# Date 2008-01-16 Time 06:17:08 PST -0800 (1200493028.48 s)
#phil __OFF__

Command line arguments: "../1080.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15067
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1080

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 48.1033, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97152
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.91924

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9715

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97152
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.91924

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2195 [2234/2263]  2011   223  10.0%
  bin  2:  4.2195 -  3.3613 [2130/2153]  1917   213  10.0%
  bin  3:  3.3613 -  2.9400 [2109/2134]  1896   213  10.1%
  bin  4:  2.9400 -  2.6728 [2089/2105]  1887   202   9.7%
  bin  5:  2.6728 -  2.4821 [2089/2133]  1877   212  10.1%
  bin  6:  2.4821 -  2.3363 [2062/2090]  1860   202   9.8%
  bin  7:  2.3363 -  2.2197 [2052/2088]  1844   208  10.1%
  bin  8:  2.2197 -  2.1234 [2058/2100]  1852   206  10.0%
  bin  9:  2.1234 -  2.0418 [2014/2074]  1811   203  10.1%
  bin 10:  2.0418 -  1.9715 [ 752/2107]   675    77  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.35 -     2.06: 11
        2.06 -     2.77: 491
        2.77 -     3.48: 4489
        3.48 -     4.19: 9279
        4.19 -     4.90: 13769
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.348 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.409 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.539 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.626 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.650 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28034 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_1080/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 48.10325 85.09415 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: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4660   r_free= 0.4490   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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: 6.278940                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.3718 0.3965       6.562      6.5627|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.4063 0.4034      6.8403       6.786|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.4423 0.3924      6.6639       6.646|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.4629 0.4637      6.5082      6.5021|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.4831 0.4855      6.3494      6.3429|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.5129 0.4540      6.2763      6.1551|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.4966 0.4294      6.2378      6.1604|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.5136 0.5044      6.1425      6.1969|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.5311 0.5018      6.1397      6.0703|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.4957 0.5076      6.0689      6.1099|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.5193 0.5123      6.0261      5.9903|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.5013 0.5105      5.9224      5.9831|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.5007 0.4046      5.8594       5.791|
| 14:  2.0207 -  1.9715 0.22    305   32 0.5512 0.5232      5.8205      5.7945|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.69  35.25   0.82     0.73      76169.12|
|  2:  4.7066 -  3.7547  1386   147  0.70  35.05   0.90     0.79     101127.67|
|  3:  3.7547 -  3.2857  1372   155  0.60  43.44   0.89     0.77     108153.09|
|  4:  3.2857 -  2.9878  1349   151  0.52  50.01   0.90     0.71      95991.74|
|  5:  2.9878 -  2.7751  1340   148  0.46  55.25   0.86     0.65      76812.59|
|  6:  2.7751 -  2.6123  1351   151  0.45  55.82   0.88     0.63      62392.65|
|  7:  2.6123 -  2.4821  1341   147  0.46  55.02   0.91     0.62      55105.14|
|  8:  2.4821 -  2.3745  1316   144  0.43  57.82   0.87     0.62      52545.25|
|  9:  2.3745 -  2.2834  1331   149  0.42  58.32   0.90     0.61      48145.95|
| 10:  2.2834 -  2.2049  1323   147  0.42  58.15   0.93     0.62      46056.67|
| 11:  2.2049 -  2.1361  1311   144  0.40  60.19   0.91     0.59      42716.66|
| 12:  2.1361 -  2.0752  1316   148  0.37  62.47   0.93     0.59      40192.04|
| 13:  2.0752 -  2.0207  1140   132  0.39  61.08   0.94     0.58      32992.96|
| 14:  2.0207 -  1.9715   305    32  0.42  58.58   0.90     0.64      25948.04|
|alpha:            min =        0.58 max =            0.79 mean =         0.66|
|beta:             min =    25948.04 max =       108153.09 mean =     64555.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.71|
|phase err.(test): min =        0.00 max =           89.99 mean =        52.63|
|-----------------------------------------------------------------------------|

