# Date 2008-01-16 Time 04:20:17 PST -0800 (1200486017.42 s)
#phil __OFF__

Command line arguments: "../272.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30314
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 272

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97048
Completeness in resolution range: 0.956868
Completeness with d_max=infinity: 0.953932

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8871
                             d_min =   1.9705

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97048
Completeness in resolution range: 0.956868
Completeness with d_max=infinity: 0.953932

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8875 -  4.2161 [2152/2176]  1933   219  10.2%
  bin  2:  4.2161 -  3.3591 [2058/2078]  1854   204   9.9%
  bin  3:  3.3591 -  2.9382 [2045/2064]  1844   201   9.8%
  bin  4:  2.9382 -  2.6713 [2007/2037]  1801   206  10.3%
  bin  5:  2.6713 -  2.4807 [2010/2029]  1810   200  10.0%
  bin  6:  2.4807 -  2.3351 [2001/2026]  1799   202  10.1%
  bin  7:  2.3351 -  2.2185 [2002/2030]  1804   198   9.9%
  bin  8:  2.2185 -  2.1222 [1955/1991]  1759   196  10.0%
  bin  9:  2.1222 -  2.0407 [1986/2028]  1790   196   9.9%
  bin 10:  2.0407 -  1.9705 [1373/2013]  1236   137  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 11
        2.09 -     2.79: 697
        2.79 -     3.49: 4554
        3.49 -     4.20: 9411
        4.20 -     4.90: 13905
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.386 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.691 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.722 3.120 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.885 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28573 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_272/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.22605 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4280   r_free= 0.4241   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.228663                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7023 0.99   1402  153 0.3321 0.3141      6.4798      6.4053|
|  2:  4.7023 -  3.7521 0.99   1344  153 0.3406 0.3454      6.6599      6.6707|
|  3:  3.7521 -  3.2836 0.99   1299  145 0.3882 0.3630      6.6029      6.5983|
|  4:  3.2836 -  2.9860 0.99   1327  140 0.4157 0.4725      6.4589       6.552|
|  5:  2.9860 -  2.7735 0.99   1281  152 0.4539 0.3734      6.3055      6.2395|
|  6:  2.7735 -  2.6109 0.99   1309  140 0.4541 0.4948      6.2202      6.1544|
|  7:  2.6109 -  2.4807 0.99   1280  147 0.4608 0.4218      6.1925      6.0831|
|  8:  2.4807 -  2.3732 0.98   1284  138 0.4885 0.4871      6.1621      6.1983|
|  9:  2.3732 -  2.2822 0.98   1271  142 0.4757 0.4998      6.0872      6.1505|
| 10:  2.2822 -  2.2037 1.00   1295  144 0.4955 0.4654      6.0893      6.0214|
| 11:  2.2037 -  2.1350 0.98   1265  141 0.4880 0.5181      6.0158      6.0425|
| 12:  2.1350 -  2.0741 0.98   1257  141 0.5095 0.4587      5.9659      5.9819|
| 13:  2.0741 -  2.0196 0.99   1275  132 0.4838 0.5033      5.8713      5.8111|
| 14:  2.0196 -  1.9705 0.57    741   91 0.5083 0.4941      5.8727      5.7478|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7023  1402   153  0.76  28.98   0.84     0.81      53378.70|
|  2:  4.7023 -  3.7521  1344   153  0.76  29.42   0.95     0.87      79171.01|
|  3:  3.7521 -  3.2836  1299   145  0.69  36.55   0.95     0.86      85201.94|
|  4:  3.2836 -  2.9860  1327   140  0.61  42.90   0.94     0.80      78889.69|
|  5:  2.9860 -  2.7735  1281   152  0.55  47.85   0.93     0.74      59847.49|
|  6:  2.7735 -  2.6109  1309   140  0.54  49.02   0.93     0.72      52470.61|
|  7:  2.6109 -  2.4807  1280   147  0.52  50.39   0.95     0.70      48125.24|
|  8:  2.4807 -  2.3732  1284   138  0.49  52.96   0.92     0.67      46610.06|
|  9:  2.3732 -  2.2822  1271   142  0.48  53.61   0.95     0.67      43826.21|
| 10:  2.2822 -  2.2037  1295   144  0.47  54.37   0.96     0.68      40260.96|
| 11:  2.2037 -  2.1350  1265   141  0.47  54.97   0.95     0.72      40046.50|
| 12:  2.1350 -  2.0741  1257   141  0.44  57.21   0.95     0.68      36756.17|
| 13:  2.0741 -  2.0196  1275   132  0.41  59.05   0.98     0.63      33076.04|
| 14:  2.0196 -  1.9705   741    91  0.40  60.46   0.99     0.55      28015.30|
|alpha:            min =        0.55 max =            0.87 mean =         0.73|
|beta:             min =    28015.30 max =        85201.94 mean =     52809.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.79|
|phase err.(test): min =        0.00 max =           89.99 mean =        47.92|
|-----------------------------------------------------------------------------|

============================== 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 = 6.477498              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.114   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.498461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.665   (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 |  1.386 -  1.738:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.738 -  2.089:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.089 -  2.440:       41 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.440 -  2.792:      656 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.792 -  3.143:     2132 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.143 -  3.494:     2422 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.494 -  3.846:     4571 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.846 -  4.197:     4840 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.197 -  4.549:     6310 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7595 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.386 |       0.440 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4280   r_free= 0.4241   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.228663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4182   r_free= 0.4149   ksol= 0.33   Bsol= 29.41   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,1.43,1.64,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.219577                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.225499              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.820017              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.418   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4182      final r-factor (work) = 0.2898          |
| start r-factor (free) = 0.4149      final r-factor (free) = 0.3222          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4174 = 5.23 * 0.50 * 6.2151 + 1.00 * 0.1790                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8788 = 5.23 * 0.50 * 6.0382 + 1.00 * 0.1024                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2898      final r-factor (work) = 0.2627          |
| start r-factor (free) = 0.3222      final r-factor (free) = 0.3379          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9575 = 0.82 * 1.00 * 6.0382 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8316 = 0.82 * 1.00 * 5.8738 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.39   18.15    None  None   None       |
|    all(noH): 2823   0      0.00    93.39   18.15    None  None   None       |
|    Sol.    : 438    0      0.99    93.39   39.12    None  None   None       |
|    Mac.    : 2385   0      0.00    71.33   14.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.339:  831   |   5:    46.695 -  56.034:  103        |
|      1:     9.339 -  18.678: 1037   |   6:    56.034 -  65.373:   58        |
|      2:    18.678 -  28.017:  431   |   7:    65.373 -  74.712:   23        |
|      3:    28.017 -  37.356:  207   |   8:    74.712 -  84.051:    0        |
