1118 0.1734      5.0608      5.3508|
|  9:  2.3853 -  2.2938 0.98   1271  146 0.1143 0.1824      5.0059      5.3213|
| 10:  2.2938 -  2.2150 0.97   1245  136 0.1100 0.1622       4.962      5.1446|
| 11:  2.2150 -  2.1459 0.99   1276  144 0.1114 0.1770       4.921      5.2775|
| 12:  2.1459 -  2.0847 0.98   1275  141 0.1077 0.1637      4.8562      5.1445|
| 13:  2.0847 -  2.0300 0.97   1256  134 0.1113 0.1671      4.7916      5.0284|
| 14:  2.0300 -  1.9806 0.67    837   98 0.1062 0.1908      4.7126      5.0094|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8647 -  4.7255  1389   154  0.94   9.09   0.97     0.95       7046.56|
|  2:  4.7255 -  3.7710  1329   150  0.95   7.88   1.01     1.00       8689.19|
|  3:  3.7710 -  3.3002  1314   149  0.94  10.83   1.03     1.02       9980.96|
|  4:  3.3002 -  3.0012  1303   133  0.92  13.15   1.01     1.00      10020.42|
|  5:  3.0012 -  2.7876  1286   148  0.90  15.55   1.00     0.96       8051.15|
|  6:  2.7876 -  2.6242  1282   143  0.90  15.96   0.98     0.95       6957.17|
|  7:  2.6242 -  2.4934  1292   146  0.91  15.04   0.98     0.96       5869.10|
|  8:  2.4934 -  2.3853  1275   137  0.91  14.66   0.99     0.97       5316.61|
|  9:  2.3853 -  2.2938  1271   146  0.91  15.44   0.99     0.96       4805.13|
| 10:  2.2938 -  2.2150  1245   136  0.90  15.59   0.99     0.95       4460.70|
| 11:  2.2150 -  2.1459  1276   144  0.91  15.50   0.99     0.95       4213.38|
| 12:  2.1459 -  2.0847  1275   141  0.91  14.96   1.00     0.98       3815.45|
| 13:  2.0847 -  2.0300  1256   134  0.90  15.96   0.99     0.98       3410.51|
| 14:  2.0300 -  1.9806   837    98  0.91  15.49   0.97     0.92       2840.19|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2840.19 max =        10020.42 mean =      6222.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.84|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1560   ksol= 0.32   Bsol= 47.48   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.36,-0.81,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1560   ksol= 0.32   Bsol= 47.48   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.36,-0.81,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131242                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1389  154 0.0982 0.1272      5.3785      5.5146|
|  2:  4.7255 -  3.7710 0.99   1329  150 0.0841 0.1075       5.424      5.6098|
|  3:  3.7710 -  3.3002 0.99   1314  149 0.1023 0.1487      5.4505      5.8446|
|  4:  3.3002 -  3.0012 0.99   1303  133 0.1173 0.1545      5.4326      5.6084|
|  5:  3.0012 -  2.7876 0.99   1286  148 0.1255 0.1637      5.3029      5.4952|
|  6:  2.7876 -  2.6242 0.98   1282  143 0.1205 0.1912      5.2027      5.4521|
|  7:  2.6242 -  2.4934 0.99   1292  146 0.1178 0.1621      5.1302       5.325|
|  8:  2.4934 -  2.3853 0.98   1275  137 0.1118 0.1733      5.0608      5.3505|
|  9:  2.3853 -  2.2938 0.98   1271  146 0.1143 0.1824       5.006      5.3214|
| 10:  2.2938 -  2.2150 0.97   1245  136 0.1100 0.1622      4.9621      5.1448|
| 11:  2.2150 -  2.1459 0.99   1276  144 0.1114 0.1770      4.9211      5.2775|
| 12:  2.1459 -  2.0847 0.98   1275  141 0.1077 0.1637      4.8561      5.1446|
| 13:  2.0847 -  2.0300 0.97   1256  134 0.1113 0.1671      4.7915      5.0282|
| 14:  2.0300 -  1.9806 0.67    837   98 0.1062 0.1908      4.7126      5.0093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8647 -  4.7255  1389   154  0.94   9.10   0.98     0.95       7062.86|
|  2:  4.7255 -  3.7710  1329   150  0.95   7.89   1.02     1.00       8698.85|
|  3:  3.7710 -  3.3002  1314   149  0.94  10.83   1.03     1.03       9982.30|
|  4:  3.3002 -  3.0012  1303   133  0.92  13.15   1.01     1.00      10018.64|
|  5:  3.0012 -  2.7876  1286   148  0.90  15.55   1.00     0.97       8047.53|
|  6:  2.7876 -  2.6242  1282   143  0.90  15.96   0.99     0.96       6953.86|
|  7:  2.6242 -  2.4934  1292   146  0.91  15.04   0.99     0.97       5866.81|
|  8:  2.4934 -  2.3853  1275   137  0.91  14.66   1.00     0.97       5315.73|
|  9:  2.3853 -  2.2938  1271   146  0.91  15.44   1.00     0.97       4805.20|
| 10:  2.2938 -  2.2150  1245   136  0.90  15.60   1.00     0.96       4461.00|
| 11:  2.2150 -  2.1459  1276   144  0.91  15.50   1.00     0.96       4213.57|
| 12:  2.1459 -  2.0847  1275   141  0.91  14.96   1.01     0.99       3814.71|
| 13:  2.0847 -  2.0300  1256   134  0.90  15.96   1.00     0.99       3409.63|
| 14:  2.0300 -  1.9806   837    98  0.91  15.49   0.98     0.93       2839.63|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2839.63 max =        10018.64 mean =      6223.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.84|
|phase err.(test): min =        0.00 max =           89.76 mean =        13.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.824)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.49   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    92.49   16.67    None  None   None       |
|    Sol.    : 438    0      5.18    77.41   39.35    None  None   None       |
|    Mac.    : 2385   0      0.00    92.49   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.252:  963   |   5:    46.246 -  55.494:   94        |
|      1:     9.252 -  18.500: 1177   |   6:    55.494 -  64.743:   66        |
|      2:    18.500 -  27.749:  233   |   7:    64.743 -  73.991:   20        |
|      3:    27.749 -  36.997:  136   |   8:    73.991 -  83.240:    4        |
|      4:    36.997 -  46.246:  126   |   9:    83.240 -  92.488:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 274         
Filter by distance & map next to the model:
   mapped sites are within: 0.570 - 4.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 274
   mapped sites are within: 0.730 - 4.636

peak=    5.681 closest distance to " CB  ARG A 275 " =    0.952
