# Date 2008-01-16 Time 06:01:44 PST -0800 (1200492104.12 s)
#phil __OFF__

Command line arguments: "../981.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32406
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 981

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.9914, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96157
Completeness in resolution range: 0.948942
Completeness with d_max=infinity: 0.946191

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9616

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96157
Completeness in resolution range: 0.948942
Completeness with d_max=infinity: 0.946191

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.1986 [2160/2187]  1947   213   9.9%
  bin  2:  4.1986 -  3.3445 [2086/2106]  1874   212  10.2%
  bin  3:  3.3445 -  2.9252 [2046/2065]  1841   205  10.0%
  bin  4:  2.9252 -  2.6593 [2032/2062]  1834   198   9.7%
  bin  5:  2.6593 -  2.4696 [2042/2061]  1839   203   9.9%
  bin  6:  2.4696 -  2.3246 [2008/2033]  1795   213  10.6%
  bin  7:  2.3246 -  2.2085 [2021/2049]  1823   198   9.8%
  bin  8:  2.2085 -  2.1126 [1975/2011]  1782   193   9.8%
  bin  9:  2.1126 -  2.0315 [1986/2028]  1791   195   9.8%
  bin 10:  2.0315 -  1.9616 [1233/2041]  1104   129  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.57 -     2.23: 22
        2.23 -     2.90: 1410
        2.90 -     3.57: 4552
        3.57 -     4.23: 9304
        4.23 -     4.90: 13304
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.567 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.856 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.892 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28587 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_981/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/model_refine_001.geo

CPU time processing inputs: 7.86


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.9914 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4599   r_free= 0.4595   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.266313                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6835 0.99   1411  159 0.3681 0.3730      6.5348      6.5564|
|  2:  4.6835 -  3.7360 0.99   1348  147 0.3920 0.3882      6.7871      6.7493|
|  3:  3.7360 -  3.2692 0.99   1318  143 0.4251 0.3974       6.649      6.7091|
|  4:  3.2692 -  2.9728 0.99   1331  156 0.4460 0.4711      6.5211      6.4891|
|  5:  2.9728 -  2.7611 0.99   1315  145 0.4885 0.4880      6.3568      6.3575|
|  6:  2.7611 -  2.5992 0.99   1300  144 0.4928 0.4949      6.2744      6.2498|
|  7:  2.5992 -  2.4696 0.99   1312  137 0.4960 0.4782      6.2341      6.2052|
|  8:  2.4696 -  2.3625 0.98   1259  150 0.5095 0.4701       6.159      6.1314|
|  9:  2.3625 -  2.2719 0.98   1304  147 0.5000 0.5164      6.1249      6.1487|
| 10:  2.2719 -  2.1937 1.00   1288  149 0.5075 0.5332      6.0752      6.1123|
| 11:  2.1937 -  2.1253 0.98   1287  128 0.5090 0.5330      6.0391      6.0673|
| 12:  2.1253 -  2.0647 0.98   1279  151 0.5170 0.5503      5.9592      5.9976|
| 13:  2.0647 -  2.0105 0.96   1242  132 0.5187 0.4837      5.8708      5.7936|
| 14:  2.0105 -  1.9616 0.48    636   71 0.5374 0.4738      5.8427      5.8125|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6835  1411   159  0.71  33.72   0.83     0.76      69838.38|
|  2:  4.6835 -  3.7360  1348   147  0.71  34.26   0.92     0.83     102484.79|
|  3:  3.7360 -  3.2692  1318   143  0.60  43.42   0.93     0.79     111619.94|
|  4:  3.2692 -  2.9728  1331   156  0.50  51.73   0.93     0.69     105490.73|
|  5:  2.9728 -  2.7611  1315   145  0.41  59.14   0.88     0.58      84344.97|
|  6:  2.7611 -  2.5992  1300   144  0.39  60.36   0.90     0.56      73390.85|
|  7:  2.5992 -  2.4696  1312   137  0.40  59.86   0.92     0.56      62368.38|
|  8:  2.4696 -  2.3625  1259   150  0.40  59.85   0.90     0.59      56105.15|
|  9:  2.3625 -  2.2719  1304   147  0.40  59.87   0.94     0.57      51038.86|
| 10:  2.2719 -  2.1937  1288   149  0.36  63.18   0.94     0.54      49312.74|
| 11:  2.1937 -  2.1253  1287   128  0.32  65.99   0.97     0.49      49144.98|
| 12:  2.1253 -  2.0647  1279   151  0.30  67.70   0.95     0.47      44523.08|
| 13:  2.0647 -  2.0105  1242   132  0.31  66.79   0.95     0.51      37315.75|
| 14:  2.0105 -  1.9616   636    71  0.38  61.88   0.94     0.57      29522.38|
|alpha:            min =        0.47 max =            0.83 mean =         0.61|
|beta:             min =    29522.38 max =       111619.94 mean =     67974.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.77|
|phase err.(test): min =        0.00 max =           90.00 mean =        56.15|
|-----------------------------------------------------------------------------|