|      4:    37.356 -  46.695:  132   |   9:    84.051 -  93.390:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2627 r_free = 0.3379             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2624 r_free = 0.3379             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2624   r_free= 0.3379   ksol= 0.33   Bsol= 29.41   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,1.43,1.64,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.892488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2611   r_free= 0.3363   ksol= 0.34   Bsol= 54.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.57,0.26,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.891191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.234493              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.051   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2611      final r-factor (work) = 0.1850          |
| start r-factor (free) = 0.3363      final r-factor (free) = 0.2425          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4838 = 5.23 * 0.50 * 5.8769 + 1.00 * 0.1024                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1555 = 5.23 * 0.50 * 5.7634 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1850      final r-factor (work) = 0.1686          |
| start r-factor (free) = 0.2425      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3867 = 0.24 * 1.00 * 5.7634 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3385 = 0.24 * 1.00 * 5.5339 + 1.00 * 0.0213                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.81   17.53    None  None   None       |
|    all(noH): 2823   0      0.00    91.81   17.53    None  None   None       |
|    Sol.    : 438    0      5.55    91.81   39.55    None  None   None       |
|    Mac.    : 2385   0      0.00    70.03   13.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.181:  775   |   5:    45.903 -  55.084:  110        |
|      1:     9.181 -  18.361: 1243   |   6:    55.084 -  64.265:   51        |
|      2:    18.361 -  27.542:  313   |   7:    64.265 -  73.445:   18        |
|      3:    27.542 -  36.723:  171   |   8:    73.445 -  82.626:    2        |
|      4:    36.723 -  45.903:  139   |   9:    82.626 -  91.806:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1686 r_free = 0.2197             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1684 r_free = 0.2190             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1684   r_free= 0.2190   ksol= 0.34   Bsol= 54.23   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-0.57,0.26,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.484571                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1682   r_free= 0.2180   ksol= 0.34   Bsol= 54.23   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.86,-0.43,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.482025                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.202953              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.960   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.694185              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.727   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1682      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.2180      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1693 = 2.20 * 0.50 * 5.5363 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9911 = 2.20 * 0.50 * 5.3920 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7908 = 0.69 * 1.00 * 5.3920 + 1.00 * 0.0477                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6724 = 0.69 * 1.00 * 5.2764 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    93.53   17.51    None  None   None       |
|    all(noH): 2823   0      0.36    93.53   17.51    None  None   None       |
|    Sol.    : 438    0      6.25    93.53   41.81    None  None   None       |
|    Mac.    : 2385   0      0.36    78.27   13.04    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:     0.357 -   9.674:  928   |   5:    46.943 -  56.260:  120        |
|      1:     9.674 -  18.991: 1185   |   6:    56.260 -  65.578:   76        |
|      2:    18.991 -  28.308:  253   |   7:    65.578 -  74.895:   19        |
|      3:    28.308 -  37.626:  116   |   8:    74.895 -  84.212:    4        |
|      4:    37.626 -  46.943:  121   |   9:    84.212 -  93.530:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1771             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1288 r_free = 0.1771             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1288   r_free= 0.1771   ksol= 0.34   Bsol= 54.23   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.86,-0.43,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1768   ksol= 0.33   Bsol= 54.23   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.36,-0.66,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258361                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.212  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.928788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.651  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1768      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2564 = 3.11 * 0.50 * 5.2770 + 1.00 * 0.0519                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1666 = 3.11 * 0.50 * 5.2115 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8500 = 0.93 * 1.00 * 5.2115 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8020 = 0.93 * 1.00 * 5.1596 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    93.94   17.37    None  None   None       |
|    all(noH): 2823   0      0.23    93.94   17.37    None  None   None       |
|    Sol.    : 438    0      5.60    93.94   41.78    None  None   None       |
|    Mac.    : 2385   0      0.23    86.69   12.89    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:     0.231 -   9.602:  971   |   5:    47.085 -  56.456:   99        |
|      1:     9.602 -  18.972: 1161   |   6:    56.456 -  65.826:   78        |
|      2:    18.972 -  28.343:  239   |   7:    65.826 -  75.197:   31        |
|      3:    28.343 -  37.714:  129   |   8:    75.197 -  84.568:    7        |
|      4:    37.714 -  47.085:  106   |   9:    84.568 -  93.939:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1606             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1606             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1606   ksol= 0.33   Bsol= 54.23   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,-2.36,-0.66,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151621                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1606   ksol= 0.33   Bsol= 54.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.27,-0.48,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.151566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.273142              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.943  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.544586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.066  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9286 = 2.27 * 0.50 * 5.1601 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9060 = 2.27 * 0.50 * 5.1460 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9581 = 1.54 * 1.00 * 5.1460 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9460 = 1.54 * 1.00 * 5.1379 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.15    94.01   17.17    None  None   None       |
|    all(noH): 2823   0      0.15    94.01   17.17    None  None   None       |
|    Sol.    : 438    0      5.45    94.01   41.54    None  None   None       |
|    Mac.    : 2385   0      0.15    88.57   12.69    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:     0.155 -   9.540: 1007   |   5:    47.081 -  56.466:   96        |
|      1:     9.540 -  18.925: 1136   |   6:    56.466 -  65.852:   75        |
|      2:    18.925 -  28.311:  230   |   7:    65.852 -  75.237:   30        |
|      3:    28.311 -  37.696:  131   |   8:    75.237 -  84.622:   10        |
|      4:    37.696 -  47.081:  105   |   9:    84.622 -  94.007:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1577             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1578             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1578   ksol= 0.33   Bsol= 54.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-2.27,-0.48,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138624                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7023 0.99   1402  153 0.0993 0.1257      5.3897      5.5297|