peak=    5.637 closest distance to " CB  GLN A 223 " =    1.395
peak=    5.056 closest distance to " NH2 ARG A  56 " =    2.292
peak=    5.036 closest distance to " CG  PRO A 213 " =    1.246
peak=    4.878 closest distance to " CG  PRO A  90 " =    1.195
peak=    4.869 closest distance to " O   HOH Z 232 " =    2.362
peak=    4.819 closest distance to " CB  SER A  63 " =    1.156
peak=    4.808 closest distance to " CA  TYR A  30 " =    0.913
peak=    4.761 closest distance to " CG  PRO A 198 " =    1.224
peak=    4.733 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.686 closest distance to " O   HOH Z 142 " =    1.617
peak=    4.682 closest distance to " O   HOH Z 126 " =    1.835
peak=    4.650 closest distance to " O   HOH Z 298 " =    1.847
peak=    4.593 closest distance to " C   PRO A 198 " =    1.461
peak=    4.548 closest distance to " CB  TYR A 169 " =    0.795
peak=    4.537 closest distance to " CB  GLU A 152 " =    1.136
peak=    4.371 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.357 closest distance to " O   HOH Z 403 " =    1.754
peak=    4.345 closest distance to " O   HOH Z 272 " =    1.876
peak=    4.332 closest distance to " NZ  LYS A 117 " =    3.230
peak=    4.300 closest distance to " CB  ARG A  79 " =    1.302
peak=    4.289 closest distance to " O   HOH Z 234 " =    3.685
peak=    4.286 closest distance to " CB  ARG A 190 " =    1.718
peak=    4.282 closest distance to " O   HOH Z 209 " =    2.224
peak=    4.282 closest distance to " O   HOH Z  78 " =    1.661
peak=    4.262 closest distance to " O   HOH Z 287 " =    2.078
peak=    4.250 closest distance to " CG  PRO A 243 " =    1.074
peak=    4.230 closest distance to " NE2 GLN A  11 " =    1.003
peak=    4.191 closest distance to " O   HOH Z 402 " =    1.454
peak=    4.158 closest distance to " CA  ALA A  21 " =    1.235
peak=    4.135 closest distance to " CA  ASN A 176 " =    1.144
peak=    4.124 closest distance to " O   HOH Z  15 " =    2.117
peak=    4.102 closest distance to " O   HOH Z  43 " =    2.039
peak=    4.087 closest distance to " O   HOH Z 427 " =    2.960
peak=    4.087 closest distance to " O   HOH Z 193 " =    1.811
peak=    4.085 closest distance to " CG1 ILE A  33 " =    1.239
peak=    4.080 closest distance to " CZ  PHE A 218 " =    1.068
peak=    4.079 closest distance to " O   HOH Z  59 " =    2.296
peak=    4.075 closest distance to " CD  ARG A 269 " =    1.043
peak=    4.073 closest distance to " O   HOH Z 369 " =    2.386
peak=    4.069 closest distance to " CA  ARG A  36 " =    1.078
peak=    4.067 closest distance to " O   HOH Z 316 " =    3.052
peak=    4.067 closest distance to " CB  GLU A 128 " =    1.124
peak=    4.058 closest distance to " CB  VAL A 265 " =    1.230
peak=    4.058 closest distance to " O   HOH Z  97 " =    1.961
peak=    4.046 closest distance to " O   HOH Z 158 " =    3.010
peak=    4.042 closest distance to " OD1 ASN A  69 " =    2.491
peak=    4.042 closest distance to " O   HOH Z 250 " =    1.444
peak=    4.033 closest distance to " CB  LEU A 228 " =    1.093
peak=    4.030 closest distance to " CG  ARG A  66 " =    2.560
peak=    4.029 closest distance to " CG2 ILE A 120 " =    1.110
peak=    3.999 closest distance to " O   SER A  87 " =    2.213
peak=    3.967 closest distance to " O   HOH Z 203 " =    1.796
peak=    3.964 closest distance to " O   HOH Z 303 " =    2.093
peak=    3.955 closest distance to " O   HOH Z 261 " =    2.028
peak=    3.951 closest distance to " NH2BARG A 145 " =    2.144
peak=    3.935 closest distance to " O   HOH Z 189 " =    2.213
peak=    3.927 closest distance to " CG1BVAL A  72 " =    1.660
peak=    3.925 closest distance to " O   HOH Z 389 " =    1.902
peak=    3.924 closest distance to " CB  SER A   3 " =    1.274
peak=    3.923 closest distance to " CD2 TRP A 179 " =    1.395
peak=    3.911 closest distance to " O   HOH Z 289 " =    1.728
peak=    3.908 closest distance to " O   HOH Z  40 " =    1.869
peak=    3.908 closest distance to " CB  ARG A  79 " =    0.886
peak=    3.895 closest distance to " O   HOH Z 368 " =    2.023
peak=    3.887 closest distance to " CB  GLU A 277 " =    3.586
peak=    3.887 closest distance to " OD2 ASP A 298 " =    3.894
peak=    3.878 closest distance to " CD2 LEU A 297 " =    0.865
peak=    3.864 closest distance to " ND2 ASN A 187 " =    1.462
peak=    3.861 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.833 closest distance to " O   HOH Z  44 " =    1.896
peak=    3.820 closest distance to " O   HOH Z 141 " =    1.770
peak=    3.811 closest distance to " O   HOH Z 280 " =    2.943
peak=    3.809 closest distance to " O   HOH Z  19 " =    1.985
peak=    3.793 closest distance to " CA  ASN A 215 " =    1.148
peak=    3.787 closest distance to " N   ASN A  39 " =    1.289
peak=    3.780 closest distance to " O   HOH Z 265 " =    2.343
peak=    3.763 closest distance to " O   HOH Z 371 " =    3.337
peak=    3.761 closest distance to " O   HOH Z  97 " =    2.448
peak=    3.755 closest distance to " CA  ARG A 195 " =    1.261
peak=    3.753 closest distance to " OD2 ASP A 286 " =    2.825
peak=    3.749 closest distance to " CB  TRP A 266 " =    0.971
peak=    3.743 closest distance to " CE  LYS A  76 " =    0.860
peak=    3.732 closest distance to " O   HOH Z 128 " =    1.983
peak=    3.722 closest distance to " CB  TRP A 179 " =    1.246
peak=    3.715 closest distance to " O   HOH Z 421 " =    1.697
peak=    3.714 closest distance to " O   HOH Z 423 " =    1.975
peak=    3.712 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.707 closest distance to " CB  ALA A 291 " =    1.304
peak=    3.702 closest distance to " O   HOH Z 344 " =    3.183
peak=    3.702 closest distance to " O   HOH Z 357 " =    1.919
peak=    3.683 closest distance to " O   HOH Z 183 " =    1.425