============================== 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 = 8.006776              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.718358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.577   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.567 -  1.901:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.901 -  2.234:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.234 -  2.567:       49 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.567 -  2.900:     1361 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.900 -  3.234:     1944 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.234 -  3.567:     2608 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.567 -  3.900:     4734 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.900 -  4.233:     4570 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.233 -  4.567:     6074 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.567 -  4.900:     7230 |
|-----------------------------------------------------------------------------|
|-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 |        0.176 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.567 |       0.395 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4599   r_free= 0.4595   ksol= 0.00   Bsol= 0.00   scale= 0.904    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.266313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4520   r_free= 0.4522   ksol= 0.34   Bsol= 34.92   scale= 0.937   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,1.88,-0.05,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.261163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.530327              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.085   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.282312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.285   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4520      final r-factor (work) = 0.3497          |
| start r-factor (free) = 0.4522      final r-factor (free) = 0.3815          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6090 = 6.53 * 0.50 * 6.2579 + 1.00 * 0.1758                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2141 = 6.53 * 0.50 * 6.1531 + 1.00 * 0.1233                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3497      final r-factor (work) = 0.3165          |
| start r-factor (free) = 0.3815      final r-factor (free) = 0.3922          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8963 = 1.28 * 1.00 * 6.1531 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7673 = 1.28 * 1.00 * 6.0410 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.81  19.21    None  None   None       |
|    all(noH): 2823   0      0.00    106.81  19.21    None  None   None       |
|    Sol.    : 438    0      0.00    106.81  37.87    None  None   None       |
|    Mac.    : 2385   0      0.00    85.71   15.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.681:  952   |   5:    53.405 -  64.086:   67        |
|      1:    10.681 -  21.362:  930   |   6:    64.086 -  74.767:   36        |
|      2:    21.362 -  32.043:  460   |   7:    74.767 -  85.448:    8        |
|      3:    32.043 -  42.724:  241   |   8:    85.448 -  96.129:    2        |
|      4:    42.724 -  53.405:  126   |   9:    96.129 - 106.810:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3165 r_free = 0.3922             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3162 r_free = 0.3925             target_work(ml) = 6.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3162   r_free= 0.3925   ksol= 0.34   Bsol= 34.92   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,1.88,-0.05,0.00,-0.00,-0.00); trace/3= 0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.044379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3160   r_free= 0.3908   ksol= 0.35   Bsol= 55.53   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.06,-0.41,-0.00,-0.00,-0.00); trace/3= -0.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.044637                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.555197              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.623   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.569569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.693  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3160      final r-factor (work) = 0.2629          |
| start r-factor (free) = 0.3908      final r-factor (free) = 0.3364          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8814 = 4.56 * 0.50 * 6.0406 + 1.00 * 0.1233                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6689 = 4.56 * 0.50 * 5.9718 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2629      final r-factor (work) = 0.2539          |
| start r-factor (free) = 0.3364      final r-factor (free) = 0.3282          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4220 = 0.57 * 1.00 * 5.9718 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3734 = 0.57 * 1.00 * 5.8861 + 1.00 * 0.0209                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.24  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    120.24  18.88    None  None   None       |
|    Sol.    : 438    0      2.32    107.18  38.08    None  None   None       |
|    Mac.    : 2385   0      0.00    120.24  15.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.025: 1140   |   5:    60.122 -  72.147:   46        |
|      1:    12.025 -  24.049:  932   |   6:    72.147 -  84.171:   11        |
|      2:    24.049 -  36.073:  402   |   7:    84.171 -  96.196:    3        |
|      3:    36.073 -  48.098:  199   |   8:    96.196 - 108.220:    1        |
|      4:    48.098 -  60.122:   88   |   9:   108.220 - 120.245:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2539 r_free = 0.3282             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2538 r_free = 0.3278             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2538   r_free= 0.3278   ksol= 0.35   Bsol= 55.53   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.06,-0.41,-0.00,-0.00,-0.00); trace/3= -0.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.873941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2544   r_free= 0.3276   ksol= 0.34   Bsol= 55.53   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.58,-0.17,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.874584                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.720429              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.486  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.411577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.678  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2544      final r-factor (work) = 0.1894          |
| start r-factor (free) = 0.3276      final r-factor (free) = 0.2516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7931 = 7.72 * 0.50 * 5.8871 + 1.00 * 0.0676                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2976 = 7.72 * 0.50 * 5.7560 + 1.00 * 0.0781                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1894      final r-factor (work) = 0.1670          |
| start r-factor (free) = 0.2516      final r-factor (free) = 0.2264          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3869 = 0.41 * 1.00 * 5.7560 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5758 = 0.41 * 1.00 * 5.5517 + 1.00 * 0.2909                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.81  18.23    None  None   None       |
|    all(noH): 2823   0      0.00    105.81  18.23    None  None   None       |
|    Sol.    : 438    0      5.37    105.81  40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    94.88   14.19    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:     0.000 -  10.581: 1069   |   5:    52.905 -  63.487:   62        |
|      1:    10.581 -  21.162:  994   |   6:    63.487 -  74.068:   31        |
|      2:    21.162 -  31.743:  301   |   7:    74.068 -  84.649:    5        |
|      3:    31.743 -  42.324:  210   |   8:    84.649 -  95.230:    5        |
|      4:    42.324 -  52.905:  145   |   9:    95.230 - 105.811:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1670 r_free = 0.2264             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1667 r_free = 0.2254             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2254   ksol= 0.34   Bsol= 55.53   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-0.58,-0.17,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.495430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2232   ksol= 0.32   Bsol= 45.83   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-2.14,-1.26,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.491672                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.123562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.072  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.955838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.819   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1659      final r-factor (work) = 0.1467          |
| start r-factor (free) = 0.2232      final r-factor (free) = 0.1983          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9783 = 2.12 * 0.50 * 5.5569 + 1.00 * 0.0781                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8263 = 2.12 * 0.50 * 5.4411 + 1.00 * 0.0490                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1467      final r-factor (work) = 0.1346          |