============================== 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 = 15.533625             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.879   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.327083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.398   (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 |  1.348 -  1.703:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.703 -  2.058:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.058 -  2.413:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.413 -  2.769:      469 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.769 -  3.124:     2191 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.124 -  3.479:     2298 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.479 -  3.834:     4387 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.834 -  4.190:     4892 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.190 -  4.545:     6214 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.545 -  4.900:     7555 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.348 |       0.471 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    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: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4660   r_free= 0.4490   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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: 6.278940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4582   r_free= 0.4402   ksol= 0.28   Bsol= 18.30   scale= 0.924   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,4.24,-0.36,0.00,-0.00,-0.00); trace/3= 0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.273250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.218048             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.121131              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.226   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4582      final r-factor (work) = 0.3521          |
| start r-factor (free) = 0.4402      final r-factor (free) = 0.3940          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.6241 = 13.22 * 0.50 * 6.2703 + 1.00 * 0.1838                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.7398 = 13.22 * 0.50 * 6.1403 + 1.00 * 0.1585                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3521      final r-factor (work) = 0.3253          |
| start r-factor (free) = 0.3940      final r-factor (free) = 0.4013          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8904 = 1.12 * 1.00 * 6.1403 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8252 = 1.12 * 1.00 * 6.0645 + 1.00 * 0.0261                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.34  17.68    None  None   None       |
|    all(noH): 2823   0      0.00    121.34  17.68    None  None   None       |
|    Sol.    : 438    0      0.00    70.22   36.36    None  None   None       |
|    Mac.    : 2385   0      0.00    121.34  14.25    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 -  12.134: 1184   |   5:    60.668 -  72.802:    9        |
|      1:    12.134 -  24.267:  955   |   6:    72.802 -  84.935:    0        |
|      2:    24.267 -  36.401:  377   |   7:    84.935 -  97.069:    0        |
|      3:    36.401 -  48.535:  213   |   8:    97.069 - 109.203:    0        |
|      4:    48.535 -  60.668:   84   |   9:   109.203 - 121.336:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3253 r_free = 0.4013             target_work(ml) = 6.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3251 r_free = 0.4004             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3251   r_free= 0.4004   ksol= 0.28   Bsol= 18.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,4.24,-0.36,0.00,-0.00,-0.00); trace/3= 0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.066288                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3243   r_free= 0.3979   ksol= 0.32   Bsol= 55.60   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,2.27,-0.64,0.00,-0.00,-0.00); trace/3= 0.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.066479                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.048047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.624  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.091803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.532  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3243      final r-factor (work) = 0.2685          |
| start r-factor (free) = 0.3979      final r-factor (free) = 0.3219          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5653 = 8.05 * 0.50 * 6.0653 + 1.00 * 0.1585                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2129 = 8.05 * 0.50 * 5.9944 + 1.00 * 0.0913                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2685      final r-factor (work) = 0.2488          |
| start r-factor (free) = 0.3219      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5664 = 1.09 * 1.00 * 5.9944 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4195 = 1.09 * 1.00 * 5.8633 + 1.00 * 0.0179                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.73   18.88    None  None   None       |
|    all(noH): 2823   0      0.00    95.73   18.88    None  None   None       |
|    Sol.    : 438    0      1.24    95.73   40.92    None  None   None       |
|    Mac.    : 2385   0      0.00    93.86   14.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.573:  971   |   5:    47.867 -  57.440:   93        |
|      1:     9.573 -  19.147:  890   |   6:    57.440 -  67.013:   61        |
|      2:    19.147 -  28.720:  379   |   7:    67.013 -  76.587:   43        |
|      3:    28.720 -  38.293:  242   |   8:    76.587 -  86.160:   12        |
|      4:    38.293 -  47.867:  121   |   9:    86.160 -  95.733:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2488 r_free = 0.3207             target_work(ml) = 5.863         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2486 r_free = 0.3205             target_work(ml) = 5.862         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2486   r_free= 0.3205   ksol= 0.32   Bsol= 55.60   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,2.27,-0.64,0.00,-0.00,-0.00); trace/3= 0.16                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.862221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2488   r_free= 0.3202   ksol= 0.32   Bsol= 67.68   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,1.56,-0.51,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.861749                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.456299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.859   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.295  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2488      final r-factor (work) = 0.2000          |
| start r-factor (free) = 0.3202      final r-factor (free) = 0.2547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0875 = 5.46 * 0.50 * 5.8634 + 1.00 * 0.0913                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8362 = 5.46 * 0.50 * 5.7758 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2000      final r-factor (work) = 0.1818          |
| start r-factor (free) = 0.2547      final r-factor (free) = 0.2318          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8275 = 0.66 * 1.00 * 5.7758 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7141 = 0.66 * 1.00 * 5.6047 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.98  18.29    None  None   None       |
|    all(noH): 2823   0      0.00    108.98  18.29    None  None   None       |
|    Sol.    : 438    0      3.86    103.26  44.10    None  None   None       |
|    Mac.    : 2385   0      0.00    108.98  13.55    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 -  10.898: 1276   |   5:    54.488 -  65.386:   87        |
|      1:    10.898 -  21.795:  859   |   6:    65.386 -  76.283:   49        |
|      2:    21.795 -  32.693:  244   |   7:    76.283 -  87.181:   22        |
|      3:    32.693 -  43.590:  152   |   8:    87.181 -  98.078:    9        |
|      4:    43.590 -  54.488:  120   |   9:    98.078 - 108.976:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1818 r_free = 0.2318             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1816 r_free = 0.2317             target_work(ml) = 5.562         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1816   r_free= 0.2317   ksol= 0.32   Bsol= 67.68   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,1.56,-0.51,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.562320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1816   r_free= 0.2318   ksol= 0.33   Bsol= 73.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,0.13,-0.98,0.00,-0.00,-0.00); trace/3= -0.76                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.562919                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.456973              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.794   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386457              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.344   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1816      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2318      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9685 = 2.46 * 0.50 * 5.6081 + 1.00 * 0.0789                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8043 = 2.46 * 0.50 * 5.4907 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1539      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.1989      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1384 = 0.39 * 1.00 * 5.4907 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0988 = 0.39 * 1.00 * 5.3958 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.34  17.63    None  None   None       |
|    all(noH): 2823   0      0.00    114.34  17.63    None  None   None       |
|    Sol.    : 438    0      4.26    107.83  43.96    None  None   None       |
|    Mac.    : 2385   0      0.00    114.34  12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.434: 1429   |   5:    57.168 -  68.602:   72        |
|      1:    11.434 -  22.867:  815   |   6:    68.602 -  80.035:   44        |
|      2:    22.867 -  34.301:  189   |   7:    80.035 -  91.469:   12        |
|      3:    34.301 -  45.734:  135   |   8:    91.469 - 102.902:    5        |
|      4:    45.734 -  57.168:  117   |   9:   102.902 - 114.336:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1468 r_free = 0.1919             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1467 r_free = 0.1918             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1918   ksol= 0.33   Bsol= 73.55   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,0.13,-0.98,0.00,-0.00,-0.00); trace/3= -0.76                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1470   r_free= 0.1923   ksol= 0.32   Bsol= 69.94   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.44,-1.06,-0.00,-0.00,-0.00); trace/3= -1.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.378612                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.550745              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.162052              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.124   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1470      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1923      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6408 = 3.55 * 0.50 * 5.3971 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5125 = 3.55 * 0.50 * 5.3161 + 1.00 * 0.0745                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1282      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1768      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8771 = 0.16 * 1.00 * 5.3161 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8870 = 0.16 * 1.00 * 5.2617 + 1.00 * 0.0344                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.02  17.57    None  None   None       |
|    all(noH): 2823   0      0.00    114.02  17.57    None  None   None       |
|    Sol.    : 438    0      4.75    107.77  43.59    None  None   None       |
|    Mac.    : 2385   0      0.00    114.02  12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.402: 1453   |   5:    57.012 -  68.414:   67        |
|      1:    11.402 -  22.805:  807   |   6:    68.414 -  79.816:   45        |
|      2:    22.805 -  34.207:  178   |   7:    79.816 -  91.219:   11        |
|      3:    34.207 -  45.609:  132   |   8:    91.219 - 102.621:    5        |
|      4:    45.609 -  57.012:  120   |   9:   102.621 - 114.023:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1267 r_free = 0.1746             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1745             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1745   ksol= 0.32   Bsol= 69.94   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.44,-1.06,-0.00,-0.00,-0.00); trace/3= -1.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.0985 0.1314      5.3933      5.5866|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.0881 0.1100      5.4548      5.6542|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.1146 0.1713      5.5342      5.9191|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.1451 0.1735      5.5726      5.7129|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.1556 0.2010      5.4599      5.6365|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.1487 0.2155      5.3429      5.5413|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.1426 0.1988      5.2787      5.4998|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.1412 0.1892      5.1815      5.4015|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.1378 0.1924      5.1336       5.342|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.1293 0.1908      5.0708      5.3426|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.1283 0.2006      5.0139      5.2994|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.1312 0.1883      4.9702      5.1974|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.1359 0.1940      4.8965      5.1154|
| 14:  2.0207 -  1.9715 0.22    305   32 0.1297 0.1741      4.7722      4.9896|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.94   9.69   0.96     0.94       7725.60|
|  2:  4.7066 -  3.7547  1386   147  0.95   8.65   1.01     0.99       9600.54|
|  3:  3.7547 -  3.2857  1372   155  0.92  12.72   1.02     1.02      11832.55|
|  4:  3.2857 -  2.9878  1349   151  0.90  16.52   1.01     0.98      13099.63|
|  5:  2.9878 -  2.7751  1340   148  0.87  19.62   1.00     0.98      11267.84|
|  6:  2.7751 -  2.6123  1351   151  0.88  18.40   0.99     0.97       8893.75|
|  7:  2.6123 -  2.4821  1341   147  0.89  17.66   0.99     0.96       7717.16|
|  8:  2.4821 -  2.3745  1316   144  0.88  18.58   1.00     0.97       6841.60|
|  9:  2.3745 -  2.2834  1331   149  0.88  17.97   0.99     0.95       5966.44|
| 10:  2.2834 -  2.2049  1323   147  0.89  17.35   0.99     0.95       5426.42|
| 11:  2.2049 -  2.1361  1311   144  0.88  18.08   0.99     0.94       5059.00|
| 12:  2.1361 -  2.0752  1316   148  0.89  18.10   0.99     0.97       4781.74|
| 13:  2.0752 -  2.0207  1140   132  0.88  18.54   0.98     0.98       4067.01|
| 14:  2.0207 -  1.9715   305    32  0.87  18.66   0.98     0.94       3207.06|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3207.06 max =        13099.63 mean =      7857.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.24|
|phase err.(test): min =        0.00 max =           89.11 mean =        15.48|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1745   ksol= 0.33   Bsol= 69.94   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-0.76,-1.11,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1745   ksol= 0.33   Bsol= 69.94   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-0.76,-1.11,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252849                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7066 0.99   1449  164 0.0986 0.1317      5.3938      5.5864|
|  2:  4.7066 -  3.7547 0.99   1386  147 0.0881 0.1101      5.4547      5.6538|
|  3:  3.7547 -  3.2857 0.99   1372  155 0.1147 0.1713      5.5345      5.9202|
|  4:  3.2857 -  2.9878 0.99   1349  151 0.1450 0.1735      5.5728      5.7126|
|  5:  2.9878 -  2.7751 0.99   1340  148 0.1555 0.2009      5.4597      5.6363|
|  6:  2.7751 -  2.6123 0.99   1351  151 0.1487 0.2151      5.3426      5.5404|
|  7:  2.6123 -  2.4821 0.98   1341  147 0.1426 0.1987      5.2782       5.499|
|  8:  2.4821 -  2.3745 0.98   1316  144 0.1410 0.1890      5.1812      5.4013|
|  9:  2.3745 -  2.2834 0.99   1331  149 0.1376 0.1927      5.1327      5.3421|
| 10:  2.2834 -  2.2049 0.98   1323  147 0.1293 0.1909      5.0706      5.3427|
| 11:  2.2049 -  2.1361 0.97   1311  144 0.1282 0.2002       5.013      5.2987|
| 12:  2.1361 -  2.0752 0.99   1316  148 0.1312 0.1887      4.9705       5.198|
| 13:  2.0752 -  2.0207 0.85   1140  132 0.1359 0.1937      4.8963      5.1143|
| 14:  2.0207 -  1.9715 0.22    305   32 0.1298 0.1738      4.7718      4.9865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7066  1449   164  0.94   9.69   0.96     0.94       7724.60|
|  2:  4.7066 -  3.7547  1386   147  0.95   8.65   1.01     0.99       9593.17|
|  3:  3.7547 -  3.2857  1372   155  0.92  12.71   1.02     1.02      11835.81|
|  4:  3.2857 -  2.9878  1349   151  0.90  16.53   1.01     0.98      13101.93|
|  5:  2.9878 -  2.7751  1340   148  0.87  19.60   1.00     0.97      11256.82|
|  6:  2.7751 -  2.6123  1351   151  0.88  18.38   0.99     0.97       8879.80|
|  7:  2.6123 -  2.4821  1341   147  0.89  17.63   0.98     0.96       7705.07|
|  8:  2.4821 -  2.3745  1316   144  0.88  18.58   1.00     0.97       6839.19|
|  9:  2.3745 -  2.2834  1331   149  0.88  17.96   0.99     0.94       5971.75|
| 10:  2.2834 -  2.2049  1323   147  0.89  17.34   0.98     0.94       5427.49|
| 11:  2.2049 -  2.1361  1311   144  0.88  18.06   0.98     0.94       5052.66|
| 12:  2.1361 -  2.0752  1316   148  0.89  18.10   0.98     0.96       4783.13|
| 13:  2.0752 -  2.0207  1140   132  0.88  18.52   0.98     0.97       4060.87|
| 14:  2.0207 -  1.9715   305    32  0.87  18.64   0.97     0.94       3194.66|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3194.66 max =        13101.93 mean =      7854.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.23|
|phase err.(test): min =        0.00 max =           89.11 mean =        15.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.154)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.03  17.57    None  None   None       |
|    all(noH): 2823   0      0.00    114.03  17.57    None  None   None       |
|    Sol.    : 438    0      4.75    107.78  43.60    None  None   None       |
|    Mac.    : 2385   0      0.00    114.03  12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.405: 1453   |   5:    57.015 -  68.417:   67        |
|      1:    11.405 -  22.808:  807   |   6:    68.417 -  79.819:   45        |
|      2:    22.808 -  34.210:  178   |   7:    79.819 -  91.222:   11        |
|      3:    34.210 -  45.612:  132   |   8:    91.222 - 102.624:    5        |
|      4:    45.612 -  57.015:  120   |   9:   102.624 - 114.026:    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)= 356         
Filter by distance & map next to the model:
   mapped sites are within: 0.508 - 5.613
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 356
   mapped sites are within: 0.711 - 5.613

