# Date 2008-01-16 Time 04:14:24 PST -0800 (1200485664.28 s)
#phil __OFF__

Command line arguments: "../235.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27917
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 235

-------------------------------------------------------------------------------
  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: (68.845, 48.1033, 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: 3.24, 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: (68.845, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.96075
Completeness in resolution range: 0.930108
Completeness with d_max=infinity: 0.927334

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0230
                             d_min =   1.9608

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: (68.845, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.96075
Completeness in resolution range: 0.930108
Completeness with d_max=infinity: 0.927334

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0234 -  4.1965 [2215/2244]  1988   227  10.2%
  bin  2:  4.1965 -  3.3430 [2118/2141]  1909   209   9.9%
  bin  3:  3.3430 -  2.9239 [2091/2116]  1885   206   9.9%
  bin  4:  2.9239 -  2.6582 [2065/2092]  1858   207  10.0%
  bin  5:  2.6582 -  2.4686 [2055/2088]  1846   209  10.2%
  bin  6:  2.4686 -  2.3236 [2062/2090]  1864   198   9.6%
  bin  7:  2.3236 -  2.2076 [2040/2076]  1835   205  10.0%
  bin  8:  2.2076 -  2.1118 [2021/2063]  1821   200   9.9%
  bin  9:  2.1118 -  2.0307 [1993/2075]  1791   202  10.1%
  bin 10:  2.0307 -  1.9607 [ 929/2076]   833    96  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/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: 0.15 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:
        1.15 -     1.90: 9
        1.90 -     2.65: 100
        2.65 -     3.40: 4381
        3.40 -     4.15: 9377
        4.15 -     4.90: 14520
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.151 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.381 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.468 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.577 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.658 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28382 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_235/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 68.845 48.10325 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: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4614   r_free= 0.4503   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.277299                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6810 0.99   1435  159 0.3802 0.4160      6.5823      6.6412|
|  2:  4.6810 -  3.7342 0.99   1380  153 0.4059 0.4063      6.8204      6.8077|
|  3:  3.7342 -  3.2678 0.99   1365  151 0.4354 0.4033      6.6666      6.6944|
|  4:  3.2678 -  2.9715 0.98   1330  144 0.4505 0.3996      6.4969      6.4226|
|  5:  2.9715 -  2.7599 0.99   1332  152 0.4895 0.4570      6.3586      6.3309|
|  6:  2.7599 -  2.5981 0.99   1349  151 0.4913 0.4669      6.2763      6.1347|
|  7:  2.5981 -  2.4686 0.98   1295  148 0.5022 0.4323      6.2296       6.159|
|  8:  2.4686 -  2.3615 0.98   1330  136 0.4964 0.5220      6.1629      6.2134|
|  9:  2.3615 -  2.2709 0.99   1310  149 0.5233 0.5004      6.1143      6.1385|
| 10:  2.2709 -  2.1928 0.99   1319  143 0.4924 0.4886      6.0981      6.0986|
| 11:  2.1928 -  2.1244 0.97   1320  148 0.5071 0.5426      6.0154      6.0311|
| 12:  2.1244 -  2.0639 0.98   1278  151 0.4921 0.4437      5.9341      5.9494|
| 13:  2.0639 -  2.0097 0.88   1151  126 0.4972 0.5249       5.856      5.8207|
| 14:  2.0097 -  1.9607 0.32    436   48 0.4961 0.5338       5.854      5.7196|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6810  1435   159  0.64  39.19   0.82     0.67      87423.37|
|  2:  4.6810 -  3.7342  1380   153  0.69  36.30   0.91     0.78     110510.04|
|  3:  3.7342 -  3.2678  1365   151  0.61  42.95   0.92     0.81     108721.15|
|  4:  3.2678 -  2.9715  1330   144  0.57  46.33   0.91     0.77      86129.01|
|  5:  2.9715 -  2.7599  1332   152  0.50  52.10   0.88     0.70      69666.78|
|  6:  2.7599 -  2.5981  1349   151  0.48  53.71   0.90     0.65      59355.30|
|  7:  2.5981 -  2.4686  1295   148  0.44  56.64   0.89     0.61      57615.83|
|  8:  2.4686 -  2.3615  1330   136  0.41  59.08   0.91     0.58      53954.67|
|  9:  2.3615 -  2.2709  1310   149  0.39  60.80   0.90     0.59      51726.36|
| 10:  2.2709 -  2.1928  1319   143  0.41  59.50   0.95     0.58      45684.62|
| 11:  2.1928 -  2.1244  1320   148  0.41  59.02   0.94     0.64      42172.00|
| 12:  2.1244 -  2.0639  1278   151  0.40  60.30   0.94     0.63      39230.09|
| 13:  2.0639 -  2.0097  1151   126  0.35  63.59   0.97     0.56      34934.60|
| 14:  2.0097 -  1.9607   436    48  0.27  69.52   0.95     0.35      30343.47|
|alpha:            min =        0.35 max =            0.81 mean =         0.65|
|beta:             min =    30343.47 max =       110510.04 mean =     65082.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.15|
|phase err.(test): min =        0.00 max =           89.84 mean =        53.03|
|-----------------------------------------------------------------------------|

============================== 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 = 10.860424             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.509   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.788267              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.308   (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 |  1.151 -  1.525:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.525 -  1.900:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.900 -  2.275:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.275 -  2.650:       81 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.650 -  3.025:     2034 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.025 -  3.400:     2347 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.400 -  3.775:     3994 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.775 -  4.150:     5383 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.150 -  4.525:     6445 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.525 -  4.900:     8075 |
|-----------------------------------------------------------------------------|
|-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 |        0.197 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.151 |       0.686 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    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: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4614   r_free= 0.4503   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.277299                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4532   r_free= 0.4387   ksol= 0.31   Bsol= 29.87   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,4.62,-1.83,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.269123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.559477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.043   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.955645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.955   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4532      final r-factor (work) = 0.3651          |
| start r-factor (free) = 0.4387      final r-factor (free) = 0.3903          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1639 = 9.56 * 0.50 * 6.2696 + 1.00 * 0.1967                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5787 = 9.56 * 0.50 * 6.1620 + 1.00 * 0.1261                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3651      final r-factor (work) = 0.3340          |
| start r-factor (free) = 0.3903      final r-factor (free) = 0.3932          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8946 = 0.96 * 1.00 * 6.1620 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8319 = 0.96 * 1.00 * 6.0848 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.87   18.98    None  None   None       |
|    all(noH): 2823   0      0.00    93.87   18.98    None  None   None       |
|    Sol.    : 438    0      0.00    93.87   36.28    None  None   None       |
|    Mac.    : 2385   0      0.00    76.72   15.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.388:  831   |   5:    46.937 -  56.325:  105        |
|      1:     9.388 -  18.775:  913   |   6:    56.325 -  65.712:   51        |
