# Date 2008-01-16 Time 06:00:23 PST -0800 (1200492023.19 s)
#phil __OFF__

Command line arguments: "../971.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21912
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 971

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.7567, 85.5261, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.95391
Completeness in resolution range: 0.938036
Completeness with d_max=infinity: 0.935348

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9539

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.95391
Completeness in resolution range: 0.938036
Completeness with d_max=infinity: 0.935348

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.1826 [2193/2220]  1976   217   9.9%
  bin  2:  4.1826 -  3.3316 [2104/2124]  1892   212  10.1%
  bin  3:  3.3316 -  2.9139 [2076/2095]  1867   209  10.1%
  bin  4:  2.9139 -  2.6490 [2051/2081]  1843   208  10.1%
  bin  5:  2.6490 -  2.4600 [2055/2074]  1860   195   9.5%
  bin  6:  2.4600 -  2.3155 [2038/2063]  1823   215  10.5%
  bin  7:  2.3155 -  2.1999 [2032/2060]  1827   205  10.1%
  bin  8:  2.1999 -  2.1044 [2014/2050]  1819   195   9.7%
  bin  9:  2.1044 -  2.0236 [2001/2051]  1802   199   9.9%
  bin 10:  2.0236 -  1.9539 [1025/2065]   921   104  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 22
        2.20 -     2.88: 1291
        2.88 -     3.55: 4528
        3.55 -     4.23: 9327
        4.23 -     4.90: 13433
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.527 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.583 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " OG BSER A 216 " - " O   HOH Z 113 "  1.789 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28596 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_971/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.75675 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4647   r_free= 0.4614   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.277298                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.6659 0.99   1420  161 0.3875 0.4024      6.5774      6.6131|
|  2:  4.6659 -  3.7217 0.99   1365  149 0.4066 0.3951      6.8145      6.7759|
|  3:  3.7217 -  3.2566 0.99   1339  146 0.4326 0.4197      6.6765      6.7106|
|  4:  3.2566 -  2.9613 0.99   1350  155 0.4592 0.4700      6.5302      6.5059|
|  5:  2.9613 -  2.7504 0.99   1327  146 0.4892 0.4892      6.3629      6.3927|
|  6:  2.7504 -  2.5891 0.99   1329  143 0.4982 0.5059      6.2741      6.2162|
|  7:  2.5891 -  2.4600 0.99   1308  141 0.4957 0.4842       6.229      6.1845|
|  8:  2.4600 -  2.3533 0.98   1295  153 0.5057 0.4764      6.1641      6.1735|
|  9:  2.3533 -  2.2630 0.98   1311  148 0.5030 0.5218      6.1179      6.1409|
| 10:  2.2630 -  2.1852 1.00   1293  156 0.5049 0.5010      6.0815      6.0732|
| 11:  2.1852 -  2.1170 0.98   1313  128 0.5047 0.4888      6.0186      6.0459|
| 12:  2.1170 -  2.0567 0.98   1282  153 0.4964 0.5111      5.9405      5.9881|
| 13:  2.0567 -  2.0027 0.92   1225  125 0.5178 0.4551      5.8663      5.8091|
| 14:  2.0027 -  1.9539 0.36    473   55 0.5261 0.4890      5.8591      5.7792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.6659  1420   161  0.67  36.50   0.81     0.74      80370.22|
|  2:  4.6659 -  3.7217  1365   149  0.68  36.90   0.90     0.80     114841.40|
|  3:  3.7217 -  3.2566  1339   146  0.57  46.08   0.92     0.76     122632.30|
|  4:  3.2566 -  2.9613  1350   155  0.46  55.04   0.92     0.65     113474.40|
|  5:  2.9613 -  2.7504  1327   146  0.38  61.51   0.89     0.54      89435.06|
|  6:  2.7504 -  2.5891  1329   143  0.36  62.93   0.89     0.52      76908.50|
|  7:  2.5891 -  2.4600  1308   141  0.37  61.99   0.92     0.53      65023.91|
|  8:  2.4600 -  2.3533  1295   153  0.38  61.71   0.92     0.54      58425.24|
|  9:  2.3533 -  2.2630  1311   148  0.37  62.37   0.93     0.54      52505.49|
| 10:  2.2630 -  2.1852  1293   156  0.36  63.34   0.94     0.53      49422.32|
| 11:  2.1852 -  2.1170  1313   128  0.34  64.37   0.98     0.54      47426.11|
| 12:  2.1170 -  2.0567  1282   153  0.36  63.30   0.96     0.57      41936.82|
| 13:  2.0567 -  2.0027  1225   125  0.38  61.42   0.95     0.62      33522.11|
| 14:  2.0027 -  1.9539   473    55  0.48  53.58   0.99     0.70      24032.51|
|alpha:            min =        0.52 max =            0.80 mean =         0.61|
|beta:             min =    24032.51 max =       122632.30 mean =     72097.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.40|
|phase err.(test): min =        0.00 max =           89.73 mean =        56.59|
|-----------------------------------------------------------------------------|

============================== 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 = 10.330705             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.680   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.811909              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.029   (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 |  1.527 -  1.864:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.864 -  2.202:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.202 -  2.539:       49 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.539 -  2.876:     1242 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.876 -  3.213:     1959 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.213 -  3.551:     2569 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.551 -  3.888:     4713 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.888 -  4.225:     4614 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.563:     6133 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7300 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.527 |       0.566 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4647   r_free= 0.4614   ksol= 0.00   Bsol= 0.00   scale= 0.897    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.277298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4563   r_free= 0.4541   ksol= 0.35   Bsol= 42.33   scale= 0.922   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,2.28,-1.31,0.00,-0.00,-0.00); trace/3= -0.04                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.271858                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.742339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.649   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.390574              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.781   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4563      final r-factor (work) = 0.3812          |
| start r-factor (free) = 0.4541      final r-factor (free) = 0.4172          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.5955 = 8.74 * 0.50 * 6.2702 + 1.00 * 0.1873                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.1870 = 8.74 * 0.50 * 6.1949 + 1.00 * 0.1079                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3812      final r-factor (work) = 0.3493          |
| start r-factor (free) = 0.4172      final r-factor (free) = 0.4265          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6208 = 1.39 * 1.00 * 6.1949 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5372 = 1.39 * 1.00 * 6.1246 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.08   19.05    None  None   None       |
|    all(noH): 2823   0      0.00    98.08   19.05    None  None   None       |
|    Sol.    : 438    0      1.32    98.08   34.77    None  None   None       |
|    Mac.    : 2385   0      0.00    85.97   16.16    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 -   9.809:  861   |   5:    49.043 -  58.851:   60        |
|      1:     9.809 -  19.617:  879   |   6:    58.851 -  68.659:   35        |
|      2:    19.617 -  29.426:  524   |   7:    68.659 -  78.468:   18        |
|      3:    29.426 -  39.234:  260   |   8:    78.468 -  88.276:    4        |
|      4:    39.234 -  49.043:  179   |   9:    88.276 -  98.085:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3493 r_free = 0.4265             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3491 r_free = 0.4264             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3491   r_free= 0.4264   ksol= 0.35   Bsol= 42.33   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,2.28,-1.31,0.00,-0.00,-0.00); trace/3= -0.04                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.127772                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3498   r_free= 0.4264   ksol= 0.36   Bsol= 67.93   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,1.08,-0.42,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.130450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.246910             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.491  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.803279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.278  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3498      final r-factor (work) = 0.2865          |
