# Date 2008-01-16 Time 03:46:10 PST -0800 (1200483970.30 s)
#phil __OFF__

Command line arguments: "../45.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11014
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 45

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.6953, 84.6622, 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: 3.27, 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: (68.4938, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6393 1.95057
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.959963

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6393
                             d_min =   1.9506

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6393 1.95057
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.959963

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6397 -  4.1730 [2137/2165]  1923   214  10.0%
  bin  2:  4.1730 -  3.3250 [2042/2062]  1839   203   9.9%
  bin  3:  3.3250 -  2.9084 [2037/2057]  1833   204  10.0%
  bin  4:  2.9084 -  2.6442 [2006/2030]  1808   198   9.9%
  bin  5:  2.6442 -  2.4556 [2001/2022]  1797   204  10.2%
  bin  6:  2.4556 -  2.3114 [1969/2015]  1776   193   9.8%
  bin  7:  2.3114 -  2.1961 [1972/2004]  1774   198  10.0%
  bin  8:  2.1961 -  2.1008 [1965/2000]  1765   200  10.2%
  bin  9:  2.1008 -  2.0201 [1948/1978]  1751   197  10.1%
  bin 10:  2.0201 -  1.9506 [1512/2009]  1364   148   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/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:
        0.93 -     1.72: 12
        1.72 -     2.52: 90
        2.52 -     3.31: 3871
        3.31 -     4.11: 9714
        4.11 -     4.90: 15437
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.926 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.043 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.361 3.040 -x+1,y+1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.497 3.440 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.515 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29119 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_45/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/model_refine_001.geo

CPU time processing inputs: 9.27


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.69535 84.6622 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: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4409   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.238367                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6539 0.99   1389  154 0.3511 0.3495      6.5097      6.5087|
|  2:  4.6539 -  3.7138 0.99   1329  150 0.3666 0.3553       6.709      6.7316|
|  3:  3.7138 -  3.2502 0.99   1317  149 0.3974 0.4238      6.6023      6.7219|
|  4:  3.2502 -  2.9557 0.99   1300  134 0.4126 0.4380       6.463      6.4915|
|  5:  2.9557 -  2.7454 0.99   1289  147 0.4518 0.4517      6.3336      6.3375|
|  6:  2.7454 -  2.5844 0.98   1284  143 0.4686 0.4899      6.2372      6.1758|
|  7:  2.5844 -  2.4556 0.99   1292  146 0.4740 0.4470      6.2201      6.1586|
|  8:  2.4556 -  2.3492 0.98   1276  139 0.4850 0.4663       6.159      6.1712|
|  9:  2.3492 -  2.2591 0.98   1268  144 0.5066 0.5004      6.1036       6.123|
| 10:  2.2591 -  2.1814 0.97   1247  136 0.4929 0.5497      6.0927       6.091|
| 11:  2.1814 -  2.1134 0.99   1274  145 0.4933 0.4819      6.0104      6.0571|
| 12:  2.1134 -  2.0531 0.98   1276  140 0.4942 0.4636      5.9662      5.9791|
| 13:  2.0531 -  1.9992 0.97   1258  134 0.4882 0.5218      5.8761      5.8628|
| 14:  1.9992 -  1.9506 0.66    831   98 0.5006 0.4613      5.8485      5.7286|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6397 -  4.6539  1389   154  0.71  33.32   0.85     0.73      65429.27|
|  2:  4.6539 -  3.7138  1329   150  0.72  33.79   0.94     0.83      97417.95|
|  3:  3.7138 -  3.2502  1317   149  0.62  42.10   0.96     0.82     105202.93|
|  4:  3.2502 -  2.9557  1300   134  0.55  48.15   0.98     0.76      94034.87|
|  5:  2.9557 -  2.7454  1289   147  0.49  52.73   0.93     0.70      74126.69|
|  6:  2.7454 -  2.5844  1284   143  0.47  54.45   0.91     0.67      62455.01|
|  7:  2.5844 -  2.4556  1292   146  0.48  53.82   0.94     0.67      56734.44|
|  8:  2.4556 -  2.3492  1276   139  0.45  55.82   0.96     0.65      51447.14|
|  9:  2.3492 -  2.2591  1268   144  0.44  57.23   0.95     0.65      47668.15|
| 10:  2.2591 -  2.1814  1247   136  0.45  56.40   0.99     0.65      42821.41|
| 11:  2.1814 -  2.1134  1274   145  0.43  57.61   0.97     0.65      40685.06|
| 12:  2.1134 -  2.0531  1276   140  0.42  58.78   1.00     0.66      38654.80|
| 13:  2.0531 -  1.9992  1258   134  0.39  60.94   1.00     0.60      34385.57|
| 14:  1.9992 -  1.9506   831    98  0.39  60.72   0.96     0.51      26364.43|
|alpha:            min =        0.51 max =            0.83 mean =         0.69|
|beta:             min =    26364.43 max =       105202.93 mean =     61032.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.41|
|phase err.(test): min =        0.00 max =           89.99 mean =        51.50|
|-----------------------------------------------------------------------------|

