# Date 2008-01-16 Time 06:43:49 PST -0800 (1200494629.38 s)
#phil __OFF__

Command line arguments: "../1266.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14601
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1266

-------------------------------------------------------------------------------
  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: (72.0062, 46.93, 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: (72.0062, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96127
Completeness in resolution range: 0.9265
Completeness with d_max=infinity: 0.923792

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9613

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: (72.0062, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96127
Completeness in resolution range: 0.9265
Completeness with d_max=infinity: 0.923792

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1984 [2217/2247]  1998   219   9.9%
  bin  2:  4.1984 -  3.3441 [2132/2151]  1919   213  10.0%
  bin  3:  3.3441 -  2.9248 [2102/2122]  1886   216  10.3%
  bin  4:  2.9248 -  2.6590 [2095/2120]  1893   202   9.6%
  bin  5:  2.6590 -  2.4693 [2062/2081]  1853   209  10.1%
  bin  6:  2.4693 -  2.3242 [2050/2097]  1842   208  10.1%
  bin  7:  2.3242 -  2.2082 [2068/2100]  1859   209  10.1%
  bin  8:  2.2082 -  2.1123 [2027/2064]  1829   198   9.8%
  bin  9:  2.1123 -  2.0312 [2019/2094]  1817   202  10.0%
  bin 10:  2.0312 -  1.9613 [ 817/2067]   734    83  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 22
        2.30 -     2.95: 1655
        2.95 -     3.60: 4530
        3.60 -     4.25: 9192
        4.25 -     4.90: 12937
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.653 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.809 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.889 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.923 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28331 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_1266/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/model_refine_001.geo

