# Date 2008-01-16 Time 06:31:22 PST -0800 (1200493882.26 s)
#phil __OFF__

Command line arguments: "../1178.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5875
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1178

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.6339, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (71.655, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96146
Completeness in resolution range: 0.917518
Completeness with d_max=infinity: 0.914818

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9615

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96146
Completeness in resolution range: 0.917518
Completeness with d_max=infinity: 0.914818

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1985 [2245/2274]  2022   223   9.9%
  bin  2:  4.1985 -  3.3443 [2146/2169]  1931   215  10.0%
  bin  3:  3.3443 -  2.9251 [2118/2143]  1902   216  10.2%
  bin  4:  2.9251 -  2.6592 [2104/2120]  1898   206   9.8%
  bin  5:  2.6592 -  2.4695 [2084/2128]  1880   204   9.8%
  bin  6:  2.4695 -  2.3244 [2081/2109]  1869   212  10.2%
  bin  7:  2.3244 -  2.2084 [2072/2108]  1861   211  10.2%
  bin  8:  2.2084 -  2.1125 [2050/2092]  1848   202   9.9%
  bin  9:  2.1125 -  2.0314 [2034/2107]  1830   204  10.0%
  bin 10:  2.0314 -  1.9615 [ 655/2100]   589    66  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/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: 0.13 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:
        1.65 -     2.30: 23
        2.30 -     2.95: 1649
        2.95 -     3.60: 4501
        3.60 -     4.25: 9155
        4.25 -     4.90: 12857
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.650 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.697 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.763 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.789 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28180 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_1178/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.63395 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4550   r_free= 0.4519   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.260948                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.3488 0.3605      6.5074       6.507|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.3774 0.3631      6.7663      6.7695|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.4195 0.3923      6.6197      6.6096|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.4509 0.4279      6.4711      6.4662|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.4633 0.4679      6.3235      6.3328|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.4986 0.5025      6.2576      6.1871|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.4973 0.4470      6.2205      6.1811|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.5079 0.5159      6.1418      6.1888|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.5299 0.5048       6.142      6.1001|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.5142 0.5615      6.0611      6.1397|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.5195 0.5850      6.0345      5.9854|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.5159 0.5344      5.9304      5.9661|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.5145 0.4660      5.8666      5.8332|
| 14:  2.0104 -  1.9615 0.20    283   25 0.5757 0.4838      5.8098      5.8178|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6835  1456   165  0.73  31.16   0.84     0.76      60228.78|
|  2:  4.6835 -  3.7359  1395   151  0.74  31.95   0.92     0.82      86781.47|
|  3:  3.7359 -  3.2691  1372   152  0.64  40.78   0.91     0.80      96482.31|
|  4:  3.2691 -  2.9727  1364   149  0.53  49.11   0.91     0.73      90843.13|
|  5:  2.9727 -  2.7610  1353   151  0.46  55.22   0.89     0.64      76122.92|
|  6:  2.7610 -  2.5991  1353   156  0.43  57.69   0.90     0.61      65840.06|
|  7:  2.5991 -  2.4695  1340   140  0.43  57.76   0.91     0.58      57400.90|
|  8:  2.4695 -  2.3624  1332   154  0.39  60.71   0.88     0.57      56142.12|
|  9:  2.3624 -  2.2718  1343   152  0.34  64.80   0.92     0.50      53998.50|
| 10:  2.2718 -  2.1936  1322   149  0.27  70.07   0.92     0.40      55481.83|
| 11:  2.1936 -  2.1252  1330   134  0.20  75.04   0.92     0.30      52923.38|
| 12:  2.1252 -  2.0646  1320   159  0.17  77.12   0.91     0.29      49876.97|
| 13:  2.0646 -  2.0104  1067   122  0.22  73.61   0.93     0.36      40884.36|
| 14:  2.0104 -  1.9615   283    25  0.30  67.39   0.86     0.48      30202.44|
|alpha:            min =        0.29 max =            0.82 mean =         0.57|
|beta:             min =    30202.44 max =        96482.31 mean =     64836.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.88|
|phase err.(test): min =        0.00 max =           89.98 mean =        56.96|
|-----------------------------------------------------------------------------|

============================== 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 = 9.406004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.242   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.889324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.860   (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 |  1.650 -  1.975:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.975 -  2.300:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.300 -  2.625:       51 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.625 -  2.950:     1598 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.950 -  3.275:     1904 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.275 -  3.600:     2597 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.600 -  3.925:     4711 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.925 -  4.250:     4444 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.250 -  4.575:     5849 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.575 -  4.900:     7008 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.650 |       0.414 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4550   r_free= 0.4519   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.260948                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4478   r_free= 0.4448   ksol= 0.30   Bsol= 35.72   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.37,1.73,1.07,0.00,0.00,0.00); trace/3= 1.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.256905                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.320927              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.395   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.266331              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.462   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4478      final r-factor (work) = 0.3440          |
| start r-factor (free) = 0.4448      final r-factor (free) = 0.3802          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0703 = 7.32 * 0.50 * 6.2536 + 1.00 * 0.1791                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5561 = 7.32 * 0.50 * 6.1323 + 1.00 * 0.1090                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3440      final r-factor (work) = 0.3125          |
| start r-factor (free) = 0.3802      final r-factor (free) = 0.3870          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7717 = 1.27 * 1.00 * 6.1323 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6425 = 1.27 * 1.00 * 6.0202 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.68  18.89    None  None   None       |
|    all(noH): 2823   0      0.00    109.68  18.89    None  None   None       |
|    Sol.    : 438    0      0.00    109.68  39.98    None  None   None       |
|    Mac.    : 2385   0      0.00    88.39   15.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.968: 1036   |   5:    54.840 -  65.808:   70        |
|      1:    10.968 -  21.936:  945   |   6:    65.808 -  76.776:   39        |
|      2:    21.936 -  32.904:  419   |   7:    76.776 -  87.744:   12        |
|      3:    32.904 -  43.872:  188   |   8:    87.744 -  98.712:    4        |