peak=    7.346 closest distance to " O   HOH Z  41 " =    1.009
peak=    6.736 closest distance to " O   HOH Z 120 " =    1.026
peak=    6.519 closest distance to " O   HOH Z 400 " =    0.723
peak=    5.634 closest distance to " O   HOH Z 210 " =    1.423
peak=    5.620 closest distance to " O   HOH Z 111 " =    2.121
peak=    5.424 closest distance to " CB  SER A  63 " =    1.341
peak=    5.066 closest distance to " CA  TYR A  30 " =    1.019
peak=    4.915 closest distance to " O   HOH Z 134 " =    2.054
peak=    4.874 closest distance to " CB  GLN A 223 " =    1.421
peak=    4.838 closest distance to " O   HOH Z 433 " =    1.936
peak=    4.825 closest distance to " CG  GLN A  77 " =    0.721
peak=    4.807 closest distance to " O   HOH Z 126 " =    1.841
peak=    4.802 closest distance to " O   HOH Z  15 " =    2.028
peak=    4.755 closest distance to " CG  PRO A  54 " =    1.214
peak=    4.738 closest distance to " O   PRO A 198 " =    1.603
peak=    4.593 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.562 closest distance to " O   HOH Z 350 " =    0.918
peak=    4.511 closest distance to " O   HOH Z 132 " =    1.309
peak=    4.472 closest distance to " O   HOH Z 209 " =    2.438
peak=    4.441 closest distance to " OE1 GLN A  77 " =    0.711
peak=    4.433 closest distance to " O   HOH Z  47 " =    1.689
peak=    4.398 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.395 closest distance to " O   HOH Z 108 " =    2.543
peak=    4.375 closest distance to " CG  PRO A 198 " =    1.409
peak=    4.372 closest distance to " O   HOH Z 232 " =    2.367
peak=    4.348 closest distance to " CG2BVAL A  41 " =    1.008
peak=    4.339 closest distance to " O   HOH Z 418 " =    1.734
peak=    4.324 closest distance to " O   HOH Z 422 " =    0.943
peak=    4.317 closest distance to " O   HOH Z 389 " =    1.904
peak=    4.316 closest distance to " CB  ARG A 275 " =    0.928
peak=    4.315 closest distance to " O   HOH Z 369 " =    2.079
peak=    4.271 closest distance to " OE1 GLN A  88 " =    0.767
peak=    4.253 closest distance to " O   HOH Z  11 " =    1.169
peak=    4.252 closest distance to " CB  LEU A 228 " =    1.173
peak=    4.251 closest distance to " O   HOH Z 196 " =    2.139
peak=    4.251 closest distance to " O   HOH Z 234 " =    3.789
peak=    4.250 closest distance to " CG  PRO A 280 " =    0.856
peak=    4.247 closest distance to " O   HOH Z 132 " =    1.994
peak=    4.225 closest distance to " CB  SER A 141 " =    1.004
peak=    4.223 closest distance to " CG2 THR A 221 " =    1.051
peak=    4.223 closest distance to " O   HOH Z 412 " =    3.254
peak=    4.211 closest distance to " O   HOH Z  80 " =    2.150
peak=    4.203 closest distance to " O   HOH Z  97 " =    1.899
peak=    4.201 closest distance to " CB  VAL A 202 " =    1.493
peak=    4.189 closest distance to " O   HOH Z 133 " =    1.729
peak=    4.185 closest distance to " O   HOH Z 357 " =    2.126
peak=    4.182 closest distance to " O   HOH Z  61 " =    1.687
peak=    4.171 closest distance to " O   HOH Z 163 " =    1.849
peak=    4.163 closest distance to " O   HOH Z  78 " =    2.271
peak=    4.159 closest distance to " CG  ARG A  66 " =    2.762
peak=    4.150 closest distance to " O   HOH Z 154 " =    1.519
peak=    4.147 closest distance to " O   HOH Z   7 " =    1.075
peak=    4.145 closest distance to " O   HOH Z  67 " =    2.049
peak=    4.127 closest distance to " O   HOH Z 142 " =    1.633
peak=    4.100 closest distance to " CG1 ILE A  33 " =    1.275
peak=    4.093 closest distance to " O   HOH Z 394 " =    1.660
peak=    4.074 closest distance to " O   HOH Z  47 " =    1.806
peak=    4.055 closest distance to " O   HOH Z 406 " =    1.454
peak=    4.043 closest distance to " CE  LYS A 119 " =    1.140
peak=    4.038 closest distance to " CA  GLY A 196 " =    1.037
peak=    4.017 closest distance to " O   HOH Z 150 " =    1.816
peak=    3.999 closest distance to " CB  GLU A 152 " =    1.152
peak=    3.988 closest distance to " CA  ASP A 191 " =    0.861
peak=    3.986 closest distance to " CB  TRP A 179 " =    1.454
peak=    3.969 closest distance to " CB  PRO A  54 " =    0.758
peak=    3.956 closest distance to " CB  GLU A 128 " =    1.109
peak=    3.920 closest distance to " O   HOH Z 124 " =    1.310
peak=    3.919 closest distance to " CB  ARG A 190 " =    1.737
peak=    3.916 closest distance to " OE1 GLN A  11 " =    2.062
peak=    3.912 closest distance to " O   HOH Z  20 " =    1.937
peak=    3.899 closest distance to " O   HOH Z 247 " =    1.421
peak=    3.892 closest distance to " CG  PRO A  90 " =    1.277
peak=    3.887 closest distance to " O   HOH Z 193 " =    2.043
peak=    3.887 closest distance to " O   HOH Z 298 " =    2.056
peak=    3.880 closest distance to " O   HOH Z  22 " =    2.391
peak=    3.880 closest distance to " O   HOH Z 118 " =    1.928
peak=    3.870 closest distance to " O   HOH Z 425 " =    1.550
peak=    3.861 closest distance to " O   HOH Z 352 " =    1.913
peak=    3.855 closest distance to " O   HOH Z 214 " =    1.153
peak=    3.842 closest distance to " O   HOH Z 431 " =    1.214
peak=    3.825 closest distance to " O   HOH Z 265 " =    2.113
peak=    3.824 closest distance to " N   ASN A  39 " =    1.209
peak=    3.808 closest distance to " O   HOH Z  40 " =    2.280
peak=    3.807 closest distance to " O   HOH Z 243 " =    0.918
peak=    3.803 closest distance to " O   HOH Z  43 " =    1.702
peak=    3.801 closest distance to " O   HOH Z 404 " =    1.590
peak=    3.798 closest distance to " CA  ASN A 176 " =    1.664
peak=    3.796 closest distance to " CB  TRP A 179 " =    1.845
peak=    3.788 closest distance to " O   HOH Z 174 " =    1.917
peak=    3.787 closest distance to " SD AMET A  47 " =    1.093
peak=    3.785 closest distance to " CB  ASN A 148 " =    1.333
peak=    3.774 closest distance to " O   HOH Z 432 " =    2.019
peak=    3.771 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.767 closest distance to " O   HOH Z 132 " =    2.399
peak=    3.762 closest distance to " O   HOH Z 189 " =    2.391
peak=    3.753 closest distance to " CD2 LEU A 297 " =    1.001
peak=    3.745 closest distance to " CB  TYR A 169 " =    0.962
peak=    3.737 closest distance to " ND1 HIS A  81 " =    1.416
peak=    3.735 closest distance to " CG2 VAL A  78 " =    1.025
peak=    3.734 closest distance to " CB  MET A 105 " =    1.119
peak=    3.733 closest distance to " O  BHOH Z 338 " =    0.843
peak=    3.732 closest distance to " CB  SER A  62 " =    0.726
peak=    3.725 closest distance to " OG  SER A  62 " =    3.145
peak=    3.725 closest distance to " O   HOH Z  54 " =    1.205
peak=    3.710 closest distance to " CD  ARG A 269 " =    0.871
peak=    3.706 closest distance to " O   SER A  87 " =    2.296
peak=    3.702 closest distance to " O   HOH Z 437 " =    1.893
peak=    3.684 closest distance to " O   THR A 251 " =    1.307
peak=    3.683 closest distance to " CA  ALA A  21 " =    1.400
peak=    3.680 closest distance to " CA  ILE A 106 " =    0.747
peak=    3.673 closest distance to " CB  GLN A  88 " =    1.104
peak=    3.664 closest distance to " CB  TRP A 266 " =    0.949
peak=    3.662 closest distance to " O   HOH Z 128 " =    2.297
peak=    3.649 closest distance to " CB  ASP A 140 " =    0.787
peak=    3.644 closest distance to " O   HOH Z  39 " =    1.600