CPU time processing inputs: 9.16


============================ 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 = 72.00625 46.93 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 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4181   r_free= 0.4225   ksol= 0.00   Bsol= 0.00   scale= 0.921    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.219259                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.3323 0.3407      6.4629      6.4726|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.3438 0.3185      6.6876      6.7075|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.3856 0.3735      6.5625      6.5876|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.3946 0.3964      6.4174      6.4117|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.4341 0.4433      6.2853      6.3026|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.4599 0.4529      6.2157      6.1926|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.4632 0.4079      6.2029      6.1203|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.4571 0.4699      6.0959      6.1423|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.4677 0.4808      6.0959      6.0568|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.4738 0.5257      6.0367      6.0998|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.4775 0.5423      6.0068       6.026|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.4720 0.5356      5.9338       5.981|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.4880 0.4870      5.8475      5.8056|
| 14:  2.0102 -  1.9613 0.27    371   31 0.5089 0.4557      5.7891      5.7576|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.75  29.71   0.84     0.78      54546.22|
|  2:  4.6835 -  3.7357  1390   152  0.76  29.55   0.94     0.86      75766.46|
|  3:  3.7357 -  3.2689  1356   151  0.68  37.28   0.93     0.85      82459.42|
|  4:  3.2689 -  2.9724  1358   155  0.61  43.38   0.95     0.80      77052.33|
|  5:  2.9724 -  2.7608  1333   147  0.51  51.00   0.92     0.69      65093.49|
|  6:  2.7608 -  2.5988  1343   149  0.50  51.99   0.92     0.69      56706.49|
|  7:  2.5988 -  2.4693  1333   144  0.52  50.40   0.93     0.69      49426.27|
|  8:  2.4693 -  2.3622  1324   151  0.52  50.59   0.93     0.74      45116.69|
|  9:  2.3622 -  2.2716  1315   151  0.49  53.31   0.97     0.69      42853.68|
| 10:  2.2716 -  2.1934  1307   148  0.41  59.29   0.95     0.59      45394.88|
| 11:  2.1934 -  2.1250  1344   137  0.33  65.45   0.98     0.49      46842.20|
| 12:  2.1250 -  2.0644  1298   146  0.29  68.60   0.96     0.45      44774.61|
| 13:  2.0644 -  2.0102  1122   136  0.32  66.25   0.95     0.50      36974.32|
| 14:  2.0102 -  1.9613   371    31  0.39  60.78   0.94     0.59      27574.97|
|alpha:            min =        0.45 max =            0.86 mean =         0.68|
|beta:             min =    27574.97 max =        82459.42 mean =     55423.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.29|
|phase err.(test): min =        0.00 max =           89.81 mean =        50.36|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.508731             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.992   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.753704              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.192   (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 |  1.653 -  1.977:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.977 -  2.302:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.302 -  2.627:       54 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.627 -  2.952:     1601 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.952 -  3.276:     1916 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.276 -  3.601:     2614 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.601 -  3.926:     4766 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.926 -  4.251:     4426 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.251 -  4.575:     5918 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.575 -  4.900:     7019 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| 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  1.653 |       0.322 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    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 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4181   r_free= 0.4225   ksol= 0.00   Bsol= 0.00   scale= 0.921    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.219259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4065   r_free= 0.4119   ksol= 0.30   Bsol= 29.32   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,-3.16,1.61,-0.00,0.00,0.00); trace/3= 0.33                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.208790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.294457             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.312   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.879152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.892   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4065      final r-factor (work) = 0.2517          |
| start r-factor (free) = 0.4119      final r-factor (free) = 0.2887          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.1206 = 10.29 * 0.50 * 6.2069 + 1.00 * 0.1721                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0844 = 10.29 * 0.50 * 6.0157 + 1.00 * 0.1200                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2517      final r-factor (work) = 0.2321          |
| start r-factor (free) = 0.2887      final r-factor (free) = 0.2946          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2955 = 0.88 * 1.00 * 6.0157 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1326 = 0.88 * 1.00 * 5.7726 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.42   17.29    None  None   None       |
|    all(noH): 2823   0      0.00    76.42   17.29    None  None   None       |
|    Sol.    : 438    0      4.72    63.32   39.12    None  None   None       |
|    Mac.    : 2385   0      0.00    76.42   13.28    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 -   7.642:  586   |   5:    38.211 -  45.853:  125        |
|      1:     7.642 -  15.284: 1065   |   6:    45.853 -  53.495:   97        |
|      2:    15.284 -  22.926:  547   |   7:    53.495 -  61.137:   57        |
|      3:    22.926 -  30.568:  196   |   8:    61.137 -  68.779:    6        |
|      4:    30.568 -  38.211:  143   |   9:    68.779 -  76.421:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2321 r_free = 0.2946             target_work(ml) = 5.782         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2317 r_free = 0.2947             target_work(ml) = 5.781         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2317   r_free= 0.2947   ksol= 0.30   Bsol= 29.32   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,-3.16,1.61,-0.00,0.00,0.00); trace/3= 0.33                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.780756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2290   r_free= 0.2904   ksol= 0.34   Bsol= 56.65   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-2.90,-0.77,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.773598                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.683921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.500   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.577019              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.696   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.1635          |
| start r-factor (free) = 0.2904      final r-factor (free) = 0.2160          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5428 = 5.68 * 0.50 * 5.7787 + 1.00 * 0.1200                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1403 = 5.68 * 0.50 * 5.6548 + 1.00 * 0.0697                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.2160      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2936 = 0.58 * 1.00 * 5.6548 + 1.00 * 0.0307                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1435 = 0.58 * 1.00 * 5.4302 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.94   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    83.94   17.73    None  None   None       |
|    Sol.    : 438    0      5.95    83.42   42.60    None  None   None       |
|    Mac.    : 2385   0      0.00    83.94   13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.395:  659   |   5:    41.972 -  50.367:  105        |
|      1:     8.395 -  16.789: 1301   |   6:    50.367 -  58.761:   90        |
|      2:    16.789 -  25.183:  346   |   7:    58.761 -  67.156:   57        |
|      3:    25.183 -  33.578:  133   |   8:    67.156 -  75.550:   22        |
|      4:    33.578 -  41.972:   97   |   9:    75.550 -  83.944:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1956             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1448 r_free = 0.1955             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1955   ksol= 0.34   Bsol= 56.65   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-2.90,-0.77,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.376416                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1951   ksol= 0.33   Bsol= 59.17   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-2.59,-1.52,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.373537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.011657              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.399  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197784              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.633  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1951      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2481 = 3.01 * 0.50 * 5.4310 + 1.00 * 0.0700                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0694 = 3.01 * 0.50 * 5.3174 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0619 = 0.20 * 1.00 * 5.3174 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0481 = 0.20 * 1.00 * 5.2330 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.28   17.34    None  None   None       |
|    all(noH): 2823   0      0.00    84.28   17.34    None  None   None       |
|    Sol.    : 438    0      6.13    79.52   40.94    None  None   None       |
|    Mac.    : 2385   0      0.00    84.28   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.429:  603   |   5:    42.142 -  50.571:  108        |