|      4:    43.872 -  54.840:  108   |   9:    98.712 - 109.680:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3125 r_free = 0.3870             target_work(ml) = 6.029         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3122 r_free = 0.3877             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3122   r_free= 0.3877   ksol= 0.30   Bsol= 35.72   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.37,1.73,1.07,0.00,0.00,0.00); trace/3= 1.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.028060                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3114   r_free= 0.3866   ksol= 0.33   Bsol= 68.31   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.74,0.05,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.028383                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.678269              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.768  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3114      final r-factor (work) = 0.2341          |
| start r-factor (free) = 0.3866      final r-factor (free) = 0.2996          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2106 = 6.68 * 0.50 * 6.0200 + 1.00 * 0.1090                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8993 = 6.68 * 0.50 * 5.9347 + 1.00 * 0.0827                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2341      final r-factor (work) = 0.2137          |
| start r-factor (free) = 0.2996      final r-factor (free) = 0.2744          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7326 = 0.63 * 1.00 * 5.9347 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6141 = 0.63 * 1.00 * 5.7563 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.20  18.30    None  None   None       |
|    all(noH): 2823   0      0.00    106.20  18.30    None  None   None       |
|    Sol.    : 438    0      5.39    106.20  41.93    None  None   None       |
|    Mac.    : 2385   0      0.00    85.14   13.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.620: 1077   |   5:    53.101 -  63.721:   88        |
|      1:    10.620 -  21.240: 1006   |   6:    63.721 -  74.341:   36        |
|      2:    21.240 -  31.860:  287   |   7:    74.341 -  84.961:   16        |
|      3:    31.860 -  42.481:  198   |   8:    84.961 -  95.581:    5        |
|      4:    42.481 -  53.101:  108   |   9:    95.581 - 106.201:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2137 r_free = 0.2744             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2136 r_free = 0.2744             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2136   r_free= 0.2744   ksol= 0.33   Bsol= 68.31   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,0.74,0.05,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.712749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2132   r_free= 0.2732   ksol= 0.33   Bsol= 68.31   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.61,-1.14,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.711296                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.157204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.256   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.458781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.088  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2132      final r-factor (work) = 0.1691          |
| start r-factor (free) = 0.2732      final r-factor (free) = 0.2168          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1740 = 3.16 * 0.50 * 5.7591 + 1.00 * 0.0827                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9292 = 3.16 * 0.50 * 5.6216 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1691      final r-factor (work) = 0.1554          |
| start r-factor (free) = 0.2168      final r-factor (free) = 0.2061          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2128 = 1.46 * 1.00 * 5.6216 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9763 = 1.46 * 1.00 * 5.4583 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.69  18.85    None  None   None       |
|    all(noH): 2823   0      0.00    115.69  18.85    None  None   None       |
|    Sol.    : 438    0      5.12    109.25  47.18    None  None   None       |
|    Mac.    : 2385   0      0.00    115.69  13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.569: 1308   |   5:    57.844 -  69.413:   68        |
|      1:    11.569 -  23.138:  906   |   6:    69.413 -  80.982:   56        |
|      2:    23.138 -  34.707:  197   |   7:    80.982 -  92.551:   24        |
|      3:    34.707 -  46.275:  137   |   8:    92.551 - 104.120:    7        |
|      4:    46.275 -  57.844:  114   |   9:   104.120 - 115.689:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1554 r_free = 0.2061             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1553 r_free = 0.2060             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1553   r_free= 0.2060   ksol= 0.33   Bsol= 68.31   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.61,-1.14,-0.00,-0.00,-0.00); trace/3= -0.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.431861                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1555   r_free= 0.2061   ksol= 0.33   Bsol= 71.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.39,-1.67,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.433512                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.166935              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.408265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.021  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1555      final r-factor (work) = 0.1309          |
| start r-factor (free) = 0.2061      final r-factor (free) = 0.1805          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7049 = 3.17 * 0.50 * 5.4626 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5547 = 3.17 * 0.50 * 5.3614 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1805      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2027 = 0.41 * 1.00 * 5.3614 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1625 = 0.41 * 1.00 * 5.2699 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    114.99  18.00    None  None   None       |
|    all(noH): 2823   0      1.49    114.99  18.00    None  None   None       |
|    Sol.    : 438    0      4.87    100.65  44.50    None  None   None       |
|    Mac.    : 2385   0      1.49    114.99  13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.493 -  12.843: 1581   |   5:    58.241 -  69.591:   66        |
|      1:    12.843 -  24.192:  710   |   6:    69.591 -  80.940:   40        |
|      2:    24.192 -  35.542:  171   |   7:    80.940 -  92.290:   17        |
|      3:    35.542 -  46.891:  121   |   8:    92.290 - 103.640:    3        |
|      4:    46.891 -  58.241:  109   |   9:   103.640 - 114.989:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1729             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1254 r_free = 0.1728             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1728   ksol= 0.33   Bsol= 71.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.39,-1.67,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248543                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1731   ksol= 0.33   Bsol= 63.99   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.39,-1.67,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.251294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.618161              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268608              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.680  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1731      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3299 = 1.62 * 0.50 * 5.2710 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2949 = 1.62 * 0.50 * 5.2457 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4199 = 0.27 * 1.00 * 5.2457 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4143 = 0.27 * 1.00 * 5.2303 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    111.71  17.36    None  None   None       |
|    all(noH): 2823   0      1.81    111.71  17.36    None  None   None       |
|    Sol.    : 438    0      4.72    92.88   41.88    None  None   None       |
|    Mac.    : 2385   0      1.81    111.71  12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.806 -  12.796: 1616   |   5:    56.758 -  67.748:   56        |
|      1:    12.796 -  23.787:  688   |   6:    67.748 -  78.739:   32        |
|      2:    23.787 -  34.777:  175   |   7:    78.739 -  89.729:   11        |
|      3:    34.777 -  45.767:  124   |   8:    89.729 - 100.719:    2        |