peak=    3.643 closest distance to " CB  GLN A  73 " =    0.827
peak=    3.636 closest distance to " O   GLY A  23 " =    2.532
peak=    3.634 closest distance to " O   HOH Z 409 " =    3.018
peak=    3.631 closest distance to " CG AARG A 275 " =    1.028
peak=    3.628 closest distance to " O   HOH Z 162 " =    1.878
peak=    3.625 closest distance to " O   ALA A 165 " =    1.332
peak=    3.623 closest distance to " NH1 ARG A 269 " =    0.737
peak=    3.618 closest distance to " CB  ASP A 132 " =    3.823
peak=    3.618 closest distance to " CB  ALA A 256 " =    1.363
peak=    3.618 closest distance to " CB  TYR A 116 " =    1.559
peak=    3.612 closest distance to " O   HOH Z   6 " =    1.068
peak=    3.611 closest distance to " CA  ALA A 299 " =    1.371
peak=    3.607 closest distance to " CG2 VAL A 197 " =    1.291
peak=    3.601 closest distance to " O   HOH Z 137 " =    1.997
peak=    3.596 closest distance to " O   HOH Z 104 " =    3.250
peak=    3.592 closest distance to " O   HOH Z 214 " =    2.057
peak=    3.588 closest distance to " CB  ALA A 100 " =    1.579
peak=    3.585 closest distance to " O   HOH Z 130 " =    1.203
peak=    3.583 closest distance to " O   GLY A  91 " =    1.198
peak=    3.583 closest distance to " O   HOH Z 316 " =    3.060
peak=    3.582 closest distance to " O   HOH Z 374 " =    2.696
peak=    3.576 closest distance to " NH2BARG A 102 " =    0.999
peak=    3.574 closest distance to " O   HOH Z 145 " =    1.897
peak=    3.564 closest distance to " NH2 ARG A 156 " =    1.219
peak=    3.556 closest distance to " O   HOH Z 387 " =    2.451
peak=    3.556 closest distance to " O   HOH Z 207 " =    2.467
peak=    3.538 closest distance to " CD1 TRP A 274 " =    1.036
peak=    3.536 closest distance to " CD BLYS A 290 " =    1.063
peak=    3.536 closest distance to " CB  PHE A  16 " =    1.497
peak=    3.519 closest distance to " CB  MET A  47 " =    1.035
peak=    3.517 closest distance to " NE2 GLN A  11 " =    1.120
peak=    3.512 closest distance to " CA  LEU A  83 " =    1.495
peak=    3.508 closest distance to " NE2 HIS A 115 " =    1.036
peak=    3.508 closest distance to " O   HOH Z 284 " =    2.859
peak=    3.500 closest distance to " O   HOH Z  88 " =    1.738
peak=    3.500 closest distance to " O   HOH Z 245 " =    1.392
peak=    3.495 closest distance to " O   HOH Z 371 " =    3.377
peak=    3.494 closest distance to " O   HOH Z 377 " =    1.466
peak=    3.493 closest distance to " CA  ALA A 160 " =    1.014
peak=    3.489 closest distance to " CB  GLN A  58 " =    0.933
peak=    3.489 closest distance to " CA  GLN A 223 " =    0.867
peak=    3.488 closest distance to " NZ  LYS A 117 " =    2.979
peak=    3.484 closest distance to " O   HOH Z 128 " =    2.182
peak=    3.484 closest distance to " CD1 LEU A 300 " =    1.242
peak=    3.476 closest distance to " O   HOH Z 108 " =    1.222
peak=    3.472 closest distance to " O   ILE A 106 " =    1.929
peak=    3.470 closest distance to " CB  ASN A 148 " =    1.831
peak=    3.465 closest distance to " O   HOH Z 126 " =    1.865
peak=    3.464 closest distance to " O   HOH Z 112 " =    1.568
peak=    3.457 closest distance to " CB  PRO A  54 " =    1.246
peak=    3.451 closest distance to " CG  PRO A 243 " =    1.139
peak=    3.446 closest distance to " CZ3 TRP A 274 " =    2.175
peak=    3.446 closest distance to " CA  TRP A 274 " =    0.985
peak=    3.445 closest distance to " OG  SER A  97 " =    3.455
peak=    3.443 closest distance to " C   SER A  32 " =    1.128
peak=    3.440 closest distance to " O   HOH Z 292 " =    1.543
peak=    3.435 closest distance to " CB  PHE A 283 " =    0.854
peak=    3.434 closest distance to " O   HOH Z 272 " =    1.226
peak=    3.433 closest distance to " O   HOH Z  48 " =    2.034
peak=    3.426 closest distance to " CA  ARG A 195 " =    1.077
peak=    3.425 closest distance to " CB  GLN A 194 " =    0.931
peak=    3.423 closest distance to " O   HOH Z 395 " =    1.446
peak=    3.423 closest distance to " CB  ILE A 199 " =    1.058
peak=    3.422 closest distance to " N   TYR A  15 " =    0.802
peak=    3.420 closest distance to " O   HOH Z  44 " =    1.770
peak=    3.416 closest distance to " CD  LYS A 166 " =    1.480
peak=    3.416 closest distance to " CA  ASP A 124 " =    0.819
peak=    3.412 closest distance to " O   HOH Z 386 " =    2.299
peak=    3.408 closest distance to " O   HOH Z 327 " =    2.520
peak=    3.403 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.401 closest distance to " CG1 VAL A 174 " =    1.199
peak=    3.401 closest distance to " CA  GLU A 152 " =    0.970
peak=    3.399 closest distance to " O   HOH Z  63 " =    2.101
peak=    3.396 closest distance to " CB  SER A   3 " =    1.479
peak=    3.396 closest distance to " CA  ASP A 149 " =    1.409
peak=    3.396 closest distance to " NH2BARG A 145 " =    1.850
peak=    3.393 closest distance to " O   HOH Z 420 " =    2.220
peak=    3.393 closest distance to " O   HOH Z 215 " =    2.211
peak=    3.392 closest distance to " O   HOH Z 403 " =    1.864
peak=    3.392 closest distance to " CB  GLU A 277 " =    3.784
peak=    3.387 closest distance to " O   HOH Z 192 " =    1.889
peak=    3.386 closest distance to " O   HOH Z 345 " =    3.039
peak=    3.381 closest distance to " CG2 THR A  42 " =    0.953
peak=    3.379 closest distance to " CB  ALA A 291 " =    1.380
peak=    3.376 closest distance to " N   TYR A 116 " =    1.911
peak=    3.372 closest distance to " CD  PRO A  54 " =    1.056
peak=    3.372 closest distance to " O   HOH Z 423 " =    3.251
peak=    3.370 closest distance to " CA  ALA A  51 " =    0.952
peak=    3.368 closest distance to " CB  SER A 276 " =    0.869
peak=    3.368 closest distance to " O   HOH Z 344 " =    3.234
peak=    3.367 closest distance to " O   HOH Z  30 " =    1.970
peak=    3.363 closest distance to " O   HOH Z   4 " =    0.936
peak=    3.360 closest distance to " O   HOH Z  19 " =    1.803
peak=    3.356 closest distance to " O   HOH Z 373 " =    1.618
peak=    3.356 closest distance to " O   HOH Z 227 " =    1.842
peak=    3.354 closest distance to " OG BSER A 164 " =    2.333
peak=    3.349 closest distance to " O   HOH Z  50 " =    3.467
peak=    3.344 closest distance to " CA  ARG A  66 " =    1.060
peak=    3.343 closest distance to " CB  ARG A  79 " =    1.344
peak=    3.341 closest distance to " O   HOH Z 301 " =    1.617
peak=    3.340 closest distance to " CB  GLU A 175 " =    1.443
peak=    3.337 closest distance to " O   HOH Z 156 " =    2.579
peak=    3.336 closest distance to " OD1 ASN A  69 " =    2.368
peak=    3.333 closest distance to " NE AARG A 275 " =    1.547
peak=    3.332 closest distance to " ND2 ASN A 110 " =    1.505
peak=    3.332 closest distance to " O   HOH Z 260 " =    1.335
peak=    3.330 closest distance to " OH  TYR A  30 " =    1.478
peak=    3.330 closest distance to " O   HOH Z 139 " =    4.536
peak=    3.330 closest distance to " CA  ASN A 127 " =    1.100
peak=    3.329 closest distance to " NZ  LYS A 117 " =    1.009
peak=    3.328 closest distance to " OG  SER A 276 " =    1.086
peak=    3.328 closest distance to " CG2AVAL A 121 " =    1.999
peak=    3.320 closest distance to " CA  SER A  32 " =    1.579
peak=    3.319 closest distance to " O   HOH Z 419 " =    2.703
peak=    3.318 closest distance to " O   HOH Z 240 " =    1.997