|      1:     8.429 -  16.857: 1404   |   6:    50.571 -  58.999:   73        |
|      2:    16.857 -  25.285:  322   |   7:    58.999 -  67.428:   46        |
|      3:    25.285 -  33.714:  125   |   8:    67.428 -  75.856:   20        |
|      4:    33.714 -  42.142:  112   |   9:    75.856 -  84.285:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1648             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1646             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1646   ksol= 0.33   Bsol= 59.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-2.59,-1.52,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.209626                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1645   ksol= 0.33   Bsol= 59.17   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.62,-1.91,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.208914                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.221794              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.728   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4925 = 3.22 * 0.50 * 5.2332 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4188 = 3.22 * 0.50 * 5.1795 + 1.00 * 0.0751                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8441 = 0.35 * 1.00 * 5.1795 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8334 = 0.35 * 1.00 * 5.1510 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    90.34   17.20    None  None   None       |
|    all(noH): 2823   0      1.42    90.34   17.20    None  None   None       |
|    Sol.    : 438    0      6.21    81.71   40.26    None  None   None       |
|    Mac.    : 2385   0      1.42    90.34   12.97    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:     1.415 -  10.308: 1084   |   5:    45.878 -  54.770:  103        |
|      1:    10.308 -  19.200: 1064   |   6:    54.770 -  63.662:   55        |
|      2:    19.200 -  28.093:  234   |   7:    63.662 -  72.555:   27        |
|      3:    28.093 -  36.985:  121   |   8:    72.555 -  81.447:   10        |
|      4:    36.985 -  45.878:  120   |   9:    81.447 -  90.340:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1582             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1581             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1581   ksol= 0.33   Bsol= 59.17   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.62,-1.91,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1577   ksol= 0.33   Bsol= 59.17   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.51,-1.96,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149304                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.423387              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.453  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.605  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7409 = 1.42 * 0.50 * 5.1507 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7289 = 1.42 * 0.50 * 5.1657 + 1.00 * 0.0525                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0060 = 0.19 * 1.00 * 5.1657 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0072 = 0.19 * 1.00 * 5.1764 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    89.78   16.83    None  None   None       |
|    all(noH): 2823   0      1.54    89.78   16.83    None  None   None       |
|    Sol.    : 438    0      6.16    79.88   38.52    None  None   None       |
|    Mac.    : 2385   0      1.54    89.78   12.85    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:     1.541 -  10.365: 1109   |   5:    45.662 -  54.486:   95        |
|      1:    10.365 -  19.189: 1051   |   6:    54.486 -  63.311:   41        |
|      2:    19.189 -  28.014:  231   |   7:    63.311 -  72.135:   22        |
|      3:    28.014 -  36.838:  138   |   8:    72.135 -  80.959:    5        |
|      4:    36.838 -  45.662:  126   |   9:    80.959 -  89.783:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1597             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1596             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1596   ksol= 0.33   Bsol= 59.17   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.51,-1.96,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.1018 0.1303       5.408      5.5779|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.0894 0.1036       5.464      5.6213|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.1092 0.1700      5.4805      5.9003|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.1281 0.1603      5.4856      5.6081|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.1359 0.1712      5.3408      5.5106|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.1277 0.1853      5.2246      5.4504|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.1277 0.1799      5.1836      5.4202|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.1177 0.1708      5.0634      5.2549|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.1212 0.1942      5.0421      5.3375|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.1156 0.1611      4.9666      5.2157|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.1192 0.1909      4.9664      5.3326|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.1181 0.1671      4.9086       5.111|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.1202 0.1713       4.809      5.0382|
| 14:  2.0102 -  1.9613 0.27    371   31 0.1073 0.1674      4.6301      4.9214|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.94   9.21   0.97     0.95       7357.26|
|  2:  4.6835 -  3.7357  1390   152  0.95   8.08   1.01     1.00       9124.19|
|  3:  3.7357 -  3.2689  1356   151  0.93  11.73   1.02     1.01      10434.04|
|  4:  3.2689 -  2.9724  1358   155  0.91  14.68   1.00     0.97      10949.16|
|  5:  2.9724 -  2.7608  1333   147  0.90  15.98   0.99     0.97       8369.94|
|  6:  2.7608 -  2.5988  1343   149  0.90  16.18   0.98     0.96       7146.50|
|  7:  2.5988 -  2.4693  1333   144  0.91  15.53   0.99     0.97       6290.85|
|  8:  2.4693 -  2.3622  1324   151  0.91  15.57   0.98     0.96       5363.91|
|  9:  2.3622 -  2.2716  1315   151  0.90  16.41   1.00     0.96       5079.68|
| 10:  2.2716 -  2.1934  1307   148  0.91  15.18   0.99     0.95       4349.16|
| 11:  2.1934 -  2.1250  1344   137  0.89  16.83   0.99     0.95       4569.23|
| 12:  2.1250 -  2.0644  1298   146  0.90  16.64   1.00     1.00       4297.88|
| 13:  2.0644 -  2.0102  1122   136  0.90  16.45   0.99     0.97       3465.55|
| 14:  2.0102 -  1.9613   371    31  0.90  15.63   0.97     0.95       2407.34|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2407.34 max =        10949.16 mean =      6657.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.44|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1596   ksol= 0.33   Bsol= 59.11   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.40,-1.90,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1596   ksol= 0.33   Bsol= 59.11   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.40,-1.90,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.1018 0.1303       5.408      5.5777|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.0894 0.1035      5.4638       5.621|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.1092 0.1700      5.4803      5.8999|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.1281 0.1603      5.4856      5.6083|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.1360 0.1712       5.341      5.5107|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.1277 0.1853      5.2246      5.4504|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.1276 0.1799      5.1834        5.42|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.1177 0.1707      5.0634      5.2548|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.1212 0.1942       5.042      5.3374|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.1156 0.1610      4.9666      5.2153|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.1193 0.1910      4.9664       5.333|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.1181 0.1672      4.9088      5.1114|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.1201 0.1714      4.8091      5.0384|
| 14:  2.0102 -  1.9613 0.27    371   31 0.1074 0.1675      4.6308      4.9226|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.94   9.21   0.97     0.95       7356.00|
|  2:  4.6835 -  3.7357  1390   152  0.95   8.07   1.01     1.00       9119.78|
|  3:  3.7357 -  3.2689  1356   151  0.93  11.73   1.02     1.01      10426.20|
|  4:  3.2689 -  2.9724  1358   155  0.91  14.68   1.00     0.97      10950.36|
|  5:  2.9724 -  2.7608  1333   147  0.90  15.98   0.99     0.97       8372.02|
|  6:  2.7608 -  2.5988  1343   149  0.90  16.18   0.98     0.96       7146.90|
|  7:  2.5988 -  2.4693  1333   144  0.91  15.53   0.99     0.97       6289.96|
|  8:  2.4693 -  2.3622  1324   151  0.91  15.56   0.99     0.96       5363.58|
|  9:  2.3622 -  2.2716  1315   151  0.90  16.41   1.00     0.96       5077.69|
| 10:  2.2716 -  2.1934  1307   148  0.91  15.19   0.99     0.95       4348.28|
| 11:  2.1934 -  2.1250  1344   137  0.89  16.82   0.99     0.95       4566.62|
| 12:  2.1250 -  2.0644  1298   146  0.90  16.65   1.00     1.00       4299.83|
| 13:  2.0644 -  2.0102  1122   136  0.90  16.46   0.99     0.97       3468.34|
| 14:  2.0102 -  1.9613   371    31  0.90  15.65   0.98     0.95       2411.61|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     2411.61 max =        10950.36 mean =      6656.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.44|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    89.73   16.78    None  None   None       |
|    all(noH): 2823   0      1.49    89.73   16.78    None  None   None       |
|    Sol.    : 438    0      6.10    79.83   38.47    None  None   None       |
|    Mac.    : 2385   0      1.49    89.73   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.486 -  10.310: 1109   |   5:    45.607 -  54.432:   95        |
|      1:    10.310 -  19.135: 1051   |   6:    54.432 -  63.256:   41        |
|      2:    19.135 -  27.959:  231   |   7:    63.256 -  72.080:   22        |
|      3:    27.959 -  36.783:  138   |   8:    72.080 -  80.904:    5        |
|      4:    36.783 -  45.607:  126   |   9:    80.904 -  89.729:    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)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.673 - 4.351
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 318
   mapped sites are within: 0.751 - 4.351

