# Date 2008-01-16 Time 05:10:17 PST -0800 (1200489017.20 s)
#phil __OFF__

Command line arguments: "../621.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18113
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 621

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 86.39, 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: (70.25, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.96293
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948758

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9629

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: (70.25, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.96293
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948758

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2009 [2165/2190]  1946   219  10.1%
  bin  2:  4.2009 -  3.3466 [2074/2094]  1870   204   9.8%
  bin  3:  3.3466 -  2.9271 [2057/2076]  1849   208  10.1%
  bin  4:  2.9271 -  2.6611 [2029/2059]  1827   202  10.0%
  bin  5:  2.6611 -  2.4713 [2011/2030]  1814   197   9.8%
  bin  6:  2.4713 -  2.3261 [2017/2042]  1812   205  10.2%
  bin  7:  2.3261 -  2.2100 [1994/2022]  1793   201  10.1%
  bin  8:  2.2100 -  2.1141 [1990/2026]  1792   198   9.9%
  bin  9:  2.1141 -  2.0329 [1988/2030]  1791   197   9.9%
  bin 10:  2.0329 -  1.9629 [1264/2016]  1136   128  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/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:
        1.81 -     2.42: 35
        2.42 -     3.04: 2232
        3.04 -     3.66: 4746
        3.66 -     4.28: 9144
        4.28 -     4.90: 12405
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.842 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.982 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28557 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_621/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/model_refine_001.geo