| start r-factor (free) = 0.1983      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6747 = 1.96 * 1.00 * 5.4411 + 1.00 * 0.0328                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4595 = 1.96 * 1.00 * 5.3418 + 1.00 * 0.0118                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.36  18.34    None  None   None       |
|    all(noH): 2823   0      0.00    104.36  18.34    None  None   None       |
|    Sol.    : 438    0      6.91    103.66  44.65    None  None   None       |
|    Mac.    : 2385   0      0.00    104.36  13.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.436: 1099   |   5:    52.181 -  62.617:  107        |
|      1:    10.436 -  20.872: 1045   |   6:    62.617 -  73.053:   54        |
|      2:    20.872 -  31.308:  229   |   7:    73.053 -  83.489:   23        |
|      3:    31.308 -  41.744:  147   |   8:    83.489 -  93.925:   10        |
|      4:    41.744 -  52.181:  106   |   9:    93.925 - 104.361:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1346 r_free = 0.1876             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1345 r_free = 0.1874             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1345   r_free= 0.1874   ksol= 0.32   Bsol= 45.83   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-2.14,-1.26,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.307830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1877   ksol= 0.31   Bsol= 45.83   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-2.55,-1.49,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306652                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.532128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.069  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1877      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1410 = 1.53 * 0.50 * 5.3417 + 1.00 * 0.0490                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0883 = 1.53 * 0.50 * 5.2753 + 1.00 * 0.0471                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1774      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3828 = 0.26 * 1.00 * 5.2753 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3704 = 0.26 * 1.00 * 5.2393 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    101.53  17.46    None  None   None       |
|    all(noH): 2823   0      0.79    101.53  17.46    None  None   None       |
|    Sol.    : 438    0      6.09    90.78   41.59    None  None   None       |
|    Mac.    : 2385   0      0.79    101.53  13.02    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:     0.785 -  10.860: 1223   |   5:    51.159 -  61.234:   83        |
|      1:    10.860 -  20.935:  973   |   6:    61.234 -  71.309:   38        |
|      2:    20.935 -  31.010:  222   |   7:    71.309 -  81.384:   19        |
|      3:    31.010 -  41.084:  131   |   8:    81.384 -  91.458:    7        |
|      4:    41.084 -  51.159:  126   |   9:    91.458 - 101.533:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1226 r_free = 0.1702             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1225 r_free = 0.1699             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1699   ksol= 0.31   Bsol= 45.83   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-2.55,-1.49,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218008                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6835 0.99   1411  159 0.0994 0.1318      5.3806      5.5798|
|  2:  4.6835 -  3.7360 0.99   1348  147 0.0893 0.1209      5.4876       5.729|
|  3:  3.7360 -  3.2692 0.99   1318  143 0.1167 0.1625      5.5507      5.8912|
|  4:  3.2692 -  2.9728 0.99   1331  156 0.1353 0.1775      5.5478      5.6866|
|  5:  2.9728 -  2.7611 0.99   1315  145 0.1472 0.1985      5.3887      5.6162|
|  6:  2.7611 -  2.5992 0.99   1300  144 0.1331 0.1707      5.2608      5.4512|
|  7:  2.5992 -  2.4696 0.99   1312  137 0.1399 0.1764      5.2285      5.4121|
|  8:  2.4696 -  2.3625 0.98   1259  150 0.1332 0.1998      5.1474      5.4502|
|  9:  2.3625 -  2.2719 0.98   1304  147 0.1295 0.1920      5.1153      5.3631|
| 10:  2.2719 -  2.1937 1.00   1288  149 0.1266 0.1839      5.0253      5.2854|
| 11:  2.1937 -  2.1253 0.98   1287  128 0.1248 0.2037      5.0399      5.3972|
| 12:  2.1253 -  2.0647 0.98   1279  151 0.1230 0.1729      4.9484      5.1342|
| 13:  2.0647 -  2.0105 0.96   1242  132 0.1302 0.2001       4.882      5.1698|
| 14:  2.0105 -  1.9616 0.48    636   71 0.1190 0.1609       4.744      4.9516|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6835  1411   159  0.94   9.37   0.98     0.95       7272.49|
|  2:  4.6835 -  3.7360  1348   147  0.95   8.50   1.02     1.02       9855.45|
|  3:  3.7360 -  3.2692  1318   143  0.93  12.46   1.04     1.04      12026.36|
|  4:  3.2692 -  2.9728  1331   156  0.90  15.70   1.02     0.99      12443.44|
|  5:  2.9728 -  2.7611  1315   145  0.90  16.37   1.01     0.99       8704.31|
|  6:  2.7611 -  2.5992  1300   144  0.90  16.50   1.00     0.98       7498.80|
|  7:  2.5992 -  2.4696  1312   137  0.90  16.46   1.01     0.98       6863.82|
|  8:  2.4696 -  2.3625  1259   150  0.89  17.19   0.99     0.97       6046.92|
|  9:  2.3625 -  2.2719  1304   147  0.90  16.75   1.01     0.98       5819.45|
| 10:  2.2719 -  2.1937  1288   149  0.89  16.81   1.01     0.98       4988.81|
| 11:  2.1937 -  2.1253  1287   128  0.88  18.09   1.01     0.96       5312.88|
| 12:  2.1253 -  2.0647  1279   151  0.89  17.28   1.01     1.00       4627.99|
| 13:  2.0647 -  2.0105  1242   132  0.89  17.56   1.01     1.01       3937.09|
| 14:  2.0105 -  1.9616   636    71  0.90  16.10   1.00     0.97       2947.93|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2947.93 max =        12443.44 mean =      7221.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.27|
|phase err.(test): min =        0.00 max =           88.40 mean =        14.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1699   ksol= 0.32   Bsol= 44.68   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.62,-1.56,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218081                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1699   ksol= 0.32   Bsol= 44.68   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-2.62,-1.56,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218081                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6835 0.99   1411  159 0.0994 0.1319      5.3811      5.5788|
|  2:  4.6835 -  3.7360 0.99   1348  147 0.0891 0.1208      5.4864      5.7279|
|  3:  3.7360 -  3.2692 0.99   1318  143 0.1166 0.1624        5.55      5.8901|
|  4:  3.2692 -  2.9728 0.99   1331  156 0.1353 0.1775      5.5476      5.6866|
|  5:  2.9728 -  2.7611 0.99   1315  145 0.1472 0.1986      5.3889      5.6167|
|  6:  2.7611 -  2.5992 0.99   1300  144 0.1331 0.1708      5.2612      5.4517|
|  7:  2.5992 -  2.4696 0.99   1312  137 0.1399 0.1764      5.2289      5.4125|
|  8:  2.4696 -  2.3625 0.98   1259  150 0.1333 0.1999      5.1477      5.4508|
|  9:  2.3625 -  2.2719 0.98   1304  147 0.1295 0.1920      5.1155       5.363|
| 10:  2.2719 -  2.1937 1.00   1288  149 0.1266 0.1840      5.0256      5.2858|
| 11:  2.1937 -  2.1253 0.98   1287  128 0.1248 0.2038        5.04      5.3973|
| 12:  2.1253 -  2.0647 0.98   1279  151 0.1230 0.1729      4.9486      5.1344|
| 13:  2.0647 -  2.0105 0.96   1242  132 0.1303 0.2001      4.8822        5.17|
| 14:  2.0105 -  1.9616 0.48    636   71 0.1190 0.1609      4.7439      4.9515|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6835  1411   159  0.94   9.37   0.98     0.95       7278.10|
|  2:  4.6835 -  3.7360  1348   147  0.95   8.49   1.02     1.01       9842.23|
|  3:  3.7360 -  3.2692  1318   143  0.93  12.44   1.04     1.04      11999.61|
|  4:  3.2692 -  2.9728  1331   156  0.90  15.69   1.02     0.99      12431.38|
|  5:  2.9728 -  2.7611  1315   145  0.90  16.37   1.00     0.99       8709.07|
|  6:  2.7611 -  2.5992  1300   144  0.90  16.51   0.99     0.97       7506.06|
|  7:  2.5992 -  2.4696  1312   137  0.90  16.47   1.00     0.97       6871.57|
|  8:  2.4696 -  2.3625  1259   150  0.89  17.20   0.99     0.96       6052.33|
|  9:  2.3625 -  2.2719  1304   147  0.90  16.75   1.01     0.98       5823.16|
| 10:  2.2719 -  2.1937  1288   149  0.89  16.81   1.00     0.97       4991.99|
| 11:  2.1937 -  2.1253  1287   128  0.88  18.09   1.00     0.95       5316.58|
| 12:  2.1253 -  2.0647  1279   151  0.89  17.28   1.01     1.00       4630.79|
| 13:  2.0647 -  2.0105  1242   132  0.89  17.56   1.00     1.00       3938.27|
| 14:  2.0105 -  1.9616   636    71  0.90  16.10   0.99     0.96       2947.72|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2947.72 max =        12431.38 mean =      7220.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.27|
|phase err.(test): min =        0.00 max =           88.46 mean =        14.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.667)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    101.51  17.43    None  None   None       |
|    all(noH): 2823   0      0.76    101.51  17.43    None  None   None       |
|    Sol.    : 438    0      6.07    90.76   41.56    None  None   None       |
|    Mac.    : 2385   0      0.76    101.51  13.00    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:     0.759 -  10.834: 1223   |   5:    51.133 -  61.207:   83        |
|      1:    10.834 -  20.908:  973   |   6:    61.207 -  71.282:   38        |
|      2:    20.908 -  30.983:  222   |   7:    71.282 -  81.357:   19        |
|      3:    30.983 -  41.058:  131   |   8:    81.357 -  91.432:    7        |
|      4:    41.058 -  51.133:  126   |   9:    91.432 - 101.507:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.681 - 5.827
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 336
   mapped sites are within: 0.712 - 5.827