peak=    6.046 closest distance to " CB  GLN A 223 " =    1.484
peak=    5.603 closest distance to " CG  PRO A  54 " =    1.288
peak=    5.571 closest distance to " O   HOH Z 111 " =    2.020
peak=    5.298 closest distance to " CG  PRO A 213 " =    1.256
peak=    5.179 closest distance to " CB  SER A  63 " =    1.349
peak=    4.921 closest distance to " CB  PRO A  54 " =    0.897
peak=    4.882 closest distance to " CG  PRO A  90 " =    1.112
peak=    4.856 closest distance to " CB  LEU A 228 " =    1.078
peak=    4.795 closest distance to " CB  GLU A 128 " =    1.049
peak=    4.776 closest distance to " CG  PRO A 198 " =    1.337
peak=    4.755 closest distance to " O   HOH Z 126 " =    1.916
peak=    4.632 closest distance to " O   HOH Z  15 " =    2.148
peak=    4.565 closest distance to " CB  GLN A 183 " =    1.227
peak=    4.565 closest distance to " O   PRO A 198 " =    1.579
peak=    4.531 closest distance to " O   HOH Z 236 " =    1.919
peak=    4.503 closest distance to " NE2 GLN A  11 " =    1.118
peak=    4.498 closest distance to " CB  ARG A 275 " =    0.897
peak=    4.446 closest distance to " O   HOH Z 135 " =    1.804
peak=    4.436 closest distance to " CB  ASN A 148 " =    1.304
peak=    4.384 closest distance to " CB  SER A 216 " =    0.836
peak=    4.376 closest distance to " NH2AARG A 102 " =    0.978
peak=    4.374 closest distance to " O   HOH Z 232 " =    2.278
peak=    4.352 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.323 closest distance to " CG  PRO A 243 " =    1.106
peak=    4.270 closest distance to " O   HOH Z 344 " =    3.243
peak=    4.269 closest distance to " O   HOH Z 108 " =    1.647
peak=    4.265 closest distance to " CA  TYR A  30 " =    1.042
peak=    4.264 closest distance to " O   HOH Z 368 " =    2.026
peak=    4.246 closest distance to " O   HOH Z 193 " =    1.701
peak=    4.241 closest distance to " CB  SER A   3 " =    1.413
peak=    4.231 closest distance to " OD2 ASP A 286 " =    2.930
peak=    4.221 closest distance to " O   HOH Z 298 " =    1.785
peak=    4.187 closest distance to " O   HOH Z 183 " =    1.583
peak=    4.185 closest distance to " CZ  PHE A 192 " =    0.939
peak=    4.179 closest distance to " CG  PRO A 280 " =    0.805
peak=    4.128 closest distance to " O   HOH Z 247 " =    1.385
peak=    4.108 closest distance to " O   HOH Z  21 " =    1.715
peak=    4.103 closest distance to " O   HOH Z 272 " =    1.927
peak=    4.072 closest distance to " O   HOH Z  78 " =    1.951
peak=    4.067 closest distance to " NH2 ARG A 156 " =    1.263
peak=    4.059 closest distance to " CB  TYR A 169 " =    0.779
peak=    4.043 closest distance to " OD1 ASN A  69 " =    2.561
peak=    4.039 closest distance to " O   HOH Z 369 " =    1.951
peak=    4.029 closest distance to " CB  VAL A 265 " =    1.240
peak=    4.018 closest distance to " O   HOH Z  88 " =    3.686
peak=    4.016 closest distance to " O   HOH Z 132 " =    2.420
peak=    4.014 closest distance to " O   HOH Z 425 " =    1.444
peak=    4.001 closest distance to " CA  THR A 264 " =    0.881
peak=    3.987 closest distance to " CA  MET A  40 " =    1.107
peak=    3.979 closest distance to " CB  TRP A 266 " =    0.916
peak=    3.965 closest distance to " CA  THR A 221 " =    0.939
peak=    3.965 closest distance to " CD  ARG A 159 " =    0.814
peak=    3.958 closest distance to " O   HOH Z 133 " =    2.424
peak=    3.953 closest distance to " O   HOH Z 234 " =    3.829
peak=    3.944 closest distance to " CA  ASP A 124 " =    0.751
peak=    3.942 closest distance to " O   HOH Z 134 " =    1.464
peak=    3.941 closest distance to " CB  VAL A 202 " =    1.614
peak=    3.934 closest distance to " O   HOH Z 303 " =    2.151
peak=    3.933 closest distance to " CD1 LEU A 300 " =    1.324
peak=    3.929 closest distance to " O   HOH Z  48 " =    1.503
peak=    3.924 closest distance to " O   HOH Z 189 " =    2.465
peak=    3.919 closest distance to " CD BLYS A 290 " =    1.084
peak=    3.917 closest distance to " CB  ASN A 187 " =    1.070
peak=    3.916 closest distance to " OD1 ASN A 217 " =    1.661
peak=    3.911 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.910 closest distance to " CA  ALA A  21 " =    1.173
peak=    3.903 closest distance to " ND2 ASN A 187 " =    1.542
peak=    3.896 closest distance to " O   HOH Z 207 " =    1.895
peak=    3.891 closest distance to " O   HOH Z  68 " =    1.751
peak=    3.889 closest distance to " O   HOH Z 112 " =    1.470
peak=    3.882 closest distance to " CB  MET A  47 " =    0.999
peak=    3.877 closest distance to " CG2 THR A 221 " =    0.963
peak=    3.866 closest distance to " O   HOH Z 126 " =    1.561
peak=    3.866 closest distance to " CG1 ILE A  33 " =    1.333
peak=    3.860 closest distance to " O   HOH Z 316 " =    3.091
peak=    3.857 closest distance to " O   HOH Z 193 " =    1.820
peak=    3.853 closest distance to " CB  ARG A  79 " =    1.422
peak=    3.852 closest distance to " N   ASN A  39 " =    1.325
peak=    3.839 closest distance to " CD  ARG A 269 " =    0.900
peak=    3.837 closest distance to " CB  GLU A 152 " =    1.506
peak=    3.829 closest distance to " CZ  PHE A 208 " =    1.180
peak=    3.826 closest distance to " CB  LEU A 143 " =    1.085
peak=    3.817 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.807 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.796 closest distance to " CA  PRO A  54 " =    1.339
peak=    3.790 closest distance to " O   HOH Z 108 " =    1.854
peak=    3.770 closest distance to " CA  ASN A 215 " =    1.292
peak=    3.755 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.753 closest distance to " CD  LYS A 119 " =    1.346
peak=    3.747 closest distance to " O   HOH Z  78 " =    1.631
peak=    3.743 closest distance to " O   HOH Z 281 " =    4.351
peak=    3.737 closest distance to " NH2BARG A 145 " =    2.055
peak=    3.734 closest distance to " CB  MET A  40 " =    0.806
peak=    3.730 closest distance to " O   HOH Z 346 " =    1.671
peak=    3.723 closest distance to " CB  ALA A 291 " =    1.320
peak=    3.722 closest distance to " N   ARG A 156 " =    1.408
peak=    3.718 closest distance to " CB  TRP A 179 " =    1.517
peak=    3.717 closest distance to " CZ  PHE A 218 " =    0.994
peak=    3.711 closest distance to " O   HOH Z 427 " =    2.989
peak=    3.710 closest distance to " O   HOH Z 389 " =    1.939
peak=    3.704 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.703 closest distance to " O   HOH Z  58 " =    1.653
peak=    3.693 closest distance to " O   HOH Z 144 " =    1.550
peak=    3.674 closest distance to " CB  ARG A 190 " =    1.648
peak=    3.664 closest distance to " O   HOH Z 437 " =    1.613