|      2:    18.775 -  28.162:  457   |   7:    65.712 -  75.100:   20        |
|      3:    28.162 -  37.550:  293   |   8:    75.100 -  84.487:    4        |
|      4:    37.550 -  46.937:  145   |   9:    84.487 -  93.875:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3340 r_free = 0.3932             target_work(ml) = 6.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3336 r_free = 0.3937             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3336   r_free= 0.3937   ksol= 0.31   Bsol= 29.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.18,4.62,-1.83,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.082622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3326   r_free= 0.3920   ksol= 0.30   Bsol= 37.15   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,2.92,-0.53,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.082803                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.371929              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.985759              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.419  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3326      final r-factor (work) = 0.2766          |
| start r-factor (free) = 0.3920      final r-factor (free) = 0.3334          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5571 = 7.37 * 0.50 * 6.0855 + 1.00 * 0.1261                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2307 = 7.37 * 0.50 * 6.0031 + 1.00 * 0.1035                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2766      final r-factor (work) = 0.2581          |
| start r-factor (free) = 0.3334      final r-factor (free) = 0.3277          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9346 = 0.99 * 1.00 * 6.0031 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8322 = 0.99 * 1.00 * 5.8986 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.77  19.21    None  None   None       |
|    all(noH): 2823   0      0.00    104.77  19.21    None  None   None       |
|    Sol.    : 438    0      2.73    104.77  38.79    None  None   None       |
|    Mac.    : 2385   0      0.00    99.21   15.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.477: 1038   |   5:    52.386 -  62.863:   76        |
|      1:    10.477 -  20.954:  879   |   6:    62.863 -  73.340:   52        |
|      2:    20.954 -  31.432:  403   |   7:    73.340 -  83.818:   22        |
|      3:    31.432 -  41.909:  219   |   8:    83.818 -  94.295:   11        |
|      4:    41.909 -  52.386:  116   |   9:    94.295 - 104.772:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2581 r_free = 0.3277             target_work(ml) = 5.893         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2578 r_free = 0.3276             target_work(ml) = 5.893         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2578   r_free= 0.3276   ksol= 0.30   Bsol= 37.15   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,2.92,-0.53,0.00,-0.00,-0.00); trace/3= 0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.892514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2576   r_free= 0.3275   ksol= 0.32   Bsol= 47.92   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,2.01,-0.00,0.00,-0.00,-0.00); trace/3= 0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.893489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.282816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.251   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.950  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2576      final r-factor (work) = 0.2087          |
| start r-factor (free) = 0.3275      final r-factor (free) = 0.2706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6347 = 6.28 * 0.50 * 5.8990 + 1.00 * 0.1035                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3240 = 6.28 * 0.50 * 5.8087 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2087      final r-factor (work) = 0.1940          |
| start r-factor (free) = 0.2706      final r-factor (free) = 0.2527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8241 = 0.48 * 1.00 * 5.8087 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7531 = 0.48 * 1.00 * 5.6638 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.16  18.44    None  None   None       |
|    all(noH): 2823   0      0.00    104.16  18.44    None  None   None       |
|    Sol.    : 438    0      3.91    104.16  40.15    None  None   None       |
|    Mac.    : 2385   0      0.00    97.98   14.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.416: 1133   |   5:    52.080 -  62.496:   83        |
|      1:    10.416 -  20.832:  900   |   6:    62.496 -  72.912:   44        |
|      2:    20.832 -  31.248:  310   |   7:    72.912 -  83.328:   18        |
|      3:    31.248 -  41.664:  204   |   8:    83.328 -  93.744:   12        |
|      4:    41.664 -  52.080:  113   |   9:    93.744 - 104.160:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1940 r_free = 0.2527             target_work(ml) = 5.629         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1938 r_free = 0.2526             target_work(ml) = 5.629         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1938   r_free= 0.2526   ksol= 0.32   Bsol= 47.92   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,2.01,-0.00,0.00,-0.00,-0.00); trace/3= 0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.628755                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1937   r_free= 0.2519   ksol= 0.32   Bsol= 54.75   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,0.34,-0.59,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.628514                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.001001              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383825              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.322   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1937      final r-factor (work) = 0.1617          |
| start r-factor (free) = 0.2519      final r-factor (free) = 0.2124          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5807 = 3.00 * 0.50 * 5.6676 + 1.00 * 0.0764                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3889 = 3.00 * 0.50 * 5.5498 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1617      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2124      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1451 = 0.38 * 1.00 * 5.5498 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0958 = 0.38 * 1.00 * 5.4320 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    101.44  17.65    None  None   None       |
|    all(noH): 2823   0      0.60    101.44  17.65    None  None   None       |
|    Sol.    : 438    0      3.65    99.80   41.83    None  None   None       |
|    Mac.    : 2385   0      0.60    101.44  13.21    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:     0.602 -  10.685: 1245   |   5:    51.019 -  61.102:  108        |
|      1:    10.685 -  20.769:  928   |   6:    61.102 -  71.185:   39        |
|      2:    20.769 -  30.852:  215   |   7:    71.185 -  81.269:   23        |
|      3:    30.852 -  40.935:  134   |   8:    81.269 -  91.352:   10        |
|      4:    40.935 -  51.019:  116   |   9:    91.352 - 101.435:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1504 r_free = 0.1980             target_work(ml) = 5.397         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1503 r_free = 0.1979             target_work(ml) = 5.397         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.1979   ksol= 0.32   Bsol= 54.75   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,0.34,-0.59,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.396915                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.1983   ksol= 0.33   Bsol= 57.49   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-0.39,-0.81,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.398442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.289410              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.282  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334915              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.041  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1983      final r-factor (free) = 0.1800          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2821 = 2.29 * 0.50 * 5.4343 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1703 = 2.29 * 0.50 * 5.3384 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1800      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7987 = 0.33 * 1.00 * 5.3384 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8951 = 0.33 * 1.00 * 5.2729 + 1.00 * 0.1291                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.71  17.43    None  None   None       |