| start r-factor (free) = 0.4264      final r-factor (free) = 0.3589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.8153 = 15.25 * 0.50 * 6.1268 + 1.00 * 0.1079                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.2771 = 15.25 * 0.50 * 6.0549 + 1.00 * 0.1178                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2865      final r-factor (work) = 0.2657          |
| start r-factor (free) = 0.3589      final r-factor (free) = 0.3467          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8842 = 0.80 * 1.00 * 6.0549 + 1.00 * 0.0205                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7835 = 0.80 * 1.00 * 5.9362 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.62   18.74    None  None   None       |
|    all(noH): 2823   0      0.00    98.62   18.74    None  None   None       |
|    Sol.    : 438    0      0.00    98.62   37.92    None  None   None       |
|    Mac.    : 2385   0      0.00    87.10   15.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.862:  916   |   5:    49.311 -  59.173:   74        |
|      1:     9.862 -  19.724:  921   |   6:    59.173 -  69.035:   46        |
|      2:    19.724 -  29.586:  450   |   7:    69.035 -  78.897:   14        |
|      3:    29.586 -  39.449:  256   |   8:    78.897 -  88.759:    7        |
|      4:    39.449 -  49.311:  138   |   9:    88.759 -  98.621:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2657 r_free = 0.3467             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2653 r_free = 0.3468             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2653   r_free= 0.3468   ksol= 0.36   Bsol= 67.93   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,1.08,-0.42,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.919410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2655   r_free= 0.3444   ksol= 0.35   Bsol= 66.85   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.33,-0.08,-0.00,-0.00,-0.00); trace/3= -0.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.915430                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.128682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.066  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255134              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2655      final r-factor (work) = 0.2116          |
| start r-factor (free) = 0.3444      final r-factor (free) = 0.2782          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2755 = 7.13 * 0.50 * 5.9360 + 1.00 * 0.1175                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8589 = 7.13 * 0.50 * 5.8321 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2116      final r-factor (work) = 0.1941          |
| start r-factor (free) = 0.2782      final r-factor (free) = 0.2508          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5030 = 0.26 * 1.00 * 5.8321 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4559 = 0.26 * 1.00 * 5.6732 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.88   17.51    None  None   None       |
|    all(noH): 2823   0      0.00    86.88   17.51    None  None   None       |
|    Sol.    : 438    0      4.78    86.41   39.70    None  None   None       |
|    Mac.    : 2385   0      0.00    86.88   13.44    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 -   8.688:  758   |   5:    43.442 -  52.130:  103        |
|      1:     8.688 -  17.377: 1187   |   6:    52.130 -  60.819:   84        |
|      2:    17.377 -  26.065:  330   |   7:    60.819 -  69.507:   25        |
|      3:    26.065 -  34.754:  192   |   8:    69.507 -  78.196:    7        |
|      4:    34.754 -  43.442:  133   |   9:    78.196 -  86.884:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1941 r_free = 0.2508             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1939 r_free = 0.2500             target_work(ml) = 5.622         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1939   r_free= 0.2500   ksol= 0.35   Bsol= 66.85   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.33,-0.08,-0.00,-0.00,-0.00); trace/3= -0.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.622440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1933   r_free= 0.2482   ksol= 0.33   Bsol= 55.35   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-1.80,-0.92,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.620371                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.376377              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.084  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.343  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1933      final r-factor (work) = 0.1587          |
| start r-factor (free) = 0.2482      final r-factor (free) = 0.2095          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8151 = 2.38 * 0.50 * 5.6758 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6308 = 2.38 * 0.50 * 5.5356 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1587      final r-factor (work) = 0.1511          |
| start r-factor (free) = 0.2095      final r-factor (free) = 0.2019          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1019 = 0.20 * 1.00 * 5.5356 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0793 = 0.20 * 1.00 * 5.4234 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    86.89   17.23    None  None   None       |
|    all(noH): 2823   0      1.67    86.89   17.23    None  None   None       |
|    Sol.    : 438    0      6.04    86.03   40.59    None  None   None       |
|    Mac.    : 2385   0      1.67    86.89   12.93    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:     1.674 -  10.196: 1076   |   5:    44.281 -  52.802:  108        |
|      1:    10.196 -  18.717: 1014   |   6:    52.802 -  61.323:   76        |
|      2:    18.717 -  27.238:  255   |   7:    61.323 -  69.844:   32        |
|      3:    27.238 -  35.759:  128   |   8:    69.844 -  78.366:    6        |
|      4:    35.759 -  44.281:  124   |   9:    78.366 -  86.887:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1511 r_free = 0.2019             target_work(ml) = 5.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1509 r_free = 0.2017             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1509   r_free= 0.2017   ksol= 0.33   Bsol= 55.35   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-1.80,-0.92,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.403422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1510   r_free= 0.2015   ksol= 0.33   Bsol= 55.35   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.54,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.403050                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.505225              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.818  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.615570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.455  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.2015      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8485 = 2.51 * 0.50 * 5.4247 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7505 = 2.51 * 0.50 * 5.3436 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2973 = 0.62 * 1.00 * 5.3436 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2435 = 0.62 * 1.00 * 5.2526 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   17.71    None  None   None       |
|    Sol.    : 438    0      5.96    95.46   44.31    None  None   None       |
|    Mac.    : 2385   0      0.00    97.05   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.705: 1013   |   5:    48.524 -  58.228:   94        |
|      1:     9.705 -  19.409: 1137   |   6:    58.228 -  67.933:   71        |
|      2:    19.409 -  29.114:  235   |   7:    67.933 -  77.638:   39        |
|      3:    29.114 -  38.819:  121   |   8:    77.638 -  87.342:   15        |