peak=    3.682 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.674 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.670 closest distance to " O   HOH Z 245 " =    1.314
peak=    3.669 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.664 closest distance to " CB  ASP A 140 " =    0.933
peak=    3.662 closest distance to " CA  ASP A 140 " =    1.131
peak=    3.653 closest distance to " O   HOH Z  61 " =    1.565
peak=    3.647 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.642 closest distance to " O   HOH Z 426 " =    1.537
peak=    3.638 closest distance to " O   HOH Z 185 " =    1.712
peak=    3.633 closest distance to " CB  ASN A  39 " =    0.870
peak=    3.632 closest distance to " O   HOH Z 383 " =    1.977
peak=    3.621 closest distance to " CB  TYR A 169 " =    0.834
peak=    3.611 closest distance to " CA  ALA A 160 " =    0.857
peak=    3.609 closest distance to " O   HOH Z 132 " =    2.546
peak=    3.606 closest distance to " O   HOH Z 392 " =    2.766
peak=    3.598 closest distance to " O   HOH Z 416 " =    2.850
peak=    3.596 closest distance to " CA  LYS A 117 " =    1.272
peak=    3.591 closest distance to " O   HOH Z 279 " =    2.127
peak=    3.589 closest distance to " CA  THR A 221 " =    0.953
peak=    3.589 closest distance to " O   HOH Z 132 " =    2.732
peak=    3.588 closest distance to " O   HOH Z  66 " =    2.094
peak=    3.586 closest distance to " O   HOH Z 214 " =    2.191
peak=    3.582 closest distance to " OG BSER A 164 " =    2.277
peak=    3.577 closest distance to " CB  SER A  62 " =    0.908
peak=    3.573 closest distance to " O   HOH Z 345 " =    3.072
peak=    3.571 closest distance to " O   HOH Z 108 " =    2.653
peak=    3.553 closest distance to " O   HOH Z 361 " =    3.660
peak=    3.551 closest distance to " NE2 GLN A  77 " =    3.206
peak=    3.547 closest distance to " CB  ALA A 248 " =    1.338
peak=    3.541 closest distance to " CD1 LEU A 300 " =    1.253
peak=    3.539 closest distance to " C   ILE A 106 " =    1.905
peak=    3.538 closest distance to " O   HOH Z  21 " =    1.788
peak=    3.533 closest distance to " CB  SER A 141 " =    1.023
peak=    3.532 closest distance to " O   HOH Z 411 " =    3.743
peak=    3.526 closest distance to " CA  GLY A  80 " =    0.934
peak=    3.524 closest distance to " CA  ALA A  51 " =    0.892
peak=    3.523 closest distance to " CB  ARG A 139 " =    0.818
peak=    3.520 closest distance to " O   HOH Z 227 " =    1.627
peak=    3.519 closest distance to " CG2 ILE A  20 " =    1.357
peak=    3.517 closest distance to " O   HOH Z 325 " =    2.375
peak=    3.499 closest distance to " CA  MET A 105 " =    1.057
peak=    3.495 closest distance to " N   ARG A 156 " =    1.388
peak=    3.494 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.493 closest distance to " OE1 GLU A   2 " =    2.263
peak=    3.492 closest distance to " CB  VAL A 202 " =    1.490
peak=    3.480 closest distance to " O   HOH Z 148 " =    3.269
peak=    3.478 closest distance to " CB  SER A  26 " =    1.696
peak=    3.475 closest distance to " O   HOH Z 126 " =    1.600
peak=    3.475 closest distance to " O   TRP A 274 " =    1.945
peak=    3.473 closest distance to " O   HOH Z 327 " =    1.640
peak=    3.468 closest distance to " O   HOH Z 247 " =    1.357
peak=    3.467 closest distance to " NH2 ARG A 156 " =    1.159
peak=    3.464 closest distance to " CB  ILE A 120 " =    1.258
peak=    3.464 closest distance to " CG  GLN A  58 " =    2.675
peak=    3.459 closest distance to " O   HOH Z 305 " =    3.639
peak=    3.457 closest distance to " CB  MET A  47 " =    0.923
peak=    3.440 closest distance to " CZ2 TRP A 179 " =    1.688
peak=    3.437 closest distance to " O   HOH Z 173 " =    1.973
peak=    3.436 closest distance to " O   HOH Z 425 " =    1.974
peak=    3.432 closest distance to " CD1 LEU A  96 " =    0.730
peak=    3.432 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.428 closest distance to " CA  ALA A 291 " =    0.801
peak=    3.413 closest distance to " CD BLYS A 290 " =    1.058
peak=    3.410 closest distance to " CG AARG A 275 " =    1.141
peak=    3.406 closest distance to " O   HOH Z 337 " =    3.645
peak=    3.398 closest distance to " O   HOH Z  35 " =    2.413
peak=    3.389 closest distance to " CG2 THR A 221 " =    1.196
peak=    3.388 closest distance to " CA  ASP A 162 " =    1.084
peak=    3.375 closest distance to " O   HOH Z 128 " =    2.194
peak=    3.370 closest distance to " O   HOH Z 124 " =    2.099
peak=    3.363 closest distance to " O   HOH Z  63 " =    1.953
peak=    3.360 closest distance to " CB  SER A 273 " =    0.874
peak=    3.358 closest distance to " O   HOH Z 298 " =    2.389
peak=    3.358 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.352 closest distance to " O   HOH Z 359 " =    1.372
peak=    3.345 closest distance to " CB  THR A  31 " =    1.691
peak=    3.342 closest distance to " CG2 VAL A 197 " =    1.150
peak=    3.339 closest distance to " CD2 HIS A  81 " =    1.122
peak=    3.339 closest distance to " CD1 ILE A 106 " =    0.875
peak=    3.333 closest distance to " CA  ALA A  84 " =    1.207
peak=    3.332 closest distance to " CG1 ILE A 151 " =    0.996
peak=    3.320 closest distance to " O   ALA A 165 " =    1.475
peak=    3.319 closest distance to " O   HOH Z 406 " =    1.519
peak=    3.317 closest distance to " CB  ALA A  34 " =    0.926
peak=    3.313 closest distance to " O   HOH Z 227 " =    2.179
peak=    3.313 closest distance to " O   HOH Z 391 " =    2.977
peak=    3.312 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.311 closest distance to " O   HOH Z  10 " =    1.731
peak=    3.309 closest distance to " O   HOH Z  88 " =    3.116
peak=    3.305 closest distance to " N   TYR A 116 " =    1.545
peak=    3.305 closest distance to " NZ  LYS A 166 " =    2.989
peak=    3.302 closest distance to " CB  SER A 212 " =    1.037