|      4:    45.767 -  56.758:  114   |   9:   100.719 - 111.710:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1225 r_free = 0.1683             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1682             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1682   ksol= 0.33   Bsol= 63.99   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.39,-1.67,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226356                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.1010 0.1291      5.3987      5.5639|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.0902 0.1095      5.4665      5.6645|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.1131 0.1731      5.5191      5.9151|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.1411 0.1614      5.5457      5.6627|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.1494 0.1976      5.4217      5.5938|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.1379 0.2059      5.2856      5.5061|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.1353 0.1724      5.2284       5.406|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.1291 0.1810      5.1246      5.3456|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.1291 0.2086      5.1029      5.3742|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.1248 0.1733      5.0365      5.2909|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.1247 0.1883      4.9917      5.2678|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.1272 0.2018      4.9453      5.2271|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.1281 0.1757      4.8601      5.0387|
| 14:  2.0104 -  1.9615 0.20    283   25 0.1208 0.1871      4.7169      5.0115|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6835  1456   165  0.94   9.07   0.97     0.94       7094.23|
|  2:  4.6835 -  3.7359  1395   151  0.95   8.20   1.01     0.99       9239.63|
|  3:  3.7359 -  3.2691  1372   152  0.93  12.41   1.02     1.02      11389.38|
|  4:  3.2691 -  2.9727  1364   149  0.90  16.23   1.00     0.97      12205.63|
|  5:  2.9727 -  2.7610  1353   151  0.88  17.94   0.99     0.97      10065.22|
|  6:  2.7610 -  2.5991  1353   156  0.89  17.44   0.99     0.96       8050.12|
|  7:  2.5991 -  2.4695  1340   140  0.90  16.47   0.99     0.97       6895.85|
|  8:  2.4695 -  2.3624  1332   154  0.89  16.90   1.00     0.96       6014.76|
|  9:  2.3624 -  2.2718  1343   152  0.89  17.61   1.00     0.96       5704.22|
| 10:  2.2718 -  2.1936  1322   149  0.90  16.51   0.99     0.95       5050.19|
| 11:  2.1936 -  2.1252  1330   134  0.89  17.29   0.99     0.94       4707.52|
| 12:  2.1252 -  2.0646  1320   159  0.89  17.65   1.00     0.99       4623.00|
| 13:  2.0646 -  2.0104  1067   122  0.88  18.23   0.99     0.98       3903.42|
| 14:  2.0104 -  1.9615   283    25  0.89  17.37   0.98     0.95       2926.98|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2926.98 max =        12205.63 mean =      7314.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.45|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1682   ksol= 0.32   Bsol= 58.52   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.61,-1.73,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226181                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1682   ksol= 0.32   Bsol= 58.52   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.61,-1.73,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226181                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.1008 0.1285      5.3964      5.5597|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.0898 0.1093      5.4634      5.6606|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.1130 0.1730      5.5178      5.9151|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.1412 0.1611       5.546      5.6621|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.1496 0.1978      5.4226      5.5946|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.1380 0.2059      5.2861      5.5063|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.1354 0.1726      5.2291      5.4063|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.1291 0.1811      5.1251      5.3466|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.1292 0.2088      5.1032      5.3757|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.1249 0.1731      5.0372       5.292|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.1248 0.1883      4.9917      5.2669|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.1272 0.2022      4.9461      5.2286|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.1281 0.1756      4.8605      5.0381|
| 14:  2.0104 -  1.9615 0.20    283   25 0.1209 0.1865      4.7166      5.0093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6835  1456   165  0.94   9.02   0.97     0.94       7048.45|
|  2:  4.6835 -  3.7359  1395   151  0.95   8.15   1.00     0.99       9172.53|
|  3:  3.7359 -  3.2691  1372   152  0.93  12.35   1.02     1.02      11333.94|
|  4:  3.2691 -  2.9727  1364   149  0.90  16.22   1.00     0.97      12198.99|
|  5:  2.9727 -  2.7610  1353   151  0.88  17.92   0.99     0.97      10067.59|
|  6:  2.7610 -  2.5991  1353   156  0.89  17.44   0.99     0.96       8057.39|
|  7:  2.5991 -  2.4695  1340   140  0.90  16.47   0.99     0.96       6903.00|
|  8:  2.4695 -  2.3624  1332   154  0.89  16.92   0.99     0.95       6025.99|
|  9:  2.3624 -  2.2718  1343   152  0.89  17.62   0.99     0.95       5715.48|
| 10:  2.2718 -  2.1936  1322   149  0.90  16.52   0.98     0.94       5062.00|
| 11:  2.1936 -  2.1252  1330   134  0.89  17.30   0.98     0.93       4713.85|
| 12:  2.1252 -  2.0646  1320   159  0.89  17.67   0.99     0.98       4631.12|
| 13:  2.0646 -  2.0104  1067   122  0.88  18.22   0.98     0.97       3902.42|
| 14:  2.0104 -  1.9615   283    25  0.89  17.36   0.97     0.94       2919.32|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2919.32 max =        12198.99 mean =      7305.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.44|
|phase err.(test): min =        0.00 max =           89.40 mean =        14.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    111.64  17.30    None  None   None       |
|    all(noH): 2823   0      1.74    111.64  17.30    None  None   None       |
|    Sol.    : 438    0      4.66    92.81   41.81    None  None   None       |
|    Mac.    : 2385   0      1.74    111.64  12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.741 -  12.732: 1616   |   5:    56.693 -  67.683:   56        |
|      1:    12.732 -  23.722:  688   |   6:    67.683 -  78.674:   32        |
|      2:    23.722 -  34.712:  175   |   7:    78.674 -  89.664:   11        |
|      3:    34.712 -  45.703:  124   |   8:    89.664 - 100.655:    2        |
|      4:    45.703 -  56.693:  114   |   9:   100.655 - 111.645:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 5.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 336
   mapped sites are within: 0.706 - 5.853

peak=    5.827 closest distance to " CB  GLN A 223 " =    1.500
peak=    5.529 closest distance to " CG  PRO A  54 " =    1.281
peak=    5.529 closest distance to " O   HOH Z 111 " =    2.141
peak=    5.511 closest distance to " CB  SER A  63 " =    1.395
peak=    5.403 closest distance to " NH2AARG A 102 " =    1.063
peak=    5.107 closest distance to " CG  PRO A 213 " =    1.292
peak=    5.099 closest distance to " CG  PRO A  90 " =    1.149
peak=    5.026 closest distance to " CG  PRO A 280 " =    0.849
peak=    5.001 closest distance to " CG  PRO A 198 " =    1.358
peak=    4.700 closest distance to " O   HOH Z  15 " =    2.063
peak=    4.695 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.652 closest distance to " O   HOH Z 247 " =    1.504
peak=    4.651 closest distance to " O   HOH Z 214 " =    1.150
peak=    4.616 closest distance to " CB  PRO A  54 " =    0.864
peak=    4.599 closest distance to " O   HOH Z 126 " =    1.700
peak=    4.573 closest distance to " CB  GLU A 128 " =    1.143
peak=    4.570 closest distance to " O   PRO A 198 " =    1.540
peak=    4.556 closest distance to " O   HOH Z 207 " =    1.877
peak=    4.463 closest distance to " NH2 ARG A 156 " =    1.267
peak=    4.461 closest distance to " O   HOH Z 134 " =    1.508
peak=    4.412 closest distance to " CA  TYR A  30 " =    1.007
peak=    4.397 closest distance to " O   HOH Z  40 " =    1.864
peak=    4.396 closest distance to " O   HOH Z 232 " =    2.228
peak=    4.386 closest distance to " O   HOH Z  80 " =    1.879
peak=    4.368 closest distance to " CB  LEU A 228 " =    1.106
peak=    4.338 closest distance to " O   HOH Z 132 " =    1.140
peak=    4.325 closest distance to " O   HOH Z  67 " =    1.910
peak=    4.319 closest distance to " O   ASP A 132 " =    3.896
peak=    4.311 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.279 closest distance to " O   HOH Z 298 " =    1.848
peak=    4.273 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.259 closest distance to " O   HOH Z 193 " =    2.140