peak=    5.892 closest distance to " NE2 GLN A  11 " =    1.355
peak=    5.642 closest distance to " O   HOH Z   7 " =    1.721
peak=    5.569 closest distance to " CG  PRO A  54 " =    1.407
peak=    5.486 closest distance to " O   HOH Z 126 " =    2.051
peak=    5.062 closest distance to " O   HOH Z 111 " =    2.021
peak=    5.042 closest distance to " O   HOH Z 214 " =    1.503
peak=    5.010 closest distance to " O   HOH Z 144 " =    1.809
peak=    4.998 closest distance to " CB  PRO A  54 " =    1.047
peak=    4.921 closest distance to " CG  PRO A 198 " =    1.321
peak=    4.920 closest distance to " CB  GLN A 223 " =    1.481
peak=    4.913 closest distance to " O   HOH Z 245 " =    1.255
peak=    4.913 closest distance to " O   HOH Z  65 " =    1.081
peak=    4.882 closest distance to " CB  SER A   3 " =    1.460
peak=    4.856 closest distance to " CG  PRO A 213 " =    1.296
peak=    4.840 closest distance to " O   HOH Z 427 " =    1.249
peak=    4.822 closest distance to " CB  GLU A 128 " =    0.995
peak=    4.818 closest distance to " O   HOH Z  78 " =    1.646
peak=    4.790 closest distance to " CB  SER A  63 " =    1.329
peak=    4.788 closest distance to " CG  PRO A  90 " =    1.149
peak=    4.773 closest distance to " O   HOH Z 425 " =    1.615
peak=    4.733 closest distance to " O   HOH Z 390 " =    1.147
peak=    4.569 closest distance to " O   HOH Z 427 " =    2.188
peak=    4.562 closest distance to " O   HOH Z 298 " =    1.974
peak=    4.552 closest distance to " O   HOH Z 403 " =    1.389
peak=    4.541 closest distance to " CB  ARG A 275 " =    1.011
peak=    4.524 closest distance to " O   HOH Z 287 " =    2.091
peak=    4.518 closest distance to " CB  ASN A 148 " =    1.324
peak=    4.503 closest distance to " O   HOH Z 232 " =    2.211
peak=    4.477 closest distance to " CG2 VAL A 257 " =    0.981
peak=    4.472 closest distance to " O   HOH Z 369 " =    1.989
peak=    4.449 closest distance to " O   HOH Z 417 " =    1.443
peak=    4.427 closest distance to " NH2BARG A 102 " =    1.011
peak=    4.427 closest distance to " CB  SER A 216 " =    0.979
peak=    4.417 closest distance to " O   HOH Z 193 " =    1.702
peak=    4.399 closest distance to " O   HOH Z 134 " =    1.465
peak=    4.391 closest distance to " O   HOH Z  63 " =    1.668
peak=    4.370 closest distance to " O   HOH Z 358 " =    1.363
peak=    4.327 closest distance to " O   HOH Z 130 " =    0.833
peak=    4.285 closest distance to " CB  GLN A 183 " =    1.115
peak=    4.284 closest distance to " OG BSER A 258 " =    0.962
peak=    4.275 closest distance to " N   GLN A 278 " =    0.973
peak=    4.272 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.240 closest distance to " O   HOH Z 423 " =    1.869
peak=    4.228 closest distance to " O   HOH Z  78 " =    1.833
peak=    4.212 closest distance to " CB  GLU A 152 " =    1.350
peak=    4.211 closest distance to " O   HOH Z 183 " =    1.548
peak=    4.203 closest distance to " O   HOH Z 389 " =    1.953
peak=    4.201 closest distance to " O   HOH Z 380 " =    1.863
peak=    4.197 closest distance to " O   SER A  87 " =    2.194
peak=    4.173 closest distance to " NZ BLYS A 290 " =    1.053
peak=    4.169 closest distance to " O   HOH Z 236 " =    1.583
peak=    4.159 closest distance to " O   HOH Z  97 " =    1.295
peak=    4.153 closest distance to " O   HOH Z  49 " =    1.378
peak=    4.150 closest distance to " O   HOH Z   1 " =    1.804
peak=    4.146 closest distance to " OG ASER A 258 " =    3.106
peak=    4.098 closest distance to " OD1BASN A 224 " =    2.192
peak=    4.095 closest distance to " O   HOH Z  11 " =    2.191
peak=    4.065 closest distance to " O   HOH Z 419 " =    2.392
peak=    4.010 closest distance to " O   HOH Z 394 " =    1.649
peak=    4.008 closest distance to " O   HOH Z 234 " =    3.758
peak=    4.002 closest distance to " CG  LEU A 167 " =    1.266
peak=    3.978 closest distance to " O   HOH Z 217 " =    2.727
peak=    3.973 closest distance to " CE3 TRP A 274 " =    2.259
peak=    3.966 closest distance to " CA  TYR A  30 " =    1.074
peak=    3.957 closest distance to " O   HOH Z 108 " =    1.797
peak=    3.952 closest distance to " NZ  LYS A 117 " =    1.198
peak=    3.941 closest distance to " O   HOH Z 145 " =    1.658
peak=    3.940 closest distance to " CB  ASN A 148 " =    1.899
peak=    3.936 closest distance to " CB  TYR A 169 " =    0.833
peak=    3.934 closest distance to " O   HOH Z 193 " =    1.843
peak=    3.934 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.887 closest distance to " ND2 ASN A 187 " =    1.543
peak=    3.873 closest distance to " O   HOH Z  59 " =    1.439
peak=    3.869 closest distance to " O   HOH Z 368 " =    1.840
peak=    3.868 closest distance to " O   HOH Z 302 " =    1.537
peak=    3.867 closest distance to " CD BLYS A 290 " =    1.114
peak=    3.867 closest distance to " CB  TRP A 179 " =    1.484
peak=    3.864 closest distance to " O   HOH Z  61 " =    1.666
peak=    3.863 closest distance to " O   HOH Z 258 " =    2.122
peak=    3.859 closest distance to " CG  TRP A 179 " =    2.170
peak=    3.855 closest distance to " O   HOH Z 282 " =    1.625
peak=    3.836 closest distance to " CB  ASP A 124 " =    0.930
peak=    3.831 closest distance to " O   HOH Z 247 " =    1.263
peak=    3.828 closest distance to " ND1 HIS A  86 " =    1.878
peak=    3.828 closest distance to " O   HOH Z  11 " =    1.506
peak=    3.814 closest distance to " NH1AARG A 145 " =    1.046
peak=    3.803 closest distance to " CA  ILE A 234 " =    1.022
peak=    3.791 closest distance to " O   HOH Z 371 " =    1.922
peak=    3.790 closest distance to " CG  GLN A 278 " =    3.815
peak=    3.787 closest distance to " O   HOH Z 222 " =    1.051
peak=    3.784 closest distance to " O   HOH Z 313 " =    1.833
peak=    3.782 closest distance to " O   HOH Z 116 " =    2.843
peak=    3.773 closest distance to " CG  GLN A  11 " =    2.086
peak=    3.769 closest distance to " NE AARG A 275 " =    1.454
peak=    3.769 closest distance to " O   HOH Z 437 " =    2.127
peak=    3.766 closest distance to " CG2 THR A 221 " =    1.274
peak=    3.761 closest distance to " O   HOH Z 261 " =    1.877
peak=    3.760 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.757 closest distance to " CB  VAL A 202 " =    1.611
peak=    3.743 closest distance to " CA  GLU A 152 " =    1.137
peak=    3.741 closest distance to " O   HOH Z  44 " =    3.084
peak=    3.728 closest distance to " CB  VAL A 265 " =    1.321
peak=    3.722 closest distance to " O   HOH Z  68 " =    1.747
peak=    3.718 closest distance to " CB  TRP A 266 " =    1.015
peak=    3.718 closest distance to " NE1 TRP A 274 " =    1.010
peak=    3.715 closest distance to " CG  GLN A  55 " =    1.822
peak=    3.677 closest distance to " O   HOH Z 352 " =    1.615
peak=    3.666 closest distance to " OD2 ASP A 286 " =    2.769
peak=    3.658 closest distance to " ND2 ASN A  60 " =    2.948
peak=    3.652 closest distance to " O   HOH Z 411 " =    3.468
peak=    3.652 closest distance to " O   ALA A 165 " =    1.312