|    all(noH): 2823   0      0.00    101.71  17.43    None  None   None       |
|    Sol.    : 438    0      0.35    99.22   41.79    None  None   None       |
|    Mac.    : 2385   0      0.00    101.71  12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.171: 1176   |   5:    50.854 -  61.025:  107        |
|      1:    10.171 -  20.342: 1008   |   6:    61.025 -  71.196:   37        |
|      2:    20.342 -  30.513:  208   |   7:    71.196 -  81.367:   23        |
|      3:    30.513 -  40.683:  132   |   8:    81.367 -  91.538:   10        |
|      4:    40.683 -  50.854:  117   |   9:    91.538 - 101.709:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1772             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1769             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1769   ksol= 0.33   Bsol= 57.49   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-0.39,-0.81,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.261898                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6810 0.99   1435  159 0.1003 0.1454       5.413      5.6367|
|  2:  4.6810 -  3.7342 0.99   1380  153 0.0914 0.1151      5.5043      5.7203|
|  3:  3.7342 -  3.2678 0.99   1365  151 0.1201 0.1725      5.5704      5.8897|
|  4:  3.2678 -  2.9715 0.98   1330  144 0.1418 0.1793      5.5619      5.7208|
|  5:  2.9715 -  2.7599 0.99   1332  152 0.1556 0.1945      5.4531      5.6201|
|  6:  2.7599 -  2.5981 0.99   1349  151 0.1483 0.2310      5.3571      5.5744|
|  7:  2.5981 -  2.4686 0.98   1295  148 0.1427 0.1786      5.2758      5.4527|
|  8:  2.4686 -  2.3615 0.98   1330  136 0.1388 0.1917       5.207      5.4409|
|  9:  2.3615 -  2.2709 0.99   1310  149 0.1339 0.2050      5.1175      5.3898|
| 10:  2.2709 -  2.1928 0.99   1319  143 0.1340 0.1795      5.1063      5.2788|
| 11:  2.1928 -  2.1244 0.97   1320  148 0.1274 0.2123      5.0155      5.3535|
| 12:  2.1244 -  2.0639 0.98   1278  151 0.1361 0.1777       4.974      5.2002|
| 13:  2.0639 -  2.0097 0.88   1151  126 0.1285 0.1976      4.8902      5.1646|
| 14:  2.0097 -  1.9607 0.32    436   48 0.1259 0.1897      4.8396      4.9811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6810  1435   159  0.93  10.13   0.97     0.94       8059.47|
|  2:  4.6810 -  3.7342  1380   153  0.94   9.23   1.02     1.02      10800.19|
|  3:  3.7342 -  3.2678  1365   151  0.92  13.23   1.03     1.02      12561.48|
|  4:  3.2678 -  2.9715  1330   144  0.90  16.06   1.02     1.01      12654.11|
|  5:  2.9715 -  2.7599  1332   152  0.88  18.49   1.01     0.99      10702.84|
|  6:  2.7599 -  2.5981  1349   151  0.87  19.04   0.98     0.93       9121.54|
|  7:  2.5981 -  2.4686  1295   148  0.89  17.74   0.99     0.96       7705.77|
|  8:  2.4686 -  2.3615  1330   136  0.88  18.07   1.01     0.98       7101.81|
|  9:  2.3615 -  2.2709  1310   149  0.89  17.95   1.00     0.95       5924.08|
| 10:  2.2709 -  2.1928  1319   143  0.88  18.40   1.00     0.96       5888.58|
| 11:  2.1928 -  2.1244  1320   148  0.88  18.21   1.00     0.96       5199.53|
| 12:  2.1244 -  2.0639  1278   151  0.89  18.03   1.00     0.98       4671.06|
| 13:  2.0639 -  2.0097  1151   126  0.88  18.56   0.99     0.99       4144.28|
| 14:  2.0097 -  1.9607   436    48  0.88  17.89   0.97     0.91       3572.51|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3572.51 max =        12654.11 mean =      8004.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.34|
|phase err.(test): min =        0.00 max =           89.25 mean =        15.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1767   ksol= 0.33   Bsol= 57.49   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-0.62,-0.72,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.263142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1767   ksol= 0.33   Bsol= 57.49   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-0.62,-0.72,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.263142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6810 0.99   1435  159 0.1024 0.1432       5.422      5.6314|
|  2:  4.6810 -  3.7342 0.99   1380  153 0.0931 0.1146      5.5105      5.7255|
|  3:  3.7342 -  3.2678 0.99   1365  151 0.1208 0.1725      5.5737      5.8894|
|  4:  3.2678 -  2.9715 0.98   1330  144 0.1421 0.1799      5.5622      5.7202|
|  5:  2.9715 -  2.7599 0.99   1332  152 0.1558 0.1941      5.4533      5.6202|
|  6:  2.7599 -  2.5981 0.99   1349  151 0.1481 0.2312      5.3562      5.5736|
|  7:  2.5981 -  2.4686 0.98   1295  148 0.1426 0.1788       5.275      5.4537|
|  8:  2.4686 -  2.3615 0.98   1330  136 0.1386 0.1917      5.2066      5.4417|
|  9:  2.3615 -  2.2709 0.99   1310  149 0.1336 0.2045      5.1163      5.3868|
| 10:  2.2709 -  2.1928 0.99   1319  143 0.1339 0.1804      5.1056       5.282|
| 11:  2.1928 -  2.1244 0.97   1320  148 0.1274 0.2121      5.0152      5.3521|
| 12:  2.1244 -  2.0639 0.98   1278  151 0.1362 0.1784      4.9747       5.202|
| 13:  2.0639 -  2.0097 0.88   1151  126 0.1288 0.1971      4.8906      5.1622|
| 14:  2.0097 -  1.9607 0.32    436   48 0.1259 0.1902       4.839      4.9807|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6810  1435   159  0.93  10.07   0.97     0.94       7938.39|
|  2:  4.6810 -  3.7342  1380   153  0.94   9.25   1.02     1.02      10762.29|
|  3:  3.7342 -  3.2678  1365   151  0.92  13.26   1.03     1.02      12601.94|
|  4:  3.2678 -  2.9715  1330   144  0.90  16.06   1.02     1.01      12644.39|
|  5:  2.9715 -  2.7599  1332   152  0.88  18.49   1.01     0.98      10693.39|
|  6:  2.7599 -  2.5981  1349   151  0.87  19.05   0.98     0.93       9133.26|
|  7:  2.5981 -  2.4686  1295   148  0.89  17.76   0.99     0.96       7711.21|
|  8:  2.4686 -  2.3615  1330   136  0.88  18.08   1.01     0.98       7105.25|
|  9:  2.3615 -  2.2709  1310   149  0.89  17.94   1.00     0.95       5921.27|
| 10:  2.2709 -  2.1928  1319   143  0.88  18.39   1.00     0.96       5883.27|
| 11:  2.1928 -  2.1244  1320   148  0.88  18.22   1.00     0.96       5200.12|
| 12:  2.1244 -  2.0639  1278   151  0.89  18.05   1.00     0.98       4680.58|
| 13:  2.0639 -  2.0097  1151   126  0.88  18.56   0.99     0.99       4142.67|
| 14:  2.0097 -  1.9607   436    48  0.88  17.86   0.97     0.91       3556.49|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3556.49 max =        12644.39 mean =      7994.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        16.34|
|phase err.(test): min =        0.00 max =           90.00 mean =        15.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.767)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.71  17.43    None  None   None       |
|    all(noH): 2823   0      0.00    101.71  17.43    None  None   None       |
|    Sol.    : 438    0      0.35    99.23   41.79    None  None   None       |
|    Mac.    : 2385   0      0.00    101.71  12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.174: 1176   |   5:    50.857 -  61.028:  107        |
|      1:    10.174 -  20.345: 1008   |   6:    61.028 -  71.199:   37        |
|      2:    20.345 -  30.516:  208   |   7:    71.199 -  81.370:   23        |
|      3:    30.516 -  40.686:  132   |   8:    81.370 -  91.541:   10        |
|      4:    40.686 -  50.857:  117   |   9:    91.541 - 101.712:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.485 - 4.011
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 328
   mapped sites are within: 0.721 - 4.011

peak=    8.257 closest distance to " O   HOH Z 400 " =    0.824
peak=    5.954 closest distance to " O   HOH Z 120 " =    1.221
peak=    5.413 closest distance to " CA  TYR A  30 " =    0.916
peak=    5.401 closest distance to " O   HOH Z 210 " =    1.319
peak=    5.069 closest distance to " O   HOH Z  49 " =    1.438
peak=    5.006 closest distance to " O   HOH Z 124 " =    1.397
peak=    4.867 closest distance to " O   HOH Z 130 " =    1.058
peak=    4.837 closest distance to " O   HOH Z  80 " =    2.095
peak=    4.794 closest distance to " O   HOH Z 422 " =    0.886
peak=    4.761 closest distance to " O   HOH Z 403 " =    2.114
peak=    4.678 closest distance to " CB  ASN A 285 " =    0.988
peak=    4.670 closest distance to " CG  PRO A 280 " =    0.781
peak=    4.664 closest distance to " O   HOH Z 401 " =    1.087