peak=    3.300 closest distance to " O   HOH Z 417 " =    2.982
peak=    3.291 closest distance to " O   HOH Z 336 " =    1.661
peak=    3.291 closest distance to " O   THR A 251 " =    1.107
peak=    3.290 closest distance to " O   HOH Z 403 " =    1.303
peak=    3.289 closest distance to " CB  ASN A 215 " =    1.158
peak=    3.289 closest distance to " CG1 VAL A 153 " =    0.950
peak=    3.283 closest distance to " ND1 HIS A  81 " =    1.576
peak=    3.282 closest distance to " O   THR A 220 " =    1.233
peak=    3.281 closest distance to " OG1 THR A 294 " =    2.358
peak=    3.280 closest distance to " CG  ARG A  66 " =    0.972
peak=    3.276 closest distance to " O   HOH Z 273 " =    2.837
peak=    3.275 closest distance to " CE  LYS A  48 " =    1.082
peak=    3.272 closest distance to " O   HOH Z 435 " =    1.884
peak=    3.271 closest distance to " O   HOH Z  64 " =    2.189
peak=    3.268 closest distance to " C   SER A  32 " =    1.093
peak=    3.266 closest distance to " CD2 TYR A  30 " =    1.049
peak=    3.265 closest distance to " O   HOH Z  61 " =    1.476
peak=    3.262 closest distance to " CE1 HIS A 108 " =    1.121
peak=    3.259 closest distance to " CA  ASN A 217 " =    1.251
peak=    3.255 closest distance to " O   ASN A  74 " =    1.487
peak=    3.255 closest distance to " C   TYR A 214 " =    1.426
peak=    3.251 closest distance to " CB  HIS A 108 " =    0.842
peak=    3.247 closest distance to " O   HOH Z 299 " =    4.404
peak=    3.243 closest distance to " C   PHE A  59 " =    0.794
peak=    3.241 closest distance to " CB  PHE A  16 " =    1.005
peak=    3.238 closest distance to " CA  MET A  40 " =    1.057
peak=    3.238 closest distance to " O   HOH Z 365 " =    2.888
peak=    3.237 closest distance to " CG2BVAL A  41 " =    0.825
peak=    3.235 closest distance to " O   HOH Z 250 " =    1.595
peak=    3.234 closest distance to " CD  LYS A 119 " =    1.219
peak=    3.234 closest distance to " O   HOH Z  80 " =    1.614
peak=    3.230 closest distance to " O   HOH Z 171 " =    1.858
peak=    3.230 closest distance to " O   HOH Z 281 " =    4.636
peak=    3.225 closest distance to " O   HOH Z 393 " =    3.305
peak=    3.224 closest distance to " O   HOH Z 298 " =    2.722
peak=    3.222 closest distance to " CB  ARG A 269 " =    0.757
peak=    3.221 closest distance to " CB  GLU A  46 " =    1.010
peak=    3.220 closest distance to " CA  VAL A  41 " =    0.946
peak=    3.218 closest distance to " CG2 VAL A 202 " =    1.150
peak=    3.216 closest distance to " CB  GLN A 278 " =    0.876
peak=    3.214 closest distance to " CB  GLN A 103 " =    0.818
peak=    3.212 closest distance to " O   HOH Z 214 " =    2.428
peak=    3.210 closest distance to " CG2AVAL A 121 " =    2.208
peak=    3.210 closest distance to " O   HOH Z 193 " =    2.130
peak=    3.209 closest distance to " OG  SER A  62 " =    2.770
peak=    3.203 closest distance to " ND2 ASN A 110 " =    1.632
peak=    3.201 closest distance to " CB  ALA A 114 " =    1.062
peak=    3.200 closest distance to " O   HOH Z 163 " =    1.890
peak=    3.197 closest distance to " NE2 GLN A  58 " =    2.803
peak=    3.195 closest distance to " O   HOH Z 152 " =    1.949
peak=    3.193 closest distance to " O   HOH Z 134 " =    1.200
peak=    3.192 closest distance to " O   HOH Z  49 " =    2.130
peak=    3.191 closest distance to " O   HOH Z  68 " =    1.669
peak=    3.190 closest distance to " O   HOH Z 163 " =    1.461
peak=    3.185 closest distance to " O   HOH Z 135 " =    1.635
peak=    3.183 closest distance to " CD1AILE A 234 " =    0.930
peak=    3.177 closest distance to " CG  GLN A  77 " =    2.199
peak=    3.175 closest distance to " O   HOH Z 374 " =    2.605
peak=    3.170 closest distance to " CB  SER A 216 " =    0.828
peak=    3.168 closest distance to " O   HOH Z 380 " =    1.907
peak=    3.167 closest distance to " CG  MET A 185 " =    1.148
peak=    3.164 closest distance to " O   HOH Z 423 " =    3.379
peak=    3.163 closest distance to " O   HOH Z 313 " =    1.872
peak=    3.160 closest distance to " CG  LEU A 167 " =    1.148
peak=    3.151 closest distance to " OH  TYR A  30 " =    1.051
peak=    3.148 closest distance to " CE  LYS A 119 " =    1.121
peak=    3.147 closest distance to " CA  ASP A 191 " =    1.224
peak=    3.144 closest distance to " CB  ASN A 110 " =    1.105
peak=    3.141 closest distance to " O   HOH Z 257 " =    2.295
peak=    3.135 closest distance to " O   HOH Z 417 " =    2.132
peak=    3.132 closest distance to " CG  LYS A  76 " =    0.984
peak=    3.127 closest distance to " O   ASP A 238 " =    0.777
peak=    3.125 closest distance to " CB  TYR A 116 " =    0.767
peak=    3.121 closest distance to " O   HOH Z 271 " =    2.187
peak=    3.114 closest distance to " OH  TYR A 116 " =    1.013
peak=    3.114 closest distance to " O   HOH Z 353 " =    2.724
peak=    3.104 closest distance to " O   ILE A  33 " =    1.357
peak=    3.100 closest distance to " CA  TYR A 116 " =    1.426
peak=    3.098 closest distance to " OD1 ASP A 238 " =    1.002
peak=    3.093 closest distance to " CG  ARG A 219 " =    1.141
peak=    3.083 closest distance to " CA  THR A 264 " =    0.909
peak=    3.076 closest distance to " O   HOH Z  88 " =    2.605
peak=    3.075 closest distance to " O   HOH Z 329 " =    3.833
peak=    3.057 closest distance to " CA  ALA A 295 " =    1.120
peak=    3.032 closest distance to " O   HOH Z 310 " =    3.604
peak=    2.889 closest distance to " O   HOH Z   9 " =    2.156

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.873 - 5.738
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 207
   mapped sites are within: 0.873 - 5.738

peak=   -4.951 closest distance to " O   HOH Z 266 " =    4.823
peak=   -4.562 closest distance to " C   HIS A 108 " =    1.083
peak=   -4.433 closest distance to " CD  GLN A  58 " =    1.113