|      4:    38.819 -  48.524:   93   |   9:    87.342 -  97.047:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1752             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1750             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1750   ksol= 0.33   Bsol= 55.35   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.54,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.242434                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.6659 0.99   1420  161 0.0996 0.1375      5.4027      5.6468|
|  2:  4.6659 -  3.7217 0.99   1365  149 0.0890 0.1228      5.5045      5.7424|
|  3:  3.7217 -  3.2566 0.99   1339  146 0.1224 0.1617      5.5815      5.8711|
|  4:  3.2566 -  2.9613 0.99   1350  155 0.1434 0.1901      5.5775      5.7307|
|  5:  2.9613 -  2.7504 0.99   1327  146 0.1504 0.2005      5.4277      5.6769|
|  6:  2.7504 -  2.5891 0.99   1329  143 0.1365 0.1942      5.2887      5.4997|
|  7:  2.5891 -  2.4600 0.99   1308  141 0.1402 0.1910      5.2479       5.441|
|  8:  2.4600 -  2.3533 0.98   1295  153 0.1349 0.1929      5.1668      5.4264|
|  9:  2.3533 -  2.2630 0.98   1311  148 0.1360 0.1920      5.1343      5.3671|
| 10:  2.2630 -  2.1852 1.00   1293  156 0.1280 0.1849       5.052      5.2764|
| 11:  2.1852 -  2.1170 0.98   1313  128 0.1257 0.2043      5.0364      5.3893|
| 12:  2.1170 -  2.0567 0.98   1282  153 0.1246 0.1981      4.9633      5.2418|
| 13:  2.0567 -  2.0027 0.92   1225  125 0.1298 0.1812      4.8771      5.0989|
| 14:  2.0027 -  1.9539 0.36    473   55 0.1092 0.1669      4.7261      4.9562|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.6659  1420   161  0.93   9.96   0.97     0.95       7937.28|
|  2:  4.6659 -  3.7217  1365   149  0.95   8.92   1.02     1.01      10779.67|
|  3:  3.7217 -  3.2566  1339   146  0.92  13.33   1.04     1.03      12801.80|
|  4:  3.2566 -  2.9613  1350   155  0.89  16.69   1.02     0.99      13350.44|
|  5:  2.9613 -  2.7504  1327   146  0.89  17.16   1.00     0.98       9728.92|
|  6:  2.7504 -  2.5891  1329   143  0.88  17.79   0.99     0.96       8219.56|
|  7:  2.5891 -  2.4600  1308   141  0.89  17.47   1.00     0.98       7408.97|
|  8:  2.4600 -  2.3533  1295   153  0.89  17.34   0.99     0.96       6370.90|
|  9:  2.3533 -  2.2630  1311   148  0.88  17.91   1.01     0.96       6023.53|
| 10:  2.2630 -  2.1852  1293   156  0.89  17.45   1.00     0.97       5326.12|
| 11:  2.1852 -  2.1170  1313   128  0.88  18.31   1.00     0.95       5365.95|
| 12:  2.1170 -  2.0567  1282   153  0.88  18.27   1.01     0.99       4926.12|
| 13:  2.0567 -  2.0027  1225   125  0.88  18.38   1.00     0.99       4044.61|
| 14:  2.0027 -  1.9539   473    55  0.90  15.98   0.98     0.95       2976.29|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2976.29 max =        13350.44 mean =      7795.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.99|
|phase err.(test): min =        0.00 max =           88.39 mean =        15.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1751   ksol= 0.32   Bsol= 55.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.55,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.242253                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1751   ksol= 0.32   Bsol= 55.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.55,-1.30,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.242253                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.6659 0.99   1420  161 0.0993 0.1376      5.3999      5.6471|
|  2:  4.6659 -  3.7217 0.99   1365  149 0.0891 0.1228      5.5049      5.7433|
|  3:  3.7217 -  3.2566 0.99   1339  146 0.1224 0.1617      5.5819      5.8719|
|  4:  3.2566 -  2.9613 0.99   1350  155 0.1434 0.1901      5.5776      5.7308|
|  5:  2.9613 -  2.7504 0.99   1327  146 0.1503 0.2004      5.4277      5.6768|
|  6:  2.7504 -  2.5891 0.99   1329  143 0.1365 0.1942      5.2886      5.4996|
|  7:  2.5891 -  2.4600 0.99   1308  141 0.1402 0.1910      5.2478      5.4409|
|  8:  2.4600 -  2.3533 0.98   1295  153 0.1348 0.1929      5.1667      5.4263|
|  9:  2.3533 -  2.2630 0.98   1311  148 0.1360 0.1920      5.1343      5.3671|
| 10:  2.2630 -  2.1852 1.00   1293  156 0.1280 0.1849       5.052      5.2763|
| 11:  2.1852 -  2.1170 0.98   1313  128 0.1257 0.2043      5.0363      5.3893|
| 12:  2.1170 -  2.0567 0.98   1282  153 0.1246 0.1981      4.9632      5.2417|
| 13:  2.0567 -  2.0027 0.92   1225  125 0.1298 0.1812      4.8771      5.0989|
| 14:  2.0027 -  1.9539 0.36    473   55 0.1092 0.1669      4.7261      4.9561|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.6659  1420   161  0.93   9.93   0.97     0.95       7908.10|
|  2:  4.6659 -  3.7217  1365   149  0.95   8.92   1.02     1.01      10777.03|
|  3:  3.7217 -  3.2566  1339   146  0.92  13.34   1.04     1.03      12822.65|
|  4:  3.2566 -  2.9613  1350   155  0.89  16.70   1.02     0.99      13359.46|
|  5:  2.9613 -  2.7504  1327   146  0.89  17.16   1.00     0.98       9729.89|
|  6:  2.7504 -  2.5891  1329   143  0.88  17.79   0.99     0.96       8217.60|
|  7:  2.5891 -  2.4600  1308   141  0.89  17.47   1.00     0.98       7406.87|
|  8:  2.4600 -  2.3533  1295   153  0.89  17.34   0.99     0.96       6369.49|
|  9:  2.3533 -  2.2630  1311   148  0.88  17.91   1.01     0.96       6022.71|
| 10:  2.2630 -  2.1852  1293   156  0.89  17.45   1.00     0.97       5325.45|
| 11:  2.1852 -  2.1170  1313   128  0.88  18.31   1.00     0.95       5365.35|
| 12:  2.1170 -  2.0567  1282   153  0.88  18.27   1.01     0.99       4925.63|
| 13:  2.0567 -  2.0027  1225   125  0.88  18.37   1.00     0.99       4044.34|
| 14:  2.0027 -  1.9539   473    55  0.90  15.98   0.98     0.95       2976.06|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2976.06 max =        13359.46 mean =      7794.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.99|
|phase err.(test): min =        0.00 max =           88.39 mean =        15.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.638)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   17.71    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   17.71    None  None   None       |
|    Sol.    : 438    0      5.97    95.46   44.31    None  None   None       |
|    Mac.    : 2385   0      0.00    97.05   12.82    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:     0.003 -   9.708: 1013   |   5:    48.526 -  58.231:   94        |
|      1:     9.708 -  19.412: 1137   |   6:    58.231 -  67.936:   71        |
|      2:    19.412 -  29.117:  235   |   7:    67.936 -  77.641:   39        |
|      3:    29.117 -  38.822:  121   |   8:    77.641 -  87.345:   15        |
|      4:    38.822 -  48.526:   93   |   9:    87.345 -  97.050:    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)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.674 - 5.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 323
   mapped sites are within: 0.706 - 5.634

peak=    7.267 closest distance to " O   HOH Z 390 " =    1.230
peak=    6.529 closest distance to " O   HOH Z 120 " =    1.354
peak=    6.446 closest distance to " O   HOH Z 385 " =    1.465
peak=    6.288 closest distance to " NE2 GLN A  11 " =    1.406
peak=    6.280 closest distance to " O   HOH Z 431 " =    1.674
peak=    6.158 closest distance to " O   HOH Z 159 " =    0.971
peak=    5.974 closest distance to " O   HOH Z 289 " =    1.423
peak=    5.956 closest distance to " O   HOH Z 214 " =    2.034
peak=    5.868 closest distance to " O   HOH Z 424 " =    2.106
peak=    5.757 closest distance to " O   HOH Z 245 " =    1.327
peak=    5.729 closest distance to " O   HOH Z  65 " =    1.458
peak=    5.267 closest distance to " O   HOH Z 427 " =    1.422
peak=    5.174 closest distance to " O   HOH Z 417 " =    2.102
peak=    5.167 closest distance to " O   HOH Z 222 " =    1.220
peak=    5.007 closest distance to " O   HOH Z  63 " =    2.038
peak=    4.933 closest distance to " CB  PRO A  54 " =    1.083
peak=    4.887 closest distance to " O   PRO A 198 " =    1.293
peak=    4.885 closest distance to " CG  PRO A  54 " =    1.400
peak=    4.822 closest distance to " CG  PRO A 213 " =    1.286
peak=    4.753 closest distance to " CA  TYR A  30 " =    1.051
peak=    4.750 closest distance to " O   HOH Z  97 " =    1.363
peak=    4.742 closest distance to " O   HOH Z 232 " =    2.187
peak=    4.693 closest distance to " O   HOH Z 144 " =    1.770
peak=    4.663 closest distance to " O   HOH Z 363 " =    1.217
peak=    4.657 closest distance to " O   HOH Z 139 " =    1.543