peak=    3.644 closest distance to " O   ALA A 233 " =    1.782
peak=    3.644 closest distance to " O   HOH Z 276 " =    1.253
peak=    3.642 closest distance to " O   HOH Z 371 " =    2.754
peak=    3.641 closest distance to " O   HOH Z 171 " =    2.652
peak=    3.639 closest distance to " CA  TYR A 186 " =    1.596
peak=    3.638 closest distance to " O   HOH Z 263 " =    2.199
peak=    3.633 closest distance to " CB  LEU A 300 " =    0.963
peak=    3.629 closest distance to " O   HOH Z   9 " =    2.047
peak=    3.626 closest distance to " CG  PRO A 243 " =    1.107
peak=    3.623 closest distance to " O   HOH Z 363 " =    1.095
peak=    3.622 closest distance to " O   HOH Z 244 " =    1.569
peak=    3.619 closest distance to " O   HOH Z 139 " =    1.382
peak=    3.617 closest distance to " O   HOH Z 135 " =    1.699
peak=    3.614 closest distance to " CB  SER A 276 " =    1.100
peak=    3.614 closest distance to " CA  THR A 264 " =    0.798
peak=    3.610 closest distance to " O   PRO A 198 " =    1.276
peak=    3.602 closest distance to " O   HOH Z 392 " =    1.337
peak=    3.597 closest distance to " O   HOH Z 414 " =    1.362
peak=    3.595 closest distance to " O   HOH Z 147 " =    1.391
peak=    3.594 closest distance to " O   HOH Z 195 " =    1.464
peak=    3.593 closest distance to " CB  MET A  47 " =    1.031
peak=    3.584 closest distance to " O   HOH Z  10 " =    1.889
peak=    3.583 closest distance to " O   HOH Z 133 " =    2.449
peak=    3.578 closest distance to " CA  THR A 221 " =    0.890
peak=    3.577 closest distance to " CD  ARG A 159 " =    0.830
peak=    3.576 closest distance to " O   HOH Z 155 " =    1.800
peak=    3.576 closest distance to " CB  LEU A 228 " =    1.061
peak=    3.575 closest distance to " CD  LYS A 166 " =    1.360
peak=    3.575 closest distance to " CA  ALA A 299 " =    0.958
peak=    3.568 closest distance to " NE2 GLN A  58 " =    3.493
peak=    3.565 closest distance to " O   HOH Z 303 " =    1.612
peak=    3.556 closest distance to " CB  ARG A 139 " =    1.176
peak=    3.553 closest distance to " O   HOH Z 146 " =    1.659
peak=    3.552 closest distance to " N   ARG A 156 " =    1.289
peak=    3.552 closest distance to " CB  THR A 157 " =    1.063
peak=    3.550 closest distance to " CB  ALA A  43 " =    0.934
peak=    3.548 closest distance to " O   HOH Z  88 " =    2.651
peak=    3.537 closest distance to " O   HOH Z  59 " =    2.166
peak=    3.532 closest distance to " O   HOH Z 119 " =    1.504
peak=    3.532 closest distance to " CB  ASN A 187 " =    1.115
peak=    3.531 closest distance to " O   HOH Z 108 " =    1.679
peak=    3.530 closest distance to " CG  GLN A  88 " =    1.030
peak=    3.529 closest distance to " O   HOH Z 405 " =    1.616
peak=    3.520 closest distance to " O   HOH Z  17 " =    2.213
peak=    3.514 closest distance to " O   HOH Z 409 " =    2.002
peak=    3.513 closest distance to " O   HOH Z  50 " =    1.598
peak=    3.510 closest distance to " O   HOH Z 207 " =    2.215
peak=    3.503 closest distance to " CG  ARG A 159 " =    0.817
peak=    3.495 closest distance to " O   HOH Z  21 " =    1.704
peak=    3.494 closest distance to " N   PHE A 130 " =    1.198
peak=    3.493 closest distance to " CZ  PHE A  38 " =    1.373
peak=    3.482 closest distance to " O   HOH Z 227 " =    1.787
peak=    3.482 closest distance to " O   HOH Z 166 " =    1.483
peak=    3.467 closest distance to " CD  LYS A 119 " =    1.186
peak=    3.465 closest distance to " CB  TYR A 116 " =    1.011
peak=    3.460 closest distance to " N   ALA A   1 " =    2.823
peak=    3.456 closest distance to " CD BARG A 102 " =    1.297
peak=    3.452 closest distance to " O   HOH Z 151 " =    1.644
peak=    3.452 closest distance to " N   TYR A  15 " =    1.041
peak=    3.449 closest distance to " CA  ALA A 154 " =    0.954
peak=    3.447 closest distance to " O   HOH Z 225 " =    1.417
peak=    3.446 closest distance to " CA  ASN A 127 " =    0.931
peak=    3.444 closest distance to " O   HOH Z 128 " =    2.052
peak=    3.436 closest distance to " O   HOH Z   1 " =    1.556
peak=    3.435 closest distance to " CD  GLN A 240 " =    1.754
peak=    3.431 closest distance to " CZ  PHE A 192 " =    0.940
peak=    3.431 closest distance to " O   HOH Z 130 " =    3.503
peak=    3.429 closest distance to " CH2 TRP A 150 " =    1.119
peak=    3.427 closest distance to " OD1 ASN A 217 " =    1.583
peak=    3.424 closest distance to " O   HOH Z 124 " =    1.317
peak=    3.424 closest distance to " O   ASN A 209 " =    1.396
peak=    3.418 closest distance to " O   HOH Z 175 " =    3.621
peak=    3.415 closest distance to " O   HOH Z 152 " =    2.316
peak=    3.409 closest distance to " CA  LEU A 282 " =    1.277
peak=    3.408 closest distance to " CA  SER A  32 " =    1.657
peak=    3.406 closest distance to " CA  ASN A 215 " =    1.192
peak=    3.405 closest distance to " O   HOH Z 181 " =    2.411
peak=    3.400 closest distance to " O   HOH Z  68 " =    2.014
peak=    3.395 closest distance to " O   HOH Z 207 " =    1.785
peak=    3.392 closest distance to " CA  GLY A 267 " =    1.297
peak=    3.389 closest distance to " OG BSER A  99 " =    2.350
peak=    3.389 closest distance to " CB  GLU A 277 " =    1.061
peak=    3.388 closest distance to " CB  ARG A 102 " =    0.818
peak=    3.387 closest distance to " O   HOH Z  17 " =    1.537
peak=    3.384 closest distance to " OD1 ASN A  69 " =    2.564
peak=    3.383 closest distance to " O   GLN A 278 " =    1.374
peak=    3.380 closest distance to " CE AMET A  47 " =    1.293
peak=    3.377 closest distance to " CA  ALA A 160 " =    0.904
peak=    3.372 closest distance to " CE  MET A  93 " =    1.357
peak=    3.366 closest distance to " CG  GLU A   2 " =    1.090
peak=    3.363 closest distance to " O   HOH Z 413 " =    1.523
peak=    3.361 closest distance to " O   HOH Z  32 " =    2.263
peak=    3.354 closest distance to " CZ3 TRP A 123 " =    1.408
peak=    3.350 closest distance to " CA  SER A  87 " =    0.991
peak=    3.349 closest distance to " O   HOH Z 209 " =    2.307
peak=    3.349 closest distance to " O   HOH Z 222 " =    2.428
peak=    3.349 closest distance to " O   HOH Z  44 " =    1.876
peak=    3.346 closest distance to " CA  ALA A  21 " =    1.187
peak=    3.345 closest distance to " CA  ARG A 195 " =    1.415
peak=    3.341 closest distance to " O   HOH Z 172 " =    2.757
peak=    3.340 closest distance to " O   HOH Z 368 " =    3.718
peak=    3.335 closest distance to " NH2AARG A 190 " =    1.347
peak=    3.332 closest distance to " NH1 ARG A  14 " =    1.044
peak=    3.331 closest distance to " O   HOH Z 373 " =    1.509
peak=    3.331 closest distance to " O   HOH Z 380 " =    3.278
peak=    3.330 closest distance to " CG2 ILE A 151 " =    1.027
peak=    3.324 closest distance to " CD  PRO A 243 " =    1.789
peak=    3.322 closest distance to " O   HOH Z 344 " =    3.189
peak=    3.322 closest distance to " O   HOH Z 345 " =    3.426
peak=    3.317 closest distance to " O   HOH Z  28 " =    1.423
peak=    3.316 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.316 closest distance to " O   HOH Z 132 " =    1.125