peak=    4.256 closest distance to " CB  VAL A 202 " =    1.600
peak=    4.253 closest distance to " O   HOH Z 132 " =    2.121
peak=    4.242 closest distance to " CD  ARG A 269 " =    0.909
peak=    4.232 closest distance to " O   HOH Z 112 " =    1.538
peak=    4.204 closest distance to " CA  ALA A  21 " =    1.300
peak=    4.196 closest distance to " O   HOH Z  48 " =    1.623
peak=    4.190 closest distance to " CB  SER A   3 " =    1.440
peak=    4.178 closest distance to " O   HOH Z 163 " =    1.744
peak=    4.175 closest distance to " O   HOH Z 389 " =    1.940
peak=    4.149 closest distance to " O   HOH Z 236 " =    1.959
peak=    4.143 closest distance to " O   HOH Z 368 " =    2.021
peak=    4.142 closest distance to " N   ASN A  39 " =    1.326
peak=    4.119 closest distance to " CG2 THR A 221 " =    0.914
peak=    4.108 closest distance to " OD2 ASP A 286 " =    2.975
peak=    4.098 closest distance to " O   HOH Z 374 " =    2.643
peak=    4.088 closest distance to " O   HOH Z 426 " =    1.517
peak=    4.071 closest distance to " O   HOH Z 132 " =    2.564
peak=    4.065 closest distance to " O   HOH Z  47 " =    1.486
peak=    4.057 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.047 closest distance to " CB  PRO A 198 " =    0.995
peak=    4.040 closest distance to " CA  ASP A 191 " =    0.816
peak=    4.025 closest distance to " O   HOH Z 272 " =    1.942
peak=    4.016 closest distance to " O   HOH Z  59 " =    2.479
peak=    4.001 closest distance to " O   HOH Z 108 " =    1.488
peak=    3.997 closest distance to " CG1 ILE A  33 " =    1.320
peak=    3.986 closest distance to " CD1 LEU A 300 " =    1.268
peak=    3.986 closest distance to " O   HOH Z  61 " =    1.727
peak=    3.983 closest distance to " CB  GLU A 277 " =    3.727
peak=    3.969 closest distance to " CB  TYR A 169 " =    0.874
peak=    3.967 closest distance to " CA  GLU A 152 " =    0.884
peak=    3.966 closest distance to " OE1 GLN A  11 " =    1.937
peak=    3.949 closest distance to " CB  PRO A  54 " =    1.348
peak=    3.942 closest distance to " O   HOH Z 189 " =    2.284
peak=    3.933 closest distance to " CB  ASN A 148 " =    1.165
peak=    3.932 closest distance to " CD BLYS A 290 " =    0.989
peak=    3.929 closest distance to " O   HOH Z 156 " =    3.422
peak=    3.927 closest distance to " O   HOH Z 425 " =    1.568
peak=    3.926 closest distance to " O   HOH Z  49 " =    2.374
peak=    3.922 closest distance to " O   HOH Z  20 " =    2.075
peak=    3.917 closest distance to " CA  GLU A 152 " =    1.574
peak=    3.916 closest distance to " O   HOH Z  78 " =    2.256
peak=    3.910 closest distance to " OD1 ASN A 217 " =    1.624
peak=    3.896 closest distance to " CB  TRP A 266 " =    0.897
peak=    3.895 closest distance to " CD  LYS A 119 " =    1.379
peak=    3.892 closest distance to " O   HOH Z  30 " =    1.596
peak=    3.889 closest distance to " CB  ILE A 199 " =    0.996
peak=    3.889 closest distance to " O   HOH Z 316 " =    3.060
peak=    3.883 closest distance to " O   HOH Z 260 " =    1.337
peak=    3.882 closest distance to " CA  ARG A  36 " =    1.180
peak=    3.875 closest distance to " O   HOH Z 183 " =    1.648
peak=    3.874 closest distance to " CB  ARG A 190 " =    1.782
peak=    3.870 closest distance to " CZ  PHE A 218 " =    1.044
peak=    3.858 closest distance to " CD  ARG A 159 " =    0.829
peak=    3.856 closest distance to " O   HOH Z 369 " =    2.172
peak=    3.846 closest distance to " O   HOH Z 124 " =    1.374
peak=    3.843 closest distance to " CG2 VAL A  78 " =    1.005
peak=    3.840 closest distance to " CB  MET A  47 " =    1.045
peak=    3.839 closest distance to " O   SER A  87 " =    2.138
peak=    3.838 closest distance to " OD1 ASN A  69 " =    2.518
peak=    3.836 closest distance to " CZ  PHE A 192 " =    0.958
peak=    3.829 closest distance to " O   HOH Z 344 " =    3.175
peak=    3.819 closest distance to " CB  SER A 216 " =    0.813
peak=    3.818 closest distance to " CB  TRP A 179 " =    1.407
peak=    3.812 closest distance to " O   HOH Z 394 " =    1.694
peak=    3.808 closest distance to " CA  ASP A 124 " =    0.780
peak=    3.807 closest distance to " CB  ARG A  79 " =    1.315
peak=    3.804 closest distance to " O   HOH Z 135 " =    1.967
peak=    3.800 closest distance to " O   HOH Z 403 " =    1.804
peak=    3.796 closest distance to " O   HOH Z 243 " =    1.268
peak=    3.791 closest distance to " CD1 TRP A 266 " =    1.241
peak=    3.790 closest distance to " O   HOH Z 411 " =    3.286
peak=    3.788 closest distance to " O   HOH Z 221 " =    1.545
peak=    3.786 closest distance to " O   HOH Z 387 " =    2.636
peak=    3.779 closest distance to " O   HOH Z 192 " =    1.894
peak=    3.774 closest distance to " O   HOH Z 227 " =    1.736
peak=    3.765 closest distance to " NH1 ARG A  56 " =    1.236
peak=    3.757 closest distance to " O   HOH Z 313 " =    2.093
peak=    3.745 closest distance to " NZ  LYS A 117 " =    3.235
peak=    3.744 closest distance to " O   HOH Z  97 " =    1.978
peak=    3.736 closest distance to " O   HOH Z  88 " =    3.643
peak=    3.736 closest distance to " C   SER A  32 " =    1.053
peak=    3.734 closest distance to " O   TRP A 274 " =    1.627
peak=    3.718 closest distance to " CA  THR A 221 " =    0.886
peak=    3.718 closest distance to " CG1 VAL A 153 " =    1.019
peak=    3.716 closest distance to " CA  GLN A 223 " =    0.980
peak=    3.714 closest distance to " O   HOH Z  54 " =    2.231
peak=    3.698 closest distance to " CB  VAL A 265 " =    1.204
peak=    3.694 closest distance to " CB  SER A 141 " =    0.987
peak=    3.692 closest distance to " CG  ARG A  66 " =    2.575
peak=    3.691 closest distance to " CB  PHE A  16 " =    1.008
peak=    3.683 closest distance to " CA  MET A  40 " =    1.085
peak=    3.659 closest distance to " O   HOH Z 108 " =    2.158
peak=    3.654 closest distance to " NH2BARG A 145 " =    2.120
peak=    3.647 closest distance to " O   HOH Z  39 " =    1.220
peak=    3.642 closest distance to " O   THR A 251 " =    1.290
peak=    3.642 closest distance to " O   HOH Z  11 " =    1.262
peak=    3.640 closest distance to " CG2 VAL A 257 " =    0.913
peak=    3.635 closest distance to " O   HOH Z 142 " =    1.596
peak=    3.629 closest distance to " O   HOH Z 345 " =    3.410
peak=    3.617 closest distance to " CB  TRP A 123 " =    1.090
peak=    3.616 closest distance to " OE1 GLN A  58 " =    1.293
peak=    3.614 closest distance to " O   HOH Z 215 " =    1.553
peak=    3.614 closest distance to " O   HOH Z 437 " =    1.625
peak=    3.613 closest distance to " O   HOH Z  21 " =    1.727
peak=    3.612 closest distance to " O   HOH Z 279 " =    2.418
peak=    3.608 closest distance to " O   HOH Z  19 " =    2.296
peak=    3.589 closest distance to " O   MET A 105 " =    1.971
peak=    3.584 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.568 closest distance to " O   HOH Z 295 " =    1.459
peak=    3.565 closest distance to " O   HOH Z 423 " =    1.867
peak=    3.559 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.558 closest distance to " O   HOH Z 209 " =    2.409
peak=    3.557 closest distance to " O   HOH Z 128 " =    2.290
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.109
peak=    3.550 closest distance to " CG2BVAL A  41 " =    0.977
peak=    3.549 closest distance to " O   HOH Z 352 " =    1.896
peak=    3.542 closest distance to " CG AARG A 275 " =    1.113
peak=    3.542 closest distance to " CD2 LEU A 255 " =    1.449
peak=    3.541 closest distance to " O   HOH Z 332 " =    1.556
peak=    3.537 closest distance to " CB  ARG A 139 " =    0.962
peak=    3.536 closest distance to " O   HOH Z 261 " =    1.916
peak=    3.533 closest distance to " OD1 ASP A 238 " =    0.912
peak=    3.521 closest distance to " CB  LEU A 143 " =    1.035
peak=    3.516 closest distance to " CB  ASN A 187 " =    1.048
peak=    3.515 closest distance to " O   HOH Z 118 " =    1.711
peak=    3.512 closest distance to " CB  MET A  40 " =    0.745
peak=    3.507 closest distance to " O   HOH Z  22 " =    2.533
peak=    3.499 closest distance to " O   HOH Z 128 " =    2.297
peak=    3.498 closest distance to " CB  ASP A 124 " =    0.780
peak=    3.496 closest distance to " ND2 ASN A 187 " =    1.559
peak=    3.496 closest distance to " CZ  PHE A 208 " =    1.095
peak=    3.493 closest distance to " O   HOH Z 368 " =    2.513
peak=    3.492 closest distance to " CB  ALA A 248 " =    1.016
peak=    3.488 closest distance to " CA  GLY A 196 " =    0.971
peak=    3.487 closest distance to " O   HOH Z 116 " =    1.747