peak=    4.656 closest distance to " O   HOH Z 403 " =    1.432
peak=    4.649 closest distance to " O   HOH Z 147 " =    1.414
peak=    4.643 closest distance to " O   HOH Z 399 " =    0.802
peak=    4.631 closest distance to " CB  GLN A 223 " =    1.446
peak=    4.624 closest distance to " O   HOH Z 158 " =    1.347
peak=    4.619 closest distance to " O   HOH Z 427 " =    1.917
peak=    4.613 closest distance to " O   HOH Z  49 " =    1.439
peak=    4.569 closest distance to " O   HOH Z  78 " =    1.625
peak=    4.518 closest distance to " CB  GLU A 128 " =    1.007
peak=    4.508 closest distance to " CB  SER A 216 " =    1.012
peak=    4.501 closest distance to " CG  PRO A 280 " =    0.857
peak=    4.488 closest distance to " O   HOH Z 130 " =    0.872
peak=    4.470 closest distance to " O   HOH Z  28 " =    1.482
peak=    4.466 closest distance to " N   GLN A 278 " =    1.045
peak=    4.453 closest distance to " O   HOH Z 111 " =    1.781
peak=    4.446 closest distance to " O   HOH Z 287 " =    2.077
peak=    4.430 closest distance to " CB  SER A   3 " =    1.499
peak=    4.415 closest distance to " O   HOH Z 316 " =    3.049
peak=    4.407 closest distance to " CB  ARG A 275 " =    1.015
peak=    4.401 closest distance to " O   HOH Z 414 " =    1.468
peak=    4.368 closest distance to " O   HOH Z 423 " =    1.985
peak=    4.314 closest distance to " NZ BLYS A 290 " =    1.006
peak=    4.301 closest distance to " CB  ASN A 148 " =    1.449
peak=    4.295 closest distance to " O   HOH Z 416 " =    1.302
peak=    4.290 closest distance to " O   HOH Z 145 " =    1.987
peak=    4.289 closest distance to " O   HOH Z 394 " =    1.876
peak=    4.269 closest distance to " O   HOH Z  29 " =    1.074
peak=    4.260 closest distance to " O   HOH Z 298 " =    2.062
peak=    4.248 closest distance to " O   HOH Z  57 " =    2.545
peak=    4.237 closest distance to " O   HOH Z 244 " =    1.464
peak=    4.226 closest distance to " O   HOH Z 369 " =    2.051
peak=    4.225 closest distance to " OE1 GLU A   2 " =    1.983
peak=    4.219 closest distance to " O   HOH Z 392 " =    1.507
peak=    4.191 closest distance to " O   HOH Z  63 " =    1.870
peak=    4.162 closest distance to " CG1BVAL A 121 " =    2.149
peak=    4.110 closest distance to " CB  SER A  63 " =    1.406
peak=    4.101 closest distance to " O   HOH Z 415 " =    1.160
peak=    4.073 closest distance to " NZ  LYS A 117 " =    1.183
peak=    4.071 closest distance to " CB  VAL A 202 " =    1.569
peak=    4.068 closest distance to " O   HOH Z 236 " =    1.576
peak=    4.066 closest distance to " O   HOH Z 258 " =    2.019
peak=    4.066 closest distance to " CB  ASP A 124 " =    0.885
peak=    4.060 closest distance to " O   HOH Z   9 " =    1.228
peak=    4.053 closest distance to " NE1 TRP A 274 " =    1.077
peak=    4.051 closest distance to " O   HOH Z 358 " =    1.346
peak=    4.050 closest distance to " CB  SER A 276 " =    1.165
peak=    4.044 closest distance to " OG BSER A 258 " =    0.945
peak=    4.037 closest distance to " O   SER A  87 " =    2.255
peak=    4.029 closest distance to " O   HOH Z 193 " =    1.770
peak=    4.027 closest distance to " CG  PRO A  90 " =    1.153
peak=    4.026 closest distance to " O   HOH Z 371 " =    1.913
peak=    4.022 closest distance to " O   HOH Z 209 " =    2.355
peak=    4.018 closest distance to " O   HOH Z  44 " =    2.770
peak=    4.017 closest distance to " O   HOH Z 171 " =    2.359
peak=    4.012 closest distance to " O   HOH Z  57 " =    1.173
peak=    4.006 closest distance to " CB  GLN A 183 " =    1.132
peak=    3.999 closest distance to " O   HOH Z 313 " =    2.115
peak=    3.983 closest distance to " OD1BASN A 224 " =    2.317
peak=    3.982 closest distance to " O   HOH Z 261 " =    2.074
peak=    3.977 closest distance to " O   HOH Z 380 " =    1.866
peak=    3.963 closest distance to " O   HOH Z 352 " =    1.524
peak=    3.945 closest distance to " O   HOH Z  44 " =    1.865
peak=    3.943 closest distance to " O   HOH Z 234 " =    3.869
peak=    3.939 closest distance to " O   HOH Z 389 " =    1.848
peak=    3.930 closest distance to " O   HOH Z   4 " =    1.089
peak=    3.918 closest distance to " O   HOH Z 239 " =    1.518
peak=    3.912 closest distance to " O   HOH Z 424 " =    1.289
peak=    3.909 closest distance to " O   HOH Z 225 " =    1.439
peak=    3.907 closest distance to " CB  TRP A 266 " =    1.009
peak=    3.904 closest distance to " CB  TRP A 179 " =    1.519
peak=    3.901 closest distance to " CG2 VAL A 257 " =    0.951
peak=    3.898 closest distance to " O   HOH Z  88 " =    3.141
peak=    3.896 closest distance to " O   HOH Z  59 " =    1.439
peak=    3.885 closest distance to " CA  ARG A 195 " =    1.516
peak=    3.880 closest distance to " O   HOH Z 334 " =    2.722
peak=    3.877 closest distance to " NH1AARG A 145 " =    1.123
peak=    3.875 closest distance to " O   HOH Z 361 " =    1.334
peak=    3.873 closest distance to " CG  LEU A 167 " =    1.296
peak=    3.871 closest distance to " OG BSER A  99 " =    2.389
peak=    3.869 closest distance to " O   HOH Z 155 " =    1.815
peak=    3.865 closest distance to " O   HOH Z 207 " =    2.165
peak=    3.849 closest distance to " O   ALA A 165 " =    1.312
peak=    3.838 closest distance to " O   HOH Z 371 " =    3.260
peak=    3.835 closest distance to " O   HOH Z 302 " =    1.521
peak=    3.834 closest distance to " O   HOH Z 217 " =    2.336
peak=    3.828 closest distance to " O   HOH Z  17 " =    2.224
peak=    3.812 closest distance to " CG  GLN A 278 " =    3.789
peak=    3.811 closest distance to " O   HOH Z 133 " =    2.466
peak=    3.808 closest distance to " CA  ILE A 234 " =    1.082
peak=    3.800 closest distance to " O   HOH Z 272 " =    1.848
peak=    3.788 closest distance to " O   HOH Z 402 " =    1.390
peak=    3.761 closest distance to " NH2 ARG A 219 " =    1.658
peak=    3.759 closest distance to " O   HOH Z  61 " =    1.560
peak=    3.757 closest distance to " CD2 TRP A 179 " =    2.162
peak=    3.757 closest distance to " N   GLU A   2 " =    1.260
peak=    3.756 closest distance to " O   HOH Z 258 " =    1.644
peak=    3.745 closest distance to " N   TYR A  15 " =    1.029
peak=    3.742 closest distance to " O   HOH Z 327 " =    2.049
peak=    3.694 closest distance to " CA  GLU A 152 " =    1.203
peak=    3.693 closest distance to " O   HOH Z 119 " =    1.428
peak=    3.677 closest distance to " OD2 ASP A 286 " =    2.672
peak=    3.675 closest distance to " O   HOH Z 115 " =    1.843
peak=    3.666 closest distance to " CA  LEU A 282 " =    1.028
peak=    3.659 closest distance to " O   HOH Z 359 " =    1.476
peak=    3.655 closest distance to " O   HOH Z 410 " =    1.779
peak=    3.653 closest distance to " O   HOH Z 193 " =    1.668
peak=    3.646 closest distance to " CB  GLU A 236 " =    1.416
peak=    3.618 closest distance to " O   HOH Z 211 " =    1.353
peak=    3.611 closest distance to " O   HOH Z 437 " =    2.284
peak=    3.610 closest distance to " O   HOH Z 116 " =    2.852
peak=    3.604 closest distance to " CA  GLY A 267 " =    1.374
peak=    3.599 closest distance to " CE  MET A  93 " =    1.393
peak=    3.599 closest distance to " CA  ALA A  21 " =    1.147
peak=    3.599 closest distance to " O   HOH Z 112 " =    1.082
peak=    3.594 closest distance to " O   HOH Z 135 " =    1.929
peak=    3.589 closest distance to " O   HOH Z 276 " =    1.261
peak=    3.588 closest distance to " O   HOH Z 134 " =    1.430
peak=    3.584 closest distance to " O   HOH Z 409 " =    1.937
peak=    3.576 closest distance to " O   HOH Z 166 " =    1.453
peak=    3.569 closest distance to " O   HOH Z 282 " =    1.562
peak=    3.568 closest distance to " O   HOH Z  51 " =    1.785
peak=    3.568 closest distance to " CD  ARG A 159 " =    0.837
peak=    3.561 closest distance to " O   HOH Z 418 " =    0.966
peak=    3.560 closest distance to " O   HOH Z 119 " =    4.247
peak=    3.554 closest distance to " N   ALA A   1 " =    2.530
peak=    3.548 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.546 closest distance to " O   HOH Z 281 " =    1.996
peak=    3.539 closest distance to " CB  GLU A 152 " =    1.188
peak=    3.538 closest distance to " O   HOH Z  88 " =    2.752
peak=    3.536 closest distance to " CE3 TRP A 274 " =    1.347
peak=    3.529 closest distance to " CB  LEU A 228 " =    1.137
peak=    3.527 closest distance to " O   HOH Z 384 " =    1.264
peak=    3.514 closest distance to " O   HOH Z 435 " =    1.995