peak=    3.315 closest distance to " O   HOH Z  58 " =    1.875
peak=    3.312 closest distance to " O   HOH Z 106 " =    2.498
peak=    3.311 closest distance to " CB  PRO A 243 " =    1.156
peak=    3.305 closest distance to " O   HOH Z 180 " =    2.067
peak=    3.302 closest distance to " CG  LYS A 166 " =    1.378
peak=    3.301 closest distance to " OD1 ASP A 238 " =    0.891
peak=    3.300 closest distance to " N   GLY A 196 " =    1.058
peak=    3.299 closest distance to " CB  ALA A 184 " =    1.074
peak=    3.298 closest distance to " CD  ARG A  66 " =    2.278
peak=    3.297 closest distance to " O   HOH Z 288 " =    1.906
peak=    3.295 closest distance to " O   HOH Z 329 " =    3.481
peak=    3.292 closest distance to " O   HOH Z 365 " =    5.827
peak=    3.290 closest distance to " CB  VAL A 230 " =    0.915
peak=    3.284 closest distance to " CE  LYS A  76 " =    0.878
peak=    3.284 closest distance to " CB  ALA A  34 " =    1.239
peak=    3.279 closest distance to " O   HOH Z  64 " =    1.991
peak=    3.278 closest distance to " ND1 HIS A  81 " =    1.583
peak=    3.276 closest distance to " CA  ARG A  36 " =    1.228
peak=    3.274 closest distance to " O   HOH Z 344 " =    1.070
peak=    3.274 closest distance to " OG1 THR A 246 " =    1.373
peak=    3.269 closest distance to " CD1 ILE A  33 " =    1.625
peak=    3.266 closest distance to " CB  GLU A 236 " =    1.378
peak=    3.265 closest distance to " C   PRO A 198 " =    1.519
peak=    3.263 closest distance to " O   HOH Z 295 " =    1.606
peak=    3.257 closest distance to " CB  LEU A 143 " =    1.112
peak=    3.257 closest distance to " CG1 VAL A 153 " =    0.888
peak=    3.254 closest distance to " NH2BARG A 190 " =    1.550
peak=    3.253 closest distance to " O   HOH Z 112 " =    0.969
peak=    3.252 closest distance to " O   HOH Z 158 " =    1.545
peak=    3.249 closest distance to " O   HOH Z 422 " =    2.842
peak=    3.248 closest distance to " O   HOH Z  88 " =    3.046
peak=    3.247 closest distance to " N   SER A 210 " =    1.102
peak=    3.247 closest distance to " CD  ARG A 138 " =    0.712
peak=    3.245 closest distance to " O   HOH Z 175 " =    2.106
peak=    3.244 closest distance to " CA  GLY A 196 " =    0.931
peak=    3.242 closest distance to " CZ3 TRP A 274 " =    1.290
peak=    3.240 closest distance to " O   HOH Z 115 " =    1.839
peak=    3.240 closest distance to " CB  ASP A 132 " =    3.894
peak=    3.240 closest distance to " CG1BVAL A  72 " =    0.931
peak=    3.239 closest distance to " O   HOH Z 334 " =    2.794
peak=    3.237 closest distance to " O   HOH Z  42 " =    1.524
peak=    3.235 closest distance to " CA  ASN A 284 " =    0.948
peak=    3.234 closest distance to " CA  TYR A  30 " =    1.078
peak=    3.233 closest distance to " CA  ALA A 158 " =    1.079
peak=    3.231 closest distance to " CG  PHE A  59 " =    1.133
peak=    3.225 closest distance to " CB  PRO A 198 " =    0.989
peak=    3.224 closest distance to " O   HOH Z 193 " =    2.066
peak=    3.220 closest distance to " N   ASN A 127 " =    1.433
peak=    3.219 closest distance to " OG  SER A  62 " =    2.878
peak=    3.217 closest distance to " CA  ALA A 180 " =    1.206
peak=    3.212 closest distance to " CA  ASP A  50 " =    1.021
peak=    3.210 closest distance to " O   HOH Z 153 " =    3.604
peak=    3.209 closest distance to " O   HOH Z 284 " =    1.460
peak=    3.209 closest distance to " N   GLU A   2 " =    1.337
peak=    3.200 closest distance to " O   ALA A 180 " =    1.232
peak=    3.199 closest distance to " O   HOH Z  48 " =    1.412
peak=    3.198 closest distance to " CB  ARG A  79 " =    1.247
peak=    3.197 closest distance to " NH2 ARG A 219 " =    1.726
peak=    3.194 closest distance to " O   HOH Z 302 " =    1.361
peak=    3.194 closest distance to " O   HOH Z 393 " =    1.261
peak=    3.190 closest distance to " OE2 GLU A  53 " =    1.968
peak=    3.190 closest distance to " O   HOH Z 225 " =    1.911
peak=    3.188 closest distance to " O   HOH Z 282 " =    2.012
peak=    3.182 closest distance to " CB  ALA A  21 " =    1.632
peak=    3.178 closest distance to " CA  LEU A 101 " =    1.540
peak=    3.177 closest distance to " O   HOH Z 213 " =    1.904
peak=    3.172 closest distance to " CB  PHE A  16 " =    1.029
peak=    3.170 closest distance to " O   HOH Z 133 " =    1.485
peak=    3.170 closest distance to " CG2AVAL A 121 " =    2.517
peak=    3.169 closest distance to " O   HOH Z 385 " =    3.604
peak=    3.165 closest distance to " CA  ARG A 102 " =    1.199
peak=    3.165 closest distance to " N   CYS A 260 " =    0.816
peak=    3.159 closest distance to " O   HOH Z 132 " =    2.070
peak=    3.156 closest distance to " O   HOH Z  73 " =    1.561
peak=    3.156 closest distance to " O   HOH Z 130 " =    2.055
peak=    3.155 closest distance to " O   HOH Z 378 " =    1.125
peak=    3.154 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.154 closest distance to " O   TYR A 116 " =    1.334
peak=    3.152 closest distance to " O   HOH Z 410 " =    1.743
peak=    3.149 closest distance to " CB  MET A  40 " =    0.871
peak=    3.147 closest distance to " O   HOH Z 126 " =    1.407
peak=    3.136 closest distance to " CG1 VAL A 202 " =    2.049
peak=    3.134 closest distance to " CD1 LEU A 300 " =    1.218
peak=    3.131 closest distance to " O   HOH Z  57 " =    1.006
peak=    3.130 closest distance to " N   SER A  97 " =    0.844
peak=    3.130 closest distance to " O   HOH Z 369 " =    1.628
peak=    3.130 closest distance to " NZ  LYS A  76 " =    1.448
peak=    3.129 closest distance to " O   HOH Z  24 " =    1.845
peak=    3.128 closest distance to " C   GLU A 277 " =    1.358
peak=    3.125 closest distance to " O   HOH Z 362 " =    1.899
peak=    3.121 closest distance to " O   HOH Z 222 " =    2.375
peak=    3.118 closest distance to " CG2 THR A 294 " =    1.167
peak=    3.116 closest distance to " CG1 VAL A 202 " =    2.064
peak=    3.114 closest distance to " O   ALA A   1 " =    1.541
peak=    3.113 closest distance to " OD1 ASN A  45 " =    1.357
peak=    3.110 closest distance to " O   MET A 105 " =    1.757
peak=    3.102 closest distance to " N   ASN A  39 " =    1.291
peak=    3.101 closest distance to " CE BMET A  47 " =    1.443
peak=    3.100 closest distance to " O   HOH Z 250 " =    1.388
peak=    3.096 closest distance to " O   HOH Z 112 " =    2.494
peak=    3.092 closest distance to " CB  LYS A 290 " =    1.193
peak=    3.089 closest distance to " CD1AILE A 234 " =    1.109
peak=    3.088 closest distance to " CA  ALA A  51 " =    1.078
peak=    3.077 closest distance to " O   HOH Z 281 " =    1.956
peak=    3.074 closest distance to " O   HOH Z 365 " =    2.717
peak=    3.063 closest distance to " O   HOH Z 217 " =    1.687
peak=    3.062 closest distance to " O   HOH Z 327 " =    1.951
peak=    3.059 closest distance to " O   THR A 220 " =    1.506
peak=    3.051 closest distance to " CG  LYS A  76 " =    1.469
peak=    3.018 closest distance to " O   HOH Z 431 " =    1.086
peak=    3.002 closest distance to " O   HOH Z 189 " =    1.835