peak=    3.486 closest distance to " O   HOH Z 427 " =    3.095
peak=    3.481 closest distance to " O   HOH Z 154 " =    1.318
peak=    3.478 closest distance to " NZ  LYS A  76 " =    1.389
peak=    3.478 closest distance to " NE2 HIS A 115 " =    0.924
peak=    3.473 closest distance to " CA  ALA A 160 " =    0.888
peak=    3.473 closest distance to " CG2 VAL A 197 " =    1.217
peak=    3.472 closest distance to " CA  GLN A  88 " =    1.341
peak=    3.463 closest distance to " O   HOH Z 193 " =    2.302
peak=    3.459 closest distance to " O   HOH Z 433 " =    1.478
peak=    3.458 closest distance to " O   HOH Z  87 " =    2.641
peak=    3.456 closest distance to " CA  ALA A  51 " =    0.913
peak=    3.448 closest distance to " CB  ASP A 140 " =    0.706
peak=    3.446 closest distance to " CD  LYS A 166 " =    1.419
peak=    3.446 closest distance to " O   HOH Z 186 " =    1.181
peak=    3.444 closest distance to " O   HOH Z 263 " =    2.205
peak=    3.440 closest distance to " O   HOH Z 197 " =    2.071
peak=    3.432 closest distance to " O   HOH Z 404 " =    1.460
peak=    3.426 closest distance to " OD1 ASP A 231 " =    1.858
peak=    3.422 closest distance to " O   HOH Z 196 " =    1.015
peak=    3.412 closest distance to " O   HOH Z 434 " =    1.460
peak=    3.410 closest distance to " O   HOH Z 284 " =    3.039
peak=    3.409 closest distance to " O   HOH Z 281 " =    4.055
peak=    3.405 closest distance to " O   HOH Z 377 " =    1.392
peak=    3.405 closest distance to " O   HOH Z 126 " =    1.778
peak=    3.404 closest distance to " CA  ASP A 140 " =    1.277
peak=    3.404 closest distance to " O   HOH Z 147 " =    1.725
peak=    3.400 closest distance to " O   HOH Z 156 " =    2.458
peak=    3.400 closest distance to " O   HOH Z 104 " =    3.090
peak=    3.400 closest distance to " NE AARG A 275 " =    1.446
peak=    3.390 closest distance to " CD  PRO A 280 " =    0.986
peak=    3.390 closest distance to " O   HOH Z 102 " =    1.297
peak=    3.384 closest distance to " O   HOH Z 406 " =    1.592
peak=    3.383 closest distance to " NH1 ARG A 269 " =    0.791
peak=    3.376 closest distance to " CB  ALA A 154 " =    1.363
peak=    3.373 closest distance to " CB  ASN A 285 " =    0.901
peak=    3.369 closest distance to " NH2AARG A 190 " =    1.545
peak=    3.369 closest distance to " O   HOH Z 383 " =    2.012
peak=    3.360 closest distance to " CB  ILE A 120 " =    1.229
peak=    3.358 closest distance to " CA  LEU A 282 " =    1.071
peak=    3.354 closest distance to " O   HOH Z  63 " =    1.816
peak=    3.353 closest distance to " C   GLY A  80 " =    1.165
peak=    3.346 closest distance to " CA  ILE A 263 " =    0.965
peak=    3.343 closest distance to " CG  ASP A 231 " =    1.091
peak=    3.341 closest distance to " OG  SER A  97 " =    3.574
peak=    3.341 closest distance to " O   HOH Z 346 " =    1.505
peak=    3.340 closest distance to " NH1AARG A 145 " =    0.978
peak=    3.337 closest distance to " N   TYR A  15 " =    0.789
peak=    3.334 closest distance to " CA  GLU A  46 " =    0.772
peak=    3.333 closest distance to " CD  ARG A  14 " =    1.288
peak=    3.333 closest distance to " O   HOH Z   6 " =    2.184
peak=    3.330 closest distance to " CA  ARG A 195 " =    1.156
peak=    3.327 closest distance to " O   HOH Z 357 " =    2.010
peak=    3.324 closest distance to " O   HOH Z 155 " =    2.933
peak=    3.323 closest distance to " CD  ARG A 219 " =    0.952
peak=    3.323 closest distance to " CB  ALA A 242 " =    0.891
peak=    3.322 closest distance to " O   HOH Z  50 " =    3.536
peak=    3.320 closest distance to " O   HOH Z  54 " =    1.695
peak=    3.319 closest distance to " CB  ASN A 148 " =    1.707
peak=    3.315 closest distance to " O   HOH Z 214 " =    1.736
peak=    3.315 closest distance to " O   HOH Z 287 " =    1.801
peak=    3.312 closest distance to " ND1 HIS A  81 " =    1.595
peak=    3.302 closest distance to " O   HOH Z 223 " =    1.096
peak=    3.299 closest distance to " CB  ALA A 256 " =    1.175
peak=    3.298 closest distance to " O   HOH Z 368 " =    3.558
peak=    3.297 closest distance to " O   HOH Z 133 " =    1.667
peak=    3.291 closest distance to " O   HOH Z  43 " =    2.273
peak=    3.291 closest distance to " CD2 LEU A 297 " =    0.883
peak=    3.289 closest distance to " CB  GLU A 236 " =    1.087
peak=    3.288 closest distance to " CG1 ILE A 120 " =    1.088
peak=    3.286 closest distance to " CD  LYS A 119 " =    1.995
peak=    3.284 closest distance to " O   HOH Z 248 " =    1.631
peak=    3.281 closest distance to " CA  ALA A 158 " =    1.044
peak=    3.281 closest distance to " NH1BARG A 145 " =    0.990
peak=    3.279 closest distance to " O   HOH Z   4 " =    1.879
peak=    3.277 closest distance to " CG1BVAL A  72 " =    1.658
peak=    3.273 closest distance to " CB  GLN A  58 " =    0.831
peak=    3.266 closest distance to " O   HOH Z 355 " =    1.639
peak=    3.266 closest distance to " O   GLY A 229 " =    1.774
peak=    3.262 closest distance to " NE  ARG A 156 " =    1.072
peak=    3.260 closest distance to " OG BSER A 258 " =    3.582
peak=    3.256 closest distance to " O   HOH Z 173 " =    1.967
peak=    3.246 closest distance to " CB  TYR A  30 " =    1.355
peak=    3.246 closest distance to " NE2 GLN A  11 " =    1.070
peak=    3.246 closest distance to " CB  THR A 235 " =    1.021
peak=    3.244 closest distance to " CB  SER A  62 " =    0.777
peak=    3.243 closest distance to " O   HOH Z 427 " =    3.092
peak=    3.243 closest distance to " O   HOH Z 174 " =    2.319
peak=    3.239 closest distance to " CD1 ILE A 106 " =    0.840
peak=    3.238 closest distance to " O   HOH Z 127 " =    1.158
peak=    3.236 closest distance to " O   HOH Z 327 " =    2.416
peak=    3.235 closest distance to " O   HOH Z 207 " =    1.858
peak=    3.227 closest distance to " O   ARG A  56 " =    1.867
peak=    3.223 closest distance to " O   HOH Z 276 " =    1.306
peak=    3.218 closest distance to " O   GLN A 278 " =    1.264
peak=    3.218 closest distance to " O   HOH Z 299 " =    2.410
peak=    3.215 closest distance to " N   ARG A 156 " =    1.449
peak=    3.206 closest distance to " O   HOH Z 171 " =    3.817
peak=    3.203 closest distance to " O   HOH Z 192 " =    1.557
peak=    3.192 closest distance to " CA  VAL A  41 " =    0.806
peak=    3.188 closest distance to " CA  ASN A 215 " =    1.157
peak=    3.184 closest distance to " O   HOH Z 432 " =    1.632
peak=    3.182 closest distance to " NZ  LYS A 117 " =    1.568
peak=    3.182 closest distance to " O   HOH Z 326 " =    1.428
peak=    3.180 closest distance to " CE3 TRP A 274 " =    3.666
peak=    3.180 closest distance to " O   HOH Z 130 " =    3.903
peak=    3.177 closest distance to " CE1 PHE A 208 " =    1.162
peak=    3.174 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.173 closest distance to " CG2 ILE A 106 " =    1.083
peak=    3.172 closest distance to " CA  GLN A 194 " =    1.001
peak=    3.172 closest distance to " CG  GLN A  77 " =    0.736
peak=    3.171 closest distance to " O   HOH Z 296 " =    1.558
peak=    3.168 closest distance to " O   HOH Z 422 " =    2.617
peak=    3.168 closest distance to " O   HOH Z 281 " =    2.555
peak=    3.165 closest distance to " CB  SER A  28 " =    1.007
peak=    3.163 closest distance to " O   HOH Z 409 " =    3.300
peak=    3.161 closest distance to " O   GLY A  57 " =    2.636
peak=    3.160 closest distance to " CZ  PHE A  38 " =    1.418
peak=    3.160 closest distance to " O   ALA A 165 " =    1.386
peak=    3.159 closest distance to " CA  TYR A 116 " =    1.531
peak=    3.159 closest distance to " O   HOH Z   1 " =    2.473
peak=    3.156 closest distance to " O   HOH Z 426 " =    3.211
peak=    3.154 closest distance to " CG2 VAL A 296 " =    0.891
peak=    3.153 closest distance to " OE1 GLN A  58 " =    5.853
peak=    3.150 closest distance to " O   THR A 220 " =    1.291
peak=    3.146 closest distance to " O   HOH Z 273 " =    2.743
peak=    3.142 closest distance to " CA  ASP A 162 " =    1.185
peak=    3.142 closest distance to " O   VAL A  72 " =    3.348
peak=    3.141 closest distance to " CG  GLN A  11 " =    1.305
peak=    3.138 closest distance to " CB  MET A 105 " =    1.253
peak=    3.138 closest distance to " CA  THR A 264 " =    0.854
peak=    3.137 closest distance to " CB  ARG A 190 " =    1.114
peak=    3.136 closest distance to " CD2 HIS A  81 " =    1.115
peak=    3.135 closest distance to " NH1 ARG A  14 " =    1.174
peak=    3.132 closest distance to " CB  GLN A  73 " =    1.077
peak=    3.131 closest distance to " CG BARG A 102 " =    1.898