peak=    3.664 closest distance to " ND1 HIS A  86 " =    1.766
peak=    3.658 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.650 closest distance to " CD  LYS A 166 " =    1.318
peak=    3.648 closest distance to " O   HOH Z 227 " =    1.649
peak=    3.631 closest distance to " O   HOH Z 426 " =    1.545
peak=    3.629 closest distance to " O   HOH Z 171 " =    3.823
peak=    3.626 closest distance to " O   HOH Z  66 " =    2.077
peak=    3.622 closest distance to " O   HOH Z 193 " =    2.169
peak=    3.620 closest distance to " NH2AARG A 190 " =    1.497
peak=    3.618 closest distance to " CE  LYS A  76 " =    0.880
peak=    3.618 closest distance to " O   HOH Z 409 " =    2.982
peak=    3.614 closest distance to " CA  ASP A 191 " =    0.759
peak=    3.595 closest distance to " CG1 ILE A 151 " =    0.917
peak=    3.591 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.590 closest distance to " O   HOH Z  40 " =    2.118
peak=    3.581 closest distance to " O   HOH Z  20 " =    2.155
peak=    3.577 closest distance to " O   HOH Z  80 " =    1.659
peak=    3.573 closest distance to " O   HOH Z 371 " =    3.078
peak=    3.572 closest distance to " O   HOH Z  85 " =    2.253
peak=    3.571 closest distance to " NH1 ARG A  56 " =    1.005
peak=    3.566 closest distance to " O   HOH Z 411 " =    3.707
peak=    3.565 closest distance to " O   HOH Z 282 " =    1.433
peak=    3.556 closest distance to " CD  ARG A 219 " =    1.056
peak=    3.555 closest distance to " CB  ILE A 234 " =    1.041
peak=    3.551 closest distance to " CD2 LEU A 255 " =    1.449
peak=    3.549 closest distance to " O   HOH Z 261 " =    1.795
peak=    3.549 closest distance to " N   TYR A  15 " =    0.784
peak=    3.548 closest distance to " O   HOH Z 313 " =    1.833
peak=    3.545 closest distance to " CB  GLU A 277 " =    3.641
peak=    3.543 closest distance to " O   THR A 220 " =    1.483
peak=    3.538 closest distance to " O   HOH Z 327 " =    2.184
peak=    3.538 closest distance to " OE1 GLN A  58 " =    1.238
peak=    3.537 closest distance to " O   HOH Z 295 " =    1.507
peak=    3.536 closest distance to " O   MET A 105 " =    1.807
peak=    3.534 closest distance to " CG  ARG A 159 " =    1.019
peak=    3.532 closest distance to " O   HOH Z  54 " =    1.676
peak=    3.530 closest distance to " CA  SER A  87 " =    0.918
peak=    3.528 closest distance to " CA  GLN A 223 " =    0.968
peak=    3.523 closest distance to " OG1 THR A 294 " =    1.663
peak=    3.521 closest distance to " O   HOH Z  49 " =    2.252
peak=    3.513 closest distance to " N   ASN A 127 " =    1.267
peak=    3.509 closest distance to " O   HOH Z   4 " =    1.958
peak=    3.507 closest distance to " CB  ALA A 248 " =    0.937
peak=    3.504 closest distance to " O   HOH Z 352 " =    1.841
peak=    3.502 closest distance to " O   HOH Z 263 " =    2.226
peak=    3.496 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.494 closest distance to " CG BARG A 275 " =    1.542
peak=    3.489 closest distance to " CB  PHE A  16 " =    1.033
peak=    3.483 closest distance to " CA  GLU A 152 " =    0.870
peak=    3.482 closest distance to " CG1 VAL A 153 " =    1.009
peak=    3.480 closest distance to " NZ  LYS A 117 " =    3.410
peak=    3.475 closest distance to " O   HOH Z 163 " =    1.606
peak=    3.470 closest distance to " CB  PRO A 198 " =    0.890
peak=    3.462 closest distance to " CD  ARG A  14 " =    1.267
peak=    3.460 closest distance to " CB  GLU A 236 " =    1.035
peak=    3.460 closest distance to " CB  TYR A 169 " =    0.790
peak=    3.459 closest distance to " O   HOH Z  93 " =    2.662
peak=    3.456 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.455 closest distance to " CD  ARG A  66 " =    2.226
peak=    3.453 closest distance to " O   HOH Z  10 " =    1.840
peak=    3.451 closest distance to " O   HOH Z  97 " =    1.911
peak=    3.441 closest distance to " CA  TYR A 186 " =    1.460
peak=    3.439 closest distance to " O   HOH Z 188 " =    2.202
peak=    3.435 closest distance to " NZ  LYS A 166 " =    3.017
peak=    3.434 closest distance to " CA  LYS A  48 " =    1.319
peak=    3.433 closest distance to " O   HOH Z 273 " =    2.662
peak=    3.432 closest distance to " CA  ILE A 234 " =    0.955
peak=    3.430 closest distance to " CB  ASP A 171 " =    0.809
peak=    3.429 closest distance to " O   HOH Z 209 " =    2.257
peak=    3.419 closest distance to " CB  SER A 212 " =    1.132
peak=    3.418 closest distance to " O   THR A 251 " =    1.209
peak=    3.417 closest distance to " O   HOH Z 383 " =    1.943
peak=    3.416 closest distance to " CB  THR A 157 " =    1.124
peak=    3.415 closest distance to " CA  ARG A  36 " =    1.243
peak=    3.413 closest distance to " O   HOH Z   6 " =    2.211
peak=    3.411 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.406 closest distance to " O   HOH Z 387 " =    2.997
peak=    3.403 closest distance to " O   HOH Z 280 " =    3.163
peak=    3.400 closest distance to " CB  ILE A 199 " =    0.959
peak=    3.397 closest distance to " O   HOH Z 368 " =    3.717
peak=    3.390 closest distance to " CG1BVAL A  72 " =    1.565
peak=    3.389 closest distance to " CB  ILE A 120 " =    1.112
peak=    3.385 closest distance to " NE AARG A 275 " =    1.501
peak=    3.384 closest distance to " O   HOH Z 213 " =    1.909
peak=    3.379 closest distance to " CG  MET A 113 " =    1.405
peak=    3.375 closest distance to " CB  TRP A 123 " =    1.032
peak=    3.375 closest distance to " CA  ALA A 158 " =    1.065
peak=    3.370 closest distance to " CB  ALA A  71 " =    1.385
peak=    3.368 closest distance to " O   HOH Z 287 " =    1.746
peak=    3.366 closest distance to " O   HOH Z 260 " =    1.131
peak=    3.363 closest distance to " CA  ARG A 102 " =    1.254
peak=    3.362 closest distance to " CG2 VAL A  78 " =    0.928
peak=    3.362 closest distance to " NE1 TRP A 266 " =    1.342
peak=    3.358 closest distance to " O   HOH Z 403 " =    1.394
peak=    3.357 closest distance to " OD1 ASP A 231 " =    1.801
peak=    3.355 closest distance to " O   HOH Z 133 " =    1.731
peak=    3.351 closest distance to " O   HOH Z 329 " =    3.570
peak=    3.348 closest distance to " CD  ARG A  66 " =    3.804
peak=    3.346 closest distance to " O   HOH Z 302 " =    2.042
peak=    3.344 closest distance to " O   ALA A 165 " =    1.444
peak=    3.344 closest distance to " CD1AILE A 234 " =    1.078
peak=    3.338 closest distance to " OE1 GLN A  11 " =    2.155
peak=    3.334 closest distance to " O   HOH Z 128 " =    2.262
peak=    3.331 closest distance to " ND1 HIS A  81 " =    1.559
peak=    3.327 closest distance to " CA  ALA A  51 " =    0.914