peak=   -4.326 closest distance to " SG  CYS A 254 " =    3.403
peak=   -4.303 closest distance to " O   VAL A  67 " =    2.645
peak=   -4.291 closest distance to " CB  PRO A 243 " =    2.646
peak=   -4.228 closest distance to " CD  ARG A 156 " =    2.070
peak=   -4.185 closest distance to " CG  GLN A 223 " =    1.827
peak=   -4.181 closest distance to " OXT GLY A 302 " =    2.771
peak=   -4.135 closest distance to " O   ILE A 109 " =    2.594
peak=   -4.117 closest distance to " O   HOH Z 372 " =    2.310
peak=   -4.104 closest distance to " O   HOH Z 377 " =    2.039
peak=   -4.060 closest distance to " OG BSER A 134 " =    1.256
peak=   -4.033 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -4.023 closest distance to " O   HOH Z  13 " =    1.622
peak=   -3.985 closest distance to " O   HOH Z 198 " =    1.989
peak=   -3.955 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.935 closest distance to " O   HOH Z 231 " =    2.322
peak=   -3.922 closest distance to " O   HOH Z 196 " =    1.956
peak=   -3.918 closest distance to " CG  ASP A 132 " =    2.345
peak=   -3.908 closest distance to " CZ3 TRP A 179 " =    1.258
peak=   -3.907 closest distance to " O   HOH Z 353 " =    2.190
peak=   -3.907 closest distance to " ND2 ASN A  45 " =    1.020
peak=   -3.882 closest distance to " O   HOH Z 389 " =    1.788
peak=   -3.881 closest distance to " O   HOH Z 114 " =    3.234
peak=   -3.863 closest distance to " O   HOH Z 407 " =    2.894
peak=   -3.849 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.844 closest distance to " O   PRO A 163 " =    2.097
peak=   -3.830 closest distance to " CB  ASN A  39 " =    2.318
peak=   -3.829 closest distance to " N   ALA A  43 " =    2.639
peak=   -3.827 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.821 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.792 closest distance to " CG1 VAL A 112 " =    2.803
peak=   -3.772 closest distance to " O   HOH Z 292 " =    4.516
peak=   -3.749 closest distance to " CB  TYR A  15 " =    2.230
peak=   -3.735 closest distance to " O   HOH Z 126 " =    1.918
peak=   -3.734 closest distance to " CA  VAL A  67 " =    2.922
peak=   -3.720 closest distance to " O   HOH Z  10 " =    1.534
peak=   -3.717 closest distance to " O   HOH Z 166 " =    1.575
peak=   -3.716 closest distance to " O   HOH Z 290 " =    1.121
peak=   -3.712 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.710 closest distance to " O   HOH Z   6 " =    2.121
peak=   -3.698 closest distance to " O   HOH Z 351 " =    1.481
peak=   -3.698 closest distance to " O   PHE A 218 " =    1.575
peak=   -3.696 closest distance to " ND2 ASN A  45 " =    1.484
peak=   -3.690 closest distance to " O   HOH Z  52 " =    1.398
peak=   -3.688 closest distance to " O   HOH Z 166 " =    1.838
peak=   -3.687 closest distance to " CG2 ILE A 263 " =    2.283
peak=   -3.674 closest distance to " CD1 LEU A 228 " =    2.122
peak=   -3.673 closest distance to " N   GLN A  58 " =    1.512
peak=   -3.669 closest distance to " O   SER A 210 " =    1.960
peak=   -3.660 closest distance to " CD1 LEU A 101 " =    2.384
peak=   -3.660 closest distance to " CG  ASP A 231 " =    0.873
peak=   -3.659 closest distance to " CB  PHE A 192 " =    2.037
peak=   -3.656 closest distance to " OG  SER A   3 " =    1.693
peak=   -3.622 closest distance to " O   ALA A 256 " =    1.568
peak=   -3.619 closest distance to " CD  ARG A 139 " =    1.532
peak=   -3.611 closest distance to " CA  GLY A 203 " =    2.377
peak=   -3.608 closest distance to " CD  ARG A 195 " =    5.143
peak=   -3.602 closest distance to " CZ  PHE A  59 " =    1.625
peak=   -3.597 closest distance to " CB  ALA A 248 " =    2.235
peak=   -3.575 closest distance to " CD1 PHE A  59 " =    1.929
peak=   -3.563 closest distance to " ND2 ASN A 187 " =    1.498
peak=   -3.546 closest distance to " O   HOH Z 435 " =    2.746
peak=   -3.546 closest distance to " CG1 VAL A  78 " =    2.911
peak=   -3.543 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.542 closest distance to " N   ALA A 248 " =    1.640
peak=   -3.531 closest distance to " CG1 VAL A 112 " =    2.856
peak=   -3.530 closest distance to " CZ  TYR A 169 " =    1.810
peak=   -3.527 closest distance to " O   HOH Z 283 " =    2.181
peak=   -3.523 closest distance to " O   HOH Z  44 " =    2.202
peak=   -3.520 closest distance to " N   THR A  52 " =    1.684
peak=   -3.510 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.495 closest distance to " O   TRP A  92 " =    1.771
peak=   -3.486 closest distance to " CB  PHE A 208 " =    2.252
peak=   -3.485 closest distance to " OD2 ASP A 171 " =    2.432
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.132
peak=   -3.478 closest distance to " OG  SER A  62 " =    1.679
peak=   -3.478 closest distance to " CB  GLN A  11 " =    1.800
peak=   -3.477 closest distance to " NE2 GLN A  88 " =    1.799
peak=   -3.475 closest distance to " O   HOH Z 252 " =    3.742
peak=   -3.471 closest distance to " NH2 ARG A  66 " =    5.406
peak=   -3.470 closest distance to " OD1 ASN A 148 " =    1.519
peak=   -3.456 closest distance to " CD2 LEU A 300 " =    2.944
peak=   -3.446 closest distance to " C   LEU A 143 " =    1.018
peak=   -3.438 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.437 closest distance to " O   HOH Z 369 " =    2.247
peak=   -3.434 closest distance to " N   ALA A 226 " =    1.996
peak=   -3.431 closest distance to " O   ALA A  34 " =    2.284
peak=   -3.426 closest distance to " NH1 ARG A 195 " =    2.614
peak=   -3.426 closest distance to " OD2 ASP A 191 " =    1.485
peak=   -3.424 closest distance to " CE1 TYR A 247 " =    2.645
peak=   -3.417 closest distance to " O   HOH Z 243 " =    2.112
peak=   -3.416 closest distance to " O   HOH Z 234 " =    4.069
peak=   -3.413 closest distance to " O   HOH Z  43 " =    1.641