peak=    3.318 closest distance to " O   HOH Z   1 " =    3.172
peak=    3.313 closest distance to " NZ  LYS A 166 " =    3.110
peak=    3.312 closest distance to " O   HOH Z 327 " =    1.614
peak=    3.312 closest distance to " O   HOH Z 303 " =    2.314
peak=    3.311 closest distance to " CB  ALA A   1 " =    1.184
peak=    3.311 closest distance to " CD2 LEU A 255 " =    1.288
peak=    3.311 closest distance to " CZ  PHE A 218 " =    1.151
peak=    3.307 closest distance to " O   HOH Z  66 " =    2.132
peak=    3.297 closest distance to " CB  PRO A 198 " =    0.981
peak=    3.297 closest distance to " O   HOH Z 185 " =    1.828
peak=    3.291 closest distance to " CA  THR A 221 " =    1.309
peak=    3.290 closest distance to " O   HOH Z 208 " =    1.769
peak=    3.288 closest distance to " O   HOH Z  21 " =    1.863
peak=    3.286 closest distance to " CA  ARG A 139 " =    1.477
peak=    3.285 closest distance to " CA  ASP A 162 " =    1.186
peak=    3.282 closest distance to " O   HOH Z 353 " =    2.578
peak=    3.280 closest distance to " O   HOH Z 364 " =    2.074
peak=    3.280 closest distance to " CA  LYS A  48 " =    1.447
peak=    3.277 closest distance to " C   VAL A 265 " =    1.246
peak=    3.275 closest distance to " O   HOH Z 418 " =    3.223
peak=    3.273 closest distance to " O   HOH Z 261 " =    1.969
peak=    3.273 closest distance to " O   HOH Z 361 " =    3.225
peak=    3.272 closest distance to " O  BHOH Z 338 " =    2.622
peak=    3.269 closest distance to " O   HOH Z  49 " =    2.023
peak=    3.268 closest distance to " O   HOH Z 279 " =    2.324
peak=    3.268 closest distance to " O   HOH Z 324 " =    1.330
peak=    3.267 closest distance to " NZ  LYS A 119 " =    1.669
peak=    3.266 closest distance to " O   HOH Z 109 " =    2.183
peak=    3.265 closest distance to " O   HOH Z 380 " =    1.947
peak=    3.263 closest distance to " CB  SER A  26 " =    0.779
peak=    3.260 closest distance to " O   HOH Z 255 " =    1.676
peak=    3.259 closest distance to " O   HOH Z 147 " =    1.601
peak=    3.258 closest distance to " CA  LEU A 282 " =    1.029
peak=    3.255 closest distance to " O   HOH Z 154 " =    2.487
peak=    3.254 closest distance to " CA  THR A 221 " =    0.898
peak=    3.254 closest distance to " CE3 TRP A 274 " =    3.591
peak=    3.253 closest distance to " CA  ASP A 132 " =    1.253
peak=    3.250 closest distance to " O   HOH Z 287 " =    1.921
peak=    3.247 closest distance to " NH1AARG A 145 " =    1.046
peak=    3.243 closest distance to " O   HOH Z  64 " =    2.261
peak=    3.243 closest distance to " O   HOH Z 368 " =    2.706
peak=    3.235 closest distance to " O   HOH Z 383 " =    1.947
peak=    3.234 closest distance to " O   HOH Z 116 " =    1.803
peak=    3.233 closest distance to " O   HOH Z 343 " =    2.366
peak=    3.230 closest distance to " N   PHE A 130 " =    1.353
peak=    3.229 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.229 closest distance to " NH2BARG A 145 " =    1.337
peak=    3.227 closest distance to " O   HOH Z 363 " =    0.978
peak=    3.224 closest distance to " NH2AARG A 190 " =    1.289
peak=    3.221 closest distance to " CA  VAL A  41 " =    0.798
peak=    3.221 closest distance to " CG2 ILE A 151 " =    0.872
peak=    3.220 closest distance to " N   SER A 164 " =    0.975
peak=    3.219 closest distance to " O   HOH Z 435 " =    1.764
peak=    3.216 closest distance to " ND2 ASN A 187 " =    1.532
peak=    3.210 closest distance to " O   HOH Z 238 " =    5.532
peak=    3.209 closest distance to " O   HOH Z 365 " =    2.981
peak=    3.207 closest distance to " CD  ARG A 159 " =    0.811
peak=    3.206 closest distance to " O   HOH Z 217 " =    2.282
peak=    3.206 closest distance to " CG2 THR A 220 " =    0.799
peak=    3.205 closest distance to " O   HOH Z 426 " =    1.344
peak=    3.203 closest distance to " O   HOH Z 287 " =    1.758
peak=    3.202 closest distance to " NH2AARG A 145 " =    2.217
peak=    3.202 closest distance to " CG2 ILE A  20 " =    1.320
peak=    3.201 closest distance to " CA  THR A 294 " =    1.753
peak=    3.200 closest distance to " CG1 ILE A 120 " =    1.083
peak=    3.199 closest distance to " CB  LEU A 261 " =    1.010
peak=    3.198 closest distance to " O   HOH Z 402 " =    1.649
peak=    3.196 closest distance to " O   HOH Z 287 " =    2.337
peak=    3.195 closest distance to " CA  ILE A  33 " =    1.474
peak=    3.194 closest distance to " CG1 ILE A  49 " =    1.597
peak=    3.189 closest distance to " CB  ALA A  71 " =    1.247
peak=    3.189 closest distance to " CA  ALA A 295 " =    1.025
peak=    3.187 closest distance to " CA  VAL A 197 " =    1.113
peak=    3.185 closest distance to " O   HOH Z 126 " =    1.844
peak=    3.182 closest distance to " CZ3 TRP A  85 " =    0.980
peak=    3.178 closest distance to " O   HOH Z 325 " =    3.711
peak=    3.170 closest distance to " N   THR A  52 " =    1.114
peak=    3.166 closest distance to " ND1 HIS A  81 " =    1.342
peak=    3.162 closest distance to " O   HOH Z 281 " =    4.113
peak=    3.161 closest distance to " O   HOH Z 261 " =    1.976
peak=    3.161 closest distance to " CA  GLY A  80 " =    1.110
peak=    3.155 closest distance to " OD2 ASP A 286 " =    2.988
peak=    3.154 closest distance to " O   GLY A 211 " =    1.176
peak=    3.152 closest distance to " OG  SER A 245 " =    1.594
peak=    3.149 closest distance to " CD1 LEU A 222 " =    0.866
peak=    3.147 closest distance to " OG1 THR A 294 " =    2.555
peak=    3.144 closest distance to " CD  LYS A 119 " =    1.497
peak=    3.143 closest distance to " CB  PHE A 204 " =    1.223
peak=    3.142 closest distance to " O   HOH Z 244 " =    1.681
peak=    3.137 closest distance to " CB  LEU A  83 " =    0.754
peak=    3.136 closest distance to " CA  SER A  12 " =    1.593
peak=    3.136 closest distance to " CG1 VAL A 153 " =    1.102
peak=    3.129 closest distance to " CB  ILE A 120 " =    1.322
peak=    3.129 closest distance to " CA  LYS A 117 " =    1.334
peak=    3.127 closest distance to " CD  PRO A 280 " =    0.984
peak=    3.127 closest distance to " O   HOH Z 420 " =    5.613
peak=    3.125 closest distance to " CD  ARG A  56 " =    1.342
peak=    3.124 closest distance to " O   HOH Z 352 " =    1.320
peak=    3.122 closest distance to " O   HOH Z 215 " =    1.454
peak=    3.121 closest distance to " O   HOH Z 336 " =    1.538
peak=    3.110 closest distance to " CD2 PHE A  59 " =    1.851
peak=    3.107 closest distance to " O   HOH Z 313 " =    2.137
peak=    3.106 closest distance to " NH1 ARG A  14 " =    1.314
peak=    3.105 closest distance to " N   ARG A 156 " =    1.445
peak=    3.103 closest distance to " CB  THR A 157 " =    1.316
peak=    3.097 closest distance to " CG2 THR A  29 " =    1.415
peak=    3.095 closest distance to " O   HOH Z 346 " =    1.600
peak=    3.094 closest distance to " O   HOH Z 142 " =    1.837
peak=    3.087 closest distance to " O   HOH Z 402 " =    2.913
peak=    3.084 closest distance to " O   HOH Z  54 " =    1.657
peak=    3.078 closest distance to " CA  SER A  87 " =    0.858
peak=    3.076 closest distance to " CB  THR A 246 " =    1.382
peak=    3.054 closest distance to " CB  PRO A  90 " =    1.310
peak=    3.047 closest distance to " O   HOH Z 358 " =    1.505
peak=    3.025 closest distance to " O   HOH Z   2 " =    1.734