peak=    3.129 closest distance to " O   HOH Z  10 " =    1.825
peak=    3.125 closest distance to " CD  ARG A 195 " =    0.965
peak=    3.119 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.117 closest distance to " O   THR A  31 " =    1.605
peak=    3.117 closest distance to " O   HOH Z 421 " =    2.126
peak=    3.116 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.116 closest distance to " CG2 VAL A 112 " =    1.249
peak=    3.111 closest distance to " NZ  LYS A 193 " =    1.545
peak=    3.110 closest distance to " O   HOH Z 155 " =    1.500
peak=    3.109 closest distance to " CA  LYS A 117 " =    1.260
peak=    3.108 closest distance to " O   HOH Z 303 " =    2.187
peak=    3.108 closest distance to " CB  ALA A  71 " =    1.277
peak=    3.108 closest distance to " O   HOH Z 305 " =    3.692
peak=    3.107 closest distance to " CG1 VAL A 202 " =    2.158
peak=    3.105 closest distance to " CB  GLU A 277 " =    1.116
peak=    3.104 closest distance to " CD2 TRP A 179 " =    1.287
peak=    3.098 closest distance to " O   HOH Z 345 " =    1.767
peak=    3.097 closest distance to " O   HOH Z 409 " =    2.921
peak=    3.088 closest distance to " O   HOH Z 109 " =    2.696
peak=    3.080 closest distance to " CA  ARG A 156 " =    0.926
peak=    3.071 closest distance to " CB  ALA A 100 " =    1.400
peak=    3.069 closest distance to " CB  GLN A 194 " =    0.882
peak=    3.066 closest distance to " CD  ARG A  66 " =    3.019
peak=    3.060 closest distance to " OG1 THR A 294 " =    4.020
peak=    3.044 closest distance to " O   HOH Z 420 " =    1.877
peak=    3.041 closest distance to " CG1 ILE A 151 " =    0.860
peak=    3.040 closest distance to " O   HOH Z 126 " =    1.471
peak=    3.034 closest distance to " O   HOH Z 329 " =    3.654
peak=    3.016 closest distance to " O   HOH Z  50 " =    1.832

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 5.441
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.789 - 5.441

peak=   -4.428 closest distance to " O   HOH Z 266 " =    4.436
peak=   -4.281 closest distance to " O   HOH Z 290 " =    0.989
peak=   -4.245 closest distance to " NH2 ARG A  66 " =    1.526
peak=   -4.231 closest distance to " O   HOH Z  19 " =    1.947
peak=   -4.145 closest distance to " N   ALA A  43 " =    2.427
peak=   -4.092 closest distance to " O   HOH Z 407 " =    3.730
peak=   -4.087 closest distance to " O   HOH Z 377 " =    0.943
peak=   -4.062 closest distance to " O   HOH Z  52 " =    1.687
peak=   -4.036 closest distance to " OG ASER A 134 " =    1.209
peak=   -4.020 closest distance to " CD2 LEU A 300 " =    3.055
peak=   -3.953 closest distance to " O   HOH Z  43 " =    1.422
peak=   -3.948 closest distance to " CG  GLU A  53 " =    1.399
peak=   -3.926 closest distance to " C   ALA A 158 " =    1.228
peak=   -3.921 closest distance to " O   HOH Z  17 " =    1.193
peak=   -3.907 closest distance to " O   HOH Z  71 " =    1.109
peak=   -3.884 closest distance to " CD2 PHE A  59 " =    2.523
peak=   -3.882 closest distance to " OXT GLY A 302 " =    2.888
peak=   -3.873 closest distance to " CD  GLN A  88 " =    0.870
peak=   -3.845 closest distance to " O   HOH Z  91 " =    2.149
peak=   -3.845 closest distance to " O   HOH Z  10 " =    1.557
peak=   -3.835 closest distance to " C   ASN A 285 " =    2.552
peak=   -3.835 closest distance to " OD2 ASP A 171 " =    2.228
peak=   -3.820 closest distance to " O   HOH Z 221 " =    1.174
peak=   -3.818 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.794 closest distance to " O   HOH Z 377 " =    1.882
peak=   -3.789 closest distance to " O   HOH Z 231 " =    1.995
peak=   -3.769 closest distance to " O   HOH Z 418 " =    1.316
peak=   -3.766 closest distance to " O   HOH Z 184 " =    1.266
peak=   -3.759 closest distance to " CH2 TRP A 179 " =    1.150
peak=   -3.753 closest distance to " CD1 LEU A 228 " =    2.482
peak=   -3.752 closest distance to " O   ILE A 109 " =    2.682
peak=   -3.748 closest distance to " O   HOH Z  13 " =    1.429
peak=   -3.743 closest distance to " OD1 ASP A 191 " =    1.550
peak=   -3.743 closest distance to " CE  MET A  93 " =    1.162
peak=   -3.740 closest distance to " O   HOH Z 283 " =    1.814
peak=   -3.735 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.729 closest distance to " CD  ARG A 156 " =    1.977
peak=   -3.724 closest distance to " O   HOH Z  11 " =    1.618
peak=   -3.717 closest distance to " O   HOH Z 166 " =    1.761
peak=   -3.709 closest distance to " OG  SER A  97 " =    2.236
peak=   -3.690 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.677 closest distance to " O   HOH Z  98 " =    1.916
peak=   -3.676 closest distance to " CG  GLN A  58 " =    1.137
peak=   -3.670 closest distance to " CG  MET A 105 " =    0.922
peak=   -3.668 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.660 closest distance to " O   GLY A 196 " =    1.166
peak=   -3.657 closest distance to " CG2 THR A   4 " =    1.929
peak=   -3.654 closest distance to " O   HOH Z  92 " =    1.455
peak=   -3.647 closest distance to " CE  MET A 105 " =    1.951
peak=   -3.645 closest distance to " CB  LEU A 167 " =    2.184
peak=   -3.632 closest distance to " CD1 PHE A  59 " =    1.862
peak=   -3.622 closest distance to " CE2 TYR A  30 " =    2.765
peak=   -3.622 closest distance to " O   HOH Z 380 " =    4.832
peak=   -3.620 closest distance to " N   ALA A 226 " =    2.104
peak=   -3.620 closest distance to " OE2 GLU A   2 " =    1.470
peak=   -3.620 closest distance to " ND2 ASN A  45 " =    0.912
peak=   -3.613 closest distance to " O   PRO A 163 " =    2.137
peak=   -3.603 closest distance to " O   HOH Z  38 " =    1.131
peak=   -3.603 closest distance to " CD2 LEU A 143 " =    2.563
peak=   -3.586 closest distance to " CB  TYR A  15 " =    2.308
peak=   -3.582 closest distance to " O   VAL A  67 " =    2.641
peak=   -3.579 closest distance to " O   HOH Z 385 " =    3.973
peak=   -3.576 closest distance to " CD2 LEU A 167 " =    1.773
peak=   -3.574 closest distance to " O   HOH Z 353 " =    2.368
peak=   -3.569 closest distance to " O   HOH Z  94 " =    2.149
peak=   -3.564 closest distance to " O   HOH Z 241 " =    1.060
peak=   -3.555 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.555 closest distance to " O   HOH Z 308 " =    1.619
peak=   -3.550 closest distance to " OD2 ASP A 171 " =    1.871
peak=   -3.545 closest distance to " SG ACYS A 201 " =    2.497
peak=   -3.543 closest distance to " CD2 LEU A 237 " =    2.414
peak=   -3.536 closest distance to " CB  CYS A 254 " =    2.353
peak=   -3.527 closest distance to " O   ALA A   7 " =    1.659
peak=   -3.523 closest distance to " O   HOH Z 252 " =    4.210
peak=   -3.523 closest distance to " O   HOH Z 231 " =    1.404
peak=   -3.520 closest distance to " CE  MET A 105 " =    2.048
peak=   -3.519 closest distance to " CA  TYR A  68 " =    2.787
peak=   -3.518 closest distance to " O   HOH Z 222 " =    1.217
peak=   -3.516 closest distance to " C   HIS A 108 " =    1.075
peak=   -3.513 closest distance to " OD1 ASN A 249 " =    1.107
peak=   -3.512 closest distance to " O   GLY A 118 " =    2.247
peak=   -3.509 closest distance to " OH  TYR A 169 " =    1.037
peak=   -3.494 closest distance to " O   HOH Z 275 " =    1.603
peak=   -3.494 closest distance to " CD  GLN A  88 " =    0.842
peak=   -3.479 closest distance to " CA  ASN A 127 " =    1.091
peak=   -3.477 closest distance to " CG  LYS A 193 " =    2.545
peak=   -3.474 closest distance to " OD1 ASN A 148 " =    1.647
peak=   -3.471 closest distance to " O   HOH Z 292 " =    4.433
peak=   -3.463 closest distance to " N   GLN A  58 " =    1.672
peak=   -3.463 closest distance to " CD  LYS A 289 " =    2.457
peak=   -3.458 closest distance to " CB  ALA A  43 " =    2.602
peak=   -3.455 closest distance to " O   HOH Z 151 " =    1.413
peak=   -3.453 closest distance to " CB  ASN A  39 " =    2.115
peak=   -3.452 closest distance to " O   HOH Z 351 " =    1.409
peak=   -3.451 closest distance to " OE1 GLN A  88 " =    0.979
peak=   -3.446 closest distance to " CA  SER A 276 " =    1.413
peak=   -3.443 closest distance to " C   ASN A 187 " =    1.886
peak=   -3.435 closest distance to " NH2AARG A 275 " =    5.441
peak=   -3.430 closest distance to " CB  PRO A 243 " =    2.610
peak=   -3.426 closest distance to " CD  ARG A 139 " =    1.612
peak=   -3.424 closest distance to " CZ  TYR A 169 " =    1.849
peak=   -3.415 closest distance to " CA  VAL A 197 " =    1.085
peak=   -3.412 closest distance to " CG  GLU A 277 " =    1.272
peak=   -3.412 closest distance to " O   HOH Z 177 " =    1.562
peak=   -3.404 closest distance to " OG  SER A  87 " =    1.574