peak=    3.326 closest distance to " CG BARG A 102 " =    1.879
peak=    3.326 closest distance to " CA  GLY A 267 " =    1.169
peak=    3.321 closest distance to " O   HOH Z 197 " =    2.761
peak=    3.315 closest distance to " CA  ALA A 160 " =    0.880
peak=    3.315 closest distance to " O   SER A  87 " =    2.282
peak=    3.312 closest distance to " O   HOH Z 271 " =    2.514
peak=    3.308 closest distance to " CA  ASP A 140 " =    1.218
peak=    3.307 closest distance to " CB  ARG A 139 " =    0.861
peak=    3.306 closest distance to " CD2 HIS A  81 " =    1.263
peak=    3.306 closest distance to " O   ALA A 233 " =    1.804
peak=    3.305 closest distance to " O   HOH Z 126 " =    1.729
peak=    3.305 closest distance to " O   HOH Z 374 " =    2.814
peak=    3.305 closest distance to " O   HOH Z   1 " =    2.208
peak=    3.299 closest distance to " O   HOH Z  44 " =    3.456
peak=    3.294 closest distance to " O   HOH Z 337 " =    3.770
peak=    3.294 closest distance to " O   HOH Z 163 " =    1.998
peak=    3.292 closest distance to " O   HOH Z 186 " =    1.225
peak=    3.289 closest distance to " CB  ALA A 184 " =    0.997
peak=    3.287 closest distance to " OD1 ASP A 238 " =    0.994
peak=    3.286 closest distance to " O   HOH Z 147 " =    1.695
peak=    3.285 closest distance to " O   TRP A 274 " =    1.708
peak=    3.284 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.283 closest distance to " NE AARG A 102 " =    1.282
peak=    3.279 closest distance to " CG  GLN A  88 " =    1.022
peak=    3.273 closest distance to " CG2 VAL A 112 " =    0.842
peak=    3.273 closest distance to " O   HOH Z 116 " =    1.854
peak=    3.273 closest distance to " O   HOH Z 263 " =    1.687
peak=    3.267 closest distance to " CD1 ILE A 106 " =    0.799
peak=    3.267 closest distance to " O   HOH Z  64 " =    2.189
peak=    3.266 closest distance to " O   HOH Z 345 " =    1.785
peak=    3.261 closest distance to " O   HOH Z 411 " =    1.822
peak=    3.258 closest distance to " CB  ASP A 140 " =    0.769
peak=    3.258 closest distance to " O   HOH Z 334 " =    1.494
peak=    3.257 closest distance to " O   ALA A   1 " =    1.512
peak=    3.251 closest distance to " CZ3 TRP A 123 " =    1.189
peak=    3.245 closest distance to " NZ ALYS A 290 " =    1.194
peak=    3.245 closest distance to " CG  GLU A 277 " =    3.062
peak=    3.239 closest distance to " C   TYR A 214 " =    1.608
peak=    3.234 closest distance to " O   HOH Z  66 " =    2.243
peak=    3.233 closest distance to " O   HOH Z 214 " =    1.938
peak=    3.228 closest distance to " O   HOH Z 184 " =    1.541
peak=    3.226 closest distance to " O   HOH Z 353 " =    2.695
peak=    3.220 closest distance to " O   HOH Z 139 " =    3.191
peak=    3.220 closest distance to " CG  GLN A 144 " =    0.887
peak=    3.212 closest distance to " CE2 TYR A 247 " =    1.333
peak=    3.205 closest distance to " CB  TYR A 116 " =    0.940
peak=    3.205 closest distance to " O   HOH Z 211 " =    2.420
peak=    3.201 closest distance to " CA  LYS A 290 " =    1.341
peak=    3.201 closest distance to " O   HOH Z 368 " =    2.515
peak=    3.200 closest distance to " O   HOH Z  44 " =    1.890
peak=    3.200 closest distance to " O   GLY A  57 " =    2.579
peak=    3.198 closest distance to " O   HOH Z 407 " =    2.347
peak=    3.196 closest distance to " CG AARG A 275 " =    1.078
peak=    3.195 closest distance to " CG2 VAL A 174 " =    1.376
peak=    3.195 closest distance to " NH1BARG A 145 " =    1.199
peak=    3.191 closest distance to " CG2BVAL A  41 " =    0.941
peak=    3.188 closest distance to " CD1 TRP A 266 " =    1.140
peak=    3.186 closest distance to " O   HOH Z 156 " =    2.772
peak=    3.182 closest distance to " N   ALA A 154 " =    0.922
peak=    3.181 closest distance to " O   HOH Z 152 " =    2.371
peak=    3.179 closest distance to " O   HOH Z 163 " =    1.734
peak=    3.178 closest distance to " CG2 THR A 220 " =    1.117
peak=    3.178 closest distance to " O   HOH Z 299 " =    2.427
peak=    3.173 closest distance to " CB  ALA A  34 " =    1.033
peak=    3.169 closest distance to " O   HOH Z  53 " =    2.557
peak=    3.165 closest distance to " CG  GLN A  55 " =    1.844
peak=    3.165 closest distance to " CB  LEU A 255 " =    0.764
peak=    3.163 closest distance to " O   HOH Z 175 " =    3.601
peak=    3.162 closest distance to " O   HOH Z 158 " =    2.864
peak=    3.160 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.159 closest distance to " CB  PHE A 283 " =    0.801
peak=    3.156 closest distance to " O   HOH Z 261 " =    2.040
peak=    3.154 closest distance to " O   HOH Z 248 " =    2.022
peak=    3.153 closest distance to " O   HOH Z 286 " =    2.205
peak=    3.150 closest distance to " CA  ILE A  33 " =    1.718
peak=    3.149 closest distance to " O   HOH Z 379 " =    1.953
peak=    3.147 closest distance to " O   HOH Z 345 " =    3.456
peak=    3.133 closest distance to " O   HOH Z 149 " =    1.881
peak=    3.130 closest distance to " O   TYR A 116 " =    1.294
peak=    3.129 closest distance to " OG BSER A 164 " =    2.474
peak=    3.128 closest distance to " CA  ASP A 162 " =    1.177
peak=    3.123 closest distance to " CB  ALA A 256 " =    1.383
peak=    3.113 closest distance to " O   HOH Z 219 " =    2.071
peak=    3.112 closest distance to " NZ  LYS A  76 " =    1.184
peak=    3.110 closest distance to " O   HOH Z 305 " =    3.693
peak=    3.110 closest distance to " O   HOH Z 332 " =    1.574
peak=    3.100 closest distance to " NH2 ARG A 219 " =    1.844
peak=    3.100 closest distance to " CD1 ILE A  33 " =    1.504
peak=    3.099 closest distance to " OD1 ASP A 171 " =    1.321
peak=    3.097 closest distance to " O   HOH Z 216 " =    2.600
peak=    3.096 closest distance to " O   HOH Z 175 " =    2.145
peak=    3.094 closest distance to " O   HOH Z 392 " =    2.105
peak=    3.091 closest distance to " CA  GLY A 196 " =    0.781
peak=    3.090 closest distance to " O   HOH Z 301 " =    1.884
peak=    3.086 closest distance to " CA  ALA A 299 " =    0.960
peak=    3.080 closest distance to " O   HOH Z 403 " =    1.670
peak=    3.063 closest distance to " CB  PHE A  16 " =    1.194
peak=    3.061 closest distance to " CB  LEU A 237 " =    0.852
peak=    3.057 closest distance to " O   HOH Z 419 " =    3.041
peak=    3.057 closest distance to " O   HOH Z 281 " =    1.906
peak=    3.050 closest distance to " CG  MET A 185 " =    1.063
peak=    3.048 closest distance to " CD  PRO A 280 " =    0.983
peak=    3.046 closest distance to " O   HOH Z 391 " =    2.958
peak=    3.037 closest distance to " CB  ARG A 138 " =    1.071
peak=    3.001 closest distance to " O   HOH Z 213 " =    2.404