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.319 - 5.518
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 225
   mapped sites are within: 0.734 - 5.518

peak=   -4.546 closest distance to " O   HOH Z 266 " =    4.687
peak=   -4.443 closest distance to " O   HOH Z 166 " =    1.834
peak=   -4.353 closest distance to " CB  LEU A 167 " =    2.105
peak=   -4.289 closest distance to " N   ARG A 275 " =    1.326
peak=   -4.272 closest distance to " C   ASN A 285 " =    2.565
peak=   -4.203 closest distance to " N   ALA A  43 " =    2.814
peak=   -4.195 closest distance to " NH2 ARG A  66 " =    1.028
peak=   -4.192 closest distance to " O   HOH Z 290 " =    0.983
peak=   -4.174 closest distance to " OG  SER A  97 " =    2.233
peak=   -4.165 closest distance to " O   HOH Z 155 " =    1.303
peak=   -4.148 closest distance to " O   HOH Z 151 " =    1.590
peak=   -4.051 closest distance to " OD2 ASP A 171 " =    2.287
peak=   -4.034 closest distance to " O   HOH Z  52 " =    1.855
peak=   -3.987 closest distance to " CD1 PHE A  59 " =    1.828
peak=   -3.960 closest distance to " OH  TYR A 169 " =    0.893
peak=   -3.959 closest distance to " CD2 LEU A 237 " =    2.562
peak=   -3.932 closest distance to " O   HOH Z  10 " =    1.607
peak=   -3.905 closest distance to " CG1 VAL A 112 " =    2.610
peak=   -3.843 closest distance to " O   ALA A   1 " =    2.028
peak=   -3.813 closest distance to " CA  GLY A 203 " =    2.220
peak=   -3.801 closest distance to " O   PRO A 198 " =    1.365
peak=   -3.797 closest distance to " O   HOH Z  58 " =    0.737
peak=   -3.796 closest distance to " N   GLN A  58 " =    1.628
peak=   -3.781 closest distance to " CB  SER A 146 " =    2.084
peak=   -3.778 closest distance to " O   HOH Z 407 " =    1.725
peak=   -3.771 closest distance to " CZ  ARG A  66 " =    1.220
peak=   -3.748 closest distance to " O   HOH Z 377 " =    0.823
peak=   -3.748 closest distance to " CG2 THR A 221 " =    2.334
peak=   -3.743 closest distance to " NE2 GLN A 223 " =    1.074
peak=   -3.722 closest distance to " CG2BVAL A  41 " =    2.790
peak=   -3.713 closest distance to " O   HOH Z  17 " =    1.177
peak=   -3.710 closest distance to " O   HOH Z 117 " =    4.815
peak=   -3.707 closest distance to " O   HOH Z  38 " =    1.087
peak=   -3.704 closest distance to " CA  SER A 276 " =    1.457
peak=   -3.702 closest distance to " O   HOH Z 185 " =    2.384
peak=   -3.701 closest distance to " O   HOH Z 210 " =    0.904
peak=   -3.694 closest distance to " O   HOH Z  19 " =    2.283
peak=   -3.679 closest distance to " CG  ASP A 231 " =    0.831
peak=   -3.678 closest distance to " O   HOH Z  71 " =    1.517
peak=   -3.674 closest distance to " OG1 THR A  82 " =    2.107
peak=   -3.665 closest distance to " OD2 ASP A 171 " =    1.940
peak=   -3.664 closest distance to " OXT GLY A 302 " =    2.917
peak=   -3.663 closest distance to " CB  PHE A 208 " =    2.340
peak=   -3.658 closest distance to " CB  ALA A 131 " =    2.361
peak=   -3.656 closest distance to " CA  SER A 164 " =    2.186
peak=   -3.655 closest distance to " O   HOH Z 350 " =    1.251
peak=   -3.654 closest distance to " O   HOH Z 399 " =    2.250
peak=   -3.648 closest distance to " CG2 ILE A  20 " =    2.961
peak=   -3.630 closest distance to " OD1 ASN A 148 " =    1.576
peak=   -3.628 closest distance to " O   HOH Z 109 " =    3.558
peak=   -3.613 closest distance to " OD1 ASP A 191 " =    1.926
peak=   -3.610 closest distance to " O   HOH Z  93 " =    1.650
peak=   -3.607 closest distance to " O   HOH Z 221 " =    1.433
peak=   -3.599 closest distance to " O   HOH Z 128 " =    4.329
peak=   -3.590 closest distance to " O   VAL A 174 " =    2.049
peak=   -3.585 closest distance to " CD2 LEU A 300 " =    3.192
peak=   -3.580 closest distance to " CD2 PHE A  59 " =    2.312
peak=   -3.566 closest distance to " O   HOH Z 221 " =    1.595
peak=   -3.552 closest distance to " C   SER A 271 " =    1.175
peak=   -3.548 closest distance to " CA  VAL A 197 " =    0.930
peak=   -3.544 closest distance to " O   HOH Z  37 " =    1.964
peak=   -3.538 closest distance to " O   HOH Z 308 " =    1.719
peak=   -3.538 closest distance to " CG  PRO A 243 " =    1.593
peak=   -3.528 closest distance to " CD1 LEU A 228 " =    2.411
peak=   -3.522 closest distance to " C   SER A 206 " =    1.378
peak=   -3.510 closest distance to " O   ALA A   7 " =    1.645
peak=   -3.510 closest distance to " CG2 ILE A  49 " =    2.609
peak=   -3.507 closest distance to " O   HOH Z 234 " =    4.265
peak=   -3.491 closest distance to " CG  TRP A 266 " =    1.861
peak=   -3.488 closest distance to " O   HOH Z  11 " =    1.341
peak=   -3.482 closest distance to " CB  TYR A  15 " =    2.299
peak=   -3.474 closest distance to " O   HOH Z 118 " =    5.518
peak=   -3.469 closest distance to " CH2 TRP A 177 " =    1.878
peak=   -3.466 closest distance to " O   HOH Z  90 " =    1.949
peak=   -3.460 closest distance to " OD1 ASP A 298 " =    1.902
peak=   -3.452 closest distance to " O   HOH Z 423 " =    2.117
peak=   -3.447 closest distance to " O   HOH Z  53 " =    2.413
peak=   -3.440 closest distance to " O   HOH Z 414 " =    1.623
peak=   -3.438 closest distance to " O   HOH Z 426 " =    1.917
peak=   -3.436 closest distance to " CB  ALA A 291 " =    2.259
peak=   -3.431 closest distance to " C   HIS A 108 " =    1.062
peak=   -3.425 closest distance to " O   HOH Z 313 " =    1.386
peak=   -3.423 closest distance to " O   HOH Z 275 " =    1.538
peak=   -3.422 closest distance to " CB  ALA A 291 " =    2.464
peak=   -3.422 closest distance to " CD  GLN A 223 " =    1.554
peak=   -3.420 closest distance to " C   THR A 279 " =    1.194
peak=   -3.417 closest distance to " O   HOH Z 388 " =    1.912
peak=   -3.410 closest distance to " OG ASER A  12 " =    1.856
peak=   -3.409 closest distance to " O   HOH Z 165 " =    2.036
peak=   -3.408 closest distance to " SG  CYS A 254 " =    3.376
peak=   -3.408 closest distance to " O   HOH Z 148 " =    3.255
peak=   -3.407 closest distance to " C   TRP A 274 " =    1.432
peak=   -3.404 closest distance to " CB  ALA A  43 " =    2.549
peak=   -3.400 closest distance to " ND2 ASN A  60 " =    1.454
peak=   -3.398 closest distance to " O   HOH Z 281 " =    4.756
peak=   -3.389 closest distance to " O   HOH Z 222 " =    1.248
peak=   -3.388 closest distance to " O   HOH Z 150 " =    1.526
peak=   -3.381 closest distance to " CE2 PHE A  38 " =    1.881
peak=   -3.375 closest distance to " SD  MET A 105 " =    0.922
peak=   -3.375 closest distance to " O   GLY A 118 " =    2.290
peak=   -3.373 closest distance to " CG  GLU A  53 " =    1.431
peak=   -3.365 closest distance to " O   HOH Z 136 " =    1.717
peak=   -3.358 closest distance to " O   HOH Z  39 " =    1.721
peak=   -3.356 closest distance to " CB  CYS A 254 " =    2.212
peak=   -3.349 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.347 closest distance to " CD2 TRP A 274 " =    2.295
peak=   -3.342 closest distance to " C   ASN A 187 " =    2.054
peak=   -3.341 closest distance to " O   HOH Z 251 " =    1.694
peak=   -3.339 closest distance to " CG  LEU A  83 " =    2.065
peak=   -3.337 closest distance to " CA  GLY A 241 " =    2.325