============================== 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 = 12.976439             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.863454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.968   (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 |  0.926 -  1.323:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.323 -  1.721:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.721 -  2.118:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.118 -  2.516:       65 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.516 -  2.913:     1493 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.913 -  3.310:     2378 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.310 -  3.708:     3818 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.708 -  4.105:     5896 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.105 -  4.503:     6813 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.503 -  4.900:     8624 |
|-----------------------------------------------------------------------------|
|-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 |        0.249 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  0.926 |       1.524 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    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: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4409   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.238367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4280   r_free= 0.4284   ksol= 0.32   Bsol= 15.13   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.64,-2.37,1.91,-0.00,0.00,0.00); trace/3= 0.06                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.229113                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.456736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.907813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.689   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4280      final r-factor (work) = 0.2616          |
| start r-factor (free) = 0.4284      final r-factor (free) = 0.2846          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8221 = 10.46 * 0.50 * 6.2301 + 1.00 * 0.2487                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.7238 = 10.46 * 0.50 * 6.0436 + 1.00 * 0.1257                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2616      final r-factor (work) = 0.2369          |
| start r-factor (free) = 0.2846      final r-factor (free) = 0.2917          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4924 = 0.91 * 1.00 * 6.0436 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2515 = 0.91 * 1.00 * 5.7692 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.44   18.81    None  None   None       |
|    all(noH): 2823   0      0.00    84.44   18.81    None  None   None       |
|    Sol.    : 438    0      5.66    84.44   42.89    None  None   None       |
|    Mac.    : 2385   0      0.00    84.37   14.39    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 -   8.444:  713   |   5:    42.222 -  50.666:  106        |
|      1:     8.444 -  16.889: 1050   |   6:    50.666 -  59.110:   87        |
|      2:    16.889 -  25.333:  439   |   7:    59.110 -  67.555:   65        |
|      3:    25.333 -  33.777:  180   |   8:    67.555 -  75.999:   23        |
|      4:    33.777 -  42.222:  145   |   9:    75.999 -  84.443:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2369 r_free = 0.2917             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2367 r_free = 0.2917             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2367   r_free= 0.2917   ksol= 0.32   Bsol= 15.13   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.64,-2.37,1.91,-0.00,0.00,0.00); trace/3= 0.06                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.780083                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2301   r_free= 0.2878   ksol= 0.32   Bsol= 29.14   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.61,-0.76,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.765810                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.642838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.587   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.569  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2301      final r-factor (work) = 0.1674          |
| start r-factor (free) = 0.2878      final r-factor (free) = 0.2193          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6438 = 3.64 * 0.50 * 5.7746 + 1.00 * 0.1258                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3399 = 3.64 * 0.50 * 5.6442 + 1.00 * 0.0595                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1674      final r-factor (work) = 0.1541          |
| start r-factor (free) = 0.2193      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1325 = 0.20 * 1.00 * 5.6442 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0879 = 0.20 * 1.00 * 5.4514 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    86.17   17.72    None  None   None       |
|    all(noH): 2823   0      1.47    86.17   17.72    None  None   None       |
|    Sol.    : 438    0      7.19    80.85   40.28    None  None   None       |
|    Mac.    : 2385   0      1.47    86.17   13.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.467 -   9.937:  933   |   5:    43.818 -  52.288:  118        |
|      1:     9.937 -  18.407: 1113   |   6:    52.288 -  60.759:   67        |
|      2:    18.407 -  26.878:  280   |   7:    60.759 -  69.229:   29        |
|      3:    26.878 -  35.348:  139   |   8:    69.229 -  77.699:    8        |
|      4:    35.348 -  43.818:  128   |   9:    77.699 -  86.169:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1541 r_free = 0.2016             target_work(ml) = 5.404         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1537 r_free = 0.2016             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1537   r_free= 0.2016   ksol= 0.32   Bsol= 29.14   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.61,-0.76,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.402305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.2005   ksol= 0.32   Bsol= 29.14   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.51,-1.62,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.398891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.273715              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.250  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1533      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.2005      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2570 = 2.27 * 0.50 * 5.4515 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0986 = 2.27 * 0.50 * 5.3143 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1271      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5473 = 0.29 * 1.00 * 5.3143 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5190 = 0.29 * 1.00 * 5.2154 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    92.77   17.69    None  None   None       |
|    all(noH): 2823   0      1.84    92.77   17.69    None  None   None       |
|    Sol.    : 438    0      4.58    83.24   41.23    None  None   None       |
|    Mac.    : 2385   0      1.84    92.77   13.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.838 -  10.932: 1138   |   5:    47.306 -  56.400:  115        |
|      1:    10.932 -  20.026: 1024   |   6:    56.400 -  65.494:   59        |
|      2:    20.026 -  29.119:  212   |   7:    65.494 -  74.587:   16        |
|      3:    29.119 -  38.213:  127   |   8:    74.587 -  83.681:   11        |
|      4:    38.213 -  47.306:  120   |   9:    83.681 -  92.775:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1653             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1654             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1654   ksol= 0.32   Bsol= 29.14   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.97,-2.51,-1.62,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.201392                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1650   ksol= 0.31   Bsol= 29.14   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.60,-1.97,-0.00,-0.00,-0.00); trace/3= -2.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.201532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.270540              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.011  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.368478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.009  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1223      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9804 = 2.27 * 0.50 * 5.2176 + 1.00 * 0.0570                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9273 = 2.27 * 0.50 * 5.1681 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9124 = 0.37 * 1.00 * 5.1681 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9037 = 0.37 * 1.00 * 5.1441 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    96.08   17.52    None  None   None       |
|    all(noH): 2823   0      2.28    96.08   17.52    None  None   None       |
|    Sol.    : 438    0      4.99    83.30   40.78    None  None   None       |