peak=    4.633 closest distance to " O   HOH Z 389 " =    2.089
peak=    4.624 closest distance to " O   HOH Z  46 " =    1.049
peak=    4.597 closest distance to " O   HOH Z 272 " =    1.339
peak=    4.593 closest distance to " CB  ARG A 275 " =    0.884
peak=    4.553 closest distance to " NH2 ARG A  56 " =    2.293
peak=    4.544 closest distance to " O   HOH Z 102 " =    1.311
peak=    4.540 closest distance to " CD2 TRP A 179 " =    1.356
peak=    4.496 closest distance to " O   HOH Z 134 " =    1.864
peak=    4.485 closest distance to " CG  PRO A  54 " =    1.183
peak=    4.472 closest distance to " O   HOH Z 236 " =    1.457
peak=    4.444 closest distance to " CG  PRO A 198 " =    1.395
peak=    4.442 closest distance to " O   HOH Z 247 " =    1.484
peak=    4.421 closest distance to " O   HOH Z 193 " =    1.670
peak=    4.418 closest distance to " O   HOH Z 357 " =    1.995
peak=    4.416 closest distance to " O   HOH Z  63 " =    2.085
peak=    4.382 closest distance to " CB  SER A  63 " =    1.179
peak=    4.382 closest distance to " CG  ARG A  66 " =    1.096
peak=    4.377 closest distance to " CB  GLN A 223 " =    1.391
peak=    4.373 closest distance to " O   HOH Z 433 " =    1.831
peak=    4.352 closest distance to " O   HOH Z 154 " =    1.917
peak=    4.351 closest distance to " CG  PRO A 213 " =    1.328
peak=    4.311 closest distance to " CG  PRO A  90 " =    1.324
peak=    4.311 closest distance to " CB  PRO A  54 " =    0.914
peak=    4.307 closest distance to " O   HOH Z 415 " =    1.686
peak=    4.279 closest distance to " O   HOH Z 428 " =    1.177
peak=    4.263 closest distance to " O   PRO A 198 " =    1.589
peak=    4.262 closest distance to " O   HOH Z 234 " =    3.710
peak=    4.252 closest distance to " CB  SER A 141 " =    1.055
peak=    4.236 closest distance to " O   HOH Z 361 " =    3.107
peak=    4.228 closest distance to " O   HOH Z  43 " =    1.960
peak=    4.212 closest distance to " CD  ARG A 269 " =    0.918
peak=    4.190 closest distance to " O   HOH Z 126 " =    1.553
peak=    4.170 closest distance to " O   HOH Z 412 " =    3.622
peak=    4.168 closest distance to " O   HOH Z  44 " =    2.053
peak=    4.164 closest distance to " CG AARG A 275 " =    1.035
peak=    4.161 closest distance to " O   HOH Z  15 " =    2.221
peak=    4.161 closest distance to " O   HOH Z 109 " =    1.976
peak=    4.158 closest distance to " O   HOH Z 117 " =    0.959
peak=    4.156 closest distance to " CB  SER A  62 " =    0.890
peak=    4.153 closest distance to " O   HOH Z 189 " =    2.129
peak=    4.152 closest distance to " O   HOH Z 209 " =    2.262
peak=    4.149 closest distance to " NZ  LYS A 117 " =    3.163
peak=    4.141 closest distance to " CB  ARG A 190 " =    1.787
peak=    4.132 closest distance to " CG2 VAL A 197 " =    1.212
peak=    4.131 closest distance to " CG1 ILE A  33 " =    1.302
peak=    4.123 closest distance to " CG  GLN A  77 " =    0.721
peak=    4.120 closest distance to " CD  LYS A 166 " =    1.581
peak=    4.120 closest distance to " O   HOH Z 431 " =    1.416
peak=    4.109 closest distance to " CE  LYS A 119 " =    1.125
peak=    4.092 closest distance to " O   HOH Z 132 " =    2.634
peak=    4.088 closest distance to " NH1AARG A 275 " =    1.153
peak=    4.074 closest distance to " O   HOH Z 146 " =    1.251
peak=    4.046 closest distance to " CG2BVAL A  41 " =    0.920
peak=    4.023 closest distance to " NH2 ARG A  36 " =    0.960
peak=    4.018 closest distance to " O   HOH Z 130 " =    2.442
peak=    4.006 closest distance to " O   HOH Z 128 " =    1.518
peak=    4.000 closest distance to " O   HOH Z  59 " =    2.230
peak=    3.990 closest distance to " NH2BARG A 145 " =    1.965
peak=    3.973 closest distance to " CB  PHE A  16 " =    1.252
peak=    3.958 closest distance to " O   HOH Z 289 " =    1.668
peak=    3.955 closest distance to " CA  ARG A  66 " =    1.320
peak=    3.932 closest distance to " O   HOH Z 272 " =    1.987
peak=    3.927 closest distance to " O   HOH Z 116 " =    1.227
peak=    3.926 closest distance to " O   GLY A  23 " =    2.514
peak=    3.925 closest distance to " O   GLN A  11 " =    0.928
peak=    3.906 closest distance to " O   HOH Z 291 " =    1.395
peak=    3.899 closest distance to " O   HOH Z 406 " =    1.661
peak=    3.898 closest distance to " O   HOH Z  40 " =    1.996
peak=    3.881 closest distance to " CG2 ILE A  20 " =    1.386
peak=    3.878 closest distance to " O   HOH Z 404 " =    1.370
peak=    3.869 closest distance to " O   HOH Z 142 " =    1.411
peak=    3.869 closest distance to " NE  ARG A  36 " =    0.876
peak=    3.863 closest distance to " O   ASN A 285 " =    0.801
peak=    3.862 closest distance to " ND2 ASN A 187 " =    1.645
peak=    3.858 closest distance to " O   HOH Z 414 " =    2.000
peak=    3.840 closest distance to " O   HOH Z 132 " =    1.930
peak=    3.838 closest distance to " O   HOH Z 245 " =    1.362
peak=    3.836 closest distance to " CB  VAL A 202 " =    1.407
peak=    3.825 closest distance to " O   HOH Z 214 " =    1.474
peak=    3.825 closest distance to " CB  TRP A 179 " =    1.236
peak=    3.818 closest distance to " O   HOH Z 437 " =    2.069
peak=    3.816 closest distance to " O   HOH Z 394 " =    1.644
peak=    3.815 closest distance to " NE2 GLN A  11 " =    1.113
peak=    3.806 closest distance to " O   HOH Z 159 " =    0.739
peak=    3.800 closest distance to " OG BSER A 210 " =    1.026
peak=    3.798 closest distance to " NH2 ARG A 156 " =    1.114
peak=    3.773 closest distance to " CA  ALA A 100 " =    1.425
peak=    3.756 closest distance to " O   HOH Z 208 " =    1.596
peak=    3.753 closest distance to " O   HOH Z 418 " =    1.787
peak=    3.746 closest distance to " CG2 THR A 220 " =    0.812
peak=    3.744 closest distance to " O   HOH Z  97 " =    1.459
peak=    3.740 closest distance to " CB  ARG A  79 " =    1.288
peak=    3.739 closest distance to " CB  SER A  26 " =    1.773
peak=    3.730 closest distance to " O   HOH Z 336 " =    1.842
peak=    3.726 closest distance to " O   HOH Z  47 " =    1.409
peak=    3.719 closest distance to " CA  ARG A 195 " =    1.088
peak=    3.717 closest distance to " N   SER A 164 " =    0.999
peak=    3.712 closest distance to " O   HOH Z   7 " =    1.181
peak=    3.712 closest distance to " O   SER A  87 " =    2.088
peak=    3.710 closest distance to " CB  GLU A 175 " =    1.372
peak=    3.706 closest distance to " O   HOH Z 403 " =    1.486
peak=    3.701 closest distance to " O   ALA A 165 " =    1.383
peak=    3.697 closest distance to " CB  GLN A 183 " =    1.226
peak=    3.696 closest distance to " O   HOH Z 227 " =    1.850
peak=    3.691 closest distance to " O   HOH Z 425 " =    1.567
peak=    3.681 closest distance to " CA  CYS A 260 " =    1.694
peak=    3.667 closest distance to " O   HOH Z 196 " =    1.389
peak=    3.665 closest distance to " O  BHOH Z 338 " =    1.074
peak=    3.664 closest distance to " O   HOH Z 203 " =    1.840
peak=    3.662 closest distance to " N   ALA A   1 " =    1.141
peak=    3.641 closest distance to " O   HOH Z 369 " =    2.071
peak=    3.635 closest distance to " O   HOH Z  48 " =    1.870
peak=    3.634 closest distance to " N   ASN A  39 " =    1.233
peak=    3.631 closest distance to " CB  THR A  52 " =    0.834
peak=    3.631 closest distance to " N   TRP A 150 " =    1.239
peak=    3.626 closest distance to " CB  GLN A  58 " =    0.933
peak=    3.624 closest distance to " O   HOH Z 232 " =    2.439
peak=    3.623 closest distance to " CB  GLU A 128 " =    1.186
peak=    3.612 closest distance to " O   HOH Z 128 " =    2.185
peak=    3.609 closest distance to " OE1 GLN A  11 " =    2.068
peak=    3.606 closest distance to " O   HOH Z 386 " =    2.167
peak=    3.605 closest distance to " CZ  PHE A 218 " =    1.120
peak=    3.590 closest distance to " CG  PRO A 243 " =    1.201
peak=    3.583 closest distance to " O   HOH Z 163 " =    1.556
peak=    3.581 closest distance to " O   HOH Z  35 " =    1.995
peak=    3.580 closest distance to " O   HOH Z 418 " =    2.869
peak=    3.573 closest distance to " CB  ARG A  79 " =    0.958
peak=    3.569 closest distance to " O   HOH Z 112 " =    2.130
peak=    3.565 closest distance to " O   HOH Z 250 " =    1.370
peak=    3.560 closest distance to " O   HOH Z  68 " =    1.980
peak=    3.555 closest distance to " O   HOH Z  18 " =    1.378
peak=    3.554 closest distance to " NH1 ARG A  36 " =    1.144
peak=    3.547 closest distance to " CD  LYS A  76 " =    1.769