peak=    3.513 closest distance to " ND2 ASN A  60 " =    3.020
peak=    3.503 closest distance to " O   HOH Z 217 " =    1.783
peak=    3.502 closest distance to " O   HOH Z 329 " =    3.556
peak=    3.501 closest distance to " NE2 GLN A  58 " =    3.750
peak=    3.496 closest distance to " NE AARG A 275 " =    1.455
peak=    3.491 closest distance to " O   HOH Z  11 " =    1.624
peak=    3.487 closest distance to " CG2 THR A 221 " =    1.361
peak=    3.485 closest distance to " CD BLYS A 290 " =    1.120
peak=    3.484 closest distance to " CB  MET A  47 " =    1.095
peak=    3.483 closest distance to " O   HOH Z 431 " =    1.357
peak=    3.480 closest distance to " CB  MET A 105 " =    1.449
peak=    3.480 closest distance to " CA  ASN A 127 " =    0.971
peak=    3.478 closest distance to " CZ  PHE A 192 " =    0.995
peak=    3.459 closest distance to " CB  VAL A 265 " =    1.299
peak=    3.447 closest distance to " CD  ARG A 138 " =    0.798
peak=    3.441 closest distance to " O   HOH Z 380 " =    2.955
peak=    3.439 closest distance to " CA  ALA A  51 " =    1.174
peak=    3.438 closest distance to " CD  LYS A 166 " =    1.592
peak=    3.433 closest distance to " ND1 HIS A  81 " =    1.469
peak=    3.433 closest distance to " O   HOH Z 151 " =    1.567
peak=    3.431 closest distance to " N   ALA A   1 " =    1.322
peak=    3.428 closest distance to " O   HOH Z 105 " =    1.302
peak=    3.427 closest distance to " O   HOH Z  50 " =    1.973
peak=    3.420 closest distance to " N   ARG A 156 " =    1.314
peak=    3.418 closest distance to " CB  ASN A 187 " =    0.983
peak=    3.408 closest distance to " O   HOH Z 422 " =    2.769
peak=    3.406 closest distance to " CB  LYS A 117 " =    1.227
peak=    3.404 closest distance to " N   SER A 210 " =    1.121
peak=    3.401 closest distance to " C   ASN A 209 " =    1.651
peak=    3.398 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.392 closest distance to " CB  TYR A 116 " =    1.111
peak=    3.391 closest distance to " CB  TYR A 169 " =    0.706
peak=    3.391 closest distance to " ND2 ASN A  60 " =    3.666
peak=    3.391 closest distance to " O   HOH Z 411 " =    3.436
peak=    3.390 closest distance to " CA  ALA A 299 " =    0.914
peak=    3.389 closest distance to " CA  MET A 105 " =    0.865
peak=    3.386 closest distance to " CA  ARG A  36 " =    1.289
peak=    3.380 closest distance to " N   PHE A 130 " =    1.151
peak=    3.377 closest distance to " O   HOH Z 405 " =    1.770
peak=    3.366 closest distance to " CD  ARG A  66 " =    2.407
peak=    3.360 closest distance to " O   HOH Z 311 " =    1.496
peak=    3.360 closest distance to " CG  ARG A 159 " =    0.783
peak=    3.359 closest distance to " O   HOH Z 413 " =    1.695
peak=    3.357 closest distance to " O   HOH Z 344 " =    3.258
peak=    3.355 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.355 closest distance to " O   HOH Z 222 " =    2.202
peak=    3.341 closest distance to " O   HOH Z 152 " =    2.128
peak=    3.335 closest distance to " O   HOH Z 365 " =    2.843
peak=    3.333 closest distance to " N   ILE A  33 " =    1.094
peak=    3.330 closest distance to " O   HOH Z 189 " =    2.055
peak=    3.326 closest distance to " O   HOH Z 130 " =    2.103
peak=    3.326 closest distance to " O   HOH Z 373 " =    1.409
peak=    3.326 closest distance to " O   HOH Z   9 " =    2.189
peak=    3.324 closest distance to " O   HOH Z 233 " =    1.518
peak=    3.322 closest distance to " O   HOH Z  40 " =    2.209
peak=    3.321 closest distance to " O   HOH Z 104 " =    1.502
peak=    3.321 closest distance to " O   HOH Z  92 " =    1.226
peak=    3.321 closest distance to " CB  LYS A 290 " =    0.839
peak=    3.321 closest distance to " CG1 ILE A 120 " =    1.433
peak=    3.318 closest distance to " O   HOH Z  10 " =    1.851
peak=    3.315 closest distance to " O   HOH Z 234 " =    2.104
peak=    3.312 closest distance to " O   HOH Z 133 " =    1.382
peak=    3.312 closest distance to " O   HOH Z 239 " =    1.563
peak=    3.309 closest distance to " O   HOH Z 434 " =    1.379
peak=    3.309 closest distance to " O   HOH Z  55 " =    1.834
peak=    3.304 closest distance to " O   HOH Z   1 " =    1.693
peak=    3.303 closest distance to " CE3 TRP A 274 " =    2.314
peak=    3.301 closest distance to " CE AMET A  47 " =    1.312
peak=    3.295 closest distance to " CA  GLU A  46 " =    0.728
peak=    3.294 closest distance to " CA  GLY A 196 " =    0.953
peak=    3.289 closest distance to " OD1 ASN A 217 " =    1.561
peak=    3.289 closest distance to " OE1 GLN A 240 " =    1.763
peak=    3.287 closest distance to " CB  LEU A 300 " =    0.923
peak=    3.286 closest distance to " O   HOH Z 345 " =    1.870
peak=    3.285 closest distance to " O   HOH Z  67 " =    1.871
peak=    3.282 closest distance to " ND1 HIS A  86 " =    1.818
peak=    3.281 closest distance to " O   HOH Z  32 " =    2.245
peak=    3.280 closest distance to " CB  ALA A  34 " =    1.226
peak=    3.280 closest distance to " O   HOH Z   7 " =    2.951
peak=    3.277 closest distance to " O   HOH Z 426 " =    1.026
peak=    3.277 closest distance to " O   HOH Z   6 " =    1.894
peak=    3.275 closest distance to " O   HOH Z 246 " =    1.286
peak=    3.274 closest distance to " OE2 GLU A  53 " =    2.037
peak=    3.273 closest distance to " CG  GLN A  89 " =    1.440
peak=    3.270 closest distance to " O   HOH Z 128 " =    1.999
peak=    3.269 closest distance to " O   HOH Z 412 " =    1.499
peak=    3.269 closest distance to " O   HOH Z 213 " =    2.042
peak=    3.266 closest distance to " CZ  ARG A  14 " =    1.685
peak=    3.265 closest distance to " O   HOH Z  65 " =    1.605
peak=    3.264 closest distance to " O   HOH Z 158 " =    2.474
peak=    3.263 closest distance to " OE1 GLN A  11 " =    2.198
peak=    3.262 closest distance to " O   HOH Z  30 " =    1.849
peak=    3.262 closest distance to " CA  PRO A 280 " =    1.551
peak=    3.255 closest distance to " CG  GLU A   2 " =    1.066
peak=    3.255 closest distance to " O   HOH Z  51 " =    1.652
peak=    3.255 closest distance to " O   HOH Z 250 " =    1.473
peak=    3.255 closest distance to " CH2 TRP A 150 " =    1.142
peak=    3.253 closest distance to " O   HOH Z 288 " =    2.187
peak=    3.243 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.243 closest distance to " NH2BARG A 102 " =    1.019
peak=    3.243 closest distance to " OG  SER A  26 " =    1.283
peak=    3.239 closest distance to " CZ3 TRP A 123 " =    1.493
peak=    3.239 closest distance to " CB  GLU A 277 " =    1.125
peak=    3.238 closest distance to " CB  MET A  40 " =    0.851
peak=    3.227 closest distance to " CA  TYR A 186 " =    1.649
peak=    3.227 closest distance to " CB  ASN A 170 " =    1.323
peak=    3.226 closest distance to " CB  ALA A 114 " =    1.014
peak=    3.223 closest distance to " O   HOH Z 276 " =    2.113
peak=    3.219 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.213 closest distance to " CG2 ILE A 106 " =    0.979
peak=    3.212 closest distance to " O   HOH Z 417 " =    1.567
peak=    3.210 closest distance to " CD  GLN A  58 " =    5.634
peak=    3.209 closest distance to " O   ARG A  56 " =    1.843
peak=    3.208 closest distance to " O  BHOH Z  74 " =    1.479
peak=    3.202 closest distance to " CB  ALA A 184 " =    1.178
peak=    3.201 closest distance to " O   HOH Z 435 " =    2.757
peak=    3.198 closest distance to " CB  ALA A 248 " =    1.026
peak=    3.197 closest distance to " CA  ALA A 292 " =    0.844
peak=    3.195 closest distance to " CZ  PHE A  38 " =    1.280
peak=    3.193 closest distance to " CD  LYS A 119 " =    1.246
peak=    3.193 closest distance to " N   VAL A 125 " =    1.398
peak=    3.190 closest distance to " OD1 ASN A  69 " =    2.394
peak=    3.188 closest distance to " N   CYS A 260 " =    0.847
peak=    3.187 closest distance to " O   HOH Z 293 " =    1.360
peak=    3.185 closest distance to " O   HOH Z 145 " =    3.408
peak=    3.183 closest distance to " O   HOH Z 393 " =    1.300
peak=    3.182 closest distance to " CB  ASN A 127 " =    0.929
peak=    3.180 closest distance to " O   HOH Z 287 " =    2.101
peak=    3.175 closest distance to " CG1 ILE A  33 " =    1.272
peak=    3.174 closest distance to " CG  GLN A  11 " =    2.087
peak=    3.174 closest distance to " O   HOH Z   9 " =    1.318
peak=    3.166 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.166 closest distance to " CB  ALA A  43 " =    0.867
peak=    3.164 closest distance to " CA  THR A 264 " =    0.836