|  2:  4.7023 -  3.7521 0.99   1344  153 0.0831 0.1113      5.4235      5.6239|
|  3:  3.7521 -  3.2836 0.99   1299  145 0.1046 0.1513      5.4655      5.8369|
|  4:  3.2836 -  2.9860 0.99   1327  140 0.1195 0.1670      5.4334      5.6173|
|  5:  2.9860 -  2.7735 0.99   1281  152 0.1297 0.1640      5.3197      5.5369|
|  6:  2.7735 -  2.6109 0.99   1309  140 0.1212 0.1990        5.21      5.4922|
|  7:  2.6109 -  2.4807 0.99   1280  147 0.1288 0.1585      5.1854      5.3159|
|  8:  2.4807 -  2.3732 0.98   1284  138 0.1159 0.1604      5.0777      5.3415|
|  9:  2.3732 -  2.2822 0.98   1271  142 0.1144 0.1831      5.0081      5.3148|
| 10:  2.2822 -  2.2037 1.00   1295  144 0.1115 0.1660      4.9415      5.1619|
| 11:  2.2037 -  2.1350 0.98   1265  141 0.1109 0.1864       4.928      5.2965|
| 12:  2.1350 -  2.0741 0.98   1257  141 0.1181 0.1637      4.9067      5.2065|
| 13:  2.0741 -  2.0196 0.99   1275  132 0.1059 0.1823      4.7678      5.0559|
| 14:  2.0196 -  1.9705 0.57    741   91 0.0892 0.1670      4.5912       4.887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7023  1402   153  0.94   9.57   0.98     0.95       7483.26|
|  2:  4.7023 -  3.7521  1344   153  0.95   7.80   1.02     1.01       9021.04|
|  3:  3.7521 -  3.2836  1299   145  0.94  11.06   1.04     1.03      10063.64|
|  4:  3.2836 -  2.9860  1327   140  0.92  13.38   1.01     1.00       9956.48|
|  5:  2.9860 -  2.7735  1281   152  0.91  15.38   1.01     0.99       8251.90|
|  6:  2.7735 -  2.6109  1309   140  0.90  16.35   0.98     0.95       7057.53|
|  7:  2.6109 -  2.4807  1280   147  0.90  15.84   0.99     0.95       6375.08|
|  8:  2.4807 -  2.3732  1284   138  0.91  15.30   0.99     0.97       5458.25|
|  9:  2.3732 -  2.2822  1271   142  0.91  14.80   1.00     0.96       4747.75|
| 10:  2.2822 -  2.2037  1295   144  0.90  15.75   1.00     0.97       4298.60|
| 11:  2.2037 -  2.1350  1265   141  0.90  15.89   0.99     0.95       4310.17|
| 12:  2.1350 -  2.0741  1257   141  0.90  16.66   1.01     1.00       4251.66|
| 13:  2.0741 -  2.0196  1275   132  0.91  15.63   0.99     0.97       3277.73|
| 14:  2.0196 -  1.9705   741    91  0.93  12.81   0.98     0.96       2295.08|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2295.08 max =        10063.64 mean =      6361.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.83 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1577   ksol= 0.32   Bsol= 54.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.16,-0.31,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138577                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1577   ksol= 0.32   Bsol= 54.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.16,-0.31,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138577                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7023 0.99   1402  153 0.0992 0.1257      5.3894      5.5301|
|  2:  4.7023 -  3.7521 0.99   1344  153 0.0832 0.1114      5.4242      5.6244|
|  3:  3.7521 -  3.2836 0.99   1299  145 0.1047 0.1514      5.4659      5.8372|
|  4:  3.2836 -  2.9860 0.99   1327  140 0.1195 0.1670      5.4334      5.6171|
|  5:  2.9860 -  2.7735 0.99   1281  152 0.1297 0.1640      5.3195      5.5363|
|  6:  2.7735 -  2.6109 0.99   1309  140 0.1211 0.1989      5.2097      5.4916|
|  7:  2.6109 -  2.4807 0.99   1280  147 0.1288 0.1585      5.1854       5.316|
|  8:  2.4807 -  2.3732 0.98   1284  138 0.1159 0.1605      5.0777      5.3416|
|  9:  2.3732 -  2.2822 0.98   1271  142 0.1144 0.1829      5.0081      5.3143|
| 10:  2.2822 -  2.2037 1.00   1295  144 0.1115 0.1662      4.9414      5.1629|
| 11:  2.2037 -  2.1350 0.98   1265  141 0.1108 0.1865      4.9281      5.2968|
| 12:  2.1350 -  2.0741 0.98   1257  141 0.1180 0.1635      4.9065       5.206|
| 13:  2.0741 -  2.0196 0.99   1275  132 0.1059 0.1822      4.7674      5.0553|
| 14:  2.0196 -  1.9705 0.57    741   91 0.0892 0.1668      4.5904      4.8858|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7023  1402   153  0.94   9.57   0.98     0.95       7481.86|
|  2:  4.7023 -  3.7521  1344   153  0.95   7.81   1.02     1.01       9028.11|
|  3:  3.7521 -  3.2836  1299   145  0.94  11.07   1.04     1.03      10072.90|
|  4:  3.2836 -  2.9860  1327   140  0.92  13.38   1.02     1.00       9955.93|
|  5:  2.9860 -  2.7735  1281   152  0.91  15.37   1.01     0.99       8246.52|
|  6:  2.7735 -  2.6109  1309   140  0.90  16.35   0.99     0.96       7053.21|
|  7:  2.6109 -  2.4807  1280   147  0.90  15.84   0.99     0.96       6374.75|
|  8:  2.4807 -  2.3732  1284   138  0.91  15.30   1.00     0.97       5456.67|
|  9:  2.3732 -  2.2822  1271   142  0.91  14.81   1.00     0.96       4748.39|
| 10:  2.2822 -  2.2037  1295   144  0.90  15.75   1.01     0.98       4299.46|
| 11:  2.2037 -  2.1350  1265   141  0.90  15.89   1.00     0.96       4312.30|
| 12:  2.1350 -  2.0741  1257   141  0.90  16.66   1.02     1.01       4251.76|
| 13:  2.0741 -  2.0196  1275   132  0.91  15.62   1.00     0.98       3273.25|
| 14:  2.0196 -  1.9705   741    91  0.93  12.78   0.99     0.97       2288.82|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2288.82 max =        10072.90 mean =      6361.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.90 mean =        13.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.633)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.15    94.00   17.16    None  None   None       |
|    all(noH): 2823   0      0.15    94.00   17.16    None  None   None       |
|    Sol.    : 438    0      5.45    94.00   41.54    None  None   None       |
|    Mac.    : 2385   0      0.15    88.56   12.69    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:     0.152 -   9.537: 1007   |   5:    47.078 -  56.464:   96        |
|      1:     9.537 -  18.923: 1136   |   6:    56.464 -  65.849:   75        |
|      2:    18.923 -  28.308:  230   |   7:    65.849 -  75.234:   30        |
|      3:    28.308 -  37.693:  131   |   8:    75.234 -  84.619:   10        |
|      4:    37.693 -  47.078:  105   |   9:    84.619 -  94.005:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 4.710
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.714 - 4.710

peak=    6.007 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.991 closest distance to " O   HOH Z 142 " =    1.881
peak=    5.451 closest distance to " CG  PRO A  54 " =    1.325
peak=    5.377 closest distance to " O   HOH Z 126 " =    2.034
peak=    5.320 closest distance to " NH2 ARG A  56 " =    2.117
peak=    5.203 closest distance to " O   HOH Z 417 " =    1.723
peak=    5.174 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.806 closest distance to " CG  PRO A 213 " =    1.256
peak=    4.805 closest distance to " O   HOH Z 375 " =    0.934
peak=    4.767 closest distance to " O   HOH Z 287 " =    1.999
peak=    4.765 closest distance to " O   HOH Z 427 " =    2.874
peak=    4.757 closest distance to " CB  PRO A  54 " =    1.016
peak=    4.677 closest distance to " CB  GLN A 223 " =    1.484
peak=    4.568 closest distance to " O   HOH Z 112 " =    1.151
peak=    4.559 closest distance to " O   HOH Z   9 " =    1.359
peak=    4.557 closest distance to " O   HOH Z 232 " =    2.347
peak=    4.556 closest distance to " O   HOH Z 369 " =    2.270
peak=    4.510 closest distance to " CB  ARG A  79 " =    1.384
peak=    4.431 closest distance to " CG2 VAL A 257 " =    0.860
peak=    4.407 closest distance to " ND2 ASN A 187 " =    1.559
peak=    4.378 closest distance to " O   HOH Z  78 " =    1.664
peak=    4.366 closest distance to " CB  SER A  63 " =    1.173
peak=    4.300 closest distance to " O   HOH Z 403 " =    1.825
peak=    4.278 closest distance to " CA  TYR A  30 " =    0.964
peak=    4.255 closest distance to " O   HOH Z  57 " =    2.426
peak=    4.253 closest distance to " O   HOH Z 423 " =    1.446