peak=   -3.411 closest distance to " OG BSER A 134 " =    1.795
peak=   -3.397 closest distance to " CG  PRO A 243 " =    1.714
peak=   -3.396 closest distance to " CE  MET A 105 " =    2.111
peak=   -3.395 closest distance to " CD2 PHE A  61 " =    2.561
peak=   -3.384 closest distance to " CB  ALA A 291 " =    2.332
peak=   -3.383 closest distance to " O   HOH Z  71 " =    1.805
peak=   -3.379 closest distance to " CB  ASP A 286 " =    1.891
peak=   -3.370 closest distance to " CB  ALA A 248 " =    2.037
peak=   -3.367 closest distance to " OG BSER A 210 " =    2.053
peak=   -3.364 closest distance to " O   GLY A  80 " =    2.602
peak=   -3.363 closest distance to " CG1 VAL A 250 " =    2.620
peak=   -3.355 closest distance to " CB  ALA A  43 " =    2.550
peak=   -3.354 closest distance to " CD1 ILE A 239 " =    2.231
peak=   -3.348 closest distance to " O   MET A  40 " =    2.670
peak=   -3.344 closest distance to " O   HOH Z 102 " =    1.548
peak=   -3.344 closest distance to " O   ALA A 160 " =    1.470
peak=   -3.337 closest distance to " O   GLY A 196 " =    1.042
peak=   -3.334 closest distance to " CA  GLY A 133 " =    2.333
peak=   -3.333 closest distance to " O   HOH Z 311 " =    3.578
peak=   -3.322 closest distance to " O   HOH Z 171 " =    1.976
peak=   -3.322 closest distance to " O   HOH Z 377 " =    1.813
peak=   -3.320 closest distance to " N   THR A 235 " =    1.350
peak=   -3.320 closest distance to " C   THR A 279 " =    1.104
peak=   -3.318 closest distance to " NH2 ARG A  79 " =    2.073
peak=   -3.318 closest distance to " O   HOH Z  37 " =    1.780
peak=   -3.316 closest distance to " O   LEU A 167 " =    1.446
peak=   -3.306 closest distance to " CB  CYS A 201 " =    2.593
peak=   -3.305 closest distance to " O   HOH Z 250 " =    1.388
peak=   -3.290 closest distance to " O   SER A 135 " =    1.503
peak=   -3.289 closest distance to " O   ALA A  10 " =    1.743
peak=   -3.288 closest distance to " O   HOH Z  38 " =    1.590
peak=   -3.286 closest distance to " O   HOH Z 414 " =    1.612
peak=   -3.283 closest distance to " O   HOH Z  11 " =    1.738
peak=   -3.282 closest distance to " O   HOH Z  93 " =    1.972
peak=   -3.282 closest distance to " CG1 VAL A 125 " =    2.302
peak=   -3.281 closest distance to " CZ2 TRP A 274 " =    1.053
peak=   -3.281 closest distance to " O   VAL A 174 " =    2.083
peak=   -3.280 closest distance to " O   VAL A 189 " =    1.711
peak=   -3.279 closest distance to " O   HOH Z 377 " =    1.753
peak=   -3.277 closest distance to " CG  PHE A 283 " =    2.558
peak=   -3.277 closest distance to " O   SER A  95 " =    1.595
peak=   -3.276 closest distance to " O   HOH Z 298 " =    1.304
peak=   -3.276 closest distance to " CE  MET A  93 " =    1.224
peak=   -3.266 closest distance to " O   ALA A 161 " =    1.635
peak=   -3.265 closest distance to " OE2 GLU A   2 " =    1.818
peak=   -3.264 closest distance to " O   HOH Z 322 " =    1.679
peak=   -3.261 closest distance to " O   HOH Z   6 " =    1.687
peak=   -3.256 closest distance to " O   GLY A  80 " =    2.389
peak=   -3.253 closest distance to " CD2 LEU A 237 " =    2.547
peak=   -3.249 closest distance to " CZ  PHE A 130 " =    0.977
peak=   -3.248 closest distance to " O   HOH Z 422 " =    1.513
peak=   -3.247 closest distance to " ND2 ASN A  69 " =    1.605
peak=   -3.245 closest distance to " O   HOH Z 211 " =    1.721
peak=   -3.239 closest distance to " SG ACYS A 201 " =    2.042
peak=   -3.237 closest distance to " CE3 TRP A 150 " =    2.165
peak=   -3.236 closest distance to " CA  GLY A 133 " =    1.933
peak=   -3.231 closest distance to " O   VAL A 189 " =    2.615
peak=   -3.230 closest distance to " CD  GLU A 236 " =    1.060
peak=   -3.230 closest distance to " CG  MET A 105 " =    0.929
peak=   -3.228 closest distance to " OD1 ASP A 171 " =    1.531
peak=   -3.226 closest distance to " O   HOH Z 191 " =    5.738
peak=   -3.218 closest distance to " CG  PRO A 280 " =    2.346
peak=   -3.213 closest distance to " O   HOH Z  41 " =    2.292
peak=   -3.211 closest distance to " CG  GLU A  53 " =    1.376
peak=   -3.210 closest distance to " OD1 ASP A 191 " =    1.605
peak=   -3.209 closest distance to " CA  PRO A 243 " =    2.396
peak=   -3.204 closest distance to " C   ALA A 158 " =    1.321
peak=   -3.200 closest distance to " O   GLY A  75 " =    1.865
peak=   -3.196 closest distance to " N   SER A 276 " =    1.348
peak=   -3.195 closest distance to " O   HOH Z 111 " =    3.788
peak=   -3.193 closest distance to " CE2 PHE A 192 " =    2.053
peak=   -3.189 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.189 closest distance to " O   HOH Z 123 " =    2.303
peak=   -3.185 closest distance to " O   HOH Z 385 " =    1.921
peak=   -3.184 closest distance to " O   HOH Z  77 " =    2.184
peak=   -3.182 closest distance to " O   HOH Z   9 " =    2.139
peak=   -3.179 closest distance to " O   HOH Z  24 " =    1.664
peak=   -3.175 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.174 closest distance to " O   HOH Z  90 " =    2.804
peak=   -3.172 closest distance to " CD1 LEU A  83 " =    2.352
peak=   -3.166 closest distance to " CG1AVAL A  41 " =    2.693
peak=   -3.163 closest distance to " O   HOH Z  60 " =    2.236
peak=   -3.155 closest distance to " CG2 VAL A 189 " =    2.226
peak=   -3.155 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.154 closest distance to " OE1 GLN A 223 " =    2.022
peak=   -3.152 closest distance to " NH2 ARG A  79 " =    1.575
peak=   -3.151 closest distance to " C   MET A 188 " =    1.550
peak=   -3.144 closest distance to " CB  TRP A  85 " =    2.401
peak=   -3.140 closest distance to " O   HOH Z 361 " =    3.393
peak=   -3.140 closest distance to " N   MET A 105 " =    2.583
peak=   -3.138 closest distance to " NH2 ARG A 159 " =    2.318