CPU time processing inputs: 8.71


============================ 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 = 70.25 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.3705   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.185290                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.3252 0.3223      6.4651      6.4613|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.3108 0.2934      6.6571      6.5502|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.3359 0.3084      6.5476      6.5948|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.3559 0.3719      6.4085      6.4306|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.3955 0.3541      6.2672      6.2186|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.3910 0.4267      6.1742      6.1466|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.3953 0.3850      6.1505      6.0849|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.4125 0.4362      6.0945      6.1424|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.4039 0.4384      6.0432      6.0773|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.4116 0.4023      6.0167      5.9799|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.4032 0.4100      5.9535      6.0053|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.4241 0.3987      5.9121      5.9413|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.4235 0.4125      5.7988      5.7478|
| 14:  2.0119 -  1.9629 0.48    631   74 0.4739 0.4399      5.8736      5.7746|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.76  29.15   0.85     0.80      54338.84|
|  2:  4.6858 -  3.7382  1348   151  0.79  26.84   0.94     0.90      68494.16|
|  3:  3.7382 -  3.2713  1328   143  0.73  32.89   0.98     0.91      71268.45|
|  4:  3.2713 -  2.9748  1325   153  0.67  37.88   0.97     0.86      65174.77|
|  5:  2.9748 -  2.7630  1309   146  0.60  43.47   0.94     0.82      53026.97|
|  6:  2.7630 -  2.6009  1305   142  0.59  44.59   0.94     0.79      47124.85|
|  7:  2.6009 -  2.4713  1287   139  0.57  46.37   0.99     0.77      44608.83|
|  8:  2.4713 -  2.3641  1289   146  0.55  48.42   0.97     0.75      41723.57|
|  9:  2.3641 -  2.2735  1269   146  0.56  47.43   0.99     0.77      37600.01|
| 10:  2.2735 -  2.1952  1303   142  0.57  46.43   1.00     0.79      32559.83|
| 11:  2.1952 -  2.1268  1281   139  0.56  47.34   1.03     0.81      31774.83|
| 12:  2.1268 -  2.0662  1262   147  0.55  48.42   1.02     0.80      29183.09|
| 13:  2.0662 -  2.0119  1289   135  0.51  51.61   1.01     0.78      26029.09|
| 14:  2.0119 -  1.9629   631    74  0.56  47.61   1.02     0.77      21221.88|
|alpha:            min =        0.75 max =            0.91 mean =         0.81|
|beta:             min =    21221.88 max =        71268.45 mean =     45736.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.95 mean =        42.38|
|phase err.(test): min =        0.00 max =           89.90 mean =        42.48|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.355364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.230   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.205266              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.226   (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 |  1.806 -  2.115:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      206 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2026 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1889 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2857 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4697 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4447 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5656 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6749 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.319 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3758   r_free= 0.3705   ksol= 0.00   Bsol= 0.00   scale= 0.946    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.185290                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3587   r_free= 0.3568   ksol= 0.35   Bsol= 50.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,3.73,-1.86,0.00,-0.00,-0.00); trace/3= -0.47                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.166264                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.660373              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.228   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635341              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.144   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3587      final r-factor (work) = 0.2729          |
| start r-factor (free) = 0.3568      final r-factor (free) = 0.3090          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6260 = 5.66 * 0.50 * 6.1675 + 1.00 * 0.1708                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0605 = 5.66 * 0.50 * 5.9894 + 1.00 * 0.1095                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2729      final r-factor (work) = 0.2488          |
| start r-factor (free) = 0.3090      final r-factor (free) = 0.3231          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8113 = 0.64 * 1.00 * 5.9894 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7326 = 0.64 * 1.00 * 5.8553 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.43   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    93.43   17.44    None  None   None       |
|    Sol.    : 438    0      3.81    93.43   38.20    None  None   None       |
|    Mac.    : 2385   0      0.00    68.33   13.63    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 -   9.343:  868   |   5:    46.713 -  56.055:  101        |
|      1:     9.343 -  18.685: 1082   |   6:    56.055 -  65.398:   40        |
|      2:    18.685 -  28.028:  397   |   7:    65.398 -  74.741:   14        |
|      3:    28.028 -  37.370:  179   |   8:    74.741 -  84.083:    0        |
|      4:    37.370 -  46.713:  141   |   9:    84.083 -  93.426:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2488 r_free = 0.3231             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2485 r_free = 0.3230             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2485   r_free= 0.3230   ksol= 0.35   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,3.73,-1.86,0.00,-0.00,-0.00); trace/3= -0.47                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.867620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2466   r_free= 0.3177   ksol= 0.34   Bsol= 52.78   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.09,-1.07,0.00,-0.00,-0.00); trace/3= -1.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.858981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.343937              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.437   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.228935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.889  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2466      final r-factor (work) = 0.1822          |
| start r-factor (free) = 0.3177      final r-factor (free) = 0.2338          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8204 = 4.34 * 0.50 * 5.8522 + 1.00 * 0.1095                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5308 = 4.34 * 0.50 * 5.7382 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1822      final r-factor (work) = 0.1673          |
| start r-factor (free) = 0.2338      final r-factor (free) = 0.2164          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3261 = 0.23 * 1.00 * 5.7382 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2741 = 0.23 * 1.00 * 5.5304 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.97   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    85.97   17.06    None  None   None       |
|    Sol.    : 438    0      5.77    85.97   38.57    None  None   None       |
|    Mac.    : 2385   0      0.00    75.56   13.11    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 -   8.597:  694   |   5:    42.985 -  51.581:  113        |
|      1:     8.597 -  17.194: 1285   |   6:    51.581 -  60.178:   67        |
|      2:    17.194 -  25.791:  343   |   7:    60.178 -  68.775:   24        |
|      3:    25.791 -  34.388:  160   |   8:    68.775 -  77.372:    3        |
|      4:    34.388 -  42.985:  133   |   9:    77.372 -  85.969:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1673 r_free = 0.2164             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1673 r_free = 0.2163             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1673   r_free= 0.2163   ksol= 0.34   Bsol= 52.78   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.09,-1.07,0.00,-0.00,-0.00); trace/3= -1.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.496636                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1666   r_free= 0.2148   ksol= 0.34   Bsol= 52.78   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.58,-0.96,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.490076                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.467192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.419  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1666      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.2148      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8883 = 2.47 * 0.50 * 5.5291 + 1.00 * 0.0676                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6999 = 2.47 * 0.50 * 5.3885 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1338      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1801      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9922 = 0.18 * 1.00 * 5.3885 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9703 = 0.18 * 1.00 * 5.2720 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.15    83.98   16.76    None  None   None       |