peak=    4.246 closest distance to " CB  ASN A 148 " =    1.366
peak=    4.242 closest distance to " CG  PRO A  90 " =    1.151
peak=    4.231 closest distance to " O   HOH Z 236 " =    1.389
peak=    4.230 closest distance to " O   HOH Z 402 " =    1.406
peak=    4.208 closest distance to " CB  ARG A 190 " =    1.684
peak=    4.205 closest distance to " O   SER A  87 " =    2.201
peak=    4.204 closest distance to " CB  VAL A 265 " =    1.284
peak=    4.190 closest distance to " NZ  LYS A 119 " =    2.551
peak=    4.188 closest distance to " CG  PRO A 198 " =    1.228
peak=    4.184 closest distance to " CD2 TRP A 179 " =    1.303
peak=    4.173 closest distance to " CB  GLN A 183 " =    1.203
peak=    4.139 closest distance to " CG  TRP A 179 " =    2.130
peak=    4.134 closest distance to " NZ  LYS A 117 " =    3.103
peak=    4.100 closest distance to " CA  ARG A 195 " =    1.213
peak=    4.096 closest distance to " C   PRO A 198 " =    1.490
peak=    4.094 closest distance to " CZ  PHE A 218 " =    1.065
peak=    4.077 closest distance to " O   HOH Z 371 " =    1.904
peak=    4.067 closest distance to " O   HOH Z 327 " =    1.564
peak=    4.058 closest distance to " O   HOH Z 346 " =    1.628
peak=    4.025 closest distance to " CD  ARG A 159 " =    0.714
peak=    4.024 closest distance to " O   HOH Z 298 " =    1.807
peak=    4.005 closest distance to " CG  ARG A  66 " =    2.590
peak=    4.000 closest distance to " OG BSER A 164 " =    2.209
peak=    3.998 closest distance to " CB  SER A  26 " =    1.777
peak=    3.991 closest distance to " O   HOH Z  61 " =    1.651
peak=    3.989 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.988 closest distance to " CB  GLU A 277 " =    3.539
peak=    3.987 closest distance to " O   HOH Z 272 " =    1.780
peak=    3.971 closest distance to " O   HOH Z 380 " =    1.699
peak=    3.964 closest distance to " CB  VAL A 202 " =    1.623
peak=    3.948 closest distance to " O   HOH Z  44 " =    1.786
peak=    3.947 closest distance to " O   HOH Z 353 " =    2.542
peak=    3.944 closest distance to " CB  THR A  31 " =    1.643
peak=    3.939 closest distance to " O   HOH Z   1 " =    1.723
peak=    3.936 closest distance to " O   HOH Z 250 " =    1.524
peak=    3.927 closest distance to " OG ASER A 258 " =    3.022
peak=    3.925 closest distance to " O   HOH Z 124 " =    2.107
peak=    3.924 closest distance to " CG  PRO A 243 " =    1.059
peak=    3.909 closest distance to " O   HOH Z 158 " =    3.021
peak=    3.883 closest distance to " O   HOH Z 425 " =    1.308
peak=    3.877 closest distance to " O   HOH Z 365 " =    2.686
peak=    3.866 closest distance to " O   HOH Z 203 " =    1.804
peak=    3.860 closest distance to " O   HOH Z 406 " =    1.616
peak=    3.858 closest distance to " O   HOH Z 368 " =    3.486
peak=    3.831 closest distance to " O   HOH Z   1 " =    1.939
peak=    3.827 closest distance to " O   HOH Z  61 " =    1.513
peak=    3.824 closest distance to " CE  LYS A  76 " =    0.870
peak=    3.809 closest distance to " O   HOH Z 248 " =    1.492
peak=    3.807 closest distance to " CB  ASN A  39 " =    0.924
peak=    3.790 closest distance to " CE  LYS A 119 " =    1.196
peak=    3.786 closest distance to " CB  ILE A 120 " =    1.454
peak=    3.780 closest distance to " O   HOH Z 425 " =    2.057
peak=    3.779 closest distance to " CB  SER A   3 " =    1.260
peak=    3.778 closest distance to " NH2AARG A 190 " =    1.898
peak=    3.773 closest distance to " CB  GLU A 152 " =    1.290
peak=    3.765 closest distance to " NH1AARG A 145 " =    1.253
peak=    3.759 closest distance to " N   PHE A 130 " =    1.270
peak=    3.750 closest distance to " O   HOH Z  40 " =    1.541
peak=    3.749 closest distance to " N   ASN A  39 " =    1.259
peak=    3.745 closest distance to " O   HOH Z 132 " =    2.151
peak=    3.741 closest distance to " CB  GLU A  46 " =    1.086
peak=    3.737 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.734 closest distance to " O   HOH Z 188 " =    2.772
peak=    3.727 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    3.726 closest distance to " O   HOH Z 126 " =    1.502
peak=    3.716 closest distance to " N   TYR A 116 " =    1.509
peak=    3.714 closest distance to " OD1 ASN A  69 " =    2.506
peak=    3.711 closest distance to " CB  LEU A 228 " =    1.081
peak=    3.706 closest distance to " CB  TRP A 266 " =    1.149
peak=    3.705 closest distance to " O   HOH Z 422 " =    2.557
peak=    3.696 closest distance to " O   HOH Z 357 " =    1.982
peak=    3.694 closest distance to " O   HOH Z 209 " =    2.189
peak=    3.692 closest distance to " O   HOH Z 261 " =    2.023
peak=    3.689 closest distance to " O   HOH Z  63 " =    1.357
peak=    3.686 closest distance to " CD  LYS A  76 " =    1.794
peak=    3.685 closest distance to " O   HOH Z 325 " =    2.241
peak=    3.678 closest distance to " O   HOH Z 193 " =    1.622
peak=    3.675 closest distance to " CG  GLN A  58 " =    0.996
peak=    3.674 closest distance to " O   HOH Z 411 " =    3.779
peak=    3.673 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.667 closest distance to " CG2 ILE A 120 " =    1.186
peak=    3.661 closest distance to " O   HOH Z   9 " =    1.999
peak=    3.660 closest distance to " CD2 LEU A 297 " =    0.989
peak=    3.654 closest distance to " O   HOH Z 394 " =    3.787
peak=    3.653 closest distance to " O   ASN A  74 " =    1.478
peak=    3.644 closest distance to " CB  TYR A 169 " =    0.924
peak=    3.632 closest distance to " CB  ASN A 187 " =    1.235
peak=    3.629 closest distance to " CA  ASN A 215 " =    1.022
peak=    3.613 closest distance to " O   HOH Z 403 " =    1.480
peak=    3.609 closest distance to " CB  ARG A 139 " =    1.107
peak=    3.597 closest distance to " O   HOH Z 234 " =    3.620
peak=    3.595 closest distance to " N   GLN A 278 " =    1.347
peak=    3.592 closest distance to " CB  PRO A  90 " =    1.142
peak=    3.587 closest distance to " O   HOH Z 286 " =    2.318
peak=    3.583 closest distance to " CB  ALA A 114 " =    1.327
peak=    3.580 closest distance to " CG1BVAL A  72 " =    1.525
peak=    3.560 closest distance to " CB  SER A 212 " =    1.204
peak=    3.559 closest distance to " CB  ASN A 142 " =    0.984
peak=    3.558 closest distance to " CB  GLU A 128 " =    0.962
peak=    3.555 closest distance to " CB  LEU A 300 " =    0.952
peak=    3.548 closest distance to " O   HOH Z  40 " =    2.363
peak=    3.530 closest distance to " O   HOH Z 421 " =    2.145
peak=    3.529 closest distance to " O   HOH Z 128 " =    2.046
peak=    3.516 closest distance to " O   HOH Z 257 " =    2.160
peak=    3.512 closest distance to " O   HOH Z  59 " =    1.582
peak=    3.501 closest distance to " O   HOH Z 180 " =    2.242
peak=    3.500 closest distance to " NE  ARG A  56 " =    3.477
peak=    3.497 closest distance to " O   HOH Z 423 " =    2.316
peak=    3.497 closest distance to " O  BHOH Z 338 " =    2.401
peak=    3.497 closest distance to " O   HOH Z 116 " =    2.833
peak=    3.493 closest distance to " CA  ALA A 233 " =    0.929
peak=    3.491 closest distance to " O   HOH Z 359 " =    1.496
peak=    3.483 closest distance to " O   HOH Z 294 " =    1.495
peak=    3.481 closest distance to " O   HOH Z   3 " =    2.047
peak=    3.480 closest distance to " O   HOH Z 371 " =    2.958
peak=    3.480 closest distance to " O   HOH Z  10 " =    1.702
peak=    3.479 closest distance to " CA  ASP A 124 " =    0.738
peak=    3.474 closest distance to " O   HOH Z 415 " =    3.742
peak=    3.468 closest distance to " O   HOH Z 405 " =    1.288
peak=    3.463 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.462 closest distance to " O   HOH Z  88 " =    2.505
peak=    3.460 closest distance to " O   HOH Z 391 " =    2.890
peak=    3.458 closest distance to " CA  SER A  87 " =    1.076
peak=    3.456 closest distance to " CB  ASN A 215 " =    1.033
peak=    3.449 closest distance to " O   HOH Z 214 " =    2.427
peak=    3.446 closest distance to " O   HOH Z 261 " =    1.661
peak=    3.436 closest distance to " CB  GLN A  89 " =    1.390