peak=    3.162 closest distance to " CG  GLU A 277 " =    4.537
peak=    3.159 closest distance to " O   HOH Z 216 " =    2.353
peak=    3.150 closest distance to " O   HOH Z 425 " =    2.116
peak=    3.150 closest distance to " CB  VAL A 121 " =    0.962
peak=    3.149 closest distance to " ND2 ASN A 187 " =    1.403
peak=    3.143 closest distance to " O   HOH Z 109 " =    2.831
peak=    3.141 closest distance to " CB  VAL A 230 " =    0.877
peak=    3.140 closest distance to " CA  ALA A 154 " =    0.932
peak=    3.135 closest distance to " O   HOH Z 172 " =    2.206
peak=    3.134 closest distance to " OD1 ASP A 238 " =    0.897
peak=    3.127 closest distance to " O   HOH Z 175 " =    3.527
peak=    3.122 closest distance to " O   HOH Z 108 " =    1.993
peak=    3.112 closest distance to " O   HOH Z 122 " =    1.833
peak=    3.112 closest distance to " CG2 ILE A  20 " =    1.839
peak=    3.108 closest distance to " CG  LYS A 119 " =    1.116
peak=    3.103 closest distance to " O   MET A 105 " =    1.811
peak=    3.098 closest distance to " O   THR A 220 " =    1.599
peak=    3.096 closest distance to " O   HOH Z 108 " =    1.652
peak=    3.093 closest distance to " O   ALA A 158 " =    1.504
peak=    3.089 closest distance to " OD1 ASP A 286 " =    1.143
peak=    3.089 closest distance to " C   GLU A 277 " =    1.406
peak=    3.088 closest distance to " O   HOH Z 172 " =    2.296
peak=    3.085 closest distance to " N   ALA A 292 " =    1.130
peak=    3.084 closest distance to " N   SER A 271 " =    1.215
peak=    3.075 closest distance to " O   HOH Z 438 " =    2.245
peak=    3.071 closest distance to " CG2 THR A 279 " =    1.069
peak=    3.067 closest distance to " O   HOH Z  73 " =    1.579
peak=    3.039 closest distance to " O   HOH Z 128 " =    2.025

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.419 - 5.634
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.737 - 5.634

peak=   -4.522 closest distance to " CG  MET A 105 " =    0.997
peak=   -4.517 closest distance to " O   HOH Z  60 " =    1.832
peak=   -4.349 closest distance to " N   THR A 157 " =    1.519
peak=   -4.346 closest distance to " CB  PRO A 243 " =    2.454
peak=   -4.267 closest distance to " CD  ARG A  14 " =    3.190
peak=   -4.160 closest distance to " O   HOH Z 409 " =    3.288
peak=   -4.146 closest distance to " O   PRO A 198 " =    1.259
peak=   -4.023 closest distance to " NE2 GLN A  55 " =    0.763
peak=   -4.009 closest distance to " CA  ASP A  27 " =    2.473
peak=   -3.947 closest distance to " O   HOH Z 166 " =    1.197
peak=   -3.931 closest distance to " NE1 TRP A 179 " =    1.186
peak=   -3.927 closest distance to " O   HOH Z 198 " =    2.194
peak=   -3.919 closest distance to " O   HOH Z 385 " =    1.150
peak=   -3.903 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.895 closest distance to " CB  ALA A 100 " =    2.021
peak=   -3.877 closest distance to " O   HOH Z  43 " =    1.467
peak=   -3.876 closest distance to " CZ  PHE A  59 " =    1.426
peak=   -3.845 closest distance to " O   HOH Z 197 " =    3.396
peak=   -3.841 closest distance to " OG  SER A  97 " =    2.236
peak=   -3.833 closest distance to " O   HOH Z 185 " =    2.118
peak=   -3.817 closest distance to " N   ARG A 159 " =    2.027
peak=   -3.811 closest distance to " CG  GLN A  88 " =    0.845
peak=   -3.810 closest distance to " O   ALA A   1 " =    1.047
peak=   -3.808 closest distance to " O   HOH Z 111 " =    1.876
peak=   -3.798 closest distance to " O   HOH Z 290 " =    1.277
peak=   -3.790 closest distance to " O   HOH Z  88 " =    2.163
peak=   -3.786 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.771 closest distance to " CB  ALA A 291 " =    2.164
peak=   -3.769 closest distance to " O   HOH Z 377 " =    1.759
peak=   -3.769 closest distance to " O   HOH Z 351 " =    1.482
peak=   -3.764 closest distance to " CB  ALA A 227 " =    2.303
peak=   -3.733 closest distance to " OG  SER A  87 " =    1.250
peak=   -3.730 closest distance to " OD1 ASP A 191 " =    1.949
peak=   -3.728 closest distance to " CG1 VAL A 265 " =    2.341
peak=   -3.726 closest distance to " NH2 ARG A 219 " =    1.797
peak=   -3.722 closest distance to " O   HOH Z  28 " =    1.791
peak=   -3.714 closest distance to " OG BSER A 134 " =    1.445
peak=   -3.674 closest distance to " CA  GLY A  23 " =    2.785
peak=   -3.671 closest distance to " CG  PRO A 163 " =    2.346
peak=   -3.666 closest distance to " CD2 TYR A 293 " =    1.791
peak=   -3.657 closest distance to " CA  GLY A 133 " =    1.981
peak=   -3.642 closest distance to " CA  ALA A  71 " =    2.107
peak=   -3.631 closest distance to " O   ALA A  51 " =    1.329
peak=   -3.617 closest distance to " CA  GLY A  98 " =    1.801
peak=   -3.613 closest distance to " O   HOH Z 432 " =    3.771
peak=   -3.609 closest distance to " O   HOH Z 143 " =    1.201
peak=   -3.602 closest distance to " O   HOH Z   1 " =    1.361
peak=   -3.602 closest distance to " OH  TYR A 214 " =    1.140
peak=   -3.596 closest distance to " CE2 TYR A  30 " =    2.636
peak=   -3.595 closest distance to " O   HOH Z 124 " =    1.256
peak=   -3.588 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.576 closest distance to " O   HOH Z 211 " =    1.621
peak=   -3.575 closest distance to " N   HIS A 115 " =    2.153
peak=   -3.557 closest distance to " O   HOH Z 231 " =    0.836
peak=   -3.555 closest distance to " CD  LYS A 166 " =    2.368
peak=   -3.555 closest distance to " OE1 GLN A  58 " =    2.757
peak=   -3.537 closest distance to " O   HOH Z 102 " =    1.776
peak=   -3.536 closest distance to " O   SER A 216 " =    1.847
peak=   -3.535 closest distance to " O   HOH Z 415 " =    1.208
peak=   -3.535 closest distance to " O   ILE A  49 " =    1.573
peak=   -3.534 closest distance to " O   HOH Z 410 " =    2.340
peak=   -3.533 closest distance to " CG2AVAL A  41 " =    2.839
peak=   -3.532 closest distance to " CD  GLN A 223 " =    1.404
peak=   -3.530 closest distance to " NH2 ARG A 159 " =    2.483
peak=   -3.529 closest distance to " CA  GLY A 241 " =    2.223
peak=   -3.528 closest distance to " CB  TYR A  15 " =    2.093
peak=   -3.523 closest distance to " CB  ALA A 158 " =    1.689
peak=   -3.518 closest distance to " O   HOH Z 352 " =    1.647
peak=   -3.503 closest distance to " O   HOH Z 298 " =    0.967
peak=   -3.499 closest distance to " OD1 ASN A 301 " =    2.088
peak=   -3.498 closest distance to " O   HOH Z 266 " =    4.413
peak=   -3.498 closest distance to " CD  ARG A 156 " =    1.901
peak=   -3.493 closest distance to " O   HOH Z 418 " =    1.267
peak=   -3.486 closest distance to " CE  MET A 113 " =    2.256
peak=   -3.485 closest distance to " OG ASER A 134 " =    1.174
peak=   -3.480 closest distance to " O   SER A  62 " =    2.473
peak=   -3.479 closest distance to " OG1 THR A 279 " =    1.493
peak=   -3.476 closest distance to " ND2 ASN A 209 " =    1.887
peak=   -3.469 closest distance to " NH2 ARG A  79 " =    1.884
peak=   -3.467 closest distance to " O   HOH Z  39 " =    1.393
peak=   -3.467 closest distance to " CB  ILE A 199 " =    2.688
peak=   -3.465 closest distance to " NE  ARG A  36 " =    1.965
peak=   -3.465 closest distance to " O   HOH Z  71 " =    2.119
peak=   -3.456 closest distance to " O   HOH Z  49 " =    1.479
peak=   -3.455 closest distance to " N   LYS A 166 " =    1.932
peak=   -3.449 closest distance to " OE2 GLU A 152 " =    2.195
peak=   -3.449 closest distance to " O   HOH Z 372 " =    2.598
peak=   -3.444 closest distance to " O   HOH Z 274 " =    3.163
peak=   -3.443 closest distance to " O   TRP A  70 " =    1.483
peak=   -3.441 closest distance to " CE3 TRP A 179 " =    1.260
peak=   -3.439 closest distance to " N   GLN A  58 " =    1.240
peak=   -3.426 closest distance to " O   HOH Z 411 " =    1.122
peak=   -3.424 closest distance to " CB  ALA A  43 " =    2.223
peak=   -3.422 closest distance to " O   HOH Z 426 " =    1.642
peak=   -3.420 closest distance to " OD2 ASP A 171 " =    1.888
peak=   -3.416 closest distance to " C   GLY A  13 " =    1.020
peak=   -3.404 closest distance to " O   HOH Z 138 " =    0.952
peak=   -3.404 closest distance to " O   ASN A 301 " =    1.361
peak=   -3.402 closest distance to " OE1 GLU A  44 " =    1.615
peak=   -3.394 closest distance to " O   HOH Z 404 " =    1.052
peak=   -3.393 closest distance to " CG  GLU A 152 " =    2.231
peak=   -3.378 closest distance to " OE1 GLN A 278 " =    1.239
peak=   -3.377 closest distance to " ND2 ASN A 285 " =    1.941