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 184         
Filter by distance & map next to the model:
   mapped sites are within: 0.508 - 5.612
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 184
   mapped sites are within: 0.712 - 5.612

peak=   -4.774 closest distance to " O   HOH Z 290 " =    1.044
peak=   -4.514 closest distance to " O   HOH Z 377 " =    1.589
peak=   -4.417 closest distance to " N   ALA A  43 " =    2.330
peak=   -4.271 closest distance to " O   HOH Z 266 " =    4.484
peak=   -4.261 closest distance to " C   ALA A 158 " =    1.297
peak=   -4.216 closest distance to " CB  PRO A 243 " =    2.576
peak=   -4.194 closest distance to " O   HOH Z 198 " =    2.477
peak=   -4.106 closest distance to " O   PRO A 198 " =    1.266
peak=   -4.097 closest distance to " ND2 ASN A  45 " =    0.921
peak=   -4.052 closest distance to " CZ3 TRP A 179 " =    1.174
peak=   -4.033 closest distance to " O   HOH Z  98 " =    1.967
peak=   -3.992 closest distance to " CD1 LEU A 228 " =    2.460
peak=   -3.951 closest distance to " CD  GLN A  88 " =    0.777
peak=   -3.931 closest distance to " O   HOH Z 231 " =    1.932
peak=   -3.924 closest distance to " O   HOH Z  19 " =    2.504
peak=   -3.891 closest distance to " CD  GLN A 223 " =    1.449
peak=   -3.878 closest distance to " CE2 TYR A  30 " =    2.833
peak=   -3.874 closest distance to " CG  MET A 105 " =    0.964
peak=   -3.862 closest distance to " O   ILE A 109 " =    2.631
peak=   -3.843 closest distance to " CG  LYS A 193 " =    2.458
peak=   -3.832 closest distance to " O   HOH Z  43 " =    1.504
peak=   -3.829 closest distance to " O   HOH Z 275 " =    1.626
peak=   -3.828 closest distance to " O   GLY A 211 " =    1.403
peak=   -3.810 closest distance to " O   HOH Z 407 " =    3.471
peak=   -3.791 closest distance to " OE1 GLN A  88 " =    1.035
peak=   -3.782 closest distance to " C   ASN A 187 " =    1.835
peak=   -3.780 closest distance to " NH2AARG A 275 " =    5.612
peak=   -3.768 closest distance to " O   HOH Z 185 " =    2.330
peak=   -3.754 closest distance to " O   HOH Z  10 " =    1.554
peak=   -3.753 closest distance to " CB  CYS A 254 " =    2.309
peak=   -3.739 closest distance to " C   ASN A 285 " =    2.551
peak=   -3.738 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.717 closest distance to " O   HOH Z  71 " =    1.115
peak=   -3.711 closest distance to " CE  MET A  93 " =    1.183
peak=   -3.703 closest distance to " CB  ASN A  39 " =    2.061
peak=   -3.696 closest distance to " OXT GLY A 302 " =    2.789
peak=   -3.684 closest distance to " CD2 LEU A 300 " =    2.991
peak=   -3.671 closest distance to " CD  ARG A 195 " =    5.137
peak=   -3.665 closest distance to " CG1 VAL A 250 " =    2.651
peak=   -3.661 closest distance to " CD  ARG A  14 " =    3.262
peak=   -3.660 closest distance to " O   HOH Z  38 " =    1.448
peak=   -3.650 closest distance to " CG  GLU A  53 " =    1.309
peak=   -3.633 closest distance to " SG  CYS A 254 " =    3.071
peak=   -3.621 closest distance to " O   HOH Z  52 " =    1.248
peak=   -3.616 closest distance to " OD1 ASP A 191 " =    1.619
peak=   -3.601 closest distance to " O   HOH Z 388 " =    1.952
peak=   -3.595 closest distance to " CD2 TYR A 293 " =    2.013
peak=   -3.592 closest distance to " CD1 LEU A 101 " =    2.632
peak=   -3.592 closest distance to " O   HOH Z 353 " =    2.181
peak=   -3.591 closest distance to " O   HOH Z 231 " =    1.184
peak=   -3.590 closest distance to " O   HOH Z 118 " =    2.736
peak=   -3.590 closest distance to " O   VAL A  67 " =    2.702
peak=   -3.587 closest distance to " CD  ARG A 156 " =    1.895
peak=   -3.578 closest distance to " CG  LEU A  83 " =    1.934
peak=   -3.569 closest distance to " O   HOH Z  98 " =    2.169
peak=   -3.564 closest distance to " CZ  TYR A 169 " =    1.714
peak=   -3.553 closest distance to " O   SER A  62 " =    2.163
peak=   -3.542 closest distance to " O   HOH Z 298 " =    1.192
peak=   -3.541 closest distance to " OD1 ASN A 148 " =    1.658
peak=   -3.538 closest distance to " O   HOH Z 222 " =    1.161
peak=   -3.516 closest distance to " CD1 ILE A 239 " =    2.050
peak=   -3.514 closest distance to " O   HOH Z  13 " =    1.235
peak=   -3.504 closest distance to " O   HOH Z 266 " =    4.960
peak=   -3.499 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.498 closest distance to " O   HOH Z 148 " =    3.547
peak=   -3.489 closest distance to " C   LEU A 143 " =    1.414
peak=   -3.485 closest distance to " O   PRO A 163 " =    1.988
peak=   -3.478 closest distance to " O   HOH Z 184 " =    1.660
peak=   -3.474 closest distance to " CB  ALA A  43 " =    2.445
peak=   -3.470 closest distance to " O   HOH Z 389 " =    1.936
peak=   -3.464 closest distance to " C   LEU A 222 " =    0.862
peak=   -3.450 closest distance to " O   GLY A 196 " =    1.164
peak=   -3.447 closest distance to " O   HOH Z 166 " =    1.833
peak=   -3.440 closest distance to " O   HOH Z 426 " =    1.742
peak=   -3.438 closest distance to " N   SER A 212 " =    1.870
peak=   -3.427 closest distance to " CD1 PHE A  59 " =    1.846
peak=   -3.425 closest distance to " CE3 TRP A 150 " =    1.800
peak=   -3.422 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.418 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.417 closest distance to " CG  GLU A 152 " =    0.848
peak=   -3.403 closest distance to " CB  PHE A 283 " =    2.770
peak=   -3.401 closest distance to " OG BSER A 134 " =    1.754
peak=   -3.401 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.397 closest distance to " CA  GLY A 241 " =    3.032
peak=   -3.391 closest distance to " O   HOH Z 252 " =    4.210
peak=   -3.391 closest distance to " OG BSER A 134 " =    1.218
peak=   -3.388 closest distance to " ND2 ASN A 249 " =    1.990
peak=   -3.380 closest distance to " OG ASER A 134 " =    1.355
peak=   -3.370 closest distance to " O   HOH Z  92 " =    1.377
peak=   -3.360 closest distance to " O   HOH Z 166 " =    1.381
peak=   -3.347 closest distance to " O   HOH Z 417 " =    2.620
peak=   -3.347 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.347 closest distance to " O   HOH Z 111 " =    2.129
peak=   -3.340 closest distance to " NH1 ARG A 195 " =    2.610
peak=   -3.337 closest distance to " O   HOH Z  11 " =    1.952
peak=   -3.335 closest distance to " CD  LYS A 289 " =    2.515
peak=   -3.327 closest distance to " C   HIS A 108 " =    1.036
peak=   -3.324 closest distance to " O   HOH Z 435 " =    2.753
peak=   -3.321 closest distance to " O   HOH Z 436 " =    1.376
peak=   -3.320 closest distance to " CD2 LEU A 237 " =    2.809
peak=   -3.319 closest distance to " O   HOH Z 283 " =    2.219
peak=   -3.319 closest distance to " CG  PRO A 163 " =    2.346
peak=   -3.311 closest distance to " OG  SER A  87 " =    1.367
peak=   -3.308 closest distance to " CA  VAL A 232 " =    2.508
peak=   -3.307 closest distance to " O   HOH Z 241 " =    1.218
peak=   -3.306 closest distance to " OD1 ASN A 249 " =    1.126
peak=   -3.305 closest distance to " CG1 VAL A 112 " =    2.563
peak=   -3.293 closest distance to " O   ALA A 161 " =    1.478
peak=   -3.292 closest distance to " O   ALA A   7 " =    1.552
peak=   -3.290 closest distance to " CE  MET A 105 " =    2.071
peak=   -3.290 closest distance to " O   ASN A 249 " =    1.561
peak=   -3.287 closest distance to " NE2 GLN A  88 " =    0.940
peak=   -3.287 closest distance to " SG ACYS A 201 " =    2.089
peak=   -3.281 closest distance to " O   HOH Z 103 " =    1.899
peak=   -3.278 closest distance to " N   GLY A  23 " =    2.168
peak=   -3.272 closest distance to " CG  ARG A 269 " =    2.473
peak=   -3.271 closest distance to " CB  LEU A 167 " =    2.122
peak=   -3.268 closest distance to " N   THR A 264 " =    1.180
peak=   -3.265 closest distance to " CZ  ARG A  66 " =    0.712
peak=   -3.260 closest distance to " NE2 GLN A  58 " =    1.241
peak=   -3.259 closest distance to " O   HOH Z  93 " =    2.362
peak=   -3.257 closest distance to " NH1BARG A 275 " =    2.007
peak=   -3.252 closest distance to " CD2 PHE A  59 " =    2.555
peak=   -3.251 closest distance to " O   HOH Z 177 " =    1.598
peak=   -3.246 closest distance to " CA  ARG A 139 " =    1.027
peak=   -3.244 closest distance to " O   HOH Z  11 " =    1.983
peak=   -3.242 closest distance to " CE3 TRP A  70 " =    1.824
peak=   -3.236 closest distance to " O   VAL A 153 " =    2.311
peak=   -3.235 closest distance to " CD  GLN A  88 " =    2.111
peak=   -3.235 closest distance to " CG  TRP A 266 " =    1.691
peak=   -3.229 closest distance to " CD  ARG A 159 " =    1.243
peak=   -3.224 closest distance to " CA  GLY A 203 " =    2.193
peak=   -3.221 closest distance to " CA  GLY A 241 " =    2.263
peak=   -3.219 closest distance to " CE  MET A 105 " =    1.922
peak=   -3.219 closest distance to " CD  GLN A  11 " =    0.759
peak=   -3.217 closest distance to " OE2 GLU A   2 " =    1.559
peak=   -3.217 closest distance to " O   HOH Z 243 " =    1.996
peak=   -3.216 closest distance to " O   HOH Z 317 " =    2.605
peak=   -3.213 closest distance to " CD1 ILE A 263 " =    2.572
peak=   -3.211 closest distance to " CB  TRP A  85 " =    2.423
peak=   -3.203 closest distance to " CZ  PHE A  59 " =    1.626
peak=   -3.186 closest distance to " CB  SER A 271 " =    1.842
peak=   -3.184 closest distance to " O   SER A  12 " =    1.532
peak=   -3.180 closest distance to " CB  PRO A 163 " =    2.634
peak=   -3.176 closest distance to " OD2 ASP A 171 " =    1.806
peak=   -3.175 closest distance to " O   HOH Z 390 " =    2.268
peak=   -3.171 closest distance to " CB  ALA A 291 " =    2.315
peak=   -3.166 closest distance to " ND2 ASN A  60 " =    1.918
peak=   -3.165 closest distance to " N   SER A 276 " =    1.327
peak=   -3.163 closest distance to " OD2 ASP A  50 " =    2.352
peak=   -3.160 closest distance to " O   HOH Z   6 " =    1.628
peak=   -3.160 closest distance to " OD2 ASP A 200 " =    1.318
peak=   -3.155 closest distance to " O   HOH Z 402 " =    1.489
peak=   -3.152 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.151 closest distance to " O   GLY A 118 " =    2.209
peak=   -3.146 closest distance to " O   HOH Z 128 " =    4.140
peak=   -3.143 closest distance to " O   HOH Z 148 " =    1.900
peak=   -3.138 closest distance to " CD1 LEU A 297 " =    2.672
peak=   -3.138 closest distance to " O   HOH Z 210 " =    0.956
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.393
peak=   -3.131 closest distance to " O   HOH Z 437 " =    2.014
peak=   -3.130 closest distance to " CD1 ILE A 199 " =    2.617
peak=   -3.129 closest distance to " O   HOH Z 176 " =    0.734
peak=   -3.122 closest distance to " CE1 TYR A 169 " =    2.455
peak=   -3.122 closest distance to " OG1 THR A 178 " =    1.334
peak=   -3.119 closest distance to " O   HOH Z  63 " =    1.280
peak=   -3.119 closest distance to " CD2 TRP A 274 " =    2.425
peak=   -3.116 closest distance to " O   HOH Z  60 " =    1.765
peak=   -3.114 closest distance to " CG1 VAL A 197 " =    2.319
peak=   -3.113 closest distance to " OG  SER A  62 " =    1.566
peak=   -3.105 closest distance to " O   HOH Z 234 " =    4.291
peak=   -3.099 closest distance to " CE2 TYR A 186 " =    2.092
peak=   -3.098 closest distance to " C   GLN A 240 " =    2.242
peak=   -3.087 closest distance to " CE2 PHE A 218 " =    2.469
peak=   -3.071 closest distance to " O   PHE A 218 " =    1.463
peak=   -3.069 closest distance to " O   HOH Z 309 " =    2.353
peak=   -3.063 closest distance to " O   HOH Z 396 " =    1.787
peak=   -3.054 closest distance to " O   VAL A 125 " =    2.224
peak=   -3.054 closest distance to " OD1 ASN A 301 " =    1.908
peak=   -3.046 closest distance to " CG1 VAL A 112 " =    2.697
peak=   -3.030 closest distance to " OG  SER A 206 " =    1.952