peak=    3.425 closest distance to " O   HOH Z 394 " =    1.718
peak=    3.423 closest distance to " O   HOH Z 227 " =    1.924
peak=    3.420 closest distance to " CA  ALA A 299 " =    0.916
peak=    3.419 closest distance to " O   HOH Z 345 " =    1.736
peak=    3.418 closest distance to " O   HOH Z 336 " =    1.756
peak=    3.411 closest distance to " O   HOH Z 156 " =    2.461
peak=    3.411 closest distance to " O   HOH Z 305 " =    3.472
peak=    3.405 closest distance to " O   HOH Z 193 " =    1.969
peak=    3.400 closest distance to " O   HOH Z 178 " =    1.182
peak=    3.399 closest distance to " O   HOH Z 290 " =    0.963
peak=    3.397 closest distance to " CA  ASN A 217 " =    1.091
peak=    3.393 closest distance to " NE2 GLN A  73 " =    3.758
peak=    3.387 closest distance to " CA  ASN A 127 " =    1.092
peak=    3.383 closest distance to " CB  TRP A 179 " =    1.315
peak=    3.382 closest distance to " O   HOH Z 175 " =    2.073
peak=    3.380 closest distance to " CB  ASN A 110 " =    1.040
peak=    3.379 closest distance to " O   HOH Z 344 " =    3.214
peak=    3.378 closest distance to " O   HOH Z 233 " =    2.003
peak=    3.376 closest distance to " CB  HIS A 108 " =    0.815
peak=    3.376 closest distance to " O   HOH Z 213 " =    2.217
peak=    3.376 closest distance to " O   HOH Z 337 " =    3.509
peak=    3.371 closest distance to " N   HIS A  86 " =    1.806
peak=    3.362 closest distance to " O   HOH Z 175 " =    2.119
peak=    3.361 closest distance to " OD2 ASP A 286 " =    3.220
peak=    3.356 closest distance to " CD2 LEU A 255 " =    1.430
peak=    3.353 closest distance to " CB  SER A 273 " =    0.868
peak=    3.352 closest distance to " O   HOH Z 128 " =    1.974
peak=    3.350 closest distance to " CG AARG A 275 " =    1.104
peak=    3.343 closest distance to " O   HOH Z  88 " =    2.460
peak=    3.338 closest distance to " O   HOH Z  40 " =    2.138
peak=    3.335 closest distance to " CA  VAL A 125 " =    1.136
peak=    3.331 closest distance to " N   GLU A   2 " =    1.478
peak=    3.331 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.323 closest distance to " O   HOH Z 386 " =    2.939
peak=    3.323 closest distance to " CB  ALA A   1 " =    4.710
peak=    3.319 closest distance to " CB  ASP A 140 " =    1.033
peak=    3.314 closest distance to " O   HOH Z 265 " =    2.068
peak=    3.314 closest distance to " O   HOH Z  66 " =    2.154
peak=    3.313 closest distance to " CE ALYS A 290 " =    1.252
peak=    3.312 closest distance to " O   HOH Z 285 " =    2.249
peak=    3.308 closest distance to " CB  PHE A 130 " =    0.966
peak=    3.307 closest distance to " O   HOH Z 291 " =    1.423
peak=    3.301 closest distance to " OG BSER A  99 " =    2.417
peak=    3.295 closest distance to " CB  ALA A 114 " =    0.850
peak=    3.292 closest distance to " NH1 ARG A  14 " =    1.227
peak=    3.290 closest distance to " O   HOH Z  21 " =    1.732
peak=    3.287 closest distance to " CD  PRO A 243 " =    1.590
peak=    3.283 closest distance to " CD1 ILE A 263 " =    1.326
peak=    3.282 closest distance to " CE AMET A  47 " =    1.414
peak=    3.280 closest distance to " O   HOH Z  93 " =    2.464
peak=    3.280 closest distance to " O   HOH Z 437 " =    1.455
peak=    3.278 closest distance to " CB  SER A  62 " =    1.242
peak=    3.277 closest distance to " CD  ARG A 269 " =    0.969
peak=    3.275 closest distance to " OG  SER A  62 " =    2.862
peak=    3.273 closest distance to " N   ASP A 162 " =    1.053
peak=    3.271 closest distance to " O   HOH Z 119 " =    4.374
peak=    3.271 closest distance to " CA  ALA A  84 " =    1.259
peak=    3.270 closest distance to " CB  MET A  47 " =    1.240
peak=    3.268 closest distance to " CA  ALA A 129 " =    1.293
peak=    3.264 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.261 closest distance to " O   HOH Z  53 " =    2.496
peak=    3.256 closest distance to " CE1 TYR A 186 " =    1.354
peak=    3.256 closest distance to " O   THR A 220 " =    1.278
peak=    3.256 closest distance to " O   HOH Z 145 " =    3.288
peak=    3.254 closest distance to " CA  ALA A  51 " =    0.970
peak=    3.254 closest distance to " CZ  PHE A  38 " =    1.181
peak=    3.253 closest distance to " CB  THR A 157 " =    1.131
peak=    3.253 closest distance to " NZ  LYS A 119 " =    1.302
peak=    3.249 closest distance to " CB  SER A 216 " =    0.845
peak=    3.246 closest distance to " CG  LEU A 101 " =    1.188
peak=    3.245 closest distance to " O   HOH Z 218 " =    1.667
peak=    3.245 closest distance to " O   HOH Z 345 " =    3.177
peak=    3.243 closest distance to " CG  MET A 113 " =    0.955
peak=    3.241 closest distance to " NH2BARG A 145 " =    2.007
peak=    3.237 closest distance to " NH1BARG A 145 " =    1.304
peak=    3.237 closest distance to " CG  LEU A 167 " =    1.286
peak=    3.233 closest distance to " O   HOH Z 153 " =    1.608
peak=    3.232 closest distance to " C   PHE A  59 " =    0.914
peak=    3.230 closest distance to " O   HOH Z  90 " =    2.159
peak=    3.230 closest distance to " NE2 GLN A  77 " =    3.010
peak=    3.224 closest distance to " O   HOH Z 368 " =    1.961
peak=    3.223 closest distance to " CG2 VAL A 197 " =    1.036
peak=    3.222 closest distance to " N   CYS A 260 " =    0.873
peak=    3.221 closest distance to " OG1 THR A 221 " =    1.248
peak=    3.216 closest distance to " O   HOH Z 280 " =    2.933
peak=    3.210 closest distance to " CG2 ILE A  20 " =    1.508
peak=    3.206 closest distance to " O   ARG A 145 " =    1.731
peak=    3.205 closest distance to " O   HOH Z 172 " =    3.043
peak=    3.201 closest distance to " CB  TYR A 116 " =    0.856
peak=    3.201 closest distance to " CA  THR A 221 " =    1.036
peak=    3.200 closest distance to " O   HOH Z 173 " =    1.894
peak=    3.198 closest distance to " O   HOH Z 389 " =    1.671
peak=    3.196 closest distance to " CB  ASP A 191 " =    1.209
peak=    3.195 closest distance to " O   HOH Z 213 " =    1.943
peak=    3.190 closest distance to " O   HOH Z 153 " =    3.814
peak=    3.189 closest distance to " CD1 LEU A  96 " =    0.735
peak=    3.184 closest distance to " O   HOH Z 244 " =    1.688
peak=    3.183 closest distance to " O   HOH Z 373 " =    1.442
peak=    3.183 closest distance to " CG  MET A 185 " =    1.379
peak=    3.180 closest distance to " CA  ALA A 158 " =    1.240
peak=    3.180 closest distance to " O   HOH Z 286 " =    2.488
peak=    3.169 closest distance to " O   HOH Z 426 " =    1.907
peak=    3.163 closest distance to " O   HOH Z 298 " =    2.556
peak=    3.163 closest distance to " CB  ARG A 219 " =    0.818
peak=    3.163 closest distance to " CA  MET A 105 " =    0.960
peak=    3.159 closest distance to " CA  ARG A  36 " =    0.992
peak=    3.157 closest distance to " O   HOH Z 130 " =    2.397
peak=    3.150 closest distance to " CD2 LEU A 261 " =    1.490
peak=    3.147 closest distance to " O   HOH Z 194 " =    1.854
peak=    3.147 closest distance to " O   HOH Z  30 " =    1.577
peak=    3.145 closest distance to " O   HOH Z 193 " =    1.421
peak=    3.143 closest distance to " CA  PRO A 280 " =    1.277
peak=    3.135 closest distance to " O   HOH Z 188 " =    1.418
peak=    3.134 closest distance to " CA  SER A  95 " =    0.991
peak=    3.130 closest distance to " O   HOH Z 219 " =    2.010
peak=    3.124 closest distance to " OE2 GLU A  53 " =    1.869
peak=    3.122 closest distance to " O   THR A 182 " =    1.471
peak=    3.119 closest distance to " O   HOH Z 260 " =    2.426
peak=    3.111 closest distance to " CG2 THR A 221 " =    1.107
peak=    3.104 closest distance to " O   HOH Z  17 " =    1.622
peak=    3.104 closest distance to " O   HOH Z 371 " =    3.128
peak=    3.104 closest distance to " O   HOH Z 329 " =    4.083
peak=    3.103 closest distance to " CG1 ILE A 151 " =    1.002
peak=    3.099 closest distance to " O   HOH Z 303 " =    2.937
peak=    3.099 closest distance to " CD2 LEU A   5 " =    1.266
peak=    3.096 closest distance to " O   HOH Z 407 " =    2.314