peak=   -3.376 closest distance to " O   HOH Z   2 " =    0.861
peak=   -3.370 closest distance to " CZ3 TRP A 123 " =    1.927
peak=   -3.365 closest distance to " O   HOH Z 231 " =    1.703
peak=   -3.363 closest distance to " O   HOH Z  13 " =    1.563
peak=   -3.359 closest distance to " O   HOH Z 438 " =    0.916
peak=   -3.355 closest distance to " O   HOH Z  61 " =    1.468
peak=   -3.355 closest distance to " CG BLYS A 290 " =    0.938
peak=   -3.347 closest distance to " NH2AARG A 275 " =    5.634
peak=   -3.346 closest distance to " O   HOH Z 139 " =    2.588
peak=   -3.344 closest distance to " O   HOH Z 388 " =    2.067
peak=   -3.342 closest distance to " O   HOH Z   4 " =    1.174
peak=   -3.342 closest distance to " CB  PRO A  90 " =    1.398
peak=   -3.340 closest distance to " O   HOH Z 121 " =    3.603
peak=   -3.339 closest distance to " CG2 ILE A  20 " =    2.817
peak=   -3.339 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.338 closest distance to " O   HOH Z 425 " =    1.012
peak=   -3.337 closest distance to " O   ARG A 145 " =    1.287
peak=   -3.336 closest distance to " O   ALA A 180 " =    1.182
peak=   -3.334 closest distance to " O   SER A 135 " =    1.574
peak=   -3.332 closest distance to " CD  GLN A  58 " =    0.887
peak=   -3.329 closest distance to " OH  TYR A 247 " =    1.536
peak=   -3.327 closest distance to " CG1BVAL A  41 " =    2.950
peak=   -3.323 closest distance to " CZ2 TRP A 274 " =    1.031
peak=   -3.321 closest distance to " N   GLN A  58 " =    1.678
peak=   -3.321 closest distance to " O   PRO A 163 " =    2.012
peak=   -3.317 closest distance to " O   HOH Z 213 " =    1.222
peak=   -3.314 closest distance to " O   HOH Z  65 " =    0.961
peak=   -3.313 closest distance to " O   HOH Z 416 " =    0.806
peak=   -3.312 closest distance to " CD2 LEU A 237 " =    2.554
peak=   -3.303 closest distance to " O   HOH Z 393 " =    2.788
peak=   -3.303 closest distance to " O   HOH Z  76 " =    1.024
peak=   -3.303 closest distance to " CB  TRP A  85 " =    2.339
peak=   -3.298 closest distance to " O   HOH Z 275 " =    1.692
peak=   -3.294 closest distance to " O   HOH Z  52 " =    1.465
peak=   -3.294 closest distance to " O   PRO A 198 " =    1.112
peak=   -3.292 closest distance to " CE2 TYR A 116 " =    3.048
peak=   -3.279 closest distance to " CG2 ILE A 151 " =    2.526
peak=   -3.279 closest distance to " O   HOH Z 417 " =    2.957
peak=   -3.278 closest distance to " CB  ASN A 285 " =    2.190
peak=   -3.278 closest distance to " CB  ASP A 132 " =    2.220
peak=   -3.271 closest distance to " CZ  ARG A  36 " =    1.408
peak=   -3.270 closest distance to " CD  ARG A 139 " =    1.657
peak=   -3.270 closest distance to " O   HOH Z 196 " =    1.857
peak=   -3.263 closest distance to " OE1 GLN A 223 " =    2.347
peak=   -3.259 closest distance to " CZ  PHE A 225 " =    1.449
peak=   -3.259 closest distance to " OG  SER A 245 " =    1.204
peak=   -3.259 closest distance to " ND2 ASN A 187 " =    1.476
peak=   -3.253 closest distance to " CD  ARG A 219 " =    2.493
peak=   -3.253 closest distance to " O   HOH Z 174 " =    2.972
peak=   -3.250 closest distance to " O   HOH Z 159 " =    0.737
peak=   -3.250 closest distance to " N   LEU A 282 " =    2.169
peak=   -3.248 closest distance to " CA  HIS A  86 " =    2.237
peak=   -3.247 closest distance to " CA  GLY A 203 " =    2.284
peak=   -3.245 closest distance to " CE  LYS A 166 " =    1.185
peak=   -3.243 closest distance to " O   HOH Z 140 " =    4.966
peak=   -3.239 closest distance to " O   ALA A 161 " =    1.861
peak=   -3.239 closest distance to " O   HOH Z 163 " =    1.512
peak=   -3.238 closest distance to " CB  ASP A  50 " =    2.413
peak=   -3.231 closest distance to " CB  CYS A 201 " =    2.096
peak=   -3.227 closest distance to " O   HOH Z  22 " =    2.841
peak=   -3.227 closest distance to " O   HOH Z 251 " =    1.156
peak=   -3.226 closest distance to " O   HOH Z 313 " =    1.869
peak=   -3.219 closest distance to " CD2 TYR A 116 " =    2.077
peak=   -3.216 closest distance to " OG  SER A  26 " =    1.077
peak=   -3.215 closest distance to " O   HOH Z 359 " =    1.407
peak=   -3.215 closest distance to " CD  GLN A  58 " =    1.370
peak=   -3.210 closest distance to " CD  GLN A  77 " =    1.441
peak=   -3.205 closest distance to " O   HOH Z 132 " =    1.076
peak=   -3.205 closest distance to " O   SER A 271 " =    2.232
peak=   -3.204 closest distance to " OE1 GLN A  88 " =    0.974
peak=   -3.201 closest distance to " O   HOH Z 409 " =    5.450
peak=   -3.194 closest distance to " OG  SER A 206 " =    1.882
peak=   -3.188 closest distance to " OG  SER A 245 " =    1.667
peak=   -3.184 closest distance to " OG BSER A 134 " =    1.872
peak=   -3.183 closest distance to " O   HOH Z 168 " =    1.454
peak=   -3.179 closest distance to " O   HOH Z 275 " =    1.772
peak=   -3.179 closest distance to " O   HOH Z 390 " =    1.061
peak=   -3.170 closest distance to " O   HOH Z 426 " =    2.226
peak=   -3.169 closest distance to " O   HOH Z 348 " =    2.093
peak=   -3.165 closest distance to " O   HOH Z 266 " =    4.426
peak=   -3.162 closest distance to " C   HIS A 108 " =    1.164
peak=   -3.159 closest distance to " CG  ARG A 259 " =    2.437
peak=   -3.148 closest distance to " CD1 ILE A  33 " =    2.134
peak=   -3.145 closest distance to " O   PRO A 243 " =    2.401
peak=   -3.144 closest distance to " O   HOH Z 247 " =    1.421
peak=   -3.142 closest distance to " ND2 ASN A 249 " =    2.217
peak=   -3.131 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.111 closest distance to " O   HOH Z   2 " =    1.253
peak=   -3.098 closest distance to " NH2BARG A 275 " =    1.721
peak=   -3.092 closest distance to " O   HOH Z  90 " =    2.197
peak=   -3.090 closest distance to " O   TYR A  30 " =    1.785
peak=   -3.089 closest distance to " O   HOH Z 198 " =    2.002
peak=   -3.087 closest distance to " C   GLU A 277 " =    2.366
peak=   -3.084 closest distance to " OG BSER A  99 " =    1.753
peak=   -3.073 closest distance to " CG  TRP A 266 " =    1.406
peak=   -3.070 closest distance to " OE1 GLN A 223 " =    2.603
peak=   -3.067 closest distance to " O   SER A  95 " =    1.078
peak=   -3.064 closest distance to " O   HOH Z 414 " =    1.440
peak=   -3.063 closest distance to " O   HOH Z 126 " =    1.866
peak=   -3.060 closest distance to " O   HOH Z 350 " =    1.839
peak=   -3.036 closest distance to " O   HOH Z  97 " =    1.424

================= 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    :  0.4647 0.4614   6.277298e+00   6.274438e+00
   1_bss:  0.4563 0.4541   6.271858e+00   6.264377e+00
   1_xyz:  0.3812 0.4172   6.168807e+00   6.214257e+00
   1_adp:  0.3493 0.4265   6.128821e+00   6.220704e+00
   1_occ:  0.3491 0.4264   6.127772e+00   6.220301e+00
   2_bss:  0.3498 0.4264   6.130450e+00   6.221248e+00
   2_xyz:  0.2865 0.3589   5.965084e+00   6.106428e+00
   2_adp:  0.2657 0.3467   5.919984e+00   6.082785e+00
   2_occ:  0.2653 0.3468   5.919410e+00   6.082807e+00
   3_bss:  0.2655 0.3444   5.915430e+00   6.077918e+00
   3_xyz:  0.2116 0.2782   5.708092e+00   5.903229e+00
   3_adp:  0.1941 0.2508   5.624393e+00   5.820649e+00
   3_occ:  0.1939 0.2500   5.622440e+00   5.818828e+00
   4_bss:  0.1933 0.2482   5.620371e+00   5.815933e+00
   4_xyz:  0.1587 0.2095   5.443847e+00   5.660762e+00
   4_adp:  0.1511 0.2019   5.404128e+00   5.623658e+00
   4_occ:  0.1509 0.2017   5.403422e+00   5.623020e+00
   5_bss:  0.1510 0.2015   5.403050e+00   5.622167e+00
   5_xyz:  0.1306 0.1782   5.272711e+00   5.503392e+00
   5_adp:  0.1251 0.1752   5.242861e+00   5.483832e+00
   5_occ:  0.1250 0.1750   5.242434e+00   5.483480e+00
   5_bss:  0.1249 0.1751   5.242253e+00   5.483584e+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:  0.350  42.334  -1.094   2.282  -1.313   0.000  -0.000  -0.000
   1_xyz:  0.350  42.334  -1.094   2.282  -1.313   0.000  -0.000  -0.000
   1_adp:  0.350  42.334  -1.094   2.282  -1.313   0.000  -0.000  -0.000
   1_occ:  0.350  42.334  -1.094   2.282  -1.313   0.000  -0.000  -0.000
   2_bss:  0.361  67.927  -0.506   1.079  -0.422   0.000  -0.000  -0.000
   2_xyz:  0.361  67.927  -0.506   1.079  -0.422   0.000  -0.000  -0.000
   2_adp:  0.361  67.927  -0.506   1.079  -0.422   0.000  -0.000  -0.000
   2_occ:  0.361  67.927  -0.506   1.079  -0.422   0.000  -0.000  -0.000
   3_bss:  0.353  66.847  -0.428  -0.333  -0.084  -0.000  -0.000  -0.000
   3_xyz:  0.353  66.847  -0.428  -0.333  -0.084  -0.000  -0.000  -0.000