peak=    3.546 closest distance to " CD  ARG A 195 " =    1.093
peak=    3.545 closest distance to " CB  ASN A 148 " =    1.336
peak=    3.540 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.531 closest distance to " O   HOH Z 364 " =    2.135
peak=    3.530 closest distance to " CG2 THR A 221 " =    1.055
peak=    3.530 closest distance to " O   HOH Z 143 " =    1.600
peak=    3.527 closest distance to " O   HOH Z 109 " =    2.484
peak=    3.525 closest distance to " O   HOH Z 412 " =    3.473
peak=    3.525 closest distance to " O   HOH Z 435 " =    1.994
peak=    3.523 closest distance to " O   HOH Z 298 " =    1.954
peak=    3.522 closest distance to " OG  SER A  62 " =    2.846
peak=    3.512 closest distance to " OE1 GLU A   2 " =    1.727
peak=    3.510 closest distance to " O   HOH Z 261 " =    2.124
peak=    3.510 closest distance to " CB  GLU A 277 " =    3.725
peak=    3.503 closest distance to " O   HOH Z 128 " =    1.880
peak=    3.499 closest distance to " O  BHOH Z  74 " =    1.300
peak=    3.492 closest distance to " O   HOH Z 393 " =    3.418
peak=    3.491 closest distance to " O   HOH Z 395 " =    1.504
peak=    3.486 closest distance to " O   HOH Z 248 " =    1.655
peak=    3.485 closest distance to " O   HOH Z 423 " =    3.214
peak=    3.482 closest distance to " C   ILE A 106 " =    1.767
peak=    3.481 closest distance to " CA  ASN A 176 " =    1.251
peak=    3.479 closest distance to " O   HOH Z 303 " =    2.118
peak=    3.479 closest distance to " CG  GLN A  11 " =    1.281
peak=    3.477 closest distance to " CA  TRP A  85 " =    1.092
peak=    3.474 closest distance to " CB  PRO A 198 " =    1.107
peak=    3.472 closest distance to " CA  SER A  12 " =    1.357
peak=    3.471 closest distance to " O   HOH Z  39 " =    2.163
peak=    3.470 closest distance to " CB  GLN A  73 " =    1.051
peak=    3.468 closest distance to " O   SER A 273 " =    1.721
peak=    3.467 closest distance to " N   CYS A 260 " =    0.845
peak=    3.459 closest distance to " O   HOH Z 380 " =    2.174
peak=    3.458 closest distance to " CB  TRP A 266 " =    1.112
peak=    3.455 closest distance to " O   HOH Z 421 " =    2.061
peak=    3.454 closest distance to " O   HOH Z 345 " =    2.410
peak=    3.453 closest distance to " CB  MET A 105 " =    0.921
peak=    3.451 closest distance to " O   HOH Z 365 " =    1.448
peak=    3.448 closest distance to " O   HOH Z 126 " =    2.074
peak=    3.442 closest distance to " O   HOH Z 427 " =    3.114
peak=    3.438 closest distance to " O   VAL A  72 " =    1.437
peak=    3.438 closest distance to " ND1 HIS A  81 " =    1.199
peak=    3.435 closest distance to " CA  ASN A 217 " =    1.366
peak=    3.434 closest distance to " O   HOH Z 250 " =    1.898
peak=    3.433 closest distance to " O   HOH Z 315 " =    1.799
peak=    3.429 closest distance to " O   HOH Z 173 " =    2.239
peak=    3.427 closest distance to " CA  ASP A 191 " =    0.926
peak=    3.425 closest distance to " CB  SER A 273 " =    0.837
peak=    3.424 closest distance to " CA  ALA A  21 " =    1.356
peak=    3.424 closest distance to " OD1 ASN A  60 " =    1.367
peak=    3.421 closest distance to " O   HOH Z  61 " =    1.483
peak=    3.420 closest distance to " CG BARG A 190 " =    1.371
peak=    3.410 closest distance to " O   HOH Z 156 " =    2.596
peak=    3.409 closest distance to " O   GLY A  91 " =    1.160
peak=    3.409 closest distance to " CB  GLU A 277 " =    1.096
peak=    3.402 closest distance to " CA  THR A  82 " =    1.748
peak=    3.398 closest distance to " CG  MET A 185 " =    1.149
peak=    3.398 closest distance to " O   HOH Z 111 " =    1.548
peak=    3.390 closest distance to " NZ  LYS A 117 " =    0.734
peak=    3.390 closest distance to " CD  ARG A  36 " =    1.170
peak=    3.388 closest distance to " CA  VAL A  41 " =    0.901
peak=    3.381 closest distance to " OD1 ASN A 301 " =    1.110
peak=    3.380 closest distance to " CA  ARG A  36 " =    1.039
peak=    3.371 closest distance to " O   HOH Z 150 " =    1.648
peak=    3.367 closest distance to " O  BHOH Z 338 " =    2.113
peak=    3.362 closest distance to " O   HOH Z 171 " =    1.868
peak=    3.357 closest distance to " O   HOH Z  88 " =    3.231
peak=    3.357 closest distance to " O   HOH Z 298 " =    2.203
peak=    3.357 closest distance to " OG  SER A 245 " =    1.437
peak=    3.357 closest distance to " O   HOH Z 371 " =    3.137
peak=    3.355 closest distance to " O   HOH Z  89 " =    1.867
peak=    3.355 closest distance to " CG2 ILE A 120 " =    1.301
peak=    3.351 closest distance to " CB  GLN A 194 " =    1.041
peak=    3.348 closest distance to " CZ  PHE A  38 " =    1.301
peak=    3.348 closest distance to " O   HOH Z 316 " =    2.738
peak=    3.348 closest distance to " CA  GLU A 152 " =    0.901
peak=    3.341 closest distance to " O   HOH Z  66 " =    2.067
peak=    3.340 closest distance to " CB  ASP A 286 " =    1.099
peak=    3.339 closest distance to " NZ  LYS A 117 " =    3.723
peak=    3.337 closest distance to " CB  PHE A 283 " =    0.839
peak=    3.330 closest distance to " O   HOH Z 162 " =    1.672
peak=    3.326 closest distance to " CB  GLU A 152 " =    1.071
peak=    3.318 closest distance to " CE1 HIS A 108 " =    1.115
peak=    3.316 closest distance to " CD1 LEU A 222 " =    0.797
peak=    3.310 closest distance to " O   HOH Z  78 " =    1.607
peak=    3.308 closest distance to " CB  VAL A 230 " =    0.988
peak=    3.301 closest distance to " NH1AARG A 275 " =    2.411
peak=    3.298 closest distance to " ND2 ASN A 301 " =    1.127
peak=    3.294 closest distance to " O   THR A 251 " =    1.321
peak=    3.293 closest distance to " CA  SER A  87 " =    0.972
peak=    3.289 closest distance to " CD  ARG A 159 " =    0.830
peak=    3.287 closest distance to " N   GLU A   2 " =    0.767
peak=    3.283 closest distance to " CG  GLU A   2 " =    0.983
peak=    3.276 closest distance to " NE2 GLN A  77 " =    3.252
peak=    3.275 closest distance to " CB  ASN A  39 " =    0.829
peak=    3.275 closest distance to " O   HOH Z   6 " =    2.344
peak=    3.272 closest distance to " O   HOH Z 279 " =    1.106
peak=    3.264 closest distance to " CB  TYR A 116 " =    1.160
peak=    3.261 closest distance to " O   HOH Z 359 " =    1.868
peak=    3.261 closest distance to " O   HOH Z 279 " =    1.981
peak=    3.260 closest distance to " O   CYS A 168 " =    1.500
peak=    3.255 closest distance to " CB  GLN A 103 " =    0.852
peak=    3.254 closest distance to " CB  VAL A 265 " =    1.316
peak=    3.253 closest distance to " O   HOH Z 265 " =    2.060
peak=    3.250 closest distance to " N   ARG A 156 " =    1.484
peak=    3.245 closest distance to " O   ASP A 200 " =    1.580
peak=    3.240 closest distance to " CA  LEU A  83 " =    1.291
peak=    3.238 closest distance to " O   HOH Z 124 " =    3.263
peak=    3.236 closest distance to " O   HOH Z 423 " =    1.826
peak=    3.235 closest distance to " CD  ARG A 139 " =    1.312
peak=    3.234 closest distance to " O   HOH Z 365 " =    2.559
peak=    3.233 closest distance to " CD  ARG A  79 " =    2.441
peak=    3.233 closest distance to " CB  LEU A 228 " =    1.218
peak=    3.230 closest distance to " O   HOH Z 435 " =    2.797
peak=    3.228 closest distance to " O   HOH Z 368 " =    1.980
peak=    3.228 closest distance to " CD  LYS A 119 " =    2.028
peak=    3.227 closest distance to " N   ASP A 286 " =    0.919
peak=    3.226 closest distance to " O   HOH Z 419 " =    2.500
peak=    3.224 closest distance to " CG1BVAL A  72 " =    3.112
peak=    3.221 closest distance to " O   HOH Z  53 " =    1.709
peak=    3.221 closest distance to " N   ASN A 252 " =    1.176
peak=    3.220 closest distance to " O   HOH Z 186 " =    1.196
peak=    3.220 closest distance to " CD  GLN A 194 " =    1.673
peak=    3.218 closest distance to " O   ALA A 242 " =    1.131
peak=    3.218 closest distance to " O   HOH Z 353 " =    2.553
peak=    3.218 closest distance to " CD2 PHE A 225 " =    0.947
peak=    3.214 closest distance to " O   HOH Z 170 " =    2.005
peak=    3.213 closest distance to " O   HOH Z  85 " =    1.397
peak=    3.211 closest distance to " CA  GLY A  80 " =    0.809
peak=    3.206 closest distance to " CB  MET A  40 " =    0.831
peak=    3.202 closest distance to " O   HOH Z 426 " =    1.401
peak=    3.200 closest distance to " O   HOH Z  48 " =    1.633
peak=    3.198 closest distance to " OE1 GLN A  73 " =    1.337
peak=    3.198 closest distance to " CD  GLN A  73 " =    1.059
peak=    3.195 closest distance to " CB  ASN A 187 " =    1.227