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.541 - 5.648
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.761 - 5.648

peak=   -4.596 closest distance to " O   PRO A 198 " =    1.240
peak=   -4.581 closest distance to " OE1 GLN A  88 " =    0.960
peak=   -4.552 closest distance to " CD  ARG A  14 " =    3.166
peak=   -4.524 closest distance to " O   HOH Z 290 " =    1.074
peak=   -4.505 closest distance to " CG  MET A 105 " =    0.921
peak=   -4.233 closest distance to " CG  GLN A  88 " =    0.865
peak=   -4.151 closest distance to " CB  PRO A 243 " =    2.530
peak=   -4.123 closest distance to " O   HOH Z 166 " =    1.139
peak=   -4.094 closest distance to " O   HOH Z 409 " =    3.445
peak=   -4.059 closest distance to " O   HOH Z  43 " =    1.527
peak=   -4.047 closest distance to " O   HOH Z  65 " =    0.961
peak=   -4.019 closest distance to " O   HOH Z  76 " =    1.071
peak=   -4.014 closest distance to " O   HOH Z 377 " =    1.153
peak=   -3.999 closest distance to " O   HOH Z 198 " =    2.336
peak=   -3.994 closest distance to " O   HOH Z 266 " =    4.495
peak=   -3.916 closest distance to " O   ALA A   1 " =    1.053
peak=   -3.897 closest distance to " CA  GLY A  98 " =    1.799
peak=   -3.875 closest distance to " O   HOH Z 185 " =    2.170
peak=   -3.867 closest distance to " CD2 LEU A 237 " =    2.818
peak=   -3.859 closest distance to " O   HOH Z 385 " =    0.984
peak=   -3.852 closest distance to " C   ALA A 158 " =    1.393
peak=   -3.839 closest distance to " O   HOH Z 124 " =    1.096
peak=   -3.835 closest distance to " CB  TYR A  15 " =    2.138
peak=   -3.832 closest distance to " O   HOH Z 438 " =    0.828
peak=   -3.831 closest distance to " O   HOH Z  60 " =    1.760
peak=   -3.815 closest distance to " OG BSER A 134 " =    1.356
peak=   -3.802 closest distance to " O   HOH Z 231 " =    1.859
peak=   -3.783 closest distance to " O   HOH Z 384 " =    2.983
peak=   -3.774 closest distance to " CA  ASP A  27 " =    2.397
peak=   -3.769 closest distance to " OG  SER A  97 " =    2.120
peak=   -3.765 closest distance to " O   HOH Z  24 " =    1.375
peak=   -3.733 closest distance to " O   HOH Z  28 " =    1.542
peak=   -3.713 closest distance to " CA  GLY A 133 " =    1.917
peak=   -3.709 closest distance to " CB  ALA A 291 " =    2.159
peak=   -3.703 closest distance to " O   ALA A  51 " =    1.426
peak=   -3.695 closest distance to " OD1 ASP A 191 " =    1.875
peak=   -3.694 closest distance to " O   HOH Z 298 " =    0.937
peak=   -3.693 closest distance to " C   ASN A 285 " =    2.357
peak=   -3.692 closest distance to " CD2 TYR A 293 " =    1.921
peak=   -3.689 closest distance to " O   HOH Z 211 " =    1.463
peak=   -3.674 closest distance to " O   HOH Z 117 " =    0.761
peak=   -3.672 closest distance to " O   HOH Z 351 " =    1.428
peak=   -3.666 closest distance to " O   HOH Z  13 " =    1.439
peak=   -3.637 closest distance to " O   GLN A 194 " =    1.249
peak=   -3.630 closest distance to " CA  GLY A 241 " =    2.149
peak=   -3.630 closest distance to " N   THR A 157 " =    1.541
peak=   -3.630 closest distance to " O   HOH Z 231 " =    0.883
peak=   -3.626 closest distance to " O   HOH Z 388 " =    1.945
peak=   -3.617 closest distance to " O   HOH Z  51 " =    1.039
peak=   -3.607 closest distance to " OG1 THR A 279 " =    1.505
peak=   -3.607 closest distance to " CB  ALA A 248 " =    2.019
peak=   -3.606 closest distance to " CZ3 TRP A 123 " =    1.569
peak=   -3.595 closest distance to " O   PRO A 243 " =    2.317
peak=   -3.594 closest distance to " CB  CYS A 201 " =    2.396
peak=   -3.585 closest distance to " O   VAL A 189 " =    2.343
peak=   -3.579 closest distance to " O   HOH Z 317 " =    2.352
peak=   -3.573 closest distance to " O   HOH Z  88 " =    2.337
peak=   -3.560 closest distance to " CB  PRO A  90 " =    1.406
peak=   -3.554 closest distance to " CD  ARG A 156 " =    1.984
peak=   -3.554 closest distance to " O   HOH Z  39 " =    1.306
peak=   -3.552 closest distance to " O   HOH Z 278 " =    1.139
peak=   -3.551 closest distance to " OG  SER A  26 " =    0.903
peak=   -3.544 closest distance to " O   HOH Z 213 " =    1.156
peak=   -3.539 closest distance to " OG BSER A 134 " =    1.738
peak=   -3.533 closest distance to " N   ALA A  43 " =    2.432
peak=   -3.527 closest distance to " O   HOH Z 168 " =    1.508
peak=   -3.523 closest distance to " O   HOH Z 221 " =    1.463
peak=   -3.520 closest distance to " O   ALA A 180 " =    1.171
peak=   -3.515 closest distance to " CD1 LEU A 255 " =    3.048
peak=   -3.514 closest distance to " O   HOH Z 298 " =    2.542
peak=   -3.507 closest distance to " CE  LYS A  76 " =    3.027
peak=   -3.505 closest distance to " CA  GLY A  23 " =    2.736
peak=   -3.504 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.502 closest distance to " O   ILE A  49 " =    1.674
peak=   -3.492 closest distance to " O   HOH Z 372 " =    2.434
peak=   -3.488 closest distance to " C   GLY A  13 " =    1.034
peak=   -3.481 closest distance to " CG  PRO A 163 " =    2.381
peak=   -3.478 closest distance to " O   SER A 135 " =    1.455
peak=   -3.478 closest distance to " O   HOH Z 247 " =    1.575
peak=   -3.477 closest distance to " O   HOH Z 404 " =    0.999
peak=   -3.474 closest distance to " OG  SER A 245 " =    1.090
peak=   -3.474 closest distance to " CE  LYS A 166 " =    1.107
peak=   -3.473 closest distance to " OE1 GLU A  44 " =    1.484
peak=   -3.469 closest distance to " CG1 VAL A 112 " =    3.016
peak=   -3.463 closest distance to " CG  ARG A 219 " =    2.331
peak=   -3.454 closest distance to " OE1 GLU A 277 " =    2.254
peak=   -3.449 closest distance to " C   LEU A 143 " =    1.238
peak=   -3.442 closest distance to " N   GLN A  58 " =    1.714
peak=   -3.440 closest distance to " CG1BVAL A  41 " =    2.848
peak=   -3.440 closest distance to " CD1 TRP A 179 " =    0.977
peak=   -3.439 closest distance to " O   HOH Z 389 " =    1.930
peak=   -3.430 closest distance to " O   HOH Z  20 " =    2.507
peak=   -3.427 closest distance to " OXT GLY A 302 " =    3.083
peak=   -3.415 closest distance to " O   HOH Z 222 " =    0.907
peak=   -3.412 closest distance to " CB  PHE A 192 " =    1.643
peak=   -3.412 closest distance to " N   GLN A 122 " =    1.452
peak=   -3.404 closest distance to " O   ASN A 301 " =    1.302
peak=   -3.404 closest distance to " OD1 ASN A  60 " =    1.073
peak=   -3.401 closest distance to " O   HOH Z 250 " =    1.334
peak=   -3.400 closest distance to " CD1 LEU A 101 " =    2.427
peak=   -3.400 closest distance to " O   HOH Z 385 " =    1.106
peak=   -3.397 closest distance to " OD1 ASN A 301 " =    1.920
peak=   -3.384 closest distance to " O   HOH Z  22 " =    2.548
peak=   -3.383 closest distance to " CA  GLY A 203 " =    2.172
peak=   -3.374 closest distance to " CG1 VAL A 265 " =    2.344
peak=   -3.369 closest distance to " O   HOH Z 102 " =    1.842
peak=   -3.369 closest distance to " O   HOH Z  52 " =    1.714
peak=   -3.364 closest distance to " ND2 ASN A  45 " =    1.056
peak=   -3.361 closest distance to " CB  TRP A  85 " =    2.310
peak=   -3.358 closest distance to " O   HOH Z 318 " =    1.498
peak=   -3.348 closest distance to " O   HOH Z 409 " =    5.648
peak=   -3.348 closest distance to " CG  GLU A 152 " =    2.342
peak=   -3.343 closest distance to " CB  PHE A 283 " =    2.636
peak=   -3.341 closest distance to " O   HOH Z 432 " =    3.730
peak=   -3.340 closest distance to " OD1 ASN A 148 " =    1.694
peak=   -3.334 closest distance to " CD1 LEU A   5 " =    2.407
peak=   -3.332 closest distance to " CE2 TYR A  30 " =    2.726
peak=   -3.330 closest distance to " CB  PRO A  54 " =    2.382
peak=   -3.329 closest distance to " O   HOH Z 111 " =    2.237
peak=   -3.324 closest distance to " O   HOH Z 431 " =    1.227
peak=   -3.324 closest distance to " OE1 GLN A  58 " =    2.842
peak=   -3.323 closest distance to " OG  SER A  87 " =    1.277
peak=   -3.323 closest distance to " O   HOH Z 300 " =    2.236
peak=   -3.314 closest distance to " C   HIS A 108 " =    1.225
peak=   -3.313 closest distance to " CD  LYS A 289 " =    2.478
peak=   -3.312 closest distance to " O   HOH Z 313 " =    1.864
peak=   -3.310 closest distance to " CE  LYS A  76 " =    2.812
peak=   -3.299 closest distance to " CB  CYS A 254 " =    2.034
peak=   -3.295 closest distance to " CE1 TYR A 169 " =    2.488
peak=   -3.289 closest distance to " O   HOH Z 209 " =    2.685
peak=   -3.287 closest distance to " N   ALA A   1 " =    1.220
peak=   -3.285 closest distance to " O   PRO A 163 " =    1.937
peak=   -3.284 closest distance to " NH2AARG A 275 " =    5.535
peak=   -3.282 closest distance to " CZ3 TRP A 179 " =    1.287
peak=   -3.279 closest distance to " O   ALA A 161 " =    1.692
peak=   -3.275 closest distance to " OD2 ASP A 171 " =    1.862
peak=   -3.267 closest distance to " O   VAL A 197 " =    1.636
peak=   -3.266 closest distance to " O   HOH Z 414 " =    1.608
peak=   -3.263 closest distance to " OG  SER A   3 " =    1.419
peak=   -3.263 closest distance to " O   HOH Z 427 " =    1.800
peak=   -3.262 closest distance to " CD  PRO A 198 " =    1.521
peak=   -3.259 closest distance to " CD  GLN A 223 " =    1.511
peak=   -3.258 closest distance to " O   HOH Z   1 " =    1.245
peak=   -3.256 closest distance to " O   GLY A  80 " =    2.290
peak=   -3.254 closest distance to " O   ASP A 162 " =    2.317
peak=   -3.248 closest distance to " O   HOH Z 416 " =    1.088
peak=   -3.247 closest distance to " N   ASP A 171 " =    2.452
peak=   -3.243 closest distance to " OG  SER A 206 " =    1.795
peak=   -3.241 closest distance to " ND2 ASN A  60 " =    4.332
peak=   -3.240 closest distance to " O   VAL A  67 " =    2.669
peak=   -3.239 closest distance to " OD2 ASP A  50 " =    1.636
peak=   -3.232 closest distance to " O   HOH Z 415 " =    1.492
peak=   -3.229 closest distance to " O   HOH Z 152 " =    4.807
peak=   -3.229 closest distance to " CG BLYS A 290 " =    0.896
peak=   -3.227 closest distance to " N   HIS A 115 " =    2.155
peak=   -3.227 closest distance to " O   VAL A  67 " =    2.667
peak=   -3.221 closest distance to " O   VAL A 174 " =    2.118
peak=   -3.220 closest distance to " CA  ASN A 127 " =    1.489
peak=   -3.214 closest distance to " O   HOH Z 411 " =    1.093
peak=   -3.208 closest distance to " ND2 ASN A 249 " =    2.371
peak=   -3.204 closest distance to " C   GLN A 205 " =    2.047
peak=   -3.198 closest distance to " O   HOH Z  71 " =    0.997
peak=   -3.196 closest distance to " O   HOH Z 139 " =    2.990
peak=   -3.193 closest distance to " CA  SER A 146 " =    2.348
peak=   -3.185 closest distance to " O   HOH Z 275 " =    1.572
peak=   -3.183 closest distance to " OG ASER A 134 " =    1.161
peak=   -3.176 closest distance to " CE2 PHE A 204 " =    2.212
peak=   -3.175 closest distance to " CD  LYS A 166 " =    2.380
peak=   -3.175 closest distance to " O   HOH Z 234 " =    4.774
peak=   -3.172 closest distance to " O   HOH Z 417 " =    2.699
peak=   -3.168 closest distance to " CD  GLN A  58 " =    1.192
peak=   -3.164 closest distance to " CG2 THR A 178 " =    2.097
peak=   -3.163 closest distance to " CZ  PHE A  59 " =    1.470
peak=   -3.158 closest distance to " N   GLN A  88 " =    1.734
peak=   -3.142 closest distance to " OE1 GLN A 223 " =    2.670
peak=   -3.142 closest distance to " O   SER A  62 " =    2.306
peak=   -3.142 closest distance to " CG1 VAL A 197 " =    2.282
peak=   -3.137 closest distance to " OE1 GLN A 278 " =    1.226
peak=   -3.136 closest distance to " CA  HIS A  86 " =    2.099
peak=   -3.135 closest distance to " OG1 THR A 246 " =    1.615
peak=   -3.133 closest distance to " O   HOH Z 234 " =    4.096
peak=   -3.131 closest distance to " N   ALA A   1 " =    3.033
peak=   -3.118 closest distance to " CG  TRP A 266 " =    1.290
peak=   -3.117 closest distance to " CD2 PHE A  61 " =    2.339
peak=   -3.114 closest distance to " O   HOH Z 111 " =    0.934
peak=   -3.113 closest distance to " NE2 GLN A 278 " =    2.043
peak=   -3.111 closest distance to " C   PHE A  59 " =    1.204
peak=   -3.104 closest distance to " O   HOH Z 359 " =    1.535
peak=   -3.095 closest distance to " C   ARG A 269 " =    1.355
peak=   -3.093 closest distance to " CB  SER A  63 " =    3.357
peak=   -3.088 closest distance to " OG1 THR A   4 " =    1.788
peak=   -3.084 closest distance to " O   HOH Z 417 " =    2.210
peak=   -3.071 closest distance to " CZ BARG A 275 " =    1.631
peak=   -3.062 closest distance to " O   HOH Z 151 " =    1.079
peak=   -3.061 closest distance to " CD  GLN A  77 " =    1.534
peak=   -3.053 closest distance to " O   ILE A 239 " =    1.288
peak=   -3.040 closest distance to " NH1BARG A 145 " =    3.948
peak=   -3.033 closest distance to " O   HOH Z  56 " =    0.943
peak=   -3.017 closest distance to " O   HOH Z  52 " =    1.793