peak=   -3.335 closest distance to " O  BHOH Z 338 " =    1.557
peak=   -3.333 closest distance to " O   HOH Z 418 " =    1.517
peak=   -3.331 closest distance to " O   HOH Z   7 " =    1.593
peak=   -3.325 closest distance to " O   HOH Z 401 " =    1.400
peak=   -3.325 closest distance to " CB  GLU A 277 " =    1.320
peak=   -3.324 closest distance to " O   HOH Z 325 " =    1.702
peak=   -3.320 closest distance to " O   HOH Z 111 " =    1.215
peak=   -3.318 closest distance to " O   HOH Z 422 " =    1.261
peak=   -3.316 closest distance to " CD  GLN A  88 " =    0.882
peak=   -3.315 closest distance to " O   HOH Z 146 " =    1.193
peak=   -3.315 closest distance to " O   HOH Z 120 " =    1.183
peak=   -3.315 closest distance to " OG ASER A 134 " =    1.266
peak=   -3.311 closest distance to " OG  SER A  26 " =    1.445
peak=   -3.310 closest distance to " O   TYR A  15 " =    1.443
peak=   -3.308 closest distance to " SG ACYS A 201 " =    1.929
peak=   -3.307 closest distance to " O   HOH Z 368 " =    2.106
peak=   -3.303 closest distance to " NE1 TRP A 177 " =    1.963
peak=   -3.301 closest distance to " CB  ALA A 161 " =    2.631
peak=   -3.299 closest distance to " O   HOH Z 377 " =    2.215
peak=   -3.286 closest distance to " O   PHE A 218 " =    1.426
peak=   -3.286 closest distance to " O   HOH Z  37 " =    1.602
peak=   -3.282 closest distance to " CZ  ARG A  36 " =    2.001
peak=   -3.281 closest distance to " O   HOH Z 184 " =    1.441
peak=   -3.279 closest distance to " CG  MET A  93 " =    2.493
peak=   -3.277 closest distance to " O   HOH Z 198 " =    1.505
peak=   -3.277 closest distance to " CE2 PHE A 218 " =    2.567
peak=   -3.272 closest distance to " O   HOH Z 298 " =    3.024
peak=   -3.261 closest distance to " O   HOH Z 322 " =    1.543
peak=   -3.261 closest distance to " CG  ARG A 269 " =    2.427
peak=   -3.258 closest distance to " O   HOH Z   7 " =    1.172
peak=   -3.256 closest distance to " O   ALA A 256 " =    1.593
peak=   -3.254 closest distance to " CA  GLY A 241 " =    3.144
peak=   -3.254 closest distance to " O   THR A  18 " =    1.510
peak=   -3.252 closest distance to " O   GLY A 196 " =    1.103
peak=   -3.251 closest distance to " O   HOH Z  64 " =    0.734
peak=   -3.251 closest distance to " CD2 HIS A 115 " =    1.073
peak=   -3.250 closest distance to " CD2 LEU A 300 " =    2.659
peak=   -3.247 closest distance to " OG BSER A 210 " =    1.190
peak=   -3.246 closest distance to " CD2 LEU A 167 " =    1.733
peak=   -3.244 closest distance to " CB  PRO A 243 " =    2.774
peak=   -3.240 closest distance to " O   HOH Z 318 " =    2.071
peak=   -3.239 closest distance to " O   SER A 210 " =    1.983
peak=   -3.238 closest distance to " O   HOH Z 423 " =    1.769
peak=   -3.238 closest distance to " O   HOH Z 396 " =    1.520
peak=   -3.238 closest distance to " ND2 ASN A  45 " =    1.725
peak=   -3.234 closest distance to " CG  PRO A 163 " =    1.851
peak=   -3.234 closest distance to " O   HOH Z 402 " =    1.187
peak=   -3.234 closest distance to " CA  VAL A 232 " =    2.324
peak=   -3.234 closest distance to " O   HOH Z 428 " =    1.382
peak=   -3.234 closest distance to " ND2 ASN A  60 " =    1.742
peak=   -3.232 closest distance to " O   TRP A  92 " =    1.866
peak=   -3.232 closest distance to " O   HOH Z 259 " =    0.887
peak=   -3.229 closest distance to " CB  ASN A 170 " =    2.046
peak=   -3.224 closest distance to " CD2 PHE A 225 " =    1.264
peak=   -3.223 closest distance to " ND2 ASN A  39 " =    1.504
peak=   -3.221 closest distance to " CE  MET A  93 " =    1.364
peak=   -3.211 closest distance to " O   HOH Z  60 " =    2.032
peak=   -3.206 closest distance to " CG1 VAL A 174 " =    2.867
peak=   -3.205 closest distance to " O   HOH Z  97 " =    1.350
peak=   -3.203 closest distance to " CG  ASP A  50 " =    2.477
peak=   -3.201 closest distance to " CD  PRO A 198 " =    1.150
peak=   -3.196 closest distance to " O   HOH Z 134 " =    2.014
peak=   -3.193 closest distance to " CE  MET A 105 " =    2.071
peak=   -3.193 closest distance to " O   HOH Z 423 " =    1.241
peak=   -3.189 closest distance to " O   HOH Z  41 " =    2.306
peak=   -3.187 closest distance to " CG  ARG A 219 " =    2.403
peak=   -3.185 closest distance to " O   HOH Z 422 " =    1.697
peak=   -3.184 closest distance to " CG2 VAL A 189 " =    2.104
peak=   -3.183 closest distance to " O   HOH Z  78 " =    2.204
peak=   -3.174 closest distance to " O   HOH Z 189 " =    1.668
peak=   -3.174 closest distance to " CZ3 TRP A  92 " =    0.970
peak=   -3.172 closest distance to " O   HOH Z 380 " =    4.359
peak=   -3.165 closest distance to " OE1 GLN A  88 " =    1.390
peak=   -3.164 closest distance to " O   HOH Z 436 " =    1.242
peak=   -3.164 closest distance to " O   HOH Z  43 " =    5.235
peak=   -3.161 closest distance to " O   HOH Z 137 " =    1.388
peak=   -3.160 closest distance to " CD  ARG A 219 " =    2.634
peak=   -3.158 closest distance to " N   LEU A 261 " =    1.139
peak=   -3.154 closest distance to " O   HOH Z 231 " =    2.291
peak=   -3.150 closest distance to " CD1 TYR A 247 " =    2.386
peak=   -3.149 closest distance to " CD2 LEU A  25 " =    2.263
peak=   -3.146 closest distance to " O   ALA A   1 " =    2.120
peak=   -3.145 closest distance to " CG2BVAL A  41 " =    1.216
peak=   -3.143 closest distance to " O   HOH Z 182 " =    2.436
peak=   -3.140 closest distance to " O   HOH Z 119 " =    4.296
peak=   -3.139 closest distance to " O   HOH Z 409 " =    4.808
peak=   -3.137 closest distance to " N   ALA A   9 " =    1.582
peak=   -3.132 closest distance to " O   HOH Z 231 " =    1.672
peak=   -3.130 closest distance to " CD2 LEU A 237 " =    2.611
peak=   -3.130 closest distance to " O   HOH Z 215 " =    3.508
peak=   -3.130 closest distance to " CD2 TYR A  30 " =    2.755
peak=   -3.127 closest distance to " CD2 PHE A  61 " =    1.821
peak=   -3.125 closest distance to " O   HOH Z 252 " =    3.901
peak=   -3.117 closest distance to " O   HOH Z 280 " =    1.980
peak=   -3.111 closest distance to " O   HOH Z 117 " =    1.936
peak=   -3.106 closest distance to " CD  PRO A 213 " =    2.262
peak=   -3.102 closest distance to " CB  ALA A 248 " =    2.062
peak=   -3.097 closest distance to " O   ARG A 275 " =    1.914
peak=   -3.096 closest distance to " O   HOH Z 366 " =    1.638
peak=   -3.095 closest distance to " CG  LYS A 193 " =    2.628
peak=   -3.093 closest distance to " NZ  LYS A 119 " =    1.519
peak=   -3.086 closest distance to " CG  GLN A  55 " =    2.072
peak=   -3.082 closest distance to " O   HOH Z 384 " =    2.279
peak=   -3.080 closest distance to " CD  ARG A 156 " =    1.950
peak=   -3.080 closest distance to " CD  ARG A 139 " =    1.542
peak=   -3.079 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.076 closest distance to " CD  GLN A  11 " =    0.783
peak=   -3.055 closest distance to " C   GLU A  46 " =    0.979
peak=   -3.049 closest distance to " O   HOH Z  43 " =    1.548
peak=   -3.038 closest distance to " O   HOH Z  48 " =    0.893
peak=   -3.038 closest distance to " CB  GLN A  55 " =    1.483
peak=   -3.037 closest distance to " OG  SER A  87 " =    1.666
peak=   -3.024 closest distance to " CB  PHE A  16 " =    2.557