peak=   -3.137 closest distance to " C   SER A 206 " =    1.569
peak=   -3.133 closest distance to " CA  GLY A 241 " =    3.144
peak=   -3.132 closest distance to " OD2 ASP A  50 " =    2.314
peak=   -3.132 closest distance to " O   HOH Z 233 " =    2.405
peak=   -3.128 closest distance to " O   HOH Z 193 " =    1.818
peak=   -3.128 closest distance to " CB  PHE A  16 " =    2.579
peak=   -3.124 closest distance to " ND2 ASN A 249 " =    2.304
peak=   -3.124 closest distance to " OE1 GLN A 183 " =    1.479
peak=   -3.122 closest distance to " O   ASP A 171 " =    1.968
peak=   -3.121 closest distance to " C   GLN A 205 " =    1.920
peak=   -3.117 closest distance to " CA  ALA A 248 " =    2.622
peak=   -3.109 closest distance to " O   ASN A  45 " =    1.896
peak=   -3.091 closest distance to " O   PRO A 198 " =    1.624
peak=   -3.091 closest distance to " O   HOH Z 353 " =    2.173
peak=   -3.076 closest distance to " O   ALA A  51 " =    1.397
peak=   -3.075 closest distance to " NH2 ARG A  66 " =    2.029
peak=   -3.062 closest distance to " O   HOH Z 280 " =    2.398
peak=   -3.037 closest distance to " OD1 ASN A 301 " =    2.010
peak=   -3.035 closest distance to " CE  LYS A 166 " =    2.959
peak=   -3.021 closest distance to " O   HOH Z  55 " =    2.528

================= 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    :  0.3092 0.3030   6.003821e+00   5.975499e+00
   1_bss:  0.2961 0.2876   5.978977e+00   5.941613e+00
   1_xyz:  0.1656 0.1829   5.429441e+00   5.521891e+00
   1_adp:  0.1500 0.1862   5.370911e+00   5.548251e+00
   1_occ:  0.1497 0.1860   5.369724e+00   5.547446e+00
   2_bss:  0.1484 0.1849   5.366027e+00   5.541345e+00
   2_xyz:  0.1199 0.1582   5.183581e+00   5.392850e+00
   2_adp:  0.1177 0.1537   5.159580e+00   5.364335e+00
   2_occ:  0.1175 0.1536   5.158733e+00   5.363744e+00
   3_bss:  0.1178 0.1531   5.159279e+00   5.362406e+00
   3_xyz:  0.1094 0.1511   5.115158e+00   5.346943e+00
   3_adp:  0.1075 0.1515   5.108443e+00   5.350886e+00
   3_occ:  0.1074 0.1516   5.108581e+00   5.351288e+00
   4_bss:  0.1074 0.1516   5.108604e+00   5.351348e+00
   4_xyz:  0.1068 0.1525   5.109451e+00   5.356632e+00
   4_adp:  0.1062 0.1539   5.111608e+00   5.365005e+00
   4_occ:  0.1062 0.1539   5.111702e+00   5.365348e+00
   5_bss:  0.1060 0.1539   5.111669e+00   5.365275e+00
   5_xyz:  0.1088 0.1556   5.129958e+00   5.375648e+00
   5_adp:  0.1088 0.1560   5.131173e+00   5.378912e+00
   5_occ:  0.1088 0.1560   5.131142e+00   5.378966e+00
   5_bss:  0.1087 0.1560   5.131242e+00   5.379032e+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:  0.306  35.901  -2.166   0.646  -1.333   0.000  -0.000  -0.000
   1_xyz:  0.306  35.901  -2.166   0.646  -1.333   0.000  -0.000  -0.000
   1_adp:  0.306  35.901  -2.166   0.646  -1.333   0.000  -0.000  -0.000
   1_occ:  0.306  35.901  -2.166   0.646  -1.333   0.000  -0.000  -0.000
   2_bss:  0.309  44.247  -3.108  -1.444  -1.729  -0.000  -0.000  -0.000
   2_xyz:  0.309  44.247  -3.108  -1.444  -1.729  -0.000  -0.000  -0.000
   2_adp:  0.309  44.247  -3.108  -1.444  -1.729  -0.000  -0.000  -0.000
   2_occ:  0.309  44.247  -3.108  -1.444  -1.729  -0.000  -0.000  -0.000
   3_bss:  0.320  45.401  -2.921  -1.761  -1.464  -0.000  -0.000  -0.000
   3_xyz:  0.320  45.401  -2.921  -1.761  -1.464  -0.000  -0.000  -0.000
   3_adp:  0.320  45.401  -2.921  -1.761  -1.464  -0.000  -0.000  -0.000
   3_occ:  0.320  45.401  -2.921  -1.761  -1.464  -0.000  -0.000  -0.000
   4_bss:  0.322  45.538  -2.746  -1.760  -1.275  -0.000  -0.000  -0.000
   4_xyz:  0.322  45.538  -2.746  -1.760  -1.275  -0.000  -0.000  -0.000
   4_adp:  0.322  45.538  -2.746  -1.760  -1.275  -0.000  -0.000  -0.000
   4_occ:  0.322  45.538  -2.746  -1.760  -1.275  -0.000  -0.000  -0.000
   5_bss:  0.322  47.233  -2.470  -1.544  -1.015  -0.000  -0.000  -0.000
   5_xyz:  0.322  47.233  -2.470  -1.544  -1.015  -0.000  -0.000  -0.000
   5_adp:  0.322  47.233  -2.470  -1.544  -1.015  -0.000  -0.000  -0.000
   5_occ:  0.322  47.233  -2.470  -1.544  -1.015  -0.000  -0.000  -0.000
   5_bss:  0.322  47.483  -2.267  -1.358  -0.813  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.234 0.7591  0.9371    25483.289
   1_bss:  28.987 0.7711  0.9193    22173.020
   1_xyz:  16.884 0.8914  1.0091     8438.242
   1_adp:  17.574 0.8847  1.0016     8821.115
   1_occ:  17.567 0.8848  1.0014     8803.432
   2_bss:  17.380 0.8864  0.9640     8658.587
   2_xyz:  14.331 0.9120  0.9757     6364.919
   2_adp:  13.688 0.9174  0.9743     6088.582
   2_occ:  13.679 0.9175  0.9742     6078.335
   3_bss:  13.643 0.9178  0.9761     6056.539
   3_xyz:  13.254 0.9209  0.9783     5884.927
   3_adp:  13.315 0.9206  0.9726     5919.432
   3_occ:  13.318 0.9206  0.9724     5920.343
   4_bss:  13.318 0.9206  0.9770     5922.880
   4_xyz:  13.391 0.9200  0.9760     5975.525
   4_adp:  13.564 0.9187  0.9680     6058.708
   4_occ:  13.569 0.9187  0.9679     6061.761
   5_bss:  13.567 0.9187  0.9768     6061.306
   5_xyz:  13.728 0.9175  0.9765     6185.800
   5_adp:  13.798 0.9170  0.9689     6221.113
   5_occ:  13.798 0.9170  0.9688     6221.488
   5_bss:  13.799 0.9169  0.9759     6222.632
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6344e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6344e-01
   1_xyz:   1.079  0.008  0.071 15.312  0.005  4.111   6.6589e-02
   1_adp:   1.079  0.008  0.071 15.312  0.005  4.111   6.6589e-02
   1_occ:   1.079  0.008  0.071 15.312  0.005  4.111   6.6589e-02
   2_bss:   1.079  0.008  0.071 15.312  0.005  4.111   6.6589e-02
   2_xyz:   0.987  0.006  0.072 14.902  0.004  4.117   5.7235e-02
   2_adp:   0.987  0.006  0.072 14.902  0.004  4.117   5.7235e-02
   2_occ:   0.987  0.006  0.072 14.902  0.004  4.117   5.7235e-02
   3_bss:   0.987  0.006  0.072 14.902  0.004  4.117   5.7235e-02
   3_xyz:   1.064  0.008  0.080 15.200  0.004  4.120   6.7523e-02