peak=    3.094 closest distance to " CA  THR A 264 " =    0.863
peak=    3.094 closest distance to " O   HOH Z  48 " =    1.561
peak=    3.089 closest distance to " O   HOH Z  28 " =    1.794
peak=    3.085 closest distance to " CB  PHE A 204 " =    0.788
peak=    3.084 closest distance to " N   ASN A 127 " =    1.315
peak=    3.078 closest distance to " O   HOH Z 287 " =    2.248
peak=    3.074 closest distance to " CB  SER A 210 " =    0.725
peak=    3.072 closest distance to " O   HOH Z   7 " =    1.414
peak=    3.071 closest distance to " CB  LYS A 290 " =    1.179
peak=    3.070 closest distance to " O   HOH Z 266 " =    3.379
peak=    3.068 closest distance to " CD1 ILE A 199 " =    1.068
peak=    3.064 closest distance to " CA  ALA A 233 " =    1.645
peak=    3.057 closest distance to " NH1 ARG A 138 " =    1.053
peak=    3.023 closest distance to " O   HOH Z 342 " =    1.433

                           ----------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: 0.925 - 5.686
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.925 - 5.686

peak=   -4.573 closest distance to " O   HOH Z 377 " =    2.032
peak=   -4.563 closest distance to " SG  CYS A 254 " =    3.375
peak=   -4.558 closest distance to " O   PRO A 198 " =    1.279
peak=   -4.545 closest distance to " CD  ARG A 156 " =    2.095
peak=   -4.375 closest distance to " OG BSER A 134 " =    1.317
peak=   -4.230 closest distance to " CG  GLN A  58 " =    1.048
peak=   -4.230 closest distance to " CB  PRO A 243 " =    2.665
peak=   -4.218 closest distance to " C   HIS A 108 " =    1.146
peak=   -4.129 closest distance to " CB  PHE A 192 " =    2.007
peak=   -4.036 closest distance to " CE  MET A 105 " =    2.437
peak=   -4.035 closest distance to " O   HOH Z 372 " =    2.369
peak=   -4.005 closest distance to " CA  VAL A  67 " =    2.968
peak=   -4.004 closest distance to " O   HOH Z 351 " =    1.535
peak=   -4.000 closest distance to " O   HOH Z 198 " =    1.470
peak=   -3.984 closest distance to " CD1 LEU A 255 " =    2.810
peak=   -3.952 closest distance to " O   HOH Z 185 " =    2.233
peak=   -3.931 closest distance to " CB  ALA A  43 " =    2.441
peak=   -3.921 closest distance to " O   VAL A  67 " =    2.670
peak=   -3.916 closest distance to " CB  ASN A  39 " =    2.351
peak=   -3.915 closest distance to " O   HOH Z 266 " =    5.160
peak=   -3.910 closest distance to " OD2 ASP A 191 " =    1.381
peak=   -3.904 closest distance to " O   HOH Z 231 " =    2.154
peak=   -3.890 closest distance to " OD1 ASP A 171 " =    1.551
peak=   -3.868 closest distance to " CG2 ILE A  49 " =    2.791
peak=   -3.857 closest distance to " ND2 ASN A 249 " =    2.147
peak=   -3.844 closest distance to " O   HOH Z 407 " =    2.802
peak=   -3.840 closest distance to " CG  GLN A 223 " =    2.132
peak=   -3.829 closest distance to " CG1 VAL A 112 " =    2.889
peak=   -3.788 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.776 closest distance to " CG2 THR A  18 " =    2.740
peak=   -3.771 closest distance to " CE BMET A  47 " =    1.165
peak=   -3.769 closest distance to " O   HOH Z  60 " =    1.821
peak=   -3.722 closest distance to " O   HOH Z 131 " =    4.055
peak=   -3.718 closest distance to " CG2 ILE A 263 " =    2.253
peak=   -3.717 closest distance to " O   HOH Z 389 " =    2.105
peak=   -3.713 closest distance to " CD2 PHE A  61 " =    2.220
peak=   -3.712 closest distance to " CB  TRP A  85 " =    2.408
peak=   -3.709 closest distance to " CZ  TYR A 169 " =    1.811
peak=   -3.702 closest distance to " N   ALA A  43 " =    2.616
peak=   -3.696 closest distance to " O   HOH Z 429 " =    1.969
peak=   -3.685 closest distance to " O   HOH Z 290 " =    1.098
peak=   -3.680 closest distance to " N   THR A 157 " =    1.494
peak=   -3.661 closest distance to " CZ3 TRP A 179 " =    1.268
peak=   -3.658 closest distance to " O   HOH Z 395 " =    5.082
peak=   -3.649 closest distance to " CD2 TYR A 293 " =    1.858
peak=   -3.644 closest distance to " OD1 ASP A 191 " =    1.777
peak=   -3.640 closest distance to " O   PRO A 243 " =    2.552
peak=   -3.637 closest distance to " CE1 PHE A  59 " =    2.136
peak=   -3.630 closest distance to " ND2 ASN A  45 " =    2.014
peak=   -3.627 closest distance to " CD1 LEU A 101 " =    2.219
peak=   -3.626 closest distance to " CG  PHE A 283 " =    2.626
peak=   -3.615 closest distance to " O   ALA A 161 " =    1.653
peak=   -3.615 closest distance to " O   HOH Z 348 " =    2.163
peak=   -3.598 closest distance to " OD1 ASN A 148 " =    1.502
peak=   -3.596 closest distance to " CD2 LEU A 237 " =    2.820
peak=   -3.586 closest distance to " O   SER A 210 " =    1.966
peak=   -3.583 closest distance to " O   TRP A  70 " =    1.427
peak=   -3.579 closest distance to " O   SER A 135 " =    1.454
peak=   -3.575 closest distance to " O   HOH Z 165 " =    2.242
peak=   -3.566 closest distance to " O   HOH Z 313 " =    1.690
peak=   -3.564 closest distance to " OD1 ASN A 187 " =    1.716
peak=   -3.560 closest distance to " O   HOH Z 298 " =    2.487
peak=   -3.558 closest distance to " OE1 GLN A 183 " =    1.527
peak=   -3.557 closest distance to " O   SER A  22 " =    2.479
peak=   -3.552 closest distance to " OXT GLY A 302 " =    3.060
peak=   -3.546 closest distance to " O   HOH Z 211 " =    1.515
peak=   -3.540 closest distance to " O   ALA A  10 " =    1.622
peak=   -3.533 closest distance to " CA  GLY A 241 " =    2.234
peak=   -3.528 closest distance to " N   ALA A 248 " =    1.612
peak=   -3.526 closest distance to " CE2 PHE A 218 " =    2.373
peak=   -3.523 closest distance to " O   PHE A 218 " =    1.417
peak=   -3.502 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.495 closest distance to " O   VAL A 189 " =    2.620
peak=   -3.482 closest distance to " O   GLU A 152 " =    1.390
peak=   -3.479 closest distance to " CA  GLY A 133 " =    1.995
peak=   -3.473 closest distance to " CE3 TRP A 274 " =    2.264
peak=   -3.470 closest distance to " ND2 ASN A  60 " =    4.078
peak=   -3.468 closest distance to " O   SER A  95 " =    1.472
peak=   -3.464 closest distance to " CA  ASN A 127 " =    1.421
peak=   -3.462 closest distance to " CA  GLY A  57 " =    2.207
peak=   -3.459 closest distance to " O   HOH Z 140 " =    1.503
peak=   -3.459 closest distance to " CB  ALA A   7 " =    2.102
peak=   -3.451 closest distance to " O   HOH Z   9 " =    1.618
peak=   -3.448 closest distance to " ND2 ASN A 187 " =    1.508
peak=   -3.444 closest distance to " C   ALA A 158 " =    1.552
peak=   -3.438 closest distance to " O   HOH Z 123 " =    2.527
peak=   -3.429 closest distance to " O   HOH Z  11 " =    1.804
peak=   -3.429 closest distance to " O   HOH Z  13 " =    1.840
peak=   -3.428 closest distance to " CB  GLN A  11 " =    1.836
peak=   -3.422 closest distance to " O   VAL A 189 " =    1.779
peak=   -3.420 closest distance to " O   HOH Z 385 " =    1.788
peak=   -3.416 closest distance to " O   HOH Z 218 " =    3.610
peak=   -3.415 closest distance to " OG  SER A  63 " =    1.181
peak=   -3.413 closest distance to " O   HOH Z 359 " =    3.145
peak=   -3.411 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.409 closest distance to " CB  SER A 210 " =    1.129
peak=   -3.407 closest distance to " O   HOH Z  90 " =    2.317
peak=   -3.406 closest distance to " NE2 GLN A 278 " =    1.546
peak=   -3.406 closest distance to " OH  TYR A 172 " =    1.817
peak=   -3.400 closest distance to " CB  ALA A 248 " =    2.237
peak=   -3.400 closest distance to " C   ASN A 285 " =    2.258
peak=   -3.393 closest distance to " O   HOH Z  15 " =    1.480
peak=   -3.393 closest distance to " O   ALA A 292 " =    2.060
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.379 closest distance to " N   GLN A  58 " =    1.652
peak=   -3.377 closest distance to " O   HOH Z 369 " =    2.291
peak=   -3.375 closest distance to " O   HOH Z 357 " =    2.153
peak=   -3.375 closest distance to " CB  ASP A 132 " =    2.399
peak=   -3.369 closest distance to " CG1 VAL A 265 " =    2.708
peak=   -3.366 closest distance to " OD1AASN A 224 " =    1.782