peak=    3.192 closest distance to " O   HOH Z 345 " =    1.917
peak=    3.178 closest distance to " CB  SER A   3 " =    1.256
peak=    3.174 closest distance to " O   HOH Z  50 " =    1.685
peak=    3.173 closest distance to " O   ALA A 158 " =    1.177
peak=    3.168 closest distance to " O   HOH Z 234 " =    3.908
peak=    3.166 closest distance to " CA  VAL A 112 " =    1.221
peak=    3.164 closest distance to " O  BHOH Z  74 " =    0.750
peak=    3.163 closest distance to " O   HOH Z 253 " =    1.909
peak=    3.156 closest distance to " O   HOH Z 313 " =    1.841
peak=    3.152 closest distance to " O   SER A 164 " =    1.342
peak=    3.151 closest distance to " O   HOH Z 344 " =    3.107
peak=    3.146 closest distance to " CG2 THR A  29 " =    1.109
peak=    3.145 closest distance to " O   HOH Z 141 " =    1.661
peak=    3.138 closest distance to " O   HOH Z 257 " =    2.275
peak=    3.135 closest distance to " CB  PRO A 243 " =    1.134
peak=    3.135 closest distance to " O   HOH Z 132 " =    1.316
peak=    3.135 closest distance to " CA  SER A  32 " =    1.591
peak=    3.134 closest distance to " O   PRO A 213 " =    1.312
peak=    3.133 closest distance to " N   TYR A  15 " =    0.784
peak=    3.129 closest distance to " O   HOH Z   4 " =    0.881
peak=    3.128 closest distance to " CB  TRP A 179 " =    1.872
peak=    3.127 closest distance to " CA  ARG A 156 " =    1.022
peak=    3.127 closest distance to " O   HOH Z 415 " =    1.047
peak=    3.123 closest distance to " CD  ARG A  36 " =    0.951
peak=    3.122 closest distance to " CA  GLY A 133 " =    4.011
peak=    3.119 closest distance to " CA  ARG A 139 " =    1.483
peak=    3.117 closest distance to " O   PHE A  61 " =    1.339
peak=    3.112 closest distance to " CB  GLU A  46 " =    1.041
peak=    3.110 closest distance to " CA  ILE A 120 " =    1.192
peak=    3.109 closest distance to " O   HOH Z 301 " =    1.638
peak=    3.108 closest distance to " CD2 LEU A 297 " =    0.825
peak=    3.103 closest distance to " CB  ALA A 114 " =    1.021
peak=    3.098 closest distance to " CB  SER A 245 " =    1.844
peak=    3.097 closest distance to " O   GLY A  57 " =    2.615
peak=    3.093 closest distance to " O   HOH Z 325 " =    3.831
peak=    3.092 closest distance to " O   HOH Z 200 " =    1.609
peak=    3.071 closest distance to " OG1 THR A 221 " =    1.012
peak=    3.069 closest distance to " CB  ALA A 248 " =    1.386
peak=    3.048 closest distance to " CD1 TRP A 274 " =    1.076
peak=    3.048 closest distance to " O   HOH Z 336 " =    3.816
peak=    3.040 closest distance to " CB  ALA A 299 " =    0.779
peak=    3.033 closest distance to " O   HOH Z 374 " =    2.609

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.708 - 5.705
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.708 - 5.705

peak=   -4.818 closest distance to " O   HOH Z 266 " =    4.762
peak=   -4.580 closest distance to " C   HIS A 108 " =    1.039
peak=   -4.281 closest distance to " CD  GLN A 223 " =    1.747
peak=   -4.252 closest distance to " O   HOH Z 422 " =    1.232
peak=   -4.228 closest distance to " O   HOH Z 120 " =    1.270
peak=   -4.209 closest distance to " O   PRO A 198 " =    1.370
peak=   -4.196 closest distance to " NE2 GLN A 223 " =    1.036
peak=   -4.184 closest distance to " CG2 ILE A  20 " =    2.855
peak=   -4.179 closest distance to " CG2 ILE A  49 " =    2.626
peak=   -4.104 closest distance to " CD2 LEU A 237 " =    2.204
peak=   -4.097 closest distance to " O  BHOH Z 338 " =    1.295
peak=   -4.077 closest distance to " CB  LEU A 167 " =    2.149
peak=   -4.063 closest distance to " CD1 PHE A  59 " =    1.914
peak=   -4.031 closest distance to " OXT GLY A 302 " =    2.868
peak=   -4.007 closest distance to " CD  GLN A  58 " =    0.941
peak=   -3.956 closest distance to " O   HOH Z   7 " =    0.968
peak=   -3.955 closest distance to " CD  ARG A  14 " =    3.317
peak=   -3.946 closest distance to " O   HOH Z  56 " =    0.938
peak=   -3.940 closest distance to " O   HOH Z 155 " =    1.693
peak=   -3.917 closest distance to " O   PHE A 218 " =    1.372
peak=   -3.913 closest distance to " CA  SER A 164 " =    1.991
peak=   -3.894 closest distance to " O   HOH Z  71 " =    1.993
peak=   -3.892 closest distance to " O   HOH Z 290 " =    0.827
peak=   -3.877 closest distance to " O   HOH Z 210 " =    1.037
peak=   -3.868 closest distance to " O   HOH Z 196 " =    1.903
peak=   -3.853 closest distance to " CD1 TRP A 179 " =    1.045
peak=   -3.837 closest distance to " O   HOH Z 234 " =    4.061
peak=   -3.827 closest distance to " O   SER A  95 " =    1.730
peak=   -3.825 closest distance to " CD  ARG A 195 " =    4.966
peak=   -3.810 closest distance to " C   ASN A 285 " =    2.177
peak=   -3.807 closest distance to " CG2 VAL A 189 " =    2.160
peak=   -3.801 closest distance to " O   HOH Z 196 " =    1.701
peak=   -3.773 closest distance to " CD1 ILE A 106 " =    2.089
peak=   -3.759 closest distance to " O   ALA A  34 " =    2.365
peak=   -3.749 closest distance to " CG  PRO A 243 " =    1.663
peak=   -3.737 closest distance to " OG  SER A  97 " =    2.242
peak=   -3.732 closest distance to " O   GLN A  11 " =    1.144
peak=   -3.730 closest distance to " NH2 ARG A  36 " =    1.285
peak=   -3.712 closest distance to " C   THR A 279 " =    1.227
peak=   -3.707 closest distance to " ND2 ASN A  69 " =    1.568
peak=   -3.699 closest distance to " CB  ALA A 161 " =    2.518
peak=   -3.694 closest distance to " CD2 TYR A  30 " =    2.686
peak=   -3.694 closest distance to " O   VAL A 174 " =    1.927
peak=   -3.686 closest distance to " O   HOH Z 377 " =    2.202
peak=   -3.678 closest distance to " CG2 THR A 182 " =    2.304
peak=   -3.678 closest distance to " O   HOH Z  52 " =    1.928
peak=   -3.665 closest distance to " O   HOH Z 423 " =    2.377
peak=   -3.660 closest distance to " N   ALA A  43 " =    2.747
peak=   -3.660 closest distance to " O   HOH Z  38 " =    1.521
peak=   -3.645 closest distance to " O   HOH Z 418 " =    1.377
peak=   -3.645 closest distance to " O   HOH Z 165 " =    1.846
peak=   -3.630 closest distance to " CG2BVAL A  41 " =    2.953
peak=   -3.629 closest distance to " CA  GLY A 133 " =    1.958
peak=   -3.626 closest distance to " CA  VAL A 197 " =    0.951
peak=   -3.613 closest distance to " O   TYR A  15 " =    1.710
peak=   -3.611 closest distance to " OG1 THR A  82 " =    1.466
peak=   -3.608 closest distance to " CD  ARG A 156 " =    2.014
peak=   -3.587 closest distance to " C   ASN A 148 " =    1.800
peak=   -3.576 closest distance to " O   HOH Z 392 " =    1.486
peak=   -3.573 closest distance to " O   HOH Z 424 " =    1.902
peak=   -3.552 closest distance to " O   ALA A   7 " =    1.500
peak=   -3.547 closest distance to " O   HOH Z  37 " =    1.617
peak=   -3.528 closest distance to " CG  GLU A  53 " =    1.267
peak=   -3.525 closest distance to " ND2 ASN A  39 " =    1.136
peak=   -3.523 closest distance to " O   HOH Z 166 " =    1.393
peak=   -3.507 closest distance to " OE1 GLN A 223 " =    2.254
peak=   -3.497 closest distance to " CG  GLN A  11 " =    1.333
peak=   -3.482 closest distance to " CG  MET A  93 " =    2.448
peak=   -3.476 closest distance to " O   HOH Z  29 " =    1.602
peak=   -3.472 closest distance to " CG2BVAL A  72 " =    1.546
peak=   -3.470 closest distance to " OD2 ASP A 171 " =    2.369
peak=   -3.462 closest distance to " O   HOH Z 424 " =    3.280
peak=   -3.461 closest distance to " O   HOH Z 250 " =    1.561
peak=   -3.456 closest distance to " ND2 ASN A 301 " =    2.015
peak=   -3.455 closest distance to " O   GLY A 302 " =    1.950
peak=   -3.454 closest distance to " O   ASP A 171 " =    0.983
peak=   -3.450 closest distance to " CG1 VAL A 112 " =    2.498
peak=   -3.445 closest distance to " CB  ALA A 248 " =    2.221
peak=   -3.438 closest distance to " C   SER A 206 " =    1.475
peak=   -3.437 closest distance to " O   LEU A 300 " =    2.401
peak=   -3.434 closest distance to " O   TRP A  92 " =    2.108
peak=   -3.422 closest distance to " O   HOH Z   6 " =    1.683
peak=   -3.415 closest distance to " CD2 PHE A 225 " =    1.344
peak=   -3.403 closest distance to " N   MET A 188 " =    2.120
peak=   -3.402 closest distance to " O   HOH Z 195 " =    3.410
peak=   -3.400 closest distance to " CH2 TRP A 150 " =    0.965
peak=   -3.400 closest distance to " OD1 ASP A 298 " =    1.876
peak=   -3.396 closest distance to " CE1 TYR A 247 " =    2.550
peak=   -3.395 closest distance to " CB  ALA A 131 " =    2.382