peak=   -3.399 closest distance to " CG  ARG A 269 " =    2.339
peak=   -3.395 closest distance to " OG  SER A  32 " =    1.034
peak=   -3.392 closest distance to " CA  ASP A 298 " =    1.077
peak=   -3.386 closest distance to " O   HOH Z 128 " =    2.383
peak=   -3.385 closest distance to " ND2BASN A 224 " =    1.930
peak=   -3.382 closest distance to " O   HOH Z 213 " =    1.413
peak=   -3.372 closest distance to " O   HOH Z  97 " =    1.663
peak=   -3.367 closest distance to " CH2 TRP A 177 " =    2.012
peak=   -3.361 closest distance to " OG BSER A 134 " =    1.866
peak=   -3.359 closest distance to " CA  PRO A 198 " =    1.102
peak=   -3.356 closest distance to " CB  THR A  82 " =    2.178
peak=   -3.355 closest distance to " CG  ASP A  50 " =    2.247
peak=   -3.346 closest distance to " O   HOH Z 389 " =    1.892
peak=   -3.339 closest distance to " NH2 ARG A  66 " =    5.344
peak=   -3.338 closest distance to " CE3 TRP A 150 " =    1.871
peak=   -3.335 closest distance to " O   HOH Z 423 " =    2.223
peak=   -3.328 closest distance to " CA  GLY A 241 " =    3.013
peak=   -3.328 closest distance to " CB  SER A 146 " =    2.179
peak=   -3.326 closest distance to " CG  ARG A  66 " =    2.384
peak=   -3.320 closest distance to " O   HOH Z 103 " =    1.965
peak=   -3.317 closest distance to " O   HOH Z 259 " =    1.055
peak=   -3.316 closest distance to " NH1 ARG A 195 " =    2.280
peak=   -3.311 closest distance to " OD2 ASP A 200 " =    1.293
peak=   -3.309 closest distance to " CA  GLY A 203 " =    2.214
peak=   -3.309 closest distance to " ND2 ASN A  60 " =    1.523
peak=   -3.308 closest distance to " CD1 LEU A 101 " =    2.688
peak=   -3.307 closest distance to " O   HOH Z 189 " =    1.925
peak=   -3.302 closest distance to " O   TRP A  92 " =    1.852
peak=   -3.302 closest distance to " O   HOH Z 388 " =    1.992
peak=   -3.292 closest distance to " C   LEU A 143 " =    1.921
peak=   -3.291 closest distance to " CB  GLN A  55 " =    1.365
peak=   -3.288 closest distance to " OE1 GLN A 223 " =    2.242
peak=   -3.287 closest distance to " O   HOH Z 402 " =    1.460
peak=   -3.286 closest distance to " O   HOH Z 312 " =    1.420
peak=   -3.284 closest distance to " NE1 TRP A 266 " =    2.153
peak=   -3.282 closest distance to " O   HOH Z 234 " =    4.403
peak=   -3.281 closest distance to " CD1 LEU A 101 " =    2.877
peak=   -3.276 closest distance to " O   HOH Z 396 " =    1.654
peak=   -3.272 closest distance to " O   HOH Z 150 " =    1.266
peak=   -3.269 closest distance to " SG  CYS A 168 " =    1.010
peak=   -3.268 closest distance to " O   HOH Z 313 " =    1.061
peak=   -3.266 closest distance to " O   HOH Z  48 " =    1.081
peak=   -3.266 closest distance to " O   HOH Z  37 " =    1.572
peak=   -3.259 closest distance to " O   HOH Z 243 " =    1.914
peak=   -3.254 closest distance to " O   ALA A 256 " =    1.439
peak=   -3.252 closest distance to " CB  ALA A 248 " =    1.928
peak=   -3.251 closest distance to " O   HOH Z 426 " =    1.858
peak=   -3.250 closest distance to " O   HOH Z 118 " =    2.875
peak=   -3.247 closest distance to " CB  PHE A 208 " =    2.285
peak=   -3.246 closest distance to " O   GLY A 211 " =    1.491
peak=   -3.244 closest distance to " ND2 ASN A  45 " =    1.158
peak=   -3.244 closest distance to " O   HOH Z 399 " =    2.181
peak=   -3.240 closest distance to " O   HOH Z 136 " =    1.389
peak=   -3.236 closest distance to " CZ  ARG A  66 " =    0.815
peak=   -3.227 closest distance to " O   ALA A 160 " =    1.495
peak=   -3.217 closest distance to " O   ASN A 187 " =    1.500
peak=   -3.214 closest distance to " O   HOH Z 437 " =    1.164
peak=   -3.211 closest distance to " O   HOH Z 265 " =    1.941
peak=   -3.202 closest distance to " O   VAL A 153 " =    2.154
peak=   -3.198 closest distance to " O   HOH Z 111 " =    1.273
peak=   -3.197 closest distance to " CD  ARG A 195 " =    5.073
peak=   -3.188 closest distance to " CG  TRP A 266 " =    1.702
peak=   -3.186 closest distance to " CD  PRO A 198 " =    1.186
peak=   -3.183 closest distance to " NH2 ARG A 156 " =    1.234
peak=   -3.182 closest distance to " C   SER A 271 " =    1.200
peak=   -3.178 closest distance to " O   ALA A  34 " =    2.528
peak=   -3.177 closest distance to " CB  TRP A  85 " =    2.358
peak=   -3.176 closest distance to " C   GLN A 240 " =    2.261
peak=   -3.170 closest distance to " CG  ASP A 231 " =    0.921
peak=   -3.167 closest distance to " CB  PRO A 163 " =    2.762
peak=   -3.165 closest distance to " O   HOH Z 390 " =    2.243
peak=   -3.164 closest distance to " O   HOH Z 165 " =    2.068
peak=   -3.162 closest distance to " NE2 HIS A  86 " =    1.061
peak=   -3.156 closest distance to " CE1 TYR A 247 " =    2.477
peak=   -3.156 closest distance to " CA  TRP A 274 " =    1.562
peak=   -3.153 closest distance to " O   HOH Z 148 " =    3.491
peak=   -3.153 closest distance to " O   VAL A 174 " =    2.023
peak=   -3.151 closest distance to " O   HOH Z 236 " =    1.425
peak=   -3.144 closest distance to " CD2 LEU A 237 " =    2.627
peak=   -3.144 closest distance to " CD2 LEU A 237 " =    2.813
peak=   -3.142 closest distance to " CA  VAL A  67 " =    2.898
peak=   -3.141 closest distance to " O   HOH Z  98 " =    1.398
peak=   -3.137 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.131 closest distance to " OD1 ASN A 187 " =    1.389
peak=   -3.118 closest distance to " CB  ALA A 291 " =    2.319
peak=   -3.115 closest distance to " CA  GLY A 133 " =    1.907
peak=   -3.115 closest distance to " O   ALA A 158 " =    1.108
peak=   -3.110 closest distance to " CB  ALA A 227 " =    2.328
peak=   -3.106 closest distance to " OG  SER A 245 " =    0.946
peak=   -3.106 closest distance to " O   HOH Z 100 " =    0.840
peak=   -3.101 closest distance to " ND2 ASN A  60 " =    1.723
peak=   -3.098 closest distance to " N   SER A 212 " =    1.990
peak=   -3.096 closest distance to " O   HOH Z 298 " =    2.813
peak=   -3.095 closest distance to " CD  GLN A 223 " =    1.243
peak=   -3.086 closest distance to " OD2 ASP A 132 " =    1.751
peak=   -3.085 closest distance to " O   HOH Z  61 " =    1.411
peak=   -3.077 closest distance to " CD1 PHE A  16 " =    2.626
peak=   -3.075 closest distance to " CG  GLN A  11 " =    1.555
peak=   -3.074 closest distance to " O   HOH Z 417 " =    2.800
peak=   -3.064 closest distance to " N   GLY A  17 " =    1.601
peak=   -3.059 closest distance to " O   HOH Z  25 " =    1.872
peak=   -3.059 closest distance to " O   HOH Z 414 " =    1.396
peak=   -3.058 closest distance to " CA  ASP A 107 " =    2.425
peak=   -3.056 closest distance to " O   ALA A   7 " =    2.115
peak=   -3.039 closest distance to " O   HOH Z 411 " =    3.177
peak=   -3.022 closest distance to " OD2 ASP A 140 " =    1.413

================= 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    :  0.4550 0.4519   6.260948e+00   6.255037e+00
   1_bss:  0.4478 0.4448   6.256905e+00   6.245312e+00
   1_xyz:  0.3440 0.3802   6.072338e+00   6.142737e+00
   1_adp:  0.3125 0.3870   6.028779e+00   6.159778e+00
   1_occ:  0.3122 0.3877   6.028060e+00   6.159607e+00
   2_bss:  0.3114 0.3866   6.028383e+00   6.158297e+00
   2_xyz:  0.2341 0.2996   5.791297e+00   5.979518e+00
   2_adp:  0.2137 0.2744   5.712923e+00   5.906792e+00
   2_occ:  0.2136 0.2744   5.712749e+00   5.906539e+00
   3_bss:  0.2132 0.2732   5.711296e+00   5.903974e+00
   3_xyz:  0.1691 0.2168   5.493971e+00   5.705614e+00
   3_adp:  0.1554 0.2061   5.432145e+00   5.650911e+00
   3_occ:  0.1553 0.2060   5.431861e+00   5.650725e+00
   4_bss:  0.1555 0.2061   5.433512e+00   5.651515e+00
   4_xyz:  0.1309 0.1805   5.284060e+00   5.520086e+00
   4_adp:  0.1255 0.1729   5.248727e+00   5.482878e+00
   4_occ:  0.1254 0.1728   5.248543e+00   5.482932e+00
   5_bss:  0.1257 0.1731   5.251294e+00   5.484477e+00
   5_xyz:  0.1229 0.1692   5.231060e+00   5.458752e+00
   5_adp:  0.1225 0.1683   5.226644e+00   5.452961e+00
   5_occ:  0.1224 0.1682   5.226356e+00   5.452841e+00
   5_bss:  0.1223 0.1682   5.226181e+00   5.452522e+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:  0.295  35.724   0.370   1.733   1.068   0.000   0.000   0.000
   1_xyz:  0.295  35.724   0.370   1.733   1.068   0.000   0.000   0.000
   1_adp:  0.295  35.724   0.370   1.733   1.068   0.000   0.000   0.000
   1_occ:  0.295  35.724   0.370   1.733   1.068   0.000   0.000   0.000
   2_bss:  0.331  68.306  -0.445   0.738   0.048   0.000   0.000   0.000
   2_xyz:  0.331  68.306  -0.445   0.738   0.048   0.000   0.000   0.000
   2_adp:  0.331  68.306  -0.445   0.738   0.048   0.000   0.000   0.000