|    Mac.    : 2385   0      2.28    96.08   13.25    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:     2.280 -  11.660: 1340   |   5:    49.181 -  58.561:   97        |
|      1:    11.660 -  21.040:  885   |   6:    58.561 -  67.941:   48        |
|      2:    21.040 -  30.420:  179   |   7:    67.941 -  77.322:   10        |
|      3:    30.420 -  39.801:  130   |   8:    77.322 -  86.702:   11        |
|      4:    39.801 -  49.181:  122   |   9:    86.702 -  96.082:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1595             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1594             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1594   ksol= 0.31   Bsol= 29.14   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.60,-1.97,-0.00,-0.00,-0.00); trace/3= -2.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141355                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1594   ksol= 0.32   Bsol= 32.36   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-2.47,-1.92,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.356489              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.349  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903380              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.856  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1209 = 2.36 * 0.50 * 5.1439 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1042 = 2.36 * 0.50 * 5.1289 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6415 = 0.90 * 1.00 * 5.1289 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6317 = 0.90 * 1.00 * 5.1174 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    101.28  17.47    None  None   None       |
|    all(noH): 2823   0      1.77    101.28  17.47    None  None   None       |
|    Sol.    : 438    0      5.99    91.24   40.85    None  None   None       |
|    Mac.    : 2385   0      1.77    101.28  13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.766 -  11.717: 1373   |   5:    51.522 -  61.474:   78        |
|      1:    11.717 -  21.669:  878   |   6:    61.474 -  71.425:   40        |
|      2:    21.669 -  31.620:  170   |   7:    71.425 -  81.376:    7        |
|      3:    31.620 -  41.571:  134   |   8:    81.376 -  91.327:    9        |
|      4:    41.571 -  51.522:  131   |   9:    91.327 - 101.279:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1578             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1578             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1578   ksol= 0.32   Bsol= 32.36   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,-2.47,-1.92,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118624                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6539 0.99   1389  154 0.1003 0.1246      5.3863       5.542|
|  2:  4.6539 -  3.7138 0.99   1329  150 0.0821 0.1139       5.417      5.6116|
|  3:  3.7138 -  3.2502 0.99   1317  149 0.1007 0.1529      5.4472      5.8405|
|  4:  3.2502 -  2.9557 0.99   1300  134 0.1155 0.1673      5.4235      5.6317|
|  5:  2.9557 -  2.7454 0.99   1289  147 0.1185 0.1565      5.2667      5.4584|
|  6:  2.7454 -  2.5844 0.98   1284  143 0.1195 0.1853      5.1789      5.4078|
|  7:  2.5844 -  2.4556 0.99   1292  146 0.1124 0.1610      5.0974      5.3306|
|  8:  2.4556 -  2.3492 0.98   1276  139 0.1103 0.1683      5.0485      5.3168|
|  9:  2.3492 -  2.2591 0.98   1268  144 0.1132 0.1918      5.0021      5.3372|
| 10:  2.2591 -  2.1814 0.97   1247  136 0.1095 0.1761       4.963       5.171|
| 11:  2.1814 -  2.1134 0.99   1274  145 0.1086 0.1729      4.9112       5.267|
| 12:  2.1134 -  2.0531 0.98   1276  140 0.1065 0.1680      4.8432      5.1346|
| 13:  2.0531 -  1.9992 0.97   1258  134 0.1080 0.1703      4.7721      5.0245|
| 14:  1.9992 -  1.9506 0.66    831   98 0.1041 0.1852       4.691      4.9627|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6397 -  4.6539  1389   154  0.94   9.08   0.99     0.97       7096.94|
|  2:  4.6539 -  3.7138  1329   150  0.95   7.95   1.04     1.02       8956.87|
|  3:  3.7138 -  3.2502  1317   149  0.94  11.08   1.05     1.04      10197.90|
|  4:  3.2502 -  2.9557  1300   134  0.93  12.91   1.02     1.02       9882.64|
|  5:  2.9557 -  2.7454  1289   147  0.91  14.90   1.00     0.97       7579.70|
|  6:  2.7454 -  2.5844  1284   143  0.90  15.69   0.99     0.96       6624.15|
|  7:  2.5844 -  2.4556  1292   146  0.91  14.70   0.99     0.96       5568.23|
|  8:  2.4556 -  2.3492  1276   139  0.92  14.48   1.01     0.99       5204.18|
|  9:  2.3492 -  2.2591  1268   144  0.91  15.31   1.01     0.99       4803.90|
| 10:  2.2591 -  2.1814  1247   136  0.90  15.71   1.01     0.98       4551.95|
| 11:  2.1814 -  2.1134  1274   145  0.90  15.87   1.01     0.98       4276.80|
| 12:  2.1134 -  2.0531  1276   140  0.91  15.04   1.02     1.01       3769.74|
| 13:  2.0531 -  1.9992  1258   134  0.90  15.84   1.01     1.01       3293.12|
| 14:  1.9992 -  1.9506   831    98  0.91  14.73   1.00     0.96       2681.95|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2681.95 max =        10197.90 mean =      6156.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.72|
|phase err.(test): min =        0.00 max =           88.66 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1578   ksol= 0.32   Bsol= 34.55   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.27,-1.73,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118269                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1578   ksol= 0.32   Bsol= 34.55   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.07,-2.27,-1.73,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118269                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6539 0.99   1389  154 0.1003 0.1248      5.3871      5.5431|
|  2:  4.6539 -  3.7138 0.99   1329  150 0.0823 0.1139      5.4183      5.6122|
|  3:  3.7138 -  3.2502 0.99   1317  149 0.1008 0.1529      5.4477      5.8411|
|  4:  3.2502 -  2.9557 0.99   1300  134 0.1155 0.1669      5.4234      5.6306|
|  5:  2.9557 -  2.7454 0.99   1289  147 0.1184 0.1565      5.2662      5.4584|
|  6:  2.7454 -  2.5844 0.98   1284  143 0.1194 0.1851      5.1783      5.4064|
|  7:  2.5844 -  2.4556 0.99   1292  146 0.1123 0.1608      5.0961      5.3296|
|  8:  2.4556 -  2.3492 0.98   1276  139 0.1102 0.1680      5.0472      5.3146|
|  9:  2.3492 -  2.2591 0.98   1268  144 0.1131 0.1919      5.0012      5.3377|
| 10:  2.2591 -  2.1814 0.97   1247  136 0.1095 0.1759      4.9624      5.1698|
| 11:  2.1814 -  2.1134 0.99   1274  145 0.1085 0.1728      4.9104      5.2667|
| 12:  2.1134 -  2.0531 0.98   1276  140 0.1063 0.1680      4.8427      5.1339|
| 13:  2.0531 -  1.9992 0.97   1258  134 0.1079 0.1705      4.7716      5.0244|
| 14:  1.9992 -  1.9506 0.66    831   98 0.1040 0.1851      4.6903      4.9624|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6397 -  4.6539  1389   154  0.94   9.10   0.99     0.97       7114.91|
|  2:  4.6539 -  3.7138  1329   150  0.95   7.96   1.04     1.03       8970.50|
|  3:  3.7138 -  3.2502  1317   149  0.94  11.09   1.05     1.04      10201.10|
|  4:  3.2502 -  2.9557  1300   134  0.93  12.91   1.03     1.02       9879.14|
|  5:  2.9557 -  2.7454  1289   147  0.91  14.90   1.01     0.98       7571.48|
|  6:  2.7454 -  2.5844  1284   143  0.90  15.67   0.99     0.96       6616.63|
|  7:  2.5844 -  2.4556  1292   146  0.91  14.67   1.00     0.97       5548.63|
|  8:  2.4556 -  2.3492  1276   139  0.92  14.44   1.01     0.99       5186.44|
|  9:  2.3492 -  2.2591  1268   144  0.91  15.28   1.02     0.99       4790.13|
| 10:  2.2591 -  2.1814  1247   136  0.90  15.71   1.02     0.99       4547.79|
| 11:  2.1814 -  2.1134  1274   145  0.90  15.86   1.02     0.99       4269.16|
| 12:  2.1134 -  2.0531  1276   140  0.91  15.03   1.03     1.01       3765.83|
| 13:  2.0531 -  1.9992  1258   134  0.90  15.84   1.02     1.01       3290.28|
| 14:  1.9992 -  1.9506   831    98  0.91  14.72   1.01     0.97       2678.85|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2678.85 max =        10201.10 mean =      6153.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.71|
|phase err.(test): min =        0.00 max =           88.77 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.259)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    101.22  17.41    None  None   None       |
|    all(noH): 2823   0      1.70    101.22  17.41    None  None   None       |
|    Sol.    : 438    0      5.92    91.18   40.79    None  None   None       |
|    Mac.    : 2385   0      1.70    101.22  13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.703 -  11.654: 1373   |   5:    51.459 -  61.410:   78        |
|      1:    11.654 -  21.605:  878   |   6:    61.410 -  71.362:   40        |
|      2:    21.605 -  31.557:  170   |   7:    71.362 -  81.313:    7        |
|      3:    31.557 -  41.508:  134   |   8:    81.313 -  91.264:    9        |
|      4:    41.508 -  51.459:  131   |   9:    91.264 - 101.215:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 283         
Filter by distance & map next to the model:
   mapped sites are within: 0.397 - 5.589
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 278 from: 283
   mapped sites are within: 0.732 - 5.589