================= 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    :  0.4181 0.4225   6.219259e+00   6.223769e+00
   1_bss:  0.4065 0.4119   6.208790e+00   6.210043e+00
   1_xyz:  0.2517 0.2887   5.823972e+00   5.933881e+00
   1_adp:  0.2321 0.2946   5.782498e+00   5.956465e+00
   1_occ:  0.2317 0.2947   5.780756e+00   5.955245e+00
   2_bss:  0.2290 0.2904   5.773598e+00   5.946217e+00
   2_xyz:  0.1635 0.2160   5.477904e+00   5.693540e+00
   2_adp:  0.1449 0.1956   5.377144e+00   5.601508e+00
   2_occ:  0.1448 0.1955   5.376416e+00   5.600841e+00
   3_bss:  0.1447 0.1951   5.373537e+00   5.597748e+00
   3_xyz:  0.1251 0.1717   5.242896e+00   5.476968e+00
   3_adp:  0.1214 0.1648   5.210236e+00   5.438620e+00
   3_occ:  0.1212 0.1646   5.209626e+00   5.438110e+00
   4_bss:  0.1211 0.1645   5.208914e+00   5.437548e+00
   4_xyz:  0.1128 0.1591   5.157378e+00   5.398032e+00
   4_adp:  0.1111 0.1582   5.148685e+00   5.394273e+00
   4_occ:  0.1110 0.1581   5.148539e+00   5.394339e+00
   5_bss:  0.1112 0.1577   5.149304e+00   5.395076e+00
   5_xyz:  0.1150 0.1595   5.174195e+00   5.409015e+00
   5_adp:  0.1155 0.1597   5.177138e+00   5.411358e+00
   5_occ:  0.1155 0.1596   5.177134e+00   5.411570e+00
   5_bss:  0.1155 0.1596   5.177129e+00   5.411543e+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:  0.300  29.323   2.552  -3.164   1.615  -0.000   0.000   0.000
   1_xyz:  0.300  29.323   2.552  -3.164   1.615  -0.000   0.000   0.000
   1_adp:  0.300  29.323   2.552  -3.164   1.615  -0.000   0.000   0.000
   1_occ:  0.300  29.323   2.552  -3.164   1.615  -0.000   0.000   0.000
   2_bss:  0.338  56.648  -0.374  -2.903  -0.772  -0.000  -0.000  -0.000
   2_xyz:  0.338  56.648  -0.374  -2.903  -0.772  -0.000  -0.000  -0.000
   2_adp:  0.338  56.648  -0.374  -2.903  -0.772  -0.000  -0.000  -0.000
   2_occ:  0.338  56.648  -0.374  -2.903  -0.772  -0.000  -0.000  -0.000
   3_bss:  0.334  59.169  -1.372  -2.587  -1.515  -0.000  -0.000  -0.000
   3_xyz:  0.334  59.169  -1.372  -2.587  -1.515  -0.000  -0.000  -0.000
   3_adp:  0.334  59.169  -1.372  -2.587  -1.515  -0.000  -0.000  -0.000
   3_occ:  0.334  59.169  -1.372  -2.587  -1.515  -0.000  -0.000  -0.000
   4_bss:  0.333  59.169  -1.904  -2.624  -1.914  -0.000  -0.000  -0.000
   4_xyz:  0.333  59.169  -1.904  -2.624  -1.914  -0.000  -0.000  -0.000
   4_adp:  0.333  59.169  -1.904  -2.624  -1.914  -0.000  -0.000  -0.000
   4_occ:  0.333  59.169  -1.904  -2.624  -1.914  -0.000  -0.000  -0.000
   5_bss:  0.333  59.169  -1.924  -2.511  -1.964  -0.000  -0.000  -0.000
   5_xyz:  0.333  59.169  -1.924  -2.511  -1.964  -0.000  -0.000  -0.000
   5_adp:  0.333  59.169  -1.924  -2.511  -1.964  -0.000  -0.000  -0.000
   5_occ:  0.333  59.169  -1.924  -2.511  -1.964  -0.000  -0.000  -0.000
   5_bss:  0.333  59.114  -1.904  -2.403  -1.897  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.299 0.5164  0.6821    55428.179
   1_bss:  48.909 0.5322  0.7151    51953.293
   1_xyz:  29.584 0.7632  0.9709    22458.236
   1_adp:  30.858 0.7479  0.9570    23708.255
   1_occ:  30.837 0.7480  0.9564    23617.103
   2_bss:  30.391 0.7528  0.9077    23106.502
   2_xyz:  21.634 0.8447  0.9783    12294.600
   2_adp:  18.958 0.8714  0.9902    10090.419
   2_occ:  18.937 0.8717  0.9902    10069.172
   3_bss:  18.837 0.8725  0.9731     9960.268
   3_xyz:  15.994 0.8979  0.9837     7595.066
   3_adp:  15.037 0.9065  0.9854     7076.988
   3_occ:  15.019 0.9067  0.9854     7068.428
   4_bss:  15.005 0.9068  0.9741     7056.959
   4_xyz:  14.200 0.9134  0.9772     6473.548
   4_adp:  14.067 0.9147  0.9748     6426.573
   4_occ:  14.064 0.9148  0.9748     6426.333
   5_bss:  14.114 0.9143  0.9752     6448.278
   5_xyz:  14.364 0.9124  0.9727     6608.400
   5_adp:  14.384 0.9123  0.9706     6656.716
   5_occ:  14.385 0.9123  0.9705     6658.742
   5_bss:  14.385 0.9123  0.9708     6657.876
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7209e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7209e-01
   1_xyz:   1.420  0.013  0.093 16.034  0.006  4.117   1.2002e-01
   1_adp:   1.420  0.013  0.093 16.034  0.006  4.117   1.2002e-01
   1_occ:   1.420  0.013  0.093 16.034  0.006  4.117   1.2002e-01
   2_bss:   1.420  0.013  0.093 16.034  0.006  4.117   1.2002e-01
   2_xyz:   1.131  0.008  0.078 14.664  0.005  4.132   6.9657e-02
   2_adp:   1.131  0.008  0.078 14.664  0.005  4.132   6.9657e-02
   2_occ:   1.131  0.008  0.078 14.664  0.005  4.132   6.9657e-02
   3_bss:   1.131  0.008  0.078 14.664  0.005  4.132   6.9657e-02
   3_xyz:   1.040  0.008  0.074 14.454  0.004  4.121   6.2325e-02
   3_adp:   1.040  0.008  0.074 14.454  0.004  4.121   6.2325e-02
   3_occ:   1.040  0.008  0.074 14.454  0.004  4.121   6.2325e-02
   4_bss:   1.040  0.008  0.074 14.454  0.004  4.121   6.2325e-02
   4_xyz:   1.151  0.010  0.080 14.746  0.004  4.127   7.5146e-02
   4_adp:   1.151  0.010  0.080 14.746  0.004  4.127   7.5146e-02
   4_occ:   1.151  0.010  0.080 14.746  0.004  4.127   7.5146e-02
   5_bss:   1.151  0.010  0.080 14.746  0.004  4.127   7.5146e-02
   5_xyz:   0.945  0.006  0.069 14.271  0.003  4.125   5.2509e-02
   5_adp:   0.945  0.006  0.069 14.271  0.003  4.125   5.2509e-02
   5_occ:   0.945  0.006  0.069 14.271  0.003  4.125   5.2509e-02
   5_bss:   0.945  0.006  0.069 14.271  0.003  4.125   5.2509e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.653   2.4109e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.653   2.4109e-01
   1_xyz:  10.910  0.082  0.392 81.987  0.031  2.173   1.1583e-01
   1_adp:  10.910  0.082  0.392 81.987  0.031  2.173   1.1583e-01
   1_occ:  10.910  0.082  0.392 81.987  0.031  2.173   1.1583e-01
   2_bss:  10.910  0.082  0.392 81.987  0.031  2.173   1.1583e-01
   2_xyz:   8.390  0.043  0.271 83.553  0.048  2.318   6.3946e-02
   2_adp:   8.390  0.043  0.271 83.553  0.048  2.318   6.3946e-02
   2_occ:   8.390  0.043  0.271 83.553  0.048  2.318   6.3946e-02
   3_bss:   8.390  0.043  0.271 83.553  0.048  2.318   6.3946e-02
   3_xyz:   8.661  0.052  0.250 82.097  0.030  2.289   4.7250e-02
   3_adp:   8.661  0.052  0.250 82.097  0.030  2.289   4.7250e-02
   3_occ:   8.661  0.052  0.250 82.097  0.030  2.289   4.7250e-02
   4_bss:   8.661  0.052  0.250 82.097  0.030  2.289   4.7250e-02
   4_xyz:   8.010  0.044  0.245 83.775  0.037  2.284   6.2319e-02
   4_adp:   8.010  0.044  0.245 83.775  0.037  2.284   6.2319e-02
   4_occ:   8.010  0.044  0.245 83.775  0.037  2.284   6.2319e-02
   5_bss:   8.010  0.044  0.245 83.775  0.037  2.284   6.2319e-02
   5_xyz:   8.030  0.046  0.209 83.621  0.030  2.390   3.7550e-02
   5_adp:   8.030  0.046  0.209 83.621  0.030  2.390   3.7550e-02
   5_occ:   8.030  0.046  0.209 83.621  0.030  2.390   3.7550e-02
   5_bss:   8.030  0.046  0.209 83.621  0.030  2.390   3.7550e-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:  76.42   0.00  17.29  76.42   0.00  13.28  63.32   4.72  39.12
   1_occ:  76.42   0.00  17.29  76.42   0.00  13.28  63.32   4.72  39.12
   2_bss:  76.42   0.00  17.29  76.42   0.00  13.28  63.32   4.72  39.12
   2_xyz:  76.42   0.00  17.29  76.42   0.00  13.28  63.32   4.72  39.12
   2_adp:  83.94   0.00  17.73  83.94   0.00  13.16  83.42   5.95  42.60
   2_occ:  83.94   0.00  17.73  83.94   0.00  13.16  83.42   5.95  42.60
   3_bss:  83.94   0.00  17.73  83.94   0.00  13.16  83.42   5.95  42.60
   3_xyz:  83.94   0.00  17.73  83.94   0.00  13.16  83.42   5.95  42.60
   3_adp:  84.28   0.00  17.34  84.28   0.00  13.01  79.52   6.13  40.94
   3_occ:  84.28   0.00  17.34  84.28   0.00  13.01  79.52   6.13  40.94
   4_bss:  84.28   0.00  17.34  84.28   0.00  13.01  79.52   6.13  40.94
   4_xyz:  84.28   0.00  17.34  84.28   0.00  13.01  79.52   6.13  40.94
   4_adp:  90.34   1.42  17.20  90.34   1.42  12.97  81.71   6.21  40.26
   4_occ:  90.34   1.42  17.20  90.34   1.42  12.97  81.71   6.21  40.26
   5_bss:  90.34   1.42  17.20  90.34   1.42  12.97  81.71   6.21  40.26
   5_xyz:  90.34   1.42  17.20  90.34   1.42  12.97  81.71   6.21  40.26
   5_adp:  89.78   1.54  16.83  89.78   1.54  12.85  79.88   6.16  38.52
   5_occ:  89.78   1.54  16.83  89.78   1.54  12.85  79.88   6.16  38.52
   5_bss:  89.73   1.49  16.78  89.73   1.49  12.79  79.83   6.10  38.47
------------------------------------------------------------------------
 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:    1.724    0.020    0.424
   1_adp:    1.724    0.020    0.424
   1_occ:    1.724    0.020    0.424
   2_bss:    1.724    0.020    0.424
   2_xyz:    1.179    0.027    0.528
   2_adp:    1.179    0.027    0.528
   2_occ:    1.179    0.027    0.528
   3_bss:    1.179    0.027    0.528
   3_xyz:    1.284    0.044    0.579
   3_adp:    1.284    0.044    0.579
   3_occ:    1.284    0.044    0.579
   4_bss:    1.284    0.044    0.579
   4_xyz:    1.241    0.019    0.601
   4_adp:    1.241    0.019    0.601
   4_occ:    1.241    0.019    0.601
   5_bss:    1.241    0.019    0.601
   5_xyz:    1.273    0.026    0.605
   5_adp:    1.273    0.026    0.605
   5_occ:    1.273    0.026    0.605
   5_bss:    1.273    0.026    0.605
------------------------------------------------------------------------

CPU time actual refinement: 330.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/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_1266/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1266/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.38 
  Macro-tasks:
    bulk solvent and scale       = 38.22  
    individual site refinement   = 133.47 
    weights calculation          = 29.93  
    collect and process          = 6.74   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.47 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 107.54 
    alpha_beta                      = 8.26   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.89 
    fmodel                         = 6.32   
    r_factors                      = 0.17   
    phase_errors                   = 10.98  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 250.35 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.774 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    615 calls, 107.21 s
gradients_fft:          560 calls, 101.47 s

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

# Date 2008-01-16 Time 06:49:34 PST -0800 (1200494974.06 s)
Start R-work = 0.4181, R-free = 0.4225 (no bulk solvent and anisotropic scale)
Final R-work = 0.1398, R-free = 0.1817 (no bulk solvent and anisotropic scale)

Start R-work = 0.4065, R-free = 0.4119
Final R-work = 0.1155, R-free = 0.1596