   2_occ:  0.331  68.306  -0.445   0.738   0.048   0.000   0.000   0.000
   3_bss:  0.331  68.306  -1.190  -0.609  -1.135  -0.000  -0.000  -0.000
   3_xyz:  0.331  68.306  -1.190  -0.609  -1.135  -0.000  -0.000  -0.000
   3_adp:  0.331  68.306  -1.190  -0.609  -1.135  -0.000  -0.000  -0.000
   3_occ:  0.331  68.306  -1.190  -0.609  -1.135  -0.000  -0.000  -0.000
   4_bss:  0.330  71.931  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   4_xyz:  0.330  71.931  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   4_adp:  0.330  71.931  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   4_occ:  0.330  71.931  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   5_bss:  0.326  63.986  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   5_xyz:  0.326  63.986  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   5_adp:  0.326  63.986  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   5_occ:  0.326  63.986  -1.873  -1.391  -1.674  -0.000  -0.000  -0.000
   5_bss:  0.320  58.518  -1.914  -1.613  -1.730  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.887 0.4318  0.5710    64832.559
   1_bss:  56.111 0.4396  0.6042    61837.436
   1_xyz:  42.378 0.6127  0.8361    40907.684
   1_adp:  44.303 0.5882  0.8078    43566.085
   1_occ:  44.323 0.5879  0.8058    43556.099
   2_bss:  44.182 0.5897  0.7841    43420.610
   2_xyz:  32.311 0.7302  0.9444    25071.804
   2_adp:  28.519 0.7733  0.9690    20562.920
   2_occ:  28.530 0.7732  0.9688    20563.926
   3_bss:  28.379 0.7747  0.9335    20359.872
   3_xyz:  21.651 0.8442  0.9818    12350.338
   3_adp:  20.054 0.8605  0.9811    11027.905
   3_occ:  20.048 0.8605  0.9811    11017.417
   4_bss:  20.050 0.8606  0.9584    11043.261
   4_xyz:  17.143 0.8874  0.9740     8366.588
   4_adp:  16.196 0.8964  0.9728     7814.322
   4_occ:  16.193 0.8964  0.9726     7811.444
   5_bss:  16.237 0.8961  0.9721     7856.717
   5_xyz:  15.567 0.9020  0.9737     7353.305
   5_adp:  15.389 0.9038  0.9692     7313.494
   5_occ:  15.384 0.9038  0.9691     7313.635
   5_bss:  15.375 0.9039  0.9634     7304.511
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7914e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7914e-01
   1_xyz:   1.420  0.011  0.089 15.516  0.005  4.115   1.0896e-01
   1_adp:   1.420  0.011  0.089 15.516  0.005  4.115   1.0896e-01
   1_occ:   1.420  0.011  0.089 15.516  0.005  4.115   1.0896e-01
   2_bss:   1.420  0.011  0.089 15.516  0.005  4.115   1.0896e-01
   2_xyz:   1.241  0.009  0.082 14.200  0.005  4.112   8.2687e-02
   2_adp:   1.241  0.009  0.082 14.200  0.005  4.112   8.2687e-02
   2_occ:   1.241  0.009  0.082 14.200  0.005  4.112   8.2687e-02
   3_bss:   1.241  0.009  0.082 14.200  0.005  4.112   8.2687e-02
   3_xyz:   0.962  0.006  0.065 14.176  0.003  4.124   5.4988e-02
   3_adp:   0.962  0.006  0.065 14.176  0.003  4.124   5.4988e-02
   3_occ:   0.962  0.006  0.065 14.176  0.003  4.124   5.4988e-02
   4_bss:   0.962  0.006  0.065 14.176  0.003  4.124   5.4988e-02
   4_xyz:   1.068  0.008  0.077 14.374  0.004  4.133   6.5129e-02
   4_adp:   1.068  0.008  0.077 14.374  0.004  4.133   6.5129e-02
   4_occ:   1.068  0.008  0.077 14.374  0.004  4.133   6.5129e-02
   5_bss:   1.068  0.008  0.077 14.374  0.004  4.133   6.5129e-02
   5_xyz:   0.922  0.006  0.067 14.130  0.003  4.123   5.0692e-02
   5_adp:   0.922  0.006  0.067 14.130  0.003  4.123   5.0692e-02
   5_occ:   0.922  0.006  0.067 14.130  0.003  4.123   5.0692e-02
   5_bss:   0.922  0.006  0.067 14.130  0.003  4.123   5.0692e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.650   2.4254e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.650   2.4254e-01
   1_xyz:   8.351  0.061  0.352 85.035  0.033  2.037   9.3225e-02
   1_adp:   8.351  0.061  0.352 85.035  0.033  2.037   9.3225e-02
   1_occ:   8.351  0.061  0.352 85.035  0.033  2.037   9.3225e-02
   2_bss:   8.351  0.061  0.352 85.035  0.033  2.037   9.3225e-02
   2_xyz:   7.251  0.043  0.289 77.098  0.037  2.307   1.0085e-01
   2_adp:   7.251  0.043  0.289 77.098  0.037  2.307   1.0085e-01
   2_occ:   7.251  0.043  0.289 77.098  0.037  2.307   1.0085e-01
   3_bss:   7.251  0.043  0.289 77.098  0.037  2.307   1.0085e-01
   3_xyz:   8.174  0.044  0.252 80.078  0.035  2.347   4.7393e-02
   3_adp:   8.174  0.044  0.252 80.078  0.035  2.347   4.7393e-02
   3_occ:   8.174  0.044  0.252 80.078  0.035  2.347   4.7393e-02
   4_bss:   8.174  0.044  0.252 80.078  0.035  2.347   4.7393e-02
   4_xyz:   7.673  0.054  0.240 81.464  0.031  2.339   5.2464e-02
   4_adp:   7.673  0.054  0.240 81.464  0.031  2.339   5.2464e-02
   4_occ:   7.673  0.054  0.240 81.464  0.031  2.339   5.2464e-02
   5_bss:   7.673  0.054  0.240 81.464  0.031  2.339   5.2464e-02
   5_xyz:   7.954  0.049  0.229 83.380  0.037  2.389   3.3343e-02
   5_adp:   7.954  0.049  0.229 83.380  0.037  2.389   3.3343e-02
   5_occ:   7.954  0.049  0.229 83.380  0.037  2.389   3.3343e-02
   5_bss:   7.954  0.049  0.229 83.380  0.037  2.389   3.3343e-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: 109.68   0.00  18.89  88.39   0.00  15.02 109.68   0.00  39.98
   1_occ: 109.68   0.00  18.89  88.39   0.00  15.02 109.68   0.00  39.98
   2_bss: 109.68   0.00  18.89  88.39   0.00  15.02 109.68   0.00  39.98
   2_xyz: 109.68   0.00  18.89  88.39   0.00  15.02 109.68   0.00  39.98
   2_adp: 106.20   0.00  18.30  85.14   0.00  13.96 106.20   5.39  41.93
   2_occ: 106.20   0.00  18.30  85.14   0.00  13.96 106.20   5.39  41.93
   3_bss: 106.20   0.00  18.30  85.14   0.00  13.96 106.20   5.39  41.93
   3_xyz: 106.20   0.00  18.30  85.14   0.00  13.96 106.20   5.39  41.93
   3_adp: 115.69   0.00  18.85 115.69   0.00  13.65 109.25   5.12  47.18
   3_occ: 115.69   0.00  18.85 115.69   0.00  13.65 109.25   5.12  47.18
   4_bss: 115.69   0.00  18.85 115.69   0.00  13.65 109.25   5.12  47.18
   4_xyz: 115.69   0.00  18.85 115.69   0.00  13.65 109.25   5.12  47.18
   4_adp: 114.99   1.49  18.00 114.99   1.49  13.14 100.65   4.87  44.50
   4_occ: 114.99   1.49  18.00 114.99   1.49  13.14 100.65   4.87  44.50
   5_bss: 114.99   1.49  18.00 114.99   1.49  13.14 100.65   4.87  44.50
   5_xyz: 114.99   1.49  18.00 114.99   1.49  13.14 100.65   4.87  44.50
   5_adp: 111.71   1.81  17.36 111.71   1.81  12.86  92.88   4.72  41.88
   5_occ: 111.71   1.81  17.36 111.71   1.81  12.86  92.88   4.72  41.88
   5_bss: 111.64   1.74  17.30 111.64   1.74  12.80  92.81   4.66  41.81
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.846    0.012    0.318
   1_adp:    1.846    0.012    0.318
   1_occ:    1.846    0.012    0.318
   2_bss:    1.846    0.012    0.318
   2_xyz:    1.341    0.045    0.531
   2_adp:    1.341    0.045    0.531
   2_occ:    1.341    0.045    0.531
   3_bss:    1.341    0.045    0.531
   3_xyz:    1.331    0.070    0.635
   3_adp:    1.331    0.070    0.635
   3_occ:    1.331    0.070    0.635
   4_bss:    1.331    0.070    0.635
   4_xyz:    1.360    0.070    0.699
   4_adp:    1.360    0.070    0.699
   4_occ:    1.360    0.070    0.699
   5_bss:    1.360    0.070    0.699
   5_xyz:    1.389    0.057    0.717
   5_adp:    1.389    0.057    0.717
   5_occ:    1.389    0.057    0.717
   5_bss:    1.389    0.057    0.717
------------------------------------------------------------------------

CPU time actual refinement: 343.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/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_1178/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1178/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.64 
  Macro-tasks:
    bulk solvent and scale       = 39.01  
    individual site refinement   = 140.78 
    weights calculation          = 30.38  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 216.93 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 113.36 
    alpha_beta                      = 8.59   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.76 
    fmodel                         = 6.17   
    r_factors                      = 0.13   
    phase_errors                   = 10.61  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 262.52 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.957 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    618 calls, 113.05 s
gradients_fft:          563 calls, 107.16 s

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

# Date 2008-01-16 Time 06:37:19 PST -0800 (1200494239.31 s)
Start R-work = 0.4550, R-free = 0.4519 (no bulk solvent and anisotropic scale)
Final R-work = 0.1433, R-free = 0.1874 (no bulk solvent and anisotropic scale)

Start R-work = 0.4478, R-free = 0.4448
Final R-work = 0.1223, R-free = 0.1682