peak=    6.547 closest distance to " O   HOH Z 142 " =    1.838
peak=    5.820 closest distance to " NE2 GLN A  11 " =    1.127
peak=    5.799 closest distance to " O   HOH Z 126 " =    1.889
peak=    5.662 closest distance to " O   HOH Z 236 " =    1.464
peak=    5.558 closest distance to " O   HOH Z 193 " =    1.736
peak=    5.549 closest distance to " O   HOH Z  52 " =    1.815
peak=    5.526 closest distance to " CB  ARG A 275 " =    0.966
peak=    5.283 closest distance to " CG  PRO A 213 " =    1.297
peak=    4.964 closest distance to " NH2 ARG A  56 " =    1.979
peak=    4.909 closest distance to " CG  PRO A  54 " =    1.148
peak=    4.839 closest distance to " C   PRO A 198 " =    1.587
peak=    4.756 closest distance to " O   HOH Z 272 " =    1.862
peak=    4.718 closest distance to " O   HOH Z  93 " =    2.443
peak=    4.702 closest distance to " CB  ASN A 148 " =    1.879
peak=    4.674 closest distance to " O   HOH Z 209 " =    2.283
peak=    4.667 closest distance to " O   HOH Z 124 " =    1.403
peak=    4.640 closest distance to " O   HOH Z 232 " =    2.354
peak=    4.595 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.552 closest distance to " CB  SER A  63 " =    1.129
peak=    4.524 closest distance to " O   HOH Z 427 " =    2.726
peak=    4.481 closest distance to " O   HOH Z  78 " =    1.770
peak=    4.461 closest distance to " O   HOH Z 213 " =    1.809
peak=    4.433 closest distance to " O   SER A  87 " =    2.398
peak=    4.425 closest distance to " O   HOH Z 407 " =    2.547
peak=    4.416 closest distance to " O   HOH Z  54 " =    1.741
peak=    4.402 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.382 closest distance to " O   HOH Z 132 " =    1.134
peak=    4.377 closest distance to " CB  ARG A  79 " =    1.359
peak=    4.375 closest distance to " CG  PRO A  90 " =    1.174
peak=    4.372 closest distance to " O   HOH Z 234 " =    3.449
peak=    4.370 closest distance to " O   HOH Z 278 " =    1.084
peak=    4.351 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.343 closest distance to " CB  GLN A 223 " =    1.548
peak=    4.331 closest distance to " NZ  LYS A 117 " =    3.015
peak=    4.322 closest distance to " O   HOH Z 402 " =    1.507
peak=    4.292 closest distance to " O   HOH Z 403 " =    1.857
peak=    4.261 closest distance to " CB  SER A   3 " =    1.316
peak=    4.256 closest distance to " O   HOH Z 327 " =    1.724
peak=    4.248 closest distance to " ND2 ASN A 187 " =    1.349
peak=    4.183 closest distance to " C   ALA A   1 " =    1.609
peak=    4.177 closest distance to " CG  PRO A 243 " =    1.172
peak=    4.175 closest distance to " O   HOH Z 369 " =    1.971
peak=    4.159 closest distance to " O   HOH Z 298 " =    1.745
peak=    4.140 closest distance to " O   HOH Z 134 " =    1.287
peak=    4.139 closest distance to " O   HOH Z 425 " =    1.285
peak=    4.137 closest distance to " CD2 TRP A 179 " =    1.410
peak=    4.126 closest distance to " O   HOH Z 416 " =    0.962
peak=    4.091 closest distance to " CB  VAL A 265 " =    1.273
peak=    4.077 closest distance to " OD2 ASP A 286 " =    2.567
peak=    4.074 closest distance to " O   HOH Z  97 " =    1.925
peak=    4.051 closest distance to " O   HOH Z 368 " =    2.008
peak=    4.043 closest distance to " O   HOH Z   6 " =    2.268
peak=    4.036 closest distance to " O   HOH Z 128 " =    2.055
peak=    4.007 closest distance to " O   HOH Z 316 " =    2.853
peak=    4.004 closest distance to " O   HOH Z 346 " =    1.644
peak=    3.998 closest distance to " O   HOH Z 112 " =    2.306
peak=    3.988 closest distance to " O   HOH Z  44 " =    1.920
peak=    3.964 closest distance to " OG BSER A 164 " =    2.182
peak=    3.961 closest distance to " O   HOH Z  92 " =    0.984
peak=    3.954 closest distance to " O   HOH Z 102 " =    1.217
peak=    3.932 closest distance to " O   HOH Z 203 " =    1.734
peak=    3.925 closest distance to " O   HOH Z  59 " =    1.847
peak=    3.912 closest distance to " O   HOH Z 389 " =    1.709
peak=    3.906 closest distance to " O   HOH Z 207 " =    1.777
peak=    3.897 closest distance to " O   HOH Z 303 " =    2.082
peak=    3.895 closest distance to " O   HOH Z 344 " =    2.909
peak=    3.894 closest distance to " O   HOH Z  42 " =    2.319
peak=    3.875 closest distance to " O   HOH Z 345 " =    3.117
peak=    3.871 closest distance to " CA  ALA A  21 " =    1.125
peak=    3.870 closest distance to " O   HOH Z 130 " =    2.881
peak=    3.864 closest distance to " O   HOH Z 219 " =    2.137
peak=    3.855 closest distance to " O   HOH Z 366 " =    2.752
peak=    3.853 closest distance to " CB  SER A  26 " =    1.588
peak=    3.852 closest distance to " O   HOH Z 108 " =    2.096
peak=    3.852 closest distance to " O   HOH Z  10 " =    1.819
peak=    3.836 closest distance to " O   HOH Z 144 " =    1.985
peak=    3.819 closest distance to " CB  TRP A 179 " =    1.095
peak=    3.818 closest distance to " NH2BARG A 145 " =    2.183
peak=    3.814 closest distance to " O   HOH Z  15 " =    2.263
peak=    3.812 closest distance to " N   ASN A  39 " =    1.218
peak=    3.799 closest distance to " CB  TYR A 169 " =    0.860
peak=    3.791 closest distance to " CG  PRO A 198 " =    1.245
peak=    3.789 closest distance to " O   HOH Z  49 " =    2.045
peak=    3.768 closest distance to " O   HOH Z  63 " =    2.024
peak=    3.767 closest distance to " O   HOH Z 156 " =    3.139
peak=    3.755 closest distance to " CB  TRP A 266 " =    1.142
peak=    3.743 closest distance to " O   HOH Z  66 " =    2.077
peak=    3.741 closest distance to " O   HOH Z  61 " =    1.682
peak=    3.740 closest distance to " CB  GLU A 128 " =    1.116
peak=    3.740 closest distance to " O   HOH Z 245 " =    1.326
peak=    3.735 closest distance to " CG1 ILE A  33 " =    1.153
peak=    3.730 closest distance to " O   HOH Z 423 " =    1.929
peak=    3.709 closest distance to " O   HOH Z 426 " =    1.467
peak=    3.706 closest distance to " O   HOH Z 128 " =    1.945
peak=    3.704 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.698 closest distance to " O   HOH Z 180 " =    2.279
peak=    3.697 closest distance to " CG2 ILE A 120 " =    1.168
peak=    3.695 closest distance to " O   HOH Z 411 " =    3.705
peak=    3.694 closest distance to " CA  ASN A 215 " =    1.161
peak=    3.688 closest distance to " CA  ASN A 176 " =    1.173
peak=    3.672 closest distance to " O   HOH Z 380 " =    1.902
peak=    3.671 closest distance to " O   HOH Z  89 " =    2.151
peak=    3.671 closest distance to " O   HOH Z 287 " =    1.694
peak=    3.655 closest distance to " O   HOH Z   3 " =    1.776
peak=    3.637 closest distance to " O   HOH Z 106 " =    2.257
peak=    3.636 closest distance to " CB  PRO A  54 " =    0.959
peak=    3.634 closest distance to " CG  ARG A  66 " =    1.010
peak=    3.632 closest distance to " NH1BARG A 145 " =    1.357
peak=    3.622 closest distance to " O   HOH Z 357 " =    1.793
peak=    3.621 closest distance to " O   HOH Z 118 " =    1.484
peak=    3.620 closest distance to " OG  SER A  62 " =    2.800
peak=    3.616 closest distance to " O   HOH Z  61 " =    1.509
peak=    3.600 closest distance to " O   HOH Z 194 " =    1.908
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.760
peak=    3.593 closest distance to " CH2 TRP A  92 " =    2.073
peak=    3.590 closest distance to " CG  GLN A  77 " =    2.052
peak=    3.585 closest distance to " O   HOH Z 173 " =    1.908
peak=    3.585 closest distance to " OD1 ASN A  69 " =    2.720
peak=    3.583 closest distance to " CB  THR A  31 " =    1.788
peak=    3.580 closest distance to " O   HOH Z 222 " =    2.344
peak=    3.579 closest distance to " O   HOH Z  35 " =    2.442
peak=    3.578 closest distance to " CB  LEU A 228 " =    1.059
peak=    3.572 closest distance to " O   HOH Z 380 " =    1.875
peak=    3.569 closest distance to " O   HOH Z 193 " =    2.036
peak=    3.564 closest distance to " CD2 LEU A 297 " =    1.029
peak=    3.563 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.556 closest distance to " O   HOH Z  43 " =    2.609
peak=    3.552 closest distance to " O   HOH Z 189 " =    1.603
peak=    3.531 closest distance to " O   HOH Z 257 " =    2.078
peak=    3.525 closest distance to " O   HOH Z 251 " =    1.638
peak=    3.524 closest distance to " O   MET A 105 " =    1.870
peak=    3.524 closest distance to " O   HOH Z  80 " =    1.720
peak=    3.523 closest distance to " CE  LYS A 119 " =    1.188
peak=    3.522 closest distance to " O   HOH Z 132 " =    2.033
peak=    3.514 closest distance to " O   HOH Z 132 " =    2.218
peak=    3.505 closest distance to " OG BSER A 258 " =    3.024
peak=    3.505 closest distance to " O   HOH Z 286 " =    2.195
peak=    3.497 closest distance to " CG  MET A 185 " =    1.258
peak=    3.492 closest distance to " O   HOH Z  94 " =    1.964