   3_adp:   1.064  0.008  0.080 15.200  0.004  4.120   6.7523e-02
   3_occ:   1.064  0.008  0.080 15.200  0.004  4.120   6.7523e-02
   4_bss:   1.064  0.008  0.080 15.200  0.004  4.120   6.7523e-02
   4_xyz:   1.030  0.008  0.078 15.022  0.004  4.120   6.4004e-02
   4_adp:   1.030  0.008  0.078 15.022  0.004  4.120   6.4004e-02
   4_occ:   1.030  0.008  0.078 15.022  0.004  4.120   6.4004e-02
   5_bss:   1.030  0.008  0.078 15.022  0.004  4.120   6.4004e-02
   5_xyz:   0.909  0.006  0.070 14.776  0.004  4.120   5.1731e-02
   5_adp:   0.909  0.006  0.070 14.776  0.004  4.120   5.1731e-02
   5_occ:   0.909  0.006  0.070 14.776  0.004  4.120   5.1731e-02
   5_bss:   0.909  0.006  0.070 14.776  0.004  4.120   5.1731e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4047e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4047e-01
   1_xyz:   6.654  0.063  0.233 84.698  0.031  2.327   6.5735e-02
   1_adp:   6.654  0.063  0.233 84.698  0.031  2.327   6.5735e-02
   1_occ:   6.654  0.063  0.233 84.698  0.031  2.327   6.5735e-02
   2_bss:   6.654  0.063  0.233 84.698  0.031  2.327   6.5735e-02
   2_xyz:   6.884  0.039  0.230 82.403  0.039  2.330   4.3877e-02
   2_adp:   6.884  0.039  0.230 82.403  0.039  2.330   4.3877e-02
   2_occ:   6.884  0.039  0.230 82.403  0.039  2.330   4.3877e-02
   3_bss:   6.884  0.039  0.230 82.403  0.039  2.330   4.3877e-02
   3_xyz:   7.919  0.048  0.256 82.950  0.039  2.314   5.0860e-02
   3_adp:   7.919  0.048  0.256 82.950  0.039  2.314   5.0860e-02
   3_occ:   7.919  0.048  0.256 82.950  0.039  2.314   5.0860e-02
   4_bss:   7.919  0.048  0.256 82.950  0.039  2.314   5.0860e-02
   4_xyz:   7.510  0.049  0.249 82.481  0.042  2.335   4.7034e-02
   4_adp:   7.510  0.049  0.249 82.481  0.042  2.335   4.7034e-02
   4_occ:   7.510  0.049  0.249 82.481  0.042  2.335   4.7034e-02
   5_bss:   7.510  0.049  0.249 82.481  0.042  2.335   4.7034e-02
   5_xyz:   6.531  0.042  0.228 82.491  0.036  2.383   2.9848e-02
   5_adp:   6.531  0.042  0.228 82.491  0.036  2.383   2.9848e-02
   5_occ:   6.531  0.042  0.228 82.491  0.036  2.383   2.9848e-02
   5_bss:   6.531  0.042  0.228 82.491  0.036  2.383   2.9848e-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:  73.76   0.00  16.96  73.76   0.00  13.08  68.09   6.73  38.12
   1_occ:  73.76   0.00  16.96  73.76   0.00  13.08  68.09   6.73  38.12
   2_bss:  73.76   0.00  16.96  73.76   0.00  13.08  68.09   6.73  38.12
   2_xyz:  73.76   0.00  16.96  73.76   0.00  13.08  68.09   6.73  38.12
   2_adp:  75.05   2.44  16.47  75.05   2.44  12.78  64.32   5.63  36.54
   2_occ:  75.05   2.44  16.47  75.05   2.44  12.78  64.32   5.63  36.54
   3_bss:  75.05   2.44  16.47  75.05   2.44  12.78  64.32   5.63  36.54
   3_xyz:  75.05   2.44  16.47  75.05   2.44  12.78  64.32   5.63  36.54
   3_adp:  80.07   1.52  16.61  80.07   1.52  12.70  66.47   5.85  37.89
   3_occ:  80.07   1.52  16.61  80.07   1.52  12.70  66.47   5.85  37.89
   4_bss:  80.07   1.52  16.61  80.07   1.52  12.70  66.47   5.85  37.89
   4_xyz:  80.07   1.52  16.61  80.07   1.52  12.70  66.47   5.85  37.89
   4_adp:  91.47   0.41  16.82  91.47   0.41  12.67  76.15   5.57  39.39
   4_occ:  91.47   0.41  16.82  91.47   0.41  12.67  76.15   5.57  39.39
   5_bss:  91.47   0.41  16.82  91.47   0.41  12.67  76.15   5.57  39.39
   5_xyz:  91.47   0.41  16.82  91.47   0.41  12.67  76.15   5.57  39.39
   5_adp:  92.49   0.00  16.66  92.49   0.00  12.50  77.40   5.18  39.35
   5_occ:  92.49   0.00  16.66  92.49   0.00  12.50  77.40   5.18  39.35
   5_bss:  92.49   0.00  16.67  92.49   0.00  12.50  77.41   5.18  39.35
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.135    0.026    0.300
   1_adp:    1.135    0.026    0.300
   1_occ:    1.135    0.026    0.300
   2_bss:    1.135    0.026    0.300
   2_xyz:    0.842    0.021    0.347
   2_adp:    0.842    0.021    0.347
   2_occ:    0.842    0.021    0.347
   3_bss:    0.842    0.021    0.347
   3_xyz:    0.761    0.057    0.379
   3_adp:    0.761    0.057    0.379
   3_occ:    0.761    0.057    0.379
   4_bss:    0.761    0.057    0.379
   4_xyz:    0.965    0.075    0.385
   4_adp:    0.965    0.075    0.385
   4_occ:    0.965    0.075    0.385
   5_bss:    0.965    0.075    0.385
   5_xyz:    1.025    0.052    0.388
   5_adp:    1.025    0.052    0.388
   5_occ:    1.025    0.052    0.388
   5_bss:    1.025    0.052    0.388
------------------------------------------------------------------------

CPU time actual refinement: 334.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/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_444/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_444/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.57 
  Macro-tasks:
    bulk solvent and scale       = 37.26  
    individual site refinement   = 144.75 
    weights calculation          = 28.57  
    collect and process          = 6.49   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 217.15 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 107.13 
    alpha_beta                      = 7.95   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.82 
    fmodel                         = 6.58   
    r_factors                      = 0.17   
    phase_errors                   = 11.28  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 254.51 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.611 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    681 calls, 106.84 s
gradients_fft:          626 calls, 103.90 s

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

# Date 2008-01-16 Time 04:50:18 PST -0800 (1200487818.68 s)
Start R-work = 0.3092, R-free = 0.3030 (no bulk solvent and anisotropic scale)
Final R-work = 0.1310, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.2961, R-free = 0.2876
Final R-work = 0.1087, R-free = 0.1560