peak=   -3.363 closest distance to " O   PRO A 163 " =    1.903
peak=   -3.358 closest distance to " CB  TYR A  15 " =    2.211
peak=   -3.351 closest distance to " O   HOH Z 166 " =    1.904
peak=   -3.350 closest distance to " CG2 THR A 178 " =    2.218
peak=   -3.342 closest distance to " CB  GLN A  55 " =    1.216
peak=   -3.334 closest distance to " O   ALA A  34 " =    2.385
peak=   -3.329 closest distance to " CG  PRO A 243 " =    1.665
peak=   -3.328 closest distance to " O   LYS A  76 " =    1.901
peak=   -3.320 closest distance to " O   HOH Z 351 " =    1.684
peak=   -3.319 closest distance to " OG  SER A  97 " =    2.105
peak=   -3.319 closest distance to " CA  GLY A  98 " =    1.772
peak=   -3.313 closest distance to " CD2 HIS A 207 " =    2.161
peak=   -3.313 closest distance to " O   HOH Z  38 " =    2.061
peak=   -3.309 closest distance to " CZ2 TRP A 274 " =    0.925
peak=   -3.307 closest distance to " C   ALA A 114 " =    2.257
peak=   -3.302 closest distance to " CZ  PHE A  59 " =    1.451
peak=   -3.288 closest distance to " CE2 TYR A  30 " =    2.608
peak=   -3.272 closest distance to " O   HOH Z  52 " =    1.382
peak=   -3.268 closest distance to " O   HOH Z 191 " =    5.686
peak=   -3.267 closest distance to " OE2 GLU A 152 " =    1.239
peak=   -3.266 closest distance to " O   HOH Z 421 " =    2.888
peak=   -3.260 closest distance to " O   HOH Z 281 " =    2.812
peak=   -3.259 closest distance to " O   HOH Z  24 " =    1.348
peak=   -3.259 closest distance to " CE2 PHE A  61 " =    2.642
peak=   -3.259 closest distance to " O   ALA A 180 " =    1.044
peak=   -3.252 closest distance to " O   HOH Z 193 " =    1.399
peak=   -3.248 closest distance to " O   VAL A 125 " =    2.142
peak=   -3.248 closest distance to " O   GLN A 240 " =    1.770
peak=   -3.246 closest distance to " OE1 GLN A  88 " =    1.079
peak=   -3.246 closest distance to " O   HOH Z 166 " =    1.467
peak=   -3.245 closest distance to " N   PHE A  59 " =    1.914
peak=   -3.245 closest distance to " CD2 PHE A 225 " =    1.182
peak=   -3.240 closest distance to " O   GLN A 144 " =    1.396
peak=   -3.240 closest distance to " O   HOH Z 348 " =    1.859
peak=   -3.234 closest distance to " NH2BARG A 275 " =    1.750
peak=   -3.234 closest distance to " CB  ALA A 291 " =    2.011
peak=   -3.232 closest distance to " CA  GLY A 203 " =    2.381
peak=   -3.230 closest distance to " O   HOH Z 318 " =    1.751
peak=   -3.227 closest distance to " O   HOH Z 345 " =    2.024
peak=   -3.221 closest distance to " O   HOH Z 394 " =    1.469
peak=   -3.220 closest distance to " O   HOH Z 288 " =    1.313
peak=   -3.218 closest distance to " CD  GLU A 277 " =    1.370
peak=   -3.217 closest distance to " O   HOH Z  43 " =    1.754
peak=   -3.211 closest distance to " O   HOH Z 265 " =    2.381
peak=   -3.207 closest distance to " O   HOH Z 427 " =    1.550
peak=   -3.207 closest distance to " O   HOH Z 201 " =    2.002
peak=   -3.202 closest distance to " OD2 ASP A 171 " =    1.723
peak=   -3.202 closest distance to " OG  SER A  87 " =    1.394
peak=   -3.197 closest distance to " O   SER A 276 " =    1.674
peak=   -3.194 closest distance to " O   HOH Z 283 " =    2.401
peak=   -3.187 closest distance to " O   HOH Z 253 " =    3.850
peak=   -3.186 closest distance to " O   HOH Z 216 " =    1.421
peak=   -3.183 closest distance to " O   HOH Z 166 " =    2.128
peak=   -3.171 closest distance to " NE2 GLN A 194 " =    1.811
peak=   -3.170 closest distance to " CG2 ILE A 151 " =    2.597
peak=   -3.169 closest distance to " O   HOH Z  60 " =    2.217
peak=   -3.166 closest distance to " OE1 GLN A 223 " =    2.103
peak=   -3.165 closest distance to " CA  GLY A 241 " =    3.076
peak=   -3.161 closest distance to " CG2 VAL A 189 " =    1.991
peak=   -3.160 closest distance to " O   HOH Z 134 " =    3.536
peak=   -3.155 closest distance to " O   HOH Z 137 " =    1.393
peak=   -3.153 closest distance to " CE1 HIS A  81 " =    1.748
peak=   -3.151 closest distance to " CG1 VAL A 268 " =    2.398
peak=   -3.150 closest distance to " O   HOH Z 292 " =    1.588
peak=   -3.150 closest distance to " CG1 VAL A  78 " =    2.624
peak=   -3.147 closest distance to " O   HOH Z 111 " =    1.996
peak=   -3.145 closest distance to " NH2AARG A 275 " =    5.175
peak=   -3.145 closest distance to " OG BSER A 134 " =    1.664
peak=   -3.143 closest distance to " O   HOH Z 213 " =    1.737
peak=   -3.138 closest distance to " OD1 ASN A 301 " =    1.851
peak=   -3.134 closest distance to " O   ASN A 252 " =    1.251
peak=   -3.127 closest distance to " O   VAL A 174 " =    2.203
peak=   -3.119 closest distance to " O   HOH Z  96 " =    4.010
peak=   -3.118 closest distance to " O   GLY A  80 " =    2.391
peak=   -3.116 closest distance to " O   HOH Z 412 " =    3.856
peak=   -3.114 closest distance to " O   HOH Z 423 " =    2.153
peak=   -3.107 closest distance to " N   MET A 188 " =    1.906
peak=   -3.106 closest distance to " CG  ARG A 269 " =    2.207
peak=   -3.102 closest distance to " O   HOH Z 174 " =    2.647
peak=   -3.101 closest distance to " O   HOH Z 219 " =    4.838
peak=   -3.095 closest distance to " O   HOH Z 250 " =    1.340
peak=   -3.091 closest distance to " C   ASP A 272 " =    2.187
peak=   -3.089 closest distance to " N   ALA A 226 " =    1.964
peak=   -3.069 closest distance to " CE  LYS A  76 " =    2.713
peak=   -3.068 closest distance to " OG  SER A 245 " =    1.426
peak=   -3.066 closest distance to " O   HOH Z 189 " =    1.964
peak=   -3.053 closest distance to " CG1 VAL A 197 " =    2.161
peak=   -3.030 closest distance to " CG1AVAL A  41 " =    2.495
peak=   -3.024 closest distance to " N   SER A 276 " =    1.243
peak=   -3.011 closest distance to " CD  GLN A  73 " =    1.184

================= 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    :  0.4280 0.4241   6.228663e+00   6.207377e+00
   1_bss:  0.4182 0.4149   6.219577e+00   6.191375e+00
   1_xyz:  0.2898 0.3222   5.940511e+00   6.001810e+00
   1_adp:  0.2627 0.3379   5.892433e+00   6.041946e+00
   1_occ:  0.2624 0.3379   5.892488e+00   6.042462e+00
   2_bss:  0.2611 0.3363   5.891191e+00   6.040978e+00
   2_xyz:  0.1850 0.2425   5.578144e+00   5.775810e+00
   2_adp:  0.1686 0.2197   5.486233e+00   5.680044e+00
   2_occ:  0.1684 0.2190   5.484571e+00   5.677994e+00
   3_bss:  0.1682 0.2180   5.482025e+00   5.673444e+00
   3_xyz:  0.1378 0.1833   5.309955e+00   5.520072e+00
   3_adp:  0.1290 0.1771   5.260817e+00   5.486504e+00
   3_occ:  0.1288 0.1771   5.260508e+00   5.486178e+00
   4_bss:  0.1289 0.1768   5.258361e+00   5.483255e+00
   4_xyz:  0.1156 0.1637   5.168647e+00   5.411894e+00
   4_adp:  0.1134 0.1606   5.151840e+00   5.398087e+00
   4_occ:  0.1133 0.1606   5.151621e+00   5.397877e+00
   5_bss:  0.1133 0.1606   5.151566e+00   5.397839e+00
   5_xyz:  0.1114 0.1584   5.141062e+00   5.390543e+00
   5_adp:  0.1107 0.1577   5.138861e+00   5.390361e+00
   5_occ:  0.1107 0.1578   5.138624e+00   5.390179e+00
   5_bss:  0.1106 0.1577   5.138577e+00   5.390129e+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:  0.329  29.415  -1.577   1.435   1.639   0.000   0.000   0.000
   1_xyz:  0.329  29.415  -1.577   1.435   1.639   0.000   0.000   0.000
   1_adp:  0.329  29.415  -1.577   1.435   1.639   0.000   0.000   0.000
   1_occ:  0.329  29.415  -1.577   1.435   1.639   0.000   0.000   0.000
   2_bss:  0.335  54.226  -2.392  -0.570   0.264  -0.000   0.000   0.000
   2_xyz:  0.335  54.226  -2.392  -0.570   0.264  -0.000   0.000   0.000
   2_adp:  0.335  54.226  -2.392  -0.570   0.264  -0.000   0.000   0.000
   2_occ:  0.335  54.226  -2.392  -0.570   0.264  -0.000   0.000   0.000
   3_bss:  0.335  54.226  -2.825  -1.864  -0.426  -0.000  -0.000  -0.000
   3_xyz:  0.335  54.226  -2.825  -1.864  -0.426  -0.000  -0.000  -0.000
   3_adp:  0.335  54.226  -2.825  -1.864  -0.426  -0.000  -0.000  -0.000
   3_occ:  0.335  54.226  -2.825  -1.864  -0.426  -0.000  -0.000  -0.000
   4_bss:  0.327  54.226  -3.003  -2.364  -0.659  -0.000  -0.000  -0.000
   4_xyz:  0.327  54.226  -3.003  -2.364  -0.659  -0.000  -0.000  -0.000