================= 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    :  0.4660 0.4490   6.278940e+00   6.254440e+00
   1_bss:  0.4582 0.4402   6.273250e+00   6.243938e+00
   1_xyz:  0.3521 0.3940   6.106619e+00   6.172356e+00
   1_adp:  0.3253 0.4013   6.067447e+00   6.176558e+00
   1_occ:  0.3251 0.4004   6.066288e+00   6.176260e+00
   2_bss:  0.3243 0.3979   6.066479e+00   6.174581e+00
   2_xyz:  0.2685 0.3219   5.896602e+00   6.034355e+00
   2_adp:  0.2488 0.3207   5.862714e+00   6.027966e+00
   2_occ:  0.2486 0.3205   5.862221e+00   6.027745e+00
   3_bss:  0.2488 0.3202   5.861749e+00   6.027949e+00
   3_xyz:  0.2000 0.2547   5.647903e+00   5.831276e+00
   3_adp:  0.1818 0.2318   5.562721e+00   5.752508e+00
   3_occ:  0.1816 0.2317   5.562320e+00   5.751938e+00
   4_bss:  0.1816 0.2318   5.562919e+00   5.751610e+00
   4_xyz:  0.1539 0.1989   5.413686e+00   5.616750e+00
   4_adp:  0.1468 0.1919   5.377231e+00   5.579660e+00
   4_occ:  0.1467 0.1918   5.376655e+00   5.579099e+00
   5_bss:  0.1470 0.1923   5.378612e+00   5.580455e+00
   5_xyz:  0.1282 0.1768   5.264873e+00   5.494231e+00
   5_adp:  0.1267 0.1746   5.253451e+00   5.479180e+00
   5_occ:  0.1266 0.1745   5.253025e+00   5.478934e+00
   5_bss:  0.1266 0.1745   5.252849e+00   5.478687e+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:  0.280  18.304  -1.304   4.236  -0.364   0.000  -0.000  -0.000
   1_xyz:  0.280  18.304  -1.304   4.236  -0.364   0.000  -0.000  -0.000
   1_adp:  0.280  18.304  -1.304   4.236  -0.364   0.000  -0.000  -0.000
   1_occ:  0.280  18.304  -1.304   4.236  -0.364   0.000  -0.000  -0.000
   2_bss:  0.319  55.598  -1.158   2.269  -0.640   0.000  -0.000  -0.000
   2_xyz:  0.319  55.598  -1.158   2.269  -0.640   0.000  -0.000  -0.000
   2_adp:  0.319  55.598  -1.158   2.269  -0.640   0.000  -0.000  -0.000
   2_occ:  0.319  55.598  -1.158   2.269  -0.640   0.000  -0.000  -0.000
   3_bss:  0.321  67.680  -0.810   1.563  -0.514   0.000  -0.000  -0.000
   3_xyz:  0.321  67.680  -0.810   1.563  -0.514   0.000  -0.000  -0.000
   3_adp:  0.321  67.680  -0.810   1.563  -0.514   0.000  -0.000  -0.000
   3_occ:  0.321  67.680  -0.810   1.563  -0.514   0.000  -0.000  -0.000
   4_bss:  0.326  73.546  -1.433   0.129  -0.976   0.000  -0.000  -0.000
   4_xyz:  0.326  73.546  -1.433   0.129  -0.976   0.000  -0.000  -0.000
   4_adp:  0.326  73.546  -1.433   0.129  -0.976   0.000  -0.000  -0.000
   4_occ:  0.326  73.546  -1.433   0.129  -0.976   0.000  -0.000  -0.000
   5_bss:  0.324  69.941  -1.636  -0.445  -1.063  -0.000  -0.000  -0.000
   5_xyz:  0.324  69.941  -1.636  -0.445  -1.063  -0.000  -0.000  -0.000
   5_adp:  0.324  69.941  -1.636  -0.445  -1.063  -0.000  -0.000  -0.000
   5_occ:  0.324  69.941  -1.636  -0.445  -1.063  -0.000  -0.000  -0.000
   5_bss:  0.327  69.944  -1.678  -0.761  -1.110  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.698 0.4884  0.6568    64547.197
   1_bss:  51.921 0.4966  0.6858    61341.871
   1_xyz:  44.966 0.5822  0.7871    46451.687
   1_adp:  45.588 0.5739  0.7743    46845.702
   1_occ:  45.527 0.5746  0.7742    46695.670
   2_bss:  45.269 0.5777  0.7637    46242.216
   2_xyz:  35.017 0.7002  0.8922    29036.833
   2_adp:  34.522 0.7063  0.8818    28826.828
   2_occ:  34.506 0.7065  0.8816    28806.032
   3_bss:  34.426 0.7073  0.8806    28684.412
   3_xyz:  26.166 0.7981  0.9657    17087.966
   3_adp:  23.151 0.8304  0.9760    14315.032
   3_occ:  23.145 0.8305  0.9760    14307.453
   4_bss:  23.074 0.8312  0.9489    14249.806
   4_xyz:  19.413 0.8668  0.9664    10319.590
   4_adp:  18.351 0.8774  0.9635     9612.361
   4_occ:  18.336 0.8775  0.9636     9607.822
   5_bss:  18.355 0.8774  0.9543     9645.723
   5_xyz:  16.513 0.8935  0.9662     8038.113
   5_adp:  16.170 0.8967  0.9691     7857.123
   5_occ:  16.162 0.8968  0.9692     7857.273
   5_bss:  16.153 0.8969  0.9651     7853.541
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8380e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8380e-01
   1_xyz:   1.738  0.014  0.107 16.501  0.006  4.107   1.5847e-01
   1_adp:   1.738  0.014  0.107 16.501  0.006  4.107   1.5847e-01
   1_occ:   1.738  0.014  0.107 16.501  0.006  4.107   1.5847e-01
   2_bss:   1.738  0.014  0.107 16.501  0.006  4.107   1.5847e-01
   2_xyz:   1.329  0.009  0.086 14.583  0.006  4.115   9.1309e-02
   2_adp:   1.329  0.009  0.086 14.583  0.006  4.115   9.1309e-02
   2_occ:   1.329  0.009  0.086 14.583  0.006  4.115   9.1309e-02
   3_bss:   1.329  0.009  0.086 14.583  0.006  4.115   9.1309e-02
   3_xyz:   1.193  0.009  0.073 14.593  0.005  4.112   7.8929e-02
   3_adp:   1.193  0.009  0.073 14.593  0.005  4.112   7.8929e-02
   3_occ:   1.193  0.009  0.073 14.593  0.005  4.112   7.8929e-02
   4_bss:   1.193  0.009  0.073 14.593  0.005  4.112   7.8929e-02
   4_xyz:   1.009  0.007  0.072 14.197  0.004  4.122   5.8988e-02
   4_adp:   1.009  0.007  0.072 14.197  0.004  4.122   5.8988e-02
   4_occ:   1.009  0.007  0.072 14.197  0.004  4.122   5.8988e-02
   5_bss:   1.009  0.007  0.072 14.197  0.004  4.122   5.8988e-02
   5_xyz:   1.149  0.010  0.079 14.684  0.004  4.132   7.4465e-02
   5_adp:   1.149  0.010  0.079 14.684  0.004  4.132   7.4465e-02
   5_occ:   1.149  0.010  0.079 14.684  0.004  4.132   7.4465e-02
   5_bss:   1.149  0.010  0.079 14.684  0.004  4.132   7.4465e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.348   2.4409e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.348   2.4409e-01
   1_xyz:  11.769  0.086  0.477 87.211  0.021  2.077   1.0840e-01
   1_adp:  11.769  0.086  0.477 87.211  0.021  2.077   1.0840e-01
   1_occ:  11.769  0.086  0.477 87.211  0.021  2.077   1.0840e-01
   2_bss:  11.769  0.086  0.477 87.211  0.021  2.077   1.0840e-01
   2_xyz:   7.377  0.052  0.263 79.821  0.036  2.215   9.9514e-02
   2_adp:   7.377  0.052  0.263 79.821  0.036  2.215   9.9514e-02
   2_occ:   7.377  0.052  0.263 79.821  0.036  2.215   9.9514e-02
   3_bss:   7.377  0.052  0.263 79.821  0.036  2.215   9.9514e-02
   3_xyz:   7.663  0.046  0.242 85.709  0.058  2.190   1.1414e-01
   3_adp:   7.663  0.046  0.242 85.709  0.058  2.190   1.1414e-01
   3_occ:   7.663  0.046  0.242 85.709  0.058  2.190   1.1414e-01
   4_bss:   7.663  0.046  0.242 85.709  0.058  2.190   1.1414e-01
   4_xyz:   7.488  0.049  0.243 85.771  0.038  2.279   4.5321e-02
   4_adp:   7.488  0.049  0.243 85.771  0.038  2.279   4.5321e-02
   4_occ:   7.488  0.049  0.243 85.771  0.038  2.279   4.5321e-02
   5_bss:   7.488  0.049  0.243 85.771  0.038  2.279   4.5321e-02
   5_xyz:   7.946  0.056  0.267 82.864  0.038  2.270   5.4398e-02
   5_adp:   7.946  0.056  0.267 82.864  0.038  2.270   5.4398e-02
   5_occ:   7.946  0.056  0.267 82.864  0.038  2.270   5.4398e-02
   5_bss:   7.946  0.056  0.267 82.864  0.038  2.270   5.4398e-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: 121.34   0.00  17.68 121.34   0.00  14.25  70.22   0.00  36.36
   1_occ: 121.34   0.00  17.68 121.34   0.00  14.25  70.22   0.00  36.36
   2_bss: 121.34   0.00  17.68 121.34   0.00  14.25  70.22   0.00  36.36
   2_xyz: 121.34   0.00  17.68 121.34   0.00  14.25  70.22   0.00  36.36
   2_adp:  95.73   0.00  18.88  93.86   0.00  14.83  95.73   1.24  40.92
   2_occ:  95.73   0.00  18.88  93.86   0.00  14.83  95.73   1.24  40.92
   3_bss:  95.73   0.00  18.88  93.86   0.00  14.83  95.73   1.24  40.92
   3_xyz:  95.73   0.00  18.88  93.86   0.00  14.83  95.73   1.24  40.92
   3_adp: 108.98   0.00  18.29 108.98   0.00  13.55 103.26   3.86  44.10
   3_occ: 108.98   0.00  18.29 108.98   0.00  13.55 103.26   3.86  44.10
   4_bss: 108.98   0.00  18.29 108.98   0.00  13.55 103.26   3.86  44.10
   4_xyz: 108.98   0.00  18.29 108.98   0.00  13.55 103.26   3.86  44.10
   4_adp: 114.34   0.00  17.63 114.34   0.00  12.79 107.83   4.26  43.96
   4_occ: 114.34   0.00  17.63 114.34   0.00  12.79 107.83   4.26  43.96
   5_bss: 114.34   0.00  17.63 114.34   0.00  12.79 107.83   4.26  43.96
   5_xyz: 114.34   0.00  17.63 114.34   0.00  12.79 107.83   4.26  43.96
   5_adp: 114.02   0.00  17.57 114.02   0.00  12.79 107.77   4.75  43.59
   5_occ: 114.02   0.00  17.57 114.02   0.00  12.79 107.77   4.75  43.59
   5_bss: 114.03   0.00  17.57 114.03   0.00  12.79 107.78   4.75  43.60
------------------------------------------------------------------------
 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:    2.173    0.026    0.427
   1_adp:    2.173    0.026    0.427
   1_occ:    2.173    0.026    0.427
   2_bss:    2.173    0.026    0.427
   2_xyz:    1.853    0.061    0.579
   2_adp:    1.853    0.061    0.579
   2_occ:    1.853    0.061    0.579
   3_bss:    1.853    0.061    0.579
   3_xyz:    1.770    0.047    0.750
   3_adp:    1.770    0.047    0.750
   3_occ:    1.770    0.047    0.750
   4_bss:    1.770    0.047    0.750
   4_xyz:    1.676    0.044    0.799
   4_adp:    1.676    0.044    0.799
   4_occ:    1.676    0.044    0.799
   5_bss:    1.676    0.044    0.799
   5_xyz:    1.684    0.065    0.855
   5_adp:    1.684    0.065    0.855
   5_occ:    1.684    0.065    0.855
   5_bss:    1.684    0.065    0.855
------------------------------------------------------------------------

CPU time actual refinement: 373.20


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/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_1080/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1080/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 373.05 
  Macro-tasks:
    bulk solvent and scale       = 45.14  
    individual site refinement   = 156.50 
    weights calculation          = 30.20  
    collect and process          = 6.51   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 238.48 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 123.16 
    alpha_beta                      = 8.46   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 131.10 
    fmodel                         = 7.52   
    r_factors                      = 0.25   
    phase_errors                   = 10.49  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 284.92 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.250 micro seconds
Total CPU time: 6.44 minutes
from_scatterers_fft:    656 calls, 122.86 s
gradients_fft:          601 calls, 117.80 s

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

# Date 2008-01-16 Time 06:23:35 PST -0800 (1200493415.88 s)
Start R-work = 0.4660, R-free = 0.4490 (no bulk solvent and anisotropic scale)
Final R-work = 0.1448, R-free = 0.1909 (no bulk solvent and anisotropic scale)

Start R-work = 0.4582, R-free = 0.4402
Final R-work = 0.1266, R-free = 0.1745