peak=    3.490 closest distance to " O   HOH Z 425 " =    2.004
peak=    3.489 closest distance to " CD BLYS A 290 " =    1.229
peak=    3.486 closest distance to " O   HOH Z  50 " =    1.688
peak=    3.482 closest distance to " O   HOH Z 359 " =    1.410
peak=    3.472 closest distance to " O   HOH Z  48 " =    1.626
peak=    3.472 closest distance to " CD  ARG A 269 " =    1.061
peak=    3.466 closest distance to " O   HOH Z 214 " =    2.204
peak=    3.463 closest distance to " O   HOH Z 260 " =    1.126
peak=    3.458 closest distance to " CB  ARG A 139 " =    1.027
peak=    3.451 closest distance to " O  BHOH Z 338 " =    2.355
peak=    3.450 closest distance to " O   HOH Z   1 " =    1.836
peak=    3.447 closest distance to " O   HOH Z 261 " =    1.638
peak=    3.445 closest distance to " O   HOH Z 172 " =    3.554
peak=    3.434 closest distance to " O   HOH Z 108 " =    1.036
peak=    3.430 closest distance to " CB  ILE A 120 " =    1.358
peak=    3.427 closest distance to " O   HOH Z 361 " =    3.419
peak=    3.426 closest distance to " O   HOH Z  85 " =    2.344
peak=    3.424 closest distance to " O   HOH Z   9 " =    2.075
peak=    3.421 closest distance to " O   HOH Z  88 " =    2.924
peak=    3.420 closest distance to " O   HOH Z 343 " =    1.285
peak=    3.419 closest distance to " CB  ALA A 291 " =    1.327
peak=    3.415 closest distance to " CB  SER A  62 " =    1.415
peak=    3.414 closest distance to " O   HOH Z  85 " =    1.526
peak=    3.406 closest distance to " O   HOH Z 305 " =    3.505
peak=    3.400 closest distance to " CG2 THR A 294 " =    1.573
peak=    3.396 closest distance to " CA  ALA A 291 " =    0.853
peak=    3.396 closest distance to " N   ARG A 156 " =    1.289
peak=    3.393 closest distance to " CG2 VAL A 257 " =    0.854
peak=    3.387 closest distance to " CD2 HIS A  81 " =    1.025
peak=    3.386 closest distance to " O   HOH Z  73 " =    1.629
peak=    3.386 closest distance to " CE BLYS A 290 " =    0.978
peak=    3.379 closest distance to " CG AARG A 275 " =    1.060
peak=    3.378 closest distance to " O   HOH Z 313 " =    1.648
peak=    3.374 closest distance to " CA  ALA A  51 " =    0.894
peak=    3.374 closest distance to " CA  GLY A  80 " =    0.732
peak=    3.373 closest distance to " O   HOH Z  71 " =    1.538
peak=    3.364 closest distance to " O   HOH Z 284 " =    2.774
peak=    3.357 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.356 closest distance to " O   HOH Z 214 " =    2.292
peak=    3.355 closest distance to " O   HOH Z 273 " =    2.810
peak=    3.353 closest distance to " OG1 THR A 294 " =    2.294
peak=    3.346 closest distance to " O   HOH Z 406 " =    1.578
peak=    3.346 closest distance to " O   HOH Z  40 " =    1.537
peak=    3.342 closest distance to " O   HOH Z 234 " =    1.872
peak=    3.342 closest distance to " O  BHOH Z  74 " =    1.443
peak=    3.341 closest distance to " O   HOH Z 427 " =    2.986
peak=    3.339 closest distance to " O   HOH Z 433 " =    1.840
peak=    3.338 closest distance to " O   HOH Z 392 " =    2.529
peak=    3.337 closest distance to " CG2 THR A 221 " =    1.096
peak=    3.336 closest distance to " N   ASP A 162 " =    1.223
peak=    3.336 closest distance to " O   HOH Z  43 " =    2.083
peak=    3.331 closest distance to " O   HOH Z 334 " =    1.276
peak=    3.331 closest distance to " CA  LYS A 117 " =    1.265
peak=    3.330 closest distance to " O   HOH Z 291 " =    1.713
peak=    3.325 closest distance to " CB  ASN A  39 " =    0.739
peak=    3.324 closest distance to " O   HOH Z 279 " =    2.135
peak=    3.321 closest distance to " NE2 GLN A 223 " =    1.908
peak=    3.318 closest distance to " CB  ARG A 190 " =    1.739
peak=    3.315 closest distance to " O   HOH Z 435 " =    1.763
peak=    3.312 closest distance to " O   HOH Z 342 " =    0.781
peak=    3.308 closest distance to " O   HOH Z 261 " =    2.177
peak=    3.307 closest distance to " O   HOH Z  19 " =    2.349
peak=    3.304 closest distance to " CA  ARG A  36 " =    0.998
peak=    3.304 closest distance to " N   TRP A 150 " =    1.353
peak=    3.304 closest distance to " CB  GLU A 277 " =    3.430
peak=    3.299 closest distance to " CA  SER A 146 " =    1.890
peak=    3.295 closest distance to " O   HOH Z  63 " =    2.308
peak=    3.294 closest distance to " O   HOH Z 368 " =    2.614
peak=    3.292 closest distance to " CA  ALA A 233 " =    0.950
peak=    3.290 closest distance to " O   HOH Z  71 " =    1.315
peak=    3.285 closest distance to " O   HOH Z 408 " =    1.409
peak=    3.278 closest distance to " CA  THR A 221 " =    0.934
peak=    3.271 closest distance to " CA  ALA A  84 " =    1.304
peak=    3.263 closest distance to " O   HOH Z 302 " =    1.663
peak=    3.263 closest distance to " O   HOH Z  59 " =    2.271
peak=    3.262 closest distance to " CB  HIS A 108 " =    0.891
peak=    3.260 closest distance to " O   HOH Z 374 " =    2.420
peak=    3.257 closest distance to " O   HOH Z 421 " =    1.576
peak=    3.257 closest distance to " O   HOH Z 353 " =    2.488
peak=    3.256 closest distance to " O   HOH Z 192 " =    1.902
peak=    3.256 closest distance to " O   HOH Z  64 " =    2.106
peak=    3.252 closest distance to " CG  GLU A 277 " =    2.034
peak=    3.250 closest distance to " CG  ARG A 269 " =    1.276
peak=    3.248 closest distance to " N   CYS A 260 " =    0.773
peak=    3.246 closest distance to " O   HOH Z  18 " =    1.212
peak=    3.241 closest distance to " CB  ASN A 110 " =    1.042
peak=    3.240 closest distance to " O   HOH Z 172 " =    5.589
peak=    3.237 closest distance to " CG1BVAL A  72 " =    1.442
peak=    3.227 closest distance to " OD1 ASP A 253 " =    1.988
peak=    3.225 closest distance to " CB  THR A 279 " =    1.567
peak=    3.223 closest distance to " CA  MET A  40 " =    1.066
peak=    3.222 closest distance to " CA  THR A 264 " =    0.775
peak=    3.215 closest distance to " O   HOH Z 303 " =    1.761
peak=    3.215 closest distance to " O   HOH Z 130 " =    2.776
peak=    3.214 closest distance to " CB  ALA A  21 " =    1.833
peak=    3.203 closest distance to " O   HOH Z 299 " =    4.268
peak=    3.198 closest distance to " CG  LYS A  76 " =    0.928
peak=    3.197 closest distance to " CG  MET A 113 " =    0.980
peak=    3.196 closest distance to " CB  ALA A  10 " =    1.309
peak=    3.195 closest distance to " O   HOH Z  88 " =    2.368
peak=    3.192 closest distance to " CG2 ILE A  20 " =    1.417
peak=    3.185 closest distance to " CB  TYR A  30 " =    1.503
peak=    3.185 closest distance to " O   HOH Z 336 " =    1.570
peak=    3.182 closest distance to " O   HOH Z 337 " =    3.324
peak=    3.182 closest distance to " N   TYR A  15 " =    1.095
peak=    3.181 closest distance to " CB  PRO A  90 " =    1.801
peak=    3.179 closest distance to " O   HOH Z 417 " =    1.993
peak=    3.172 closest distance to " CG  MET A 185 " =    0.944
peak=    3.168 closest distance to " N   ASN A 127 " =    1.206
peak=    3.167 closest distance to " CA  ASP A 140 " =    1.102
peak=    3.166 closest distance to " O   HOH Z 267 " =    2.034
peak=    3.162 closest distance to " O   HOH Z 163 " =    1.669
peak=    3.162 closest distance to " NZ  LYS A  76 " =    1.439
peak=    3.161 closest distance to " N   PHE A 130 " =    1.356
peak=    3.159 closest distance to " CB  ALA A 248 " =    1.448
peak=    3.154 closest distance to " O   HOH Z 293 " =    2.034
peak=    3.153 closest distance to " O   HOH Z 211 " =    2.630
peak=    3.153 closest distance to " O   HOH Z 423 " =    2.935
peak=    3.150 closest distance to " N   TYR A 116 " =    1.631
peak=    3.144 closest distance to " O   HOH Z 112 " =    1.205
peak=    3.139 closest distance to " CB  ASN A 127 " =    0.753
peak=    3.139 closest distance to " CG1 ILE A 120 " =    1.266
peak=    3.136 closest distance to " OG BSER A  99 " =    2.192
peak=    3.132 closest distance to " CH2 TRP A 150 " =    1.129
peak=    3.130 closest distance to " O   HOH Z 125 " =    2.403
peak=    3.130 closest distance to " CG2 THR A  29 " =    1.242
peak=    3.130 closest distance to " CB  GLN A 278 " =    0.777
peak=    3.110 closest distance to " O   HOH Z 114 " =    3.871
peak=    3.108 closest distance to " OG  SER A  22 " =    2.615
peak=    3.103 closest distance to " O   HOH Z 329 " =    3.564
peak=    3.102 closest distance to " CG  LYS A 119 " =    1.147
peak=    3.095 closest distance to " O   HOH Z  40 " =    2.273
peak=    3.092 closest distance to " O   HOH Z 194 " =    1.930
peak=    3.080 closest distance to " O   HOH Z 299 " =    2.253
peak=    3.063 closest distance to " CA  ILE A  33 " =    1.232
peak=    3.051 closest distance to " O   HOH Z 325 " =    3.603
peak=    3.027 closest distance to " O   HOH Z  68 " =    1.467
peak=    3.020 closest distance to " O   HOH Z 134 " =    1.322
peak=    3.019 closest distance to " O   HOH Z 250 " =    1.901