peak=   -3.392 closest distance to " CA  SER A 276 " =    1.421
peak=   -3.389 closest distance to " N   THR A 235 " =    1.218
peak=   -3.388 closest distance to " O   HOH Z 250 " =    1.506
peak=   -3.385 closest distance to " OXT GLY A 302 " =    3.323
peak=   -3.384 closest distance to " O   HOH Z 345 " =    3.090
peak=   -3.377 closest distance to " O   HOH Z 151 " =    1.508
peak=   -3.376 closest distance to " O   HOH Z 189 " =    1.189
peak=   -3.376 closest distance to " CB  SER A 210 " =    1.353
peak=   -3.370 closest distance to " OD2 ASP A 171 " =    1.855
peak=   -3.369 closest distance to " CD2 PHE A  61 " =    2.108
peak=   -3.366 closest distance to " O   HOH Z 109 " =    2.704
peak=   -3.358 closest distance to " O   HOH Z 348 " =    2.340
peak=   -3.351 closest distance to " ND2 ASN A 187 " =    1.455
peak=   -3.351 closest distance to " O   HOH Z 407 " =    1.335
peak=   -3.345 closest distance to " O   HOH Z 198 " =    1.121
peak=   -3.342 closest distance to " O   HOH Z   1 " =    1.893
peak=   -3.333 closest distance to " CG  ASP A 162 " =    1.613
peak=   -3.330 closest distance to " O   PHE A  59 " =    2.427
peak=   -3.328 closest distance to " O   MET A  40 " =    2.752
peak=   -3.325 closest distance to " CG  LEU A  83 " =    1.897
peak=   -3.325 closest distance to " CD  GLN A  73 " =    0.708
peak=   -3.321 closest distance to " CA  PRO A 280 " =    1.020
peak=   -3.319 closest distance to " OD1 ASN A 148 " =    1.456
peak=   -3.318 closest distance to " OE2 GLU A   2 " =    0.933
peak=   -3.316 closest distance to " CB  ASP A 132 " =    2.343
peak=   -3.316 closest distance to " CD2 PHE A  59 " =    2.255
peak=   -3.316 closest distance to " CG  ASN A 252 " =    1.388
peak=   -3.313 closest distance to " CB  PRO A 213 " =    1.542
peak=   -3.311 closest distance to " CA  GLY A 203 " =    2.346
peak=   -3.306 closest distance to " OG1 THR A   4 " =    1.466
peak=   -3.304 closest distance to " OH  TYR A 169 " =    0.837
peak=   -3.303 closest distance to " CD2 PHE A 192 " =    2.115
peak=   -3.302 closest distance to " OG BSER A 134 " =    1.435
peak=   -3.295 closest distance to " CE1 PHE A 204 " =    2.453
peak=   -3.286 closest distance to " C   VAL A 265 " =    0.889
peak=   -3.285 closest distance to " O   HOH Z 130 " =    2.136
peak=   -3.277 closest distance to " O   HOH Z 176 " =    1.662
peak=   -3.272 closest distance to " O   HOH Z 174 " =    2.073
peak=   -3.269 closest distance to " O   ASN A 187 " =    1.533
peak=   -3.266 closest distance to " O   HOH Z 299 " =    1.982
peak=   -3.266 closest distance to " O   HOH Z 221 " =    1.298
peak=   -3.264 closest distance to " O   THR A  52 " =    1.991
peak=   -3.260 closest distance to " O   HOH Z 109 " =    5.705
peak=   -3.255 closest distance to " O   HOH Z 157 " =    3.618
peak=   -3.251 closest distance to " O   HOH Z 197 " =    1.754
peak=   -3.249 closest distance to " CD2 HIS A 115 " =    1.042
peak=   -3.247 closest distance to " OG  SER A   3 " =    1.460
peak=   -3.245 closest distance to " O   HOH Z 351 " =    1.595
peak=   -3.243 closest distance to " O   HOH Z 118 " =    4.724
peak=   -3.239 closest distance to " O   HOH Z 146 " =    1.535
peak=   -3.234 closest distance to " CD1 PHE A 130 " =    2.216
peak=   -3.227 closest distance to " O   HOH Z 135 " =    1.618
peak=   -3.224 closest distance to " O   HOH Z 150 " =    1.785
peak=   -3.220 closest distance to " CG  GLN A  88 " =    0.976
peak=   -3.218 closest distance to " O   ALA A 161 " =    1.398
peak=   -3.217 closest distance to " ND2 ASN A  60 " =    1.253
peak=   -3.217 closest distance to " O   HOH Z 231 " =    1.174
peak=   -3.215 closest distance to " O   HOH Z 313 " =    1.215
peak=   -3.212 closest distance to " CG1 VAL A 197 " =    1.979
peak=   -3.208 closest distance to " O   HOH Z  49 " =    0.828
peak=   -3.206 closest distance to " O   HOH Z  41 " =    1.958
peak=   -3.205 closest distance to " O   HOH Z 393 " =    1.110
peak=   -3.201 closest distance to " C   GLY A 133 " =    1.223
peak=   -3.198 closest distance to " O   GLY A  75 " =    1.588
peak=   -3.195 closest distance to " OE1 GLN A 183 " =    1.660
peak=   -3.190 closest distance to " O   HOH Z 222 " =    1.171
peak=   -3.189 closest distance to " CB  SER A 146 " =    2.087
peak=   -3.188 closest distance to " O   HOH Z 139 " =    3.491
peak=   -3.184 closest distance to " O   HOH Z 145 " =    2.588
peak=   -3.179 closest distance to " CD  GLU A 236 " =    0.961
peak=   -3.173 closest distance to " O   HOH Z 126 " =    1.491
peak=   -3.171 closest distance to " CE  MET A 105 " =    2.021
peak=   -3.169 closest distance to " O   HOH Z 368 " =    1.940
peak=   -3.168 closest distance to " O   HOH Z 401 " =    0.868
peak=   -3.156 closest distance to " O   HOH Z 200 " =    1.265
peak=   -3.150 closest distance to " C   GLY A  91 " =    1.228
peak=   -3.150 closest distance to " CA  GLU A 277 " =    1.318
peak=   -3.149 closest distance to " O   HOH Z  78 " =    1.687
peak=   -3.148 closest distance to " CZ  TYR A 169 " =    1.890
peak=   -3.145 closest distance to " O   HOH Z 384 " =    1.877
peak=   -3.144 closest distance to " O   HOH Z 426 " =    1.719
peak=   -3.138 closest distance to " O   GLY A 196 " =    0.950
peak=   -3.132 closest distance to " CG1BVAL A  72 " =    1.862
peak=   -3.126 closest distance to " O   HOH Z 377 " =    1.100
peak=   -3.126 closest distance to " NH1 ARG A 195 " =    2.358
peak=   -3.125 closest distance to " CE  MET A  93 " =    1.393
peak=   -3.123 closest distance to " N   ASP A 272 " =    1.210
peak=   -3.120 closest distance to " SD  MET A  40 " =    1.947
peak=   -3.120 closest distance to " CB  ALA A  43 " =    2.687
peak=   -3.119 closest distance to " O   ARG A  66 " =    1.203
peak=   -3.116 closest distance to " C   GLN A 144 " =    0.859
peak=   -3.116 closest distance to " O   GLY A 241 " =    2.139
peak=   -3.110 closest distance to " NH2 ARG A  66 " =    5.606
peak=   -3.102 closest distance to " O   HOH Z 196 " =    2.026
peak=   -3.095 closest distance to " O   HOH Z 210 " =    1.433
peak=   -3.085 closest distance to " O   HOH Z 115 " =    1.410
peak=   -3.064 closest distance to " CG  LYS A 181 " =    2.329
peak=   -3.064 closest distance to " O   HOH Z 422 " =    0.994
peak=   -3.063 closest distance to " O   HOH Z 166 " =    0.878
peak=   -3.061 closest distance to " SD  MET A  40 " =    2.012
peak=   -3.033 closest distance to " CG2BVAL A  41 " =    1.837
peak=   -3.015 closest distance to " NH2 ARG A  66 " =    1.523

================= 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    :  0.4614 0.4503   6.277299e+00   6.260374e+00
   1_bss:  0.4532 0.4387   6.269123e+00   6.250739e+00
   1_xyz:  0.3651 0.3903   6.136573e+00   6.176088e+00
   1_adp:  0.3340 0.3932   6.083545e+00   6.181285e+00
   1_occ:  0.3336 0.3937   6.082622e+00   6.180941e+00
   2_bss:  0.3326 0.3920   6.082803e+00   6.180725e+00
   2_xyz:  0.2766 0.3334   5.927605e+00   6.061613e+00
   2_adp:  0.2581 0.3277   5.893173e+00   6.050697e+00
   2_occ:  0.2578 0.3276   5.892514e+00   6.050614e+00
   3_bss:  0.2576 0.3275   5.893489e+00   6.050542e+00
   3_xyz:  0.2087 0.2706   5.693071e+00   5.888813e+00
   3_adp:  0.1940 0.2527   5.629256e+00   5.824589e+00
   3_occ:  0.1938 0.2526   5.628755e+00   5.824807e+00
   4_bss:  0.1937 0.2519   5.628514e+00   5.821891e+00
   4_xyz:  0.1617 0.2124   5.461542e+00   5.673731e+00
   4_adp:  0.1504 0.1980   5.397422e+00   5.607081e+00
   4_occ:  0.1503 0.1979   5.396915e+00   5.606775e+00
   5_bss:  0.1506 0.1983   5.398442e+00   5.607071e+00
   5_xyz:  0.1315 0.1800   5.286014e+00   5.510411e+00
   5_adp:  0.1278 0.1772   5.262633e+00   5.489375e+00
   5_occ:  0.1277 0.1769   5.261898e+00   5.488955e+00
   5_bss:  0.1282 0.1767   5.263142e+00   5.488808e+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:  0.307  29.868  -1.182   4.624  -1.829   0.000  -0.000  -0.000
   1_xyz:  0.307  29.868  -1.182   4.624  -1.829   0.000  -0.000  -0.000
   1_adp:  0.307  29.868  -1.182   4.624  -1.829   0.000  -0.000  -0.000
   1_occ:  0.307  29.868  -1.182   4.624  -1.829   0.000  -0.000  -0.000
   2_bss:  0.299  37.145  -1.617   2.920  -0.529   0.000  -0.000  -0.000
   2_xyz:  0.299  37.145  -1.617   2.920  -0.529   0.000  -0.000  -0.000
   2_adp:  0.299  37.145  -1.617   2.920  -0.529   0.000  -0.000  -0.000
   2_occ:  0.299  37.145  -1.617   2.920  -0.529   0.000  -0.000  -0.000
   3_bss:  0.316  47.921  -1.328   2.007  -0.002   0.000  -0.000  -0.000
   3_xyz:  0.316  47.921  -1.328   2.007  -0.002   0.000  -0.000  -0.000