   4_adp:  0.327  54.226  -3.003  -2.364  -0.659  -0.000  -0.000  -0.000
   4_occ:  0.327  54.226  -3.003  -2.364  -0.659  -0.000  -0.000  -0.000
   5_bss:  0.327  54.226  -2.772  -2.267  -0.481  -0.000  -0.000  -0.000
   5_xyz:  0.327  54.226  -2.772  -2.267  -0.481  -0.000  -0.000  -0.000
   5_adp:  0.327  54.226  -2.772  -2.267  -0.481  -0.000  -0.000  -0.000
   5_occ:  0.327  54.226  -2.772  -2.267  -0.481  -0.000  -0.000  -0.000
   5_bss:  0.323  54.223  -2.589  -2.156  -0.308  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.807 0.5490  0.7282    52806.700
   1_bss:  46.569 0.5625  0.7611    49456.318
   1_xyz:  32.327 0.7328  0.9494    26846.050
   1_adp:  34.764 0.7035  0.9203    30164.347
   1_occ:  34.846 0.7026  0.9185    30229.642
   2_bss:  34.591 0.7054  0.8790    29890.138
   2_xyz:  23.735 0.8238  0.9885    14798.775
   2_adp:  20.623 0.8560  1.0085    12055.493
   2_occ:  20.570 0.8565  1.0084    11982.839
   3_bss:  20.398 0.8580  0.9806    11802.683
   3_xyz:  16.895 0.8904  0.9915     8460.000
   3_adp:  16.131 0.8973  0.9838     7929.117
   3_occ:  16.126 0.8973  0.9837     7921.395
   4_bss:  16.069 0.8977  0.9732     7856.426
   4_xyz:  14.568 0.9099  0.9822     6687.346
   4_adp:  14.219 0.9131  0.9774     6501.123
   4_occ:  14.215 0.9131  0.9773     6496.209
   5_bss:  14.213 0.9131  0.9834     6497.518
   5_xyz:  13.986 0.9152  0.9825     6380.802
   5_adp:  13.953 0.9156  0.9750     6364.376
   5_occ:  13.949 0.9156  0.9750     6361.156
   5_bss:  13.948 0.9156  0.9805     6361.055
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7896e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7896e-01
   1_xyz:   1.375  0.010  0.088 15.406  0.006  4.106   1.0241e-01
   1_adp:   1.375  0.010  0.088 15.406  0.006  4.106   1.0241e-01
   1_occ:   1.375  0.010  0.088 15.406  0.006  4.106   1.0241e-01
   2_bss:   1.375  0.010  0.088 15.406  0.006  4.106   1.0241e-01
   2_xyz:   1.122  0.008  0.078 14.911  0.005  4.109   7.1220e-02
   2_adp:   1.122  0.008  0.078 14.911  0.005  4.109   7.1220e-02
   2_occ:   1.122  0.008  0.078 14.911  0.005  4.109   7.1220e-02
   3_bss:   1.122  0.008  0.078 14.911  0.005  4.109   7.1220e-02
   3_xyz:   0.926  0.006  0.066 14.692  0.004  4.114   5.1921e-02
   3_adp:   0.926  0.006  0.066 14.692  0.004  4.114   5.1921e-02
   3_occ:   0.926  0.006  0.066 14.692  0.004  4.114   5.1921e-02
   4_bss:   0.926  0.006  0.066 14.692  0.004  4.114   5.1921e-02
   4_xyz:   1.046  0.007  0.076 14.858  0.004  4.110   6.3845e-02
   4_adp:   1.046  0.007  0.076 14.858  0.004  4.110   6.3845e-02
   4_occ:   1.046  0.007  0.076 14.858  0.004  4.110   6.3845e-02
   5_bss:   1.046  0.007  0.076 14.858  0.004  4.110   6.3845e-02
   5_xyz:   0.976  0.007  0.073 14.654  0.004  4.111   5.7267e-02
   5_adp:   0.976  0.007  0.073 14.654  0.004  4.111   5.7267e-02
   5_occ:   0.976  0.007  0.073 14.654  0.004  4.111   5.7267e-02
   5_bss:   0.976  0.007  0.073 14.654  0.004  4.111   5.7267e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.386   2.3983e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.386   2.3983e-01
   1_xyz:  10.457  0.062  0.325 88.207  0.048  1.967   9.4889e-02
   1_adp:  10.457  0.062  0.325 88.207  0.048  1.967   9.4889e-02
   1_occ:  10.457  0.062  0.325 88.207  0.048  1.967   9.4889e-02
   2_bss:  10.457  0.062  0.325 88.207  0.048  1.967   9.4889e-02
   2_xyz:   6.729  0.064  0.261 85.125  0.033  2.350   9.2537e-02
   2_adp:   6.729  0.064  0.261 85.125  0.033  2.350   9.2537e-02
   2_occ:   6.729  0.064  0.261 85.125  0.033  2.350   9.2537e-02
   3_bss:   6.729  0.064  0.261 85.125  0.033  2.350   9.2537e-02
   3_xyz:   7.016  0.044  0.206 80.271  0.029  2.329   3.7766e-02
   3_adp:   7.016  0.044  0.206 80.271  0.029  2.329   3.7766e-02
   3_occ:   7.016  0.044  0.206 80.271  0.029  2.329   3.7766e-02
   4_bss:   7.016  0.044  0.206 80.271  0.029  2.329   3.7766e-02
   4_xyz:   6.817  0.046  0.254 83.361  0.039  2.211   4.9505e-02
   4_adp:   6.817  0.046  0.254 83.361  0.039  2.211   4.9505e-02
   4_occ:   6.817  0.046  0.254 83.361  0.039  2.211   4.9505e-02
   5_bss:   6.817  0.046  0.254 83.361  0.039  2.211   4.9505e-02
   5_xyz:   6.336  0.048  0.244 83.362  0.037  2.319   5.0143e-02
   5_adp:   6.336  0.048  0.244 83.362  0.037  2.319   5.0143e-02
   5_occ:   6.336  0.048  0.244 83.362  0.037  2.319   5.0143e-02
   5_bss:   6.336  0.048  0.244 83.362  0.037  2.319   5.0143e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  93.39   0.00  18.15  71.33   0.00  14.30  93.39   0.99  39.12
   1_occ:  93.39   0.00  18.15  71.33   0.00  14.30  93.39   0.99  39.12
   2_bss:  93.39   0.00  18.15  71.33   0.00  14.30  93.39   0.99  39.12
   2_xyz:  93.39   0.00  18.15  71.33   0.00  14.30  93.39   0.99  39.12
   2_adp:  91.81   0.00  17.53  70.03   0.00  13.48  91.81   5.55  39.55
   2_occ:  91.81   0.00  17.53  70.03   0.00  13.48  91.81   5.55  39.55
   3_bss:  91.81   0.00  17.53  70.03   0.00  13.48  91.81   5.55  39.55
   3_xyz:  91.81   0.00  17.53  70.03   0.00  13.48  91.81   5.55  39.55
   3_adp:  93.53   0.36  17.51  78.27   0.36  13.04  93.53   6.25  41.81
   3_occ:  93.53   0.36  17.51  78.27   0.36  13.04  93.53   6.25  41.81
   4_bss:  93.53   0.36  17.51  78.27   0.36  13.04  93.53   6.25  41.81
   4_xyz:  93.53   0.36  17.51  78.27   0.36  13.04  93.53   6.25  41.81
   4_adp:  93.94   0.23  17.37  86.69   0.23  12.89  93.94   5.60  41.78
   4_occ:  93.94   0.23  17.37  86.69   0.23  12.89  93.94   5.60  41.78
   5_bss:  93.94   0.23  17.37  86.69   0.23  12.89  93.94   5.60  41.78
   5_xyz:  93.94   0.23  17.37  86.69   0.23  12.89  93.94   5.60  41.78
   5_adp:  94.01   0.15  17.17  88.57   0.15  12.69  94.01   5.45  41.54
   5_occ:  94.01   0.15  17.17  88.57   0.15  12.69  94.01   5.45  41.54
   5_bss:  94.00   0.15  17.16  88.56   0.15  12.69  94.00   5.45  41.54
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.253    0.025    0.330
   1_adp:    2.253    0.025    0.330
   1_occ:    2.253    0.025    0.330
   2_bss:    2.253    0.025    0.330
   2_xyz:    1.670    0.015    0.509
   2_adp:    1.670    0.015    0.509
   2_occ:    1.670    0.015    0.509
   3_bss:    1.670    0.015    0.509
   3_xyz:    1.599    0.067    0.588
   3_adp:    1.599    0.067    0.588
   3_occ:    1.599    0.067    0.588
   4_bss:    1.599    0.067    0.588
   4_xyz:    1.432    0.062    0.615
   4_adp:    1.432    0.062    0.615
   4_occ:    1.432    0.062    0.615
   5_bss:    1.432    0.062    0.615
   5_xyz:    1.518    0.054    0.630
   5_adp:    1.518    0.054    0.630
   5_occ:    1.518    0.054    0.630
   5_bss:    1.518    0.054    0.630
------------------------------------------------------------------------

CPU time actual refinement: 336.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/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_272/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_272/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.88 
  Macro-tasks:
    bulk solvent and scale       = 38.16  
    individual site refinement   = 138.42 
    weights calculation          = 30.10  
    collect and process          = 6.66   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 213.47 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 107.18 
    alpha_beta                      = 8.35   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 115.67 
    fmodel                         = 6.69   
    r_factors                      = 0.22   
    phase_errors                   = 10.76  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 252.13 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.761 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    652 calls, 106.85 s
gradients_fft:          597 calls, 102.09 s

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

# Date 2008-01-16 Time 04:26:07 PST -0800 (1200486367.39 s)
Start R-work = 0.4280, R-free = 0.4241 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1763 (no bulk solvent and anisotropic scale)

Start R-work = 0.4182, R-free = 0.4149
Final R-work = 0.1106, R-free = 0.1577