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.649 - 5.647
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.725 - 5.647

peak=   -4.593 closest distance to " O   HOH Z 266 " =    4.513
peak=   -4.463 closest distance to " O   HOH Z 372 " =    2.346
peak=   -4.460 closest distance to " CA  VAL A  67 " =    2.812
peak=   -4.424 closest distance to " C   HIS A 108 " =    1.085
peak=   -4.393 closest distance to " OXT GLY A 302 " =    2.688
peak=   -4.393 closest distance to " O   VAL A  67 " =    2.709
peak=   -4.354 closest distance to " SG  CYS A 254 " =    3.212
peak=   -4.301 closest distance to " OD1 ASN A  39 " =    2.115
peak=   -4.298 closest distance to " OG BSER A 134 " =    1.314
peak=   -4.216 closest distance to " N   GLN A  58 " =    1.643
peak=   -4.147 closest distance to " O   PRO A 198 " =    1.294
peak=   -4.146 closest distance to " CD  ARG A 156 " =    2.028
peak=   -4.135 closest distance to " NH1 ARG A  56 " =    2.533
peak=   -4.113 closest distance to " O   HOH Z 407 " =    2.679
peak=   -4.050 closest distance to " CB  PRO A 243 " =    2.638
peak=   -4.037 closest distance to " N   HIS A 115 " =    1.969
peak=   -3.987 closest distance to " O   HOH Z 166 " =    1.520
peak=   -3.986 closest distance to " ND2 ASN A  45 " =    1.078
peak=   -3.964 closest distance to " N   ALA A 248 " =    1.660
peak=   -3.963 closest distance to " O   HOH Z 290 " =    1.119
peak=   -3.959 closest distance to " O   HOH Z 377 " =    2.078
peak=   -3.945 closest distance to " OD2 ASP A 191 " =    1.403
peak=   -3.934 closest distance to " O   HOH Z 198 " =    1.878
peak=   -3.923 closest distance to " O   HOH Z 126 " =    1.830
peak=   -3.919 closest distance to " CD1 LEU A 101 " =    2.346
peak=   -3.909 closest distance to " NH2 ARG A  66 " =    4.524
peak=   -3.890 closest distance to " C   GLY A  91 " =    1.323
peak=   -3.888 closest distance to " O   HOH Z  52 " =    2.103
peak=   -3.844 closest distance to " O   HOH Z   6 " =    2.005
peak=   -3.830 closest distance to " O   HOH Z  13 " =    1.587
peak=   -3.824 closest distance to " O   SER A 146 " =    0.865
peak=   -3.818 closest distance to " CD1 LEU A 255 " =    2.667
peak=   -3.801 closest distance to " O   ALA A 161 " =    1.638
peak=   -3.793 closest distance to " OG  SER A   3 " =    1.514
peak=   -3.791 closest distance to " N   GLN A 122 " =    1.464
peak=   -3.784 closest distance to " O   TRP A  92 " =    1.691
peak=   -3.773 closest distance to " O   HOH Z  92 " =    1.898
peak=   -3.768 closest distance to " O   TRP A  70 " =    1.486
peak=   -3.767 closest distance to " O   HOH Z 385 " =    1.921
peak=   -3.766 closest distance to " O   HOH Z  43 " =    1.733
peak=   -3.761 closest distance to " O   HOH Z   3 " =    1.822
peak=   -3.751 closest distance to " CB  PRO A 163 " =    2.642
peak=   -3.747 closest distance to " CB  ALA A 291 " =    2.406
peak=   -3.744 closest distance to " CG  PHE A 283 " =    2.598
peak=   -3.741 closest distance to " O   HOH Z 250 " =    1.363
peak=   -3.738 closest distance to " C   ASP A 231 " =    2.491
peak=   -3.738 closest distance to " O   PRO A 163 " =    1.784
peak=   -3.735 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.729 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.718 closest distance to " CD1 LEU A  25 " =    2.462
peak=   -3.689 closest distance to " O   ALA A  51 " =    1.221
peak=   -3.682 closest distance to " CD2 LEU A 300 " =    2.845
peak=   -3.680 closest distance to " O   HOH Z 313 " =    1.898
peak=   -3.677 closest distance to " O   HOH Z 388 " =    1.953
peak=   -3.673 closest distance to " O   HOH Z  11 " =    1.658
peak=   -3.672 closest distance to " CB  ASN A  39 " =    2.245
peak=   -3.662 closest distance to " CD  ARG A 139 " =    1.397
peak=   -3.637 closest distance to " CA  GLY A  98 " =    1.932
peak=   -3.637 closest distance to " C   GLN A 205 " =    1.812
peak=   -3.633 closest distance to " O   SER A 135 " =    1.454
peak=   -3.629 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.628 closest distance to " O   HOH Z  24 " =    1.335
peak=   -3.627 closest distance to " O   ARG A 145 " =    1.641
peak=   -3.626 closest distance to " CG  ARG A 219 " =    2.283
peak=   -3.609 closest distance to " O   MET A  40 " =    2.703
peak=   -3.605 closest distance to " CA  GLY A 133 " =    1.827
peak=   -3.605 closest distance to " CZ  TYR A 169 " =    1.728
peak=   -3.604 closest distance to " C   ALA A 158 " =    1.224
peak=   -3.601 closest distance to " CD2 LEU A 237 " =    2.281
peak=   -3.597 closest distance to " O   HOH Z 362 " =    5.647
peak=   -3.593 closest distance to " CG1 VAL A  78 " =    3.138
peak=   -3.586 closest distance to " CD1 LEU A 228 " =    2.052
peak=   -3.584 closest distance to " O   HOH Z 401 " =    0.884
peak=   -3.578 closest distance to " OD1 ASP A 191 " =    1.587
peak=   -3.561 closest distance to " OG  SER A  97 " =    2.023
peak=   -3.550 closest distance to " O   HOH Z 263 " =    2.975
peak=   -3.548 closest distance to " O   HOH Z 385 " =    1.955
peak=   -3.547 closest distance to " O   ASP A 270 " =    1.920
peak=   -3.546 closest distance to " ND2 ASN A  39 " =    1.298
peak=   -3.538 closest distance to " OD1 ASP A 191 " =    1.434
peak=   -3.538 closest distance to " O   HOH Z 197 " =    4.883
peak=   -3.523 closest distance to " O   HOH Z 393 " =    3.542
peak=   -3.523 closest distance to " O   PRO A 198 " =    1.243
peak=   -3.521 closest distance to " O   HOH Z 114 " =    2.940
peak=   -3.518 closest distance to " O   HOH Z 423 " =    2.117
peak=   -3.508 closest distance to " CD1 PHE A  59 " =    1.928
peak=   -3.487 closest distance to " O   ALA A  34 " =    2.399
peak=   -3.473 closest distance to " O   HOH Z 231 " =    2.231
peak=   -3.466 closest distance to " CD  LYS A 289 " =    2.377
peak=   -3.463 closest distance to " CG  GLN A  58 " =    1.303
peak=   -3.454 closest distance to " O   HOH Z 395 " =    5.012
peak=   -3.445 closest distance to " CE2 TYR A  30 " =    2.904
peak=   -3.442 closest distance to " CB  ALA A 244 " =    2.054
peak=   -3.442 closest distance to " N   SER A 276 " =    1.164
peak=   -3.439 closest distance to " OD2 ASP A  50 " =    1.368
peak=   -3.438 closest distance to " O   HOH Z 427 " =    1.453
peak=   -3.427 closest distance to " CB  PHE A 192 " =    1.835
peak=   -3.425 closest distance to " O   HOH Z  88 " =    1.907
peak=   -3.421 closest distance to " OH  TYR A 172 " =    1.688
peak=   -3.418 closest distance to " N   ASP A 286 " =    2.210
peak=   -3.415 closest distance to " CG1 VAL A 112 " =    2.832
peak=   -3.409 closest distance to " O   HOH Z 421 " =    3.219
peak=   -3.395 closest distance to " O   HOH Z 137 " =    1.444