================= 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    :  0.4599 0.4595   6.266313e+00   6.264545e+00
   1_bss:  0.4520 0.4522   6.261163e+00   6.253851e+00
   1_xyz:  0.3497 0.3815   6.097394e+00   6.148803e+00
   1_adp:  0.3165 0.3922   6.045497e+00   6.162279e+00
   1_occ:  0.3162 0.3925   6.044379e+00   6.161603e+00
   2_bss:  0.3160 0.3908   6.044637e+00   6.160290e+00
   2_xyz:  0.2629 0.3364   5.897910e+00   6.054875e+00
   2_adp:  0.2539 0.3282   5.874445e+00   6.037402e+00
   2_occ:  0.2538 0.3278   5.873941e+00   6.037049e+00
   3_bss:  0.2544 0.3276   5.874584e+00   6.037399e+00
   3_xyz:  0.1894 0.2516   5.611404e+00   5.815202e+00
   3_adp:  0.1670 0.2264   5.498138e+00   5.727477e+00
   3_occ:  0.1667 0.2254   5.495430e+00   5.724441e+00
   4_bss:  0.1659 0.2232   5.491672e+00   5.718536e+00
   4_xyz:  0.1467 0.1983   5.378321e+00   5.608023e+00
   4_adp:  0.1346 0.1876   5.308261e+00   5.546460e+00
   4_occ:  0.1345 0.1874   5.307830e+00   5.545826e+00
   5_bss:  0.1344 0.1877   5.306652e+00   5.545241e+00
   5_xyz:  0.1246 0.1774   5.242351e+00   5.491406e+00
   5_adp:  0.1226 0.1702   5.218852e+00   5.459513e+00
   5_occ:  0.1225 0.1699   5.218008e+00   5.458503e+00
   5_bss:  0.1225 0.1699   5.218081e+00   5.458463e+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:  0.340  34.917  -0.907   1.878  -0.054   0.000  -0.000  -0.000
   1_xyz:  0.340  34.917  -0.907   1.878  -0.054   0.000  -0.000  -0.000
   1_adp:  0.340  34.917  -0.907   1.878  -0.054   0.000  -0.000  -0.000
   1_occ:  0.340  34.917  -0.907   1.878  -0.054   0.000  -0.000  -0.000
   2_bss:  0.347  55.530  -0.964  -0.064  -0.414  -0.000  -0.000  -0.000
   2_xyz:  0.347  55.530  -0.964  -0.064  -0.414  -0.000  -0.000  -0.000
   2_adp:  0.347  55.530  -0.964  -0.064  -0.414  -0.000  -0.000  -0.000
   2_occ:  0.347  55.530  -0.964  -0.064  -0.414  -0.000  -0.000  -0.000
   3_bss:  0.345  55.530  -0.728  -0.578  -0.174  -0.000  -0.000  -0.000
   3_xyz:  0.345  55.530  -0.728  -0.578  -0.174  -0.000  -0.000  -0.000
   3_adp:  0.345  55.530  -0.728  -0.578  -0.174  -0.000  -0.000  -0.000
   3_occ:  0.345  55.530  -0.728  -0.578  -0.174  -0.000  -0.000  -0.000
   4_bss:  0.323  45.833  -1.683  -2.142  -1.259  -0.000  -0.000  -0.000
   4_xyz:  0.323  45.833  -1.683  -2.142  -1.259  -0.000  -0.000  -0.000
   4_adp:  0.323  45.833  -1.683  -2.142  -1.259  -0.000  -0.000  -0.000
   4_occ:  0.323  45.833  -1.683  -2.142  -1.259  -0.000  -0.000  -0.000
   5_bss:  0.313  45.833  -1.872  -2.545  -1.485  -0.000  -0.000  -0.000
   5_xyz:  0.313  45.833  -1.872  -2.545  -1.485  -0.000  -0.000  -0.000
   5_adp:  0.313  45.833  -1.872  -2.545  -1.485  -0.000  -0.000  -0.000
   5_occ:  0.313  45.833  -1.872  -2.545  -1.485  -0.000  -0.000  -0.000
   5_bss:  0.315  44.681  -1.952  -2.625  -1.559  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.809 0.4476  0.6130    67977.873
   1_bss:  54.933 0.4572  0.6351    64953.442
   1_xyz:  42.014 0.6189  0.8300    42517.706
   1_adp:  43.179 0.6036  0.8167    43768.221
   1_occ:  43.185 0.6035  0.8156    43726.726
   2_bss:  42.954 0.6062  0.7984    43338.476
   2_xyz:  35.821 0.6904  0.8929    30876.845
   2_adp:  34.112 0.7110  0.9074    29202.854
   2_occ:  34.098 0.7111  0.9069    29157.587
   3_bss:  34.054 0.7115  0.9068    29071.065
   3_xyz:  25.055 0.8103  0.9997    16258.318
   3_adp:  22.083 0.8413  1.0217    13197.150
   3_occ:  21.973 0.8423  1.0221    13051.484
   4_bss:  21.804 0.8436  0.9791    12780.271
   4_xyz:  18.941 0.8711  0.9903     9940.519
   4_adp:  17.402 0.8860  0.9883     8837.517
   4_occ:  17.386 0.8861  0.9882     8825.450
   5_bss:  17.373 0.8862  0.9785     8818.109
   5_xyz:  16.114 0.8971  0.9860     7749.434
   5_adp:  15.244 0.9049  0.9868     7241.955
   5_occ:  15.220 0.9051  0.9868     7221.930
   5_bss:  15.221 0.9050  0.9831     7221.368
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7584e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7584e-01
   1_xyz:   1.469  0.012  0.098 15.468  0.006  4.105   1.2326e-01
   1_adp:   1.469  0.012  0.098 15.468  0.006  4.105   1.2326e-01
   1_occ:   1.469  0.012  0.098 15.468  0.006  4.105   1.2326e-01
   2_bss:   1.469  0.012  0.098 15.468  0.006  4.105   1.2326e-01
   2_xyz:   1.129  0.007  0.077 14.304  0.005  4.107   6.7636e-02
   2_adp:   1.129  0.007  0.077 14.304  0.005  4.107   6.7636e-02
   2_occ:   1.129  0.007  0.077 14.304  0.005  4.107   6.7636e-02
   3_bss:   1.129  0.007  0.077 14.304  0.005  4.107   6.7636e-02
   3_xyz:   1.175  0.009  0.079 14.660  0.004  4.112   7.8099e-02
   3_adp:   1.175  0.009  0.079 14.660  0.004  4.112   7.8099e-02
   3_occ:   1.175  0.009  0.079 14.660  0.004  4.112   7.8099e-02
   4_bss:   1.175  0.009  0.079 14.660  0.004  4.112   7.8099e-02
   4_xyz:   0.899  0.005  0.065 14.187  0.003  4.109   4.8985e-02
   4_adp:   0.899  0.005  0.065 14.187  0.003  4.109   4.8985e-02
   4_occ:   0.899  0.005  0.065 14.187  0.003  4.109   4.8985e-02
   5_bss:   0.899  0.005  0.065 14.187  0.003  4.109   4.8985e-02
   5_xyz:   0.871  0.005  0.064 14.182  0.003  4.112   4.7092e-02
   5_adp:   0.871  0.005  0.064 14.182  0.003  4.112   4.7092e-02
   5_occ:   0.871  0.005  0.064 14.182  0.003  4.112   4.7092e-02
   5_bss:   0.871  0.005  0.064 14.182  0.003  4.112   4.7092e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.567   2.3940e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.567   2.3940e-01
   1_xyz:   9.434  0.089  0.472 87.835  0.035  2.014   2.0847e-01
   1_adp:   9.434  0.089  0.472 87.835  0.035  2.014   2.0847e-01
   1_occ:   9.434  0.089  0.472 87.835  0.035  2.014   2.0847e-01
   2_bss:   9.434  0.089  0.472 87.835  0.035  2.014   2.0847e-01
   2_xyz:   7.739  0.044  0.232 83.615  0.043  2.286   4.9955e-02
   2_adp:   7.739  0.044  0.232 83.615  0.043  2.286   4.9955e-02
   2_occ:   7.739  0.044  0.232 83.615  0.043  2.286   4.9955e-02
   3_bss:   7.739  0.044  0.232 83.615  0.043  2.286   4.9955e-02
   3_xyz:   8.227  0.046  0.331 82.524  0.022  2.142   8.1814e-02
   3_adp:   8.227  0.046  0.331 82.524  0.022  2.142   8.1814e-02
   3_occ:   8.227  0.046  0.331 82.524  0.022  2.142   8.1814e-02
   4_bss:   8.227  0.046  0.331 82.524  0.022  2.142   8.1814e-02
   4_xyz:   7.228  0.043  0.204 80.562  0.028  2.374   3.1578e-02
   4_adp:   7.228  0.043  0.204 80.562  0.028  2.374   3.1578e-02
   4_occ:   7.228  0.043  0.204 80.562  0.028  2.374   3.1578e-02
   5_bss:   7.228  0.043  0.204 80.562  0.028  2.374   3.1578e-02
   5_xyz:   7.894  0.034  0.199 83.352  0.030  2.335   3.0413e-02
   5_adp:   7.894  0.034  0.199 83.352  0.030  2.335   3.0413e-02
   5_occ:   7.894  0.034  0.199 83.352  0.030  2.335   3.0413e-02
   5_bss:   7.894  0.034  0.199 83.352  0.030  2.335   3.0413e-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: 106.81   0.00  19.21  85.71   0.00  15.78 106.81   0.00  37.87
   1_occ: 106.81   0.00  19.21  85.71   0.00  15.78 106.81   0.00  37.87
   2_bss: 106.81   0.00  19.21  85.71   0.00  15.78 106.81   0.00  37.87
   2_xyz: 106.81   0.00  19.21  85.71   0.00  15.78 106.81   0.00  37.87
   2_adp: 120.24   0.00  18.88 120.24   0.00  15.35 107.18   2.32  38.08
   2_occ: 120.24   0.00  18.88 120.24   0.00  15.35 107.18   2.32  38.08
   3_bss: 120.24   0.00  18.88 120.24   0.00  15.35 107.18   2.32  38.08
   3_xyz: 120.24   0.00  18.88 120.24   0.00  15.35 107.18   2.32  38.08
   3_adp: 105.81   0.00  18.23  94.88   0.00  14.19 105.81   5.37  40.21
   3_occ: 105.81   0.00  18.23  94.88   0.00  14.19 105.81   5.37  40.21
   4_bss: 105.81   0.00  18.23  94.88   0.00  14.19 105.81   5.37  40.21
   4_xyz: 105.81   0.00  18.23  94.88   0.00  14.19 105.81   5.37  40.21
   4_adp: 104.36   0.00  18.34 104.36   0.00  13.50 103.66   6.91  44.65
   4_occ: 104.36   0.00  18.34 104.36   0.00  13.50 103.66   6.91  44.65
   5_bss: 104.36   0.00  18.34 104.36   0.00  13.50 103.66   6.91  44.65
   5_xyz: 104.36   0.00  18.34 104.36   0.00  13.50 103.66   6.91  44.65
   5_adp: 101.53   0.79  17.46 101.53   0.79  13.02  90.78   6.09  41.59
   5_occ: 101.53   0.79  17.46 101.53   0.79  13.02  90.78   6.09  41.59
   5_bss: 101.51   0.76  17.43 101.51   0.76  13.00  90.76   6.07  41.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.892    0.004    0.316
   1_adp:    1.892    0.004    0.316
   1_occ:    1.892    0.004    0.316
   2_bss:    1.892    0.004    0.316
   2_xyz:    1.298    0.017    0.438
   2_adp:    1.298    0.017    0.438
   2_occ:    1.298    0.017    0.438
   3_bss:    1.298    0.017    0.438
   3_xyz:    1.537    0.040    0.666
   3_adp:    1.537    0.040    0.666
   3_occ:    1.537    0.040    0.666
   4_bss:    1.537    0.040    0.666
   4_xyz:    1.576    0.086    0.698
   4_adp:    1.576    0.086    0.698
   4_occ:    1.576    0.086    0.698
   5_bss:    1.576    0.086    0.698
   5_xyz:    1.634    0.056    0.727
   5_adp:    1.634    0.056    0.727
   5_occ:    1.634    0.056    0.727
   5_bss:    1.634    0.056    0.727
------------------------------------------------------------------------

CPU time actual refinement: 290.88


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/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_981/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_981/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 290.75 
  Macro-tasks:
    bulk solvent and scale       = 30.88  
    individual site refinement   = 123.85 
    weights calculation          = 24.95  
    collect and process          = 5.39   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 185.15 
  Micro-tasks:
    mask                            = 2.06   
    f_calc                          = 96.66  
    alpha_beta                      = 6.80   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 103.46 
    fmodel                         = 5.49   
    r_factors                      = 0.14   
    phase_errors                   = 8.67   
    foms                           = 0.34   
    TOTAL for micro-tasks          = 224.58 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.144 micro seconds
Total CPU time: 5.04 minutes
from_scatterers_fft:    634 calls, 96.43 s
gradients_fft:          579 calls, 92.18 s

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

# Date 2008-01-16 Time 06:06:46 PST -0800 (1200492406.56 s)
Start R-work = 0.4599, R-free = 0.4595 (no bulk solvent and anisotropic scale)
Final R-work = 0.1460, R-free = 0.1902 (no bulk solvent and anisotropic scale)

Start R-work = 0.4520, R-free = 0.4522
Final R-work = 0.1225, R-free = 0.1699