   3_adp:  0.353  66.847  -0.428  -0.333  -0.084  -0.000  -0.000  -0.000
   3_occ:  0.353  66.847  -0.428  -0.333  -0.084  -0.000  -0.000  -0.000
   4_bss:  0.331  55.350  -1.499  -1.805  -0.918  -0.000  -0.000  -0.000
   4_xyz:  0.331  55.350  -1.499  -1.805  -0.918  -0.000  -0.000  -0.000
   4_adp:  0.331  55.350  -1.499  -1.805  -0.918  -0.000  -0.000  -0.000
   4_occ:  0.331  55.350  -1.499  -1.805  -0.918  -0.000  -0.000  -0.000
   5_bss:  0.328  55.350  -1.886  -2.545  -1.296  -0.000  -0.000  -0.000
   5_xyz:  0.328  55.350  -1.886  -2.545  -1.296  -0.000  -0.000  -0.000
   5_adp:  0.328  55.350  -1.886  -2.545  -1.296  -0.000  -0.000  -0.000
   5_occ:  0.328  55.350  -1.886  -2.545  -1.296  -0.000  -0.000  -0.000
   5_bss:  0.322  55.353  -1.889  -2.548  -1.299  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.420 0.4406  0.6114    72095.181
   1_bss:  55.760 0.4479  0.6243    69583.032
   1_xyz:  48.872 0.5339  0.7229    54569.074
   1_adp:  49.748 0.5226  0.7096    55987.881
   1_occ:  49.728 0.5228  0.7092    55919.660
   2_bss:  49.651 0.5238  0.7144    55881.932
   2_xyz:  39.705 0.6450  0.8702    37024.355
   2_adp:  37.682 0.6693  0.8874    34485.171
   2_occ:  37.702 0.6690  0.8863    34433.923
   3_bss:  37.391 0.6721  0.8790    33682.263
   3_xyz:  28.599 0.7718  0.9724    20416.127
   3_adp:  25.082 0.8106  0.9931    16628.020
   3_occ:  25.023 0.8111  0.9929    16519.678
   4_bss:  24.917 0.8120  0.9543    16347.641
   4_xyz:  20.419 0.8570  0.9832    11391.433
   4_adp:  19.361 0.8677  0.9861    10596.483
   4_occ:  19.336 0.8679  0.9858    10566.378
   5_bss:  19.300 0.8682  0.9683    10523.767
   5_xyz:  16.473 0.8940  0.9807     8094.006
   5_adp:  15.963 0.8988  0.9774     7806.872
   5_occ:  15.948 0.8989  0.9774     7795.285
   5_bss:  15.946 0.8989  0.9774     7794.446
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8734e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8734e-01
   1_xyz:   1.438  0.010  0.099 15.476  0.005  4.103   1.0788e-01
   1_adp:   1.438  0.010  0.099 15.476  0.005  4.103   1.0788e-01
   1_occ:   1.438  0.010  0.099 15.476  0.005  4.103   1.0788e-01
   2_bss:   1.438  0.010  0.099 15.476  0.005  4.103   1.0788e-01
   2_xyz:   1.442  0.011  0.099 15.727  0.006  4.104   1.1778e-01
   2_adp:   1.442  0.011  0.099 15.727  0.006  4.104   1.1778e-01
   2_occ:   1.442  0.011  0.099 15.727  0.006  4.104   1.1778e-01
   3_bss:   1.442  0.011  0.099 15.727  0.006  4.104   1.1778e-01
   3_xyz:   1.090  0.008  0.074 14.835  0.004  4.115   7.1246e-02
   3_adp:   1.090  0.008  0.074 14.835  0.004  4.115   7.1246e-02
   3_occ:   1.090  0.008  0.074 14.835  0.004  4.115   7.1246e-02
   4_bss:   1.090  0.008  0.074 14.835  0.004  4.115   7.1246e-02
   4_xyz:   0.930  0.005  0.066 14.409  0.003  4.107   5.3422e-02
   4_adp:   0.930  0.005  0.066 14.409  0.003  4.107   5.3422e-02
   4_occ:   0.930  0.005  0.066 14.409  0.003  4.107   5.3422e-02
   5_bss:   0.930  0.005  0.066 14.409  0.003  4.107   5.3422e-02
   5_xyz:   0.974  0.006  0.070 14.500  0.004  4.108   5.7076e-02
   5_adp:   0.974  0.006  0.070 14.500  0.004  4.108   5.7076e-02
   5_occ:   0.974  0.006  0.070 14.500  0.004  4.108   5.7076e-02
   5_bss:   0.974  0.006  0.070 14.500  0.004  4.108   5.7076e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.527   2.4001e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.527   2.4001e-01
   1_xyz:   9.430  0.096  0.523 89.587  0.032  2.013   7.8093e-02
   1_adp:   9.430  0.096  0.523 89.587  0.032  2.013   7.8093e-02
   1_occ:   9.430  0.096  0.523 89.587  0.032  2.013   7.8093e-02
   2_bss:   9.430  0.096  0.523 89.587  0.032  2.013   7.8093e-02
   2_xyz:   8.978  0.063  0.384 82.950  0.055  1.977   1.1859e-01
   2_adp:   8.978  0.063  0.384 82.950  0.055  1.977   1.1859e-01
   2_occ:   8.978  0.063  0.384 82.950  0.055  1.977   1.1859e-01
   3_bss:   8.978  0.063  0.384 82.950  0.055  1.977   1.1859e-01
   3_xyz:   8.091  0.046  0.283 77.380  0.016  2.299   7.1083e-02
   3_adp:   8.091  0.046  0.283 77.380  0.016  2.299   7.1083e-02
   3_occ:   8.091  0.046  0.283 77.380  0.016  2.299   7.1083e-02
   4_bss:   8.091  0.046  0.283 77.380  0.016  2.299   7.1083e-02
   4_xyz:   7.219  0.036  0.213 76.827  0.030  2.335   4.8683e-02
   4_adp:   7.219  0.036  0.213 76.827  0.030  2.335   4.8683e-02
   4_occ:   7.219  0.036  0.213 76.827  0.030  2.335   4.8683e-02
   5_bss:   7.219  0.036  0.213 76.827  0.030  2.335   4.8683e-02
   5_xyz:   8.053  0.042  0.214 84.294  0.032  2.322   4.6500e-02
   5_adp:   8.053  0.042  0.214 84.294  0.032  2.322   4.6500e-02
   5_occ:   8.053  0.042  0.214 84.294  0.032  2.322   4.6500e-02
   5_bss:   8.053  0.042  0.214 84.294  0.032  2.322   4.6500e-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:  98.08   0.00  19.05  85.97   0.00  16.16  98.08   1.32  34.77
   1_occ:  98.08   0.00  19.05  85.97   0.00  16.16  98.08   1.32  34.77
   2_bss:  98.08   0.00  19.05  85.97   0.00  16.16  98.08   1.32  34.77
   2_xyz:  98.08   0.00  19.05  85.97   0.00  16.16  98.08   1.32  34.77
   2_adp:  98.62   0.00  18.74  87.10   0.00  15.21  98.62   0.00  37.92
   2_occ:  98.62   0.00  18.74  87.10   0.00  15.21  98.62   0.00  37.92
   3_bss:  98.62   0.00  18.74  87.10   0.00  15.21  98.62   0.00  37.92
   3_xyz:  98.62   0.00  18.74  87.10   0.00  15.21  98.62   0.00  37.92
   3_adp:  86.88   0.00  17.51  86.88   0.00  13.44  86.41   4.78  39.70
   3_occ:  86.88   0.00  17.51  86.88   0.00  13.44  86.41   4.78  39.70
   4_bss:  86.88   0.00  17.51  86.88   0.00  13.44  86.41   4.78  39.70
   4_xyz:  86.88   0.00  17.51  86.88   0.00  13.44  86.41   4.78  39.70
   4_adp:  86.89   1.67  17.23  86.89   1.67  12.93  86.03   6.04  40.59
   4_occ:  86.89   1.67  17.23  86.89   1.67  12.93  86.03   6.04  40.59
   5_bss:  86.89   1.67  17.23  86.89   1.67  12.93  86.03   6.04  40.59
   5_xyz:  86.89   1.67  17.23  86.89   1.67  12.93  86.03   6.04  40.59
   5_adp:  97.05   0.00  17.71  97.05   0.00  12.82  95.46   5.96  44.31
   5_occ:  97.05   0.00  17.71  97.05   0.00  12.82  95.46   5.96  44.31
   5_bss:  97.05   0.00  17.71  97.05   0.00  12.82  95.46   5.97  44.31
------------------------------------------------------------------------
 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:    1.632    0.019    0.282
   1_adp:    1.632    0.019    0.282
   1_occ:    1.632    0.019    0.282
   2_bss:    1.632    0.019    0.282
   2_xyz:    1.593    0.051    0.563
   2_adp:    1.593    0.051    0.563
   2_occ:    1.593    0.051    0.563
   3_bss:    1.593    0.051    0.563
   3_xyz:    1.734    0.058    0.702
   3_adp:    1.734    0.058    0.702
   3_occ:    1.734    0.058    0.702
   4_bss:    1.734    0.058    0.702
   4_xyz:    1.720    0.048    0.774
   4_adp:    1.720    0.048    0.774
   4_occ:    1.720    0.048    0.774
   5_bss:    1.720    0.048    0.774
   5_xyz:    1.765    0.074    0.819
   5_adp:    1.765    0.074    0.819
   5_occ:    1.765    0.074    0.819
   5_bss:    1.765    0.074    0.819
------------------------------------------------------------------------

CPU time actual refinement: 342.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/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_971/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_971/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.84 
  Macro-tasks:
    bulk solvent and scale       = 37.95  
    individual site refinement   = 137.39 
    weights calculation          = 30.18  
    collect and process          = 6.43   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.05 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 113.71 
    alpha_beta                      = 8.07   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.51 
    fmodel                         = 6.12   
    r_factors                      = 0.16   
    phase_errors                   = 10.46  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 261.94 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.962 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    630 calls, 113.38 s
gradients_fft:          575 calls, 107.12 s

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

# Date 2008-01-16 Time 06:06:19 PST -0800 (1200492379.54 s)
Start R-work = 0.4647, R-free = 0.4614 (no bulk solvent and anisotropic scale)
Final R-work = 0.1466, R-free = 0.1922 (no bulk solvent and anisotropic scale)

Start R-work = 0.4563, R-free = 0.4541
Final R-work = 0.1249, R-free = 0.1751