peak=   -3.393 closest distance to " O   HOH Z 351 " =    1.554
peak=   -3.388 closest distance to " OD2 ASP A 171 " =    2.306
peak=   -3.385 closest distance to " CB  ALA A 248 " =    2.083
peak=   -3.383 closest distance to " CG  ASP A 231 " =    0.725
peak=   -3.382 closest distance to " O   HOH Z 165 " =    2.071
peak=   -3.378 closest distance to " SG ACYS A 201 " =    1.702
peak=   -3.376 closest distance to " CD1 ILE A 239 " =    2.554
peak=   -3.374 closest distance to " O   HOH Z  37 " =    1.503
peak=   -3.372 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.371 closest distance to " N   THR A 220 " =    2.281
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.254
peak=   -3.364 closest distance to " O   HOH Z 193 " =    1.393
peak=   -3.363 closest distance to " CG2 ILE A 263 " =    2.181
peak=   -3.360 closest distance to " O   GLU A 152 " =    1.564
peak=   -3.358 closest distance to " O   ASP A 162 " =    2.157
peak=   -3.357 closest distance to " OG1 THR A 178 " =    1.212
peak=   -3.351 closest distance to " OG ASER A 134 " =    1.142
peak=   -3.350 closest distance to " CE3 TRP A 274 " =    2.240
peak=   -3.341 closest distance to " O   HOH Z 185 " =    2.146
peak=   -3.338 closest distance to " O   VAL A 174 " =    2.044
peak=   -3.337 closest distance to " CE  MET A 105 " =    2.263
peak=   -3.333 closest distance to " CZ  PHE A 130 " =    0.836
peak=   -3.321 closest distance to " OG  SER A  63 " =    1.166
peak=   -3.313 closest distance to " CZ  PHE A  59 " =    1.520
peak=   -3.312 closest distance to " C   LEU A 143 " =    1.046
peak=   -3.306 closest distance to " CG1BVAL A  41 " =    2.747
peak=   -3.305 closest distance to " NH1BARG A 145 " =    3.364
peak=   -3.300 closest distance to " C   GLN A 144 " =    1.000
peak=   -3.297 closest distance to " O   PRO A 163 " =    1.293
peak=   -3.295 closest distance to " ND2 ASN A 142 " =    1.866
peak=   -3.293 closest distance to " CB  GLN A  11 " =    1.858
peak=   -3.292 closest distance to " CG  GLU A 152 " =    1.078
peak=   -3.290 closest distance to " O   HOH Z 210 " =    1.934
peak=   -3.284 closest distance to " O   HOH Z  60 " =    1.823
peak=   -3.283 closest distance to " O   HOH Z 113 " =    1.997
peak=   -3.282 closest distance to " O   SER A 146 " =    0.910
peak=   -3.281 closest distance to " ND2 ASN A 173 " =    1.440
peak=   -3.278 closest distance to " O   HOH Z 211 " =    1.676
peak=   -3.272 closest distance to " O   HOH Z 139 " =    3.015
peak=   -3.270 closest distance to " ND2 ASN A 209 " =    1.740
peak=   -3.267 closest distance to " O   HOH Z  97 " =    1.216
peak=   -3.266 closest distance to " N   SER A 210 " =    1.417
peak=   -3.260 closest distance to " N   PHE A  59 " =    1.723
peak=   -3.258 closest distance to " O   SER A   3 " =    1.073
peak=   -3.255 closest distance to " CD1 TYR A 247 " =    2.295
peak=   -3.247 closest distance to " O   THR A 182 " =    1.263
peak=   -3.246 closest distance to " O   HOH Z 389 " =    1.730
peak=   -3.243 closest distance to " O   HOH Z 107 " =    1.690
peak=   -3.240 closest distance to " O   HOH Z 191 " =    5.416
peak=   -3.234 closest distance to " O   SER A 210 " =    1.857
peak=   -3.233 closest distance to " O   HOH Z  52 " =    1.575
peak=   -3.232 closest distance to " N   PRO A 163 " =    1.457
peak=   -3.230 closest distance to " NH1 ARG A 195 " =    2.554
peak=   -3.224 closest distance to " O   ILE A 120 " =    1.362
peak=   -3.222 closest distance to " O   HOH Z  63 " =    1.449
peak=   -3.221 closest distance to " CE1 HIS A  81 " =    1.662
peak=   -3.216 closest distance to " OG  SER A  22 " =    4.353
peak=   -3.216 closest distance to " O   HOH Z 326 " =    1.652
peak=   -3.216 closest distance to " O   SER A  22 " =    2.131
peak=   -3.214 closest distance to " O   HOH Z 218 " =    3.112
peak=   -3.214 closest distance to " OE2 GLU A 152 " =    1.350
peak=   -3.211 closest distance to " O   GLN A  89 " =    1.550
peak=   -3.208 closest distance to " O   HOH Z 310 " =    3.506
peak=   -3.206 closest distance to " CG  TRP A 266 " =    1.927
peak=   -3.204 closest distance to " N   ALA A  43 " =    2.285
peak=   -3.203 closest distance to " CB  ASP A 132 " =    2.301
peak=   -3.200 closest distance to " O   ASN A  45 " =    1.828
peak=   -3.200 closest distance to " C   LEU A 101 " =    1.382
peak=   -3.198 closest distance to " O   HOH Z 234 " =    3.801
peak=   -3.198 closest distance to " O   HOH Z 123 " =    2.335
peak=   -3.195 closest distance to " OG  SER A  26 " =    1.203
peak=   -3.192 closest distance to " O   HOH Z 251 " =    1.340
peak=   -3.188 closest distance to " CG  PRO A 243 " =    1.536
peak=   -3.187 closest distance to " O   ASP A 231 " =    2.337
peak=   -3.174 closest distance to " CB  TRP A 274 " =    2.773
peak=   -3.169 closest distance to " O   HOH Z 361 " =    3.457
peak=   -3.167 closest distance to " CE  MET A 105 " =    1.944
peak=   -3.166 closest distance to " O   LEU A 222 " =    1.345
peak=   -3.156 closest distance to " O   HOH Z 256 " =    1.359
peak=   -3.156 closest distance to " O   VAL A 125 " =    1.949
peak=   -3.154 closest distance to " CE  MET A  93 " =    1.162
peak=   -3.154 closest distance to " ND2 ASN A 215 " =    2.098
peak=   -3.150 closest distance to " O   HOH Z 424 " =    2.857
peak=   -3.147 closest distance to " O   HOH Z  90 " =    2.403
peak=   -3.141 closest distance to " O   HOH Z  60 " =    1.901
peak=   -3.139 closest distance to " CD  GLN A  88 " =    0.963
peak=   -3.137 closest distance to " O   HOH Z 168 " =    1.510
peak=   -3.136 closest distance to " C   THR A 264 " =    1.374
peak=   -3.115 closest distance to " CB  ILE A  33 " =    2.877
peak=   -3.114 closest distance to " O   HOH Z 174 " =    4.201
peak=   -3.114 closest distance to " CG2 THR A 178 " =    2.191
peak=   -3.112 closest distance to " CG1 VAL A 125 " =    2.288
peak=   -3.102 closest distance to " O   HOH Z 385 " =    1.649
peak=   -3.102 closest distance to " CB  ALA A  43 " =    2.276
peak=   -3.091 closest distance to " ND2 ASN A  60 " =    1.576
peak=   -3.087 closest distance to " O   HOH Z 200 " =    3.280
peak=   -3.073 closest distance to " CB  PHE A 208 " =    2.170
peak=   -3.049 closest distance to " OE1 GLN A  88 " =    1.064
peak=   -3.047 closest distance to " CZ3 TRP A 179 " =    1.328
peak=   -3.043 closest distance to " CE2 PHE A 204 " =    2.195
peak=   -3.037 closest distance to " CG2BVAL A  72 " =    1.855
peak=   -3.033 closest distance to " O   HOH Z 281 " =    2.736
peak=   -3.023 closest distance to " CG  ARG A 269 " =    2.166
peak=   -3.018 closest distance to " OD1 ASN A 301 " =    2.014