   3_adp:  0.316  47.921  -1.328   2.007  -0.002   0.000  -0.000  -0.000
   3_occ:  0.316  47.921  -1.328   2.007  -0.002   0.000  -0.000  -0.000
   4_bss:  0.320  54.750  -2.156   0.337  -0.591   0.000  -0.000  -0.000
   4_xyz:  0.320  54.750  -2.156   0.337  -0.591   0.000  -0.000  -0.000
   4_adp:  0.320  54.750  -2.156   0.337  -0.591   0.000  -0.000  -0.000
   4_occ:  0.320  54.750  -2.156   0.337  -0.591   0.000  -0.000  -0.000
   5_bss:  0.325  57.491  -2.516  -0.394  -0.809  -0.000  -0.000  -0.000
   5_xyz:  0.325  57.491  -2.516  -0.394  -0.809  -0.000  -0.000  -0.000
   5_adp:  0.325  57.491  -2.516  -0.394  -0.809  -0.000  -0.000  -0.000
   5_occ:  0.325  57.491  -2.516  -0.394  -0.809  -0.000  -0.000  -0.000
   5_bss:  0.325  57.494  -2.512  -0.620  -0.716  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.134 0.4830  0.6525    65073.331
   1_bss:  51.801 0.4987  0.6884    61413.086
   1_xyz:  45.192 0.5794  0.7759    46250.800
   1_adp:  44.816 0.5839  0.7893    46234.095
   1_occ:  44.758 0.5846  0.7878    45985.913
   2_bss:  44.479 0.5880  0.7874    45582.293
   2_xyz:  37.021 0.6762  0.8884    31664.160
   2_adp:  36.105 0.6872  0.8812    30597.471
   2_occ:  36.072 0.6876  0.8814    30558.992
   3_bss:  36.028 0.6882  0.8826    30585.306
   3_xyz:  28.038 0.7781  0.9706    19299.185
   3_adp:  25.285 0.8086  0.9881    16671.945
   3_occ:  25.261 0.8088  0.9885    16664.646
   4_bss:  25.124 0.8101  0.9549    16486.055
   4_xyz:  20.741 0.8540  0.9811    11546.986
   4_adp:  18.878 0.8723  0.9817    10010.659
   4_occ:  18.867 0.8724  0.9818    10008.026
   5_bss:  18.856 0.8726  0.9672    10001.515
   5_xyz:  16.796 0.8912  0.9780     8251.870
   5_adp:  16.310 0.8958  0.9744     8014.505
   5_occ:  16.296 0.8959  0.9744     8003.287
   5_bss:  16.292 0.8959  0.9731     7993.340
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9670e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9670e-01
   1_xyz:   1.547  0.012  0.092 15.886  0.006  4.103   1.2607e-01
   1_adp:   1.547  0.012  0.092 15.886  0.006  4.103   1.2607e-01
   1_occ:   1.547  0.012  0.092 15.886  0.006  4.103   1.2607e-01
   2_bss:   1.547  0.012  0.092 15.886  0.006  4.103   1.2607e-01
   2_xyz:   1.407  0.010  0.090 15.376  0.005  4.109   1.0353e-01
   2_adp:   1.407  0.010  0.090 15.376  0.005  4.109   1.0353e-01
   2_occ:   1.407  0.010  0.090 15.376  0.005  4.109   1.0353e-01
   3_bss:   1.407  0.010  0.090 15.376  0.005  4.109   1.0353e-01
   3_xyz:   1.162  0.009  0.073 14.636  0.004  4.116   7.6556e-02
   3_adp:   1.162  0.009  0.073 14.636  0.004  4.116   7.6556e-02
   3_occ:   1.162  0.009  0.073 14.636  0.004  4.116   7.6556e-02
   4_bss:   1.162  0.009  0.073 14.636  0.004  4.116   7.6556e-02
   4_xyz:   1.041  0.007  0.069 14.267  0.004  4.118   6.1436e-02
   4_adp:   1.041  0.007  0.069 14.267  0.004  4.118   6.1436e-02
   4_occ:   1.041  0.007  0.069 14.267  0.004  4.118   6.1436e-02
   5_bss:   1.041  0.007  0.069 14.267  0.004  4.118   6.1436e-02
   5_xyz:   1.013  0.007  0.071 14.431  0.004  4.111   5.9413e-02
   5_adp:   1.013  0.007  0.071 14.431  0.004  4.111   5.9413e-02
   5_occ:   1.013  0.007  0.071 14.431  0.004  4.111   5.9413e-02
   5_bss:   1.013  0.007  0.071 14.431  0.004  4.111   5.9413e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.151   2.4261e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.151   2.4261e-01
   1_xyz:   8.447  0.070  0.433 85.461  0.036  1.762   1.0585e-01
   1_adp:   8.447  0.070  0.433 85.461  0.036  1.762   1.0585e-01
   1_occ:   8.447  0.070  0.433 85.461  0.036  1.762   1.0585e-01
   2_bss:   8.447  0.070  0.433 85.461  0.036  1.762   1.0585e-01
   2_xyz:  11.001  0.057  0.322 87.345  0.035  2.101   1.4247e-01
   2_adp:  11.001  0.057  0.322 87.345  0.035  2.101   1.4247e-01
   2_occ:  11.001  0.057  0.322 87.345  0.035  2.101   1.4247e-01
   3_bss:  11.001  0.057  0.322 87.345  0.035  2.101   1.4247e-01
   3_xyz:   7.310  0.047  0.342 81.841  0.033  2.268   6.8760e-02
   3_adp:   7.310  0.047  0.342 81.841  0.033  2.268   6.8760e-02
   3_occ:   7.310  0.047  0.342 81.841  0.033  2.268   6.8760e-02
   4_bss:   7.310  0.047  0.342 81.841  0.033  2.268   6.8760e-02
   4_xyz:   7.435  0.053  0.218 78.044  0.031  2.336   4.4957e-02
   4_adp:   7.435  0.053  0.218 78.044  0.031  2.336   4.4957e-02
   4_occ:   7.435  0.053  0.218 78.044  0.031  2.336   4.4957e-02
   5_bss:   7.435  0.053  0.218 78.044  0.031  2.336   4.4957e-02
   5_xyz:   7.201  0.046  0.234 79.921  0.031  2.378   4.0235e-02
   5_adp:   7.201  0.046  0.234 79.921  0.031  2.378   4.0235e-02
   5_occ:   7.201  0.046  0.234 79.921  0.031  2.378   4.0235e-02
   5_bss:   7.201  0.046  0.234 79.921  0.031  2.378   4.0235e-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:  93.87   0.00  18.98  76.72   0.00  15.80  93.87   0.00  36.28
   1_occ:  93.87   0.00  18.98  76.72   0.00  15.80  93.87   0.00  36.28
   2_bss:  93.87   0.00  18.98  76.72   0.00  15.80  93.87   0.00  36.28
   2_xyz:  93.87   0.00  18.98  76.72   0.00  15.80  93.87   0.00  36.28
   2_adp: 104.77   0.00  19.21  99.21   0.00  15.61 104.77   2.73  38.79
   2_occ: 104.77   0.00  19.21  99.21   0.00  15.61 104.77   2.73  38.79
   3_bss: 104.77   0.00  19.21  99.21   0.00  15.61 104.77   2.73  38.79
   3_xyz: 104.77   0.00  19.21  99.21   0.00  15.61 104.77   2.73  38.79
   3_adp: 104.16   0.00  18.44  97.98   0.00  14.45 104.16   3.91  40.15
   3_occ: 104.16   0.00  18.44  97.98   0.00  14.45 104.16   3.91  40.15
   4_bss: 104.16   0.00  18.44  97.98   0.00  14.45 104.16   3.91  40.15
   4_xyz: 104.16   0.00  18.44  97.98   0.00  14.45 104.16   3.91  40.15
   4_adp: 101.44   0.60  17.65 101.44   0.60  13.21  99.80   3.65  41.83
   4_occ: 101.44   0.60  17.65 101.44   0.60  13.21  99.80   3.65  41.83
   5_bss: 101.44   0.60  17.65 101.44   0.60  13.21  99.80   3.65  41.83
   5_xyz: 101.44   0.60  17.65 101.44   0.60  13.21  99.80   3.65  41.83
   5_adp: 101.71   0.00  17.43 101.71   0.00  12.96  99.22   0.35  41.79
   5_occ: 101.71   0.00  17.43 101.71   0.00  12.96  99.22   0.35  41.79
   5_bss: 101.71   0.00  17.43 101.71   0.00  12.96  99.23   0.35  41.79
------------------------------------------------------------------------
 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:    2.341    0.018    0.337
   1_adp:    2.341    0.018    0.337
   1_occ:    2.341    0.018    0.337
   2_bss:    2.341    0.018    0.337
   2_xyz:    1.869    0.014    0.537
   2_adp:    1.869    0.014    0.537
   2_occ:    1.869    0.014    0.537
   3_bss:    1.869    0.014    0.537
   3_xyz:    1.789    0.034    0.685
   3_adp:    1.789    0.034    0.685
   3_occ:    1.789    0.034    0.685
   4_bss:    1.789    0.034    0.685
   4_xyz:    1.794    0.058    0.763
   4_adp:    1.794    0.058    0.763
   4_occ:    1.794    0.058    0.763
   5_bss:    1.794    0.058    0.763
   5_xyz:    1.884    0.075    0.824
   5_adp:    1.884    0.075    0.824
   5_occ:    1.884    0.075    0.824
   5_bss:    1.884    0.075    0.824
------------------------------------------------------------------------

CPU time actual refinement: 336.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/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_235/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_235/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.49 
  Macro-tasks:
    bulk solvent and scale       = 38.77  
    individual site refinement   = 138.03 
    weights calculation          = 29.22  
    collect and process          = 6.38   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 212.52 
  Micro-tasks:
    mask                            = 2.91   
    f_calc                          = 108.71 
    alpha_beta                      = 8.09   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 116.94 
    fmodel                         = 6.22   
    r_factors                      = 0.16   
    phase_errors                   = 10.51  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.94 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.803 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    646 calls, 108.33 s
gradients_fft:          591 calls, 103.85 s

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

# Date 2008-01-16 Time 04:20:13 PST -0800 (1200486013.14 s)
Start R-work = 0.4614, R-free = 0.4503 (no bulk solvent and anisotropic scale)
Final R-work = 0.1482, R-free = 0.1939 (no bulk solvent and anisotropic scale)

Start R-work = 0.4532, R-free = 0.4387
Final R-work = 0.1282, R-free = 0.1767