================= 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    :  0.4374 0.4409   6.238367e+00   6.241813e+00
   1_bss:  0.4280 0.4284   6.229113e+00   6.221229e+00
   1_xyz:  0.2616 0.2846   5.841266e+00   5.920389e+00
   1_adp:  0.2369 0.2917   5.780591e+00   5.944038e+00
   1_occ:  0.2367 0.2917   5.780083e+00   5.943907e+00
   2_bss:  0.2301 0.2878   5.765810e+00   5.933464e+00
   2_xyz:  0.1674 0.2193   5.488044e+00   5.691584e+00
   2_adp:  0.1541 0.2016   5.403554e+00   5.603542e+00
   2_occ:  0.1537 0.2016   5.402305e+00   5.602786e+00
   3_bss:  0.1533 0.2005   5.398891e+00   5.597159e+00
   3_xyz:  0.1271 0.1695   5.235055e+00   5.448973e+00
   3_adp:  0.1221 0.1653   5.201773e+00   5.422305e+00
   3_occ:  0.1219 0.1654   5.201392e+00   5.422231e+00
   4_bss:  0.1223 0.1650   5.201532e+00   5.419898e+00
   4_xyz:  0.1131 0.1601   5.150039e+00   5.389066e+00
   4_adp:  0.1116 0.1595   5.141689e+00   5.384412e+00
   4_occ:  0.1115 0.1594   5.141355e+00   5.384276e+00
   5_bss:  0.1114 0.1594   5.140846e+00   5.383765e+00
   5_xyz:  0.1080 0.1573   5.121522e+00   5.371584e+00
   5_adp:  0.1072 0.1578   5.118758e+00   5.373693e+00
   5_occ:  0.1072 0.1578   5.118624e+00   5.373706e+00
   5_bss:  0.1071 0.1578   5.118269e+00   5.373332e+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:  0.317  15.130   0.643  -2.367   1.907  -0.000   0.000   0.000
   1_xyz:  0.317  15.130   0.643  -2.367   1.907  -0.000   0.000   0.000
   1_adp:  0.317  15.130   0.643  -2.367   1.907  -0.000   0.000   0.000
   1_occ:  0.317  15.130   0.643  -2.367   1.907  -0.000   0.000   0.000
   2_bss:  0.316  29.145  -2.102  -2.606  -0.760  -0.000  -0.000  -0.000
   2_xyz:  0.316  29.145  -2.102  -2.606  -0.760  -0.000  -0.000  -0.000
   2_adp:  0.316  29.145  -2.102  -2.606  -0.760  -0.000  -0.000  -0.000
   2_occ:  0.316  29.145  -2.102  -2.606  -0.760  -0.000  -0.000  -0.000
   3_bss:  0.319  29.145  -2.974  -2.507  -1.620  -0.000  -0.000  -0.000
   3_xyz:  0.319  29.145  -2.974  -2.507  -1.620  -0.000  -0.000  -0.000
   3_adp:  0.319  29.145  -2.974  -2.507  -1.620  -0.000  -0.000  -0.000
   3_occ:  0.319  29.145  -2.974  -2.507  -1.620  -0.000  -0.000  -0.000
   4_bss:  0.312  29.145  -3.277  -2.597  -1.969  -0.000  -0.000  -0.000
   4_xyz:  0.312  29.145  -3.277  -2.597  -1.969  -0.000  -0.000  -0.000
   4_adp:  0.312  29.145  -3.277  -2.597  -1.969  -0.000  -0.000  -0.000
   4_occ:  0.312  29.145  -3.277  -2.597  -1.969  -0.000  -0.000  -0.000
   5_bss:  0.319  32.355  -3.238  -2.474  -1.922  -0.000  -0.000  -0.000
   5_xyz:  0.319  32.355  -3.238  -2.474  -1.922  -0.000  -0.000  -0.000
   5_adp:  0.319  32.355  -3.238  -2.474  -1.922  -0.000  -0.000  -0.000
   5_occ:  0.319  32.355  -3.238  -2.474  -1.922  -0.000  -0.000  -0.000
   5_bss:  0.322  34.547  -3.073  -2.269  -1.730  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.416 0.5043  0.6891    61024.918
   1_bss:  49.845 0.5223  0.7185    56495.822
   1_xyz:  28.260 0.7785  1.0034    21217.772
   1_adp:  29.591 0.7629  0.9949    22429.164
   1_occ:  29.579 0.7630  0.9950    22430.525
   2_bss:  29.120 0.7674  0.9348    21645.176
   2_xyz:  21.101 0.8505  0.9973    11964.709
   2_adp:  18.502 0.8764  1.0132     9986.207
   2_occ:  18.490 0.8765  1.0129     9957.693
   3_bss:  18.349 0.8777  0.9915     9799.090
   3_xyz:  15.347 0.9037  1.0029     7165.072
   3_adp:  14.733 0.9092  1.0023     6856.927
   3_occ:  14.728 0.9092  1.0022     6849.867
   4_bss:  14.664 0.9097  0.9933     6797.409
   4_xyz:  14.018 0.9149  0.9949     6313.229
   4_adp:  13.910 0.9159  0.9924     6284.266
   4_occ:  13.904 0.9159  0.9923     6279.845
   5_bss:  13.892 0.9160  0.9951     6277.058
   5_xyz:  13.673 0.9177  0.9951     6145.686
   5_adp:  13.688 0.9177  0.9899     6158.045
   5_occ:  13.685 0.9177  0.9899     6155.928
   5_bss:  13.677 0.9177  0.9946     6152.015
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.4866e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.4866e-01
   1_xyz:   1.504  0.012  0.093 16.073  0.007  4.102   1.2574e-01
   1_adp:   1.504  0.012  0.093 16.073  0.007  4.102   1.2574e-01
   1_occ:   1.504  0.012  0.093 16.073  0.007  4.102   1.2574e-01
   2_bss:   1.504  0.012  0.093 16.073  0.007  4.102   1.2574e-01
   2_xyz:   1.030  0.006  0.070 14.580  0.004  4.115   5.9500e-02
   2_adp:   1.030  0.006  0.070 14.580  0.004  4.115   5.9500e-02
   2_occ:   1.030  0.006  0.070 14.580  0.004  4.115   5.9500e-02
   3_bss:   1.030  0.006  0.070 14.580  0.004  4.115   5.9500e-02
   3_xyz:   0.978  0.006  0.066 14.666  0.004  4.106   5.7017e-02
   3_adp:   0.978  0.006  0.066 14.666  0.004  4.106   5.7017e-02
   3_occ:   0.978  0.006  0.066 14.666  0.004  4.106   5.7017e-02
   4_bss:   0.978  0.006  0.066 14.666  0.004  4.106   5.7017e-02
   4_xyz:   1.025  0.006  0.070 14.831  0.004  4.107   6.0143e-02
   4_adp:   1.025  0.006  0.070 14.831  0.004  4.107   6.0143e-02
   4_occ:   1.025  0.006  0.070 14.831  0.004  4.107   6.0143e-02
   5_bss:   1.025  0.006  0.070 14.831  0.004  4.107   6.0143e-02
   5_xyz:   1.040  0.007  0.071 14.718  0.004  4.106   6.1187e-02
   5_adp:   1.040  0.007  0.071 14.718  0.004  4.106   6.1187e-02
   5_occ:   1.040  0.007  0.071 14.718  0.004  4.106   6.1187e-02
   5_bss:   1.040  0.007  0.071 14.718  0.004  4.106   6.1187e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.926   2.4313e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.926   2.4313e-01
   1_xyz:   9.677  0.066  0.383 86.068  0.070  1.977   8.6525e-02
   1_adp:   9.677  0.066  0.383 86.068  0.070  1.977   8.6525e-02
   1_occ:   9.677  0.066  0.383 86.068  0.070  1.977   8.6525e-02
   2_bss:   9.677  0.066  0.383 86.068  0.070  1.977   8.6525e-02
   2_xyz:   7.776  0.043  0.210 83.506  0.048  2.234   5.5669e-02
   2_adp:   7.776  0.043  0.210 83.506  0.048  2.234   5.5669e-02
   2_occ:   7.776  0.043  0.210 83.506  0.048  2.234   5.5669e-02
   3_bss:   7.776  0.043  0.210 83.506  0.048  2.234   5.5669e-02
   3_xyz:   6.759  0.044  0.224 83.932  0.038  2.240   4.3119e-02
   3_adp:   6.759  0.044  0.224 83.932  0.038  2.240   4.3119e-02
   3_occ:   6.759  0.044  0.224 83.932  0.038  2.240   4.3119e-02
   4_bss:   6.759  0.044  0.224 83.932  0.038  2.240   4.3119e-02
   4_xyz:   6.700  0.040  0.215 83.678  0.047  2.297   5.5704e-02
   4_adp:   6.700  0.040  0.215 83.678  0.047  2.297   5.5704e-02
   4_occ:   6.700  0.040  0.215 83.678  0.047  2.297   5.5704e-02
   5_bss:   6.700  0.040  0.215 83.678  0.047  2.297   5.5704e-02
   5_xyz:   6.936  0.045  0.227 82.922  0.044  2.286   4.2804e-02
   5_adp:   6.936  0.045  0.227 82.922  0.044  2.286   4.2804e-02
   5_occ:   6.936  0.045  0.227 82.922  0.044  2.286   4.2804e-02
   5_bss:   6.936  0.045  0.227 82.922  0.044  2.286   4.2804e-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:  84.44   0.00  18.81  84.37   0.00  14.39  84.44   5.66  42.89
   1_occ:  84.44   0.00  18.81  84.37   0.00  14.39  84.44   5.66  42.89
   2_bss:  84.44   0.00  18.81  84.37   0.00  14.39  84.44   5.66  42.89
   2_xyz:  84.44   0.00  18.81  84.37   0.00  14.39  84.44   5.66  42.89
   2_adp:  86.17   1.47  17.72  86.17   1.47  13.57  80.85   7.19  40.28
   2_occ:  86.17   1.47  17.72  86.17   1.47  13.57  80.85   7.19  40.28
   3_bss:  86.17   1.47  17.72  86.17   1.47  13.57  80.85   7.19  40.28
   3_xyz:  86.17   1.47  17.72  86.17   1.47  13.57  80.85   7.19  40.28
   3_adp:  92.77   1.84  17.69  92.77   1.84  13.37  83.24   4.58  41.23
   3_occ:  92.77   1.84  17.69  92.77   1.84  13.37  83.24   4.58  41.23
   4_bss:  92.77   1.84  17.69  92.77   1.84  13.37  83.24   4.58  41.23
   4_xyz:  92.77   1.84  17.69  92.77   1.84  13.37  83.24   4.58  41.23
   4_adp:  96.08   2.28  17.52  96.08   2.28  13.25  83.30   4.99  40.78
   4_occ:  96.08   2.28  17.52  96.08   2.28  13.25  83.30   4.99  40.78
   5_bss:  96.08   2.28  17.52  96.08   2.28  13.25  83.30   4.99  40.78
   5_xyz:  96.08   2.28  17.52  96.08   2.28  13.25  83.30   4.99  40.78
   5_adp: 101.28   1.77  17.47 101.28   1.77  13.18  91.24   5.99  40.85
   5_occ: 101.28   1.77  17.47 101.28   1.77  13.18  91.24   5.99  40.85
   5_bss: 101.22   1.70  17.41 101.22   1.70  13.12  91.18   5.92  40.79
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    3.267    0.022    0.464
   1_adp:    3.267    0.022    0.464
   1_occ:    3.267    0.022    0.464
   2_bss:    3.267    0.022    0.464
   2_xyz:    2.896    0.020    0.537
   2_adp:    2.896    0.020    0.537
   2_occ:    2.896    0.020    0.537
   3_bss:    2.896    0.020    0.537
   3_xyz:    2.908    0.029    0.594
   3_adp:    2.908    0.029    0.594
   3_occ:    2.908    0.029    0.594
   4_bss:    2.908    0.029    0.594
   4_xyz:    2.846    0.085    0.619
   4_adp:    2.846    0.085    0.619
   4_occ:    2.846    0.085    0.619
   5_bss:    2.846    0.085    0.619
   5_xyz:    2.774    0.083    0.631
   5_adp:    2.774    0.083    0.631
   5_occ:    2.774    0.083    0.631
   5_bss:    2.774    0.083    0.631
------------------------------------------------------------------------

CPU time actual refinement: 338.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/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_45/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_45/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.83 
  Macro-tasks:
    bulk solvent and scale       = 43.52  
    individual site refinement   = 133.04 
    weights calculation          = 30.76  
    collect and process          = 6.70   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.14 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 106.16 
    alpha_beta                      = 8.48   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 113.75 
    fmodel                         = 7.57   
    r_factors                      = 0.22   
    phase_errors                   = 10.92  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 250.38 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.826 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    651 calls, 105.84 s
gradients_fft:          596 calls, 100.79 s

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

# Date 2008-01-16 Time 03:52:02 PST -0800 (1200484322.51 s)
Start R-work = 0.4374, R-free = 0.4409 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1800 (no bulk solvent and anisotropic scale)

Start R-work = 0.4280, R-free = 0.4284
Final R-work = 0.1071, R-free = 0.1578