|    all(noH): 2823   0      1.15    83.98   16.76    None  None   None       |
|    Sol.    : 438    0      4.40    83.98   38.62    None  None   None       |
|    Mac.    : 2385   0      1.15    75.50   12.74    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:     1.149 -   9.432:  896   |   5:    42.567 -  50.850:  121        |
|      1:     9.432 -  17.716: 1177   |   6:    50.850 -  59.134:   67        |
|      2:    17.716 -  25.999:  268   |   7:    59.134 -  67.417:   27        |
|      3:    25.999 -  34.283:  141   |   8:    67.417 -  75.701:    6        |
|      4:    34.283 -  42.567:  119   |   9:    75.701 -  83.984:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1739             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1738             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1738   ksol= 0.34   Bsol= 52.78   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.58,-0.96,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253789                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1734   ksol= 0.34   Bsol= 52.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.34,-1.15,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.252808                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.267772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.736  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.524120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.914  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0323 = 2.27 * 0.50 * 5.2736 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9653 = 2.27 * 0.50 * 5.2123 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9515 = 1.52 * 1.00 * 5.2123 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8621 = 1.52 * 1.00 * 5.1522 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.49   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    89.49   17.22    None  None   None       |
|    Sol.    : 438    0      4.31    89.49   41.38    None  None   None       |
|    Mac.    : 2385   0      0.00    88.06   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.950:  821   |   5:    44.747 -  53.697:   93        |
|      1:     8.950 -  17.899: 1268   |   6:    53.697 -  62.646:   81        |
|      2:    17.899 -  26.848:  265   |   7:    62.646 -  71.596:   40        |
|      3:    26.848 -  35.798:  130   |   8:    71.596 -  80.545:   12        |
|      4:    35.798 -  44.747:  107   |   9:    80.545 -  89.495:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1597             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1596             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1596   ksol= 0.34   Bsol= 52.78   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.34,-1.15,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1595   ksol= 0.32   Bsol= 52.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.37,-1.01,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149256                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.841779              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.846  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.369086              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.870  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7993 = 1.84 * 0.50 * 5.1518 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7868 = 1.84 * 0.50 * 5.1429 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9077 = 0.37 * 1.00 * 5.1429 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9053 = 0.37 * 1.00 * 5.1381 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.55   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    90.55   16.85    None  None   None       |
|    Sol.    : 438    0      5.74    87.62   40.10    None  None   None       |
|    Mac.    : 2385   0      0.00    90.55   12.58    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 -   9.055:  886   |   5:    45.273 -  54.328:   90        |
|      1:     9.055 -  18.109: 1231   |   6:    54.328 -  63.382:   62        |
|      2:    18.109 -  27.164:  249   |   7:    63.382 -  72.437:   35        |
|      3:    27.164 -  36.219:  139   |   8:    72.437 -  81.492:   10        |
|      4:    36.219 -  45.273:  116   |   9:    81.492 -  90.546:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1560             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1561             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1561   ksol= 0.32   Bsol= 52.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.37,-1.01,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.0950 0.1218      5.3395      5.5311|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.0839 0.1134      5.4252      5.6038|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.1073 0.1494      5.4777      5.8409|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.1225 0.1665      5.4476      5.5918|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.1322 0.1757      5.3134      5.5543|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.1164 0.1878      5.1794      5.4799|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.1240 0.1504      5.1559      5.2867|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.1164 0.1630       5.053      5.2921|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.1167 0.1666      5.0271      5.2659|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.1101 0.1749      4.9323      5.2188|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.1109 0.1775      4.9334      5.2737|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.1111 0.1692      4.8577        5.17|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.1138 0.1780      4.7805      5.0552|
| 14:  2.0119 -  1.9629 0.48    631   74 0.1012 0.1456      4.6795      4.8328|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.94   8.58   0.98     0.95       6419.29|
|  2:  4.6858 -  3.7382  1348   151  0.95   7.61   1.02     1.01       8685.82|
|  3:  3.7382 -  3.2713  1328   143  0.94  11.18   1.03     1.03      10260.36|
|  4:  3.2713 -  2.9748  1325   153  0.92  13.73   1.01     0.99      10113.47|
|  5:  2.9748 -  2.7630  1309   146  0.90  15.47   1.00     0.98       8035.11|
|  6:  2.7630 -  2.6009  1305   142  0.90  15.84   0.99     0.96       6710.21|
|  7:  2.6009 -  2.4713  1287   139  0.91  15.27   0.99     0.96       5998.70|
|  8:  2.4713 -  2.3641  1289   146  0.91  15.10   0.99     0.97       5104.81|
|  9:  2.3641 -  2.2735  1269   146  0.91  15.02   1.00     0.97       4914.36|
| 10:  2.2735 -  2.1952  1303   142  0.90  15.57   1.00     0.97       4219.13|
| 11:  2.1952 -  2.1268  1281   139  0.90  15.90   0.99     0.94       4285.39|
| 12:  2.1268 -  2.0662  1262   147  0.91  15.14   1.01     1.00       3820.44|
| 13:  2.0662 -  2.0119  1289   135  0.90  16.42   1.00     0.98       3325.33|
| 14:  2.0119 -  1.9629   631    74  0.92  14.06   0.98     0.96       2689.53|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2689.53 max =        10260.36 mean =      6202.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.74 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1560   ksol= 0.32   Bsol= 52.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.28,-0.81,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1560   ksol= 0.32   Bsol= 52.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.28,-0.81,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.135349                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.0951 0.1220      5.3405      5.5327|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.0840 0.1134      5.4257      5.6038|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.1073 0.1494      5.4778      5.8409|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.1226 0.1665      5.4476      5.5916|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.1322 0.1756      5.3131      5.5539|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.1164 0.1875       5.179       5.479|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.1241 0.1505      5.1559      5.2869|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.1164 0.1630      5.0528      5.2917|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.1168 0.1664      5.0271      5.2653|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.1100 0.1751      4.9323        5.22|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.1109 0.1776      4.9337      5.2742|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.1110 0.1691      4.8576        5.17|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.1138 0.1777      4.7799      5.0535|
| 14:  2.0119 -  1.9629 0.48    631   74 0.1011 0.1453      4.6781      4.8312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.94   8.59   0.98     0.95       6433.00|
|  2:  4.6858 -  3.7382  1348   151  0.95   7.62   1.02     1.01       8697.10|
|  3:  3.7382 -  3.2713  1328   143  0.94  11.18   1.03     1.03      10263.01|
|  4:  3.2713 -  2.9748  1325   153  0.92  13.73   1.02     0.99      10110.85|
|  5:  2.9748 -  2.7630  1309   146  0.90  15.47   1.00     0.98       8027.05|
|  6:  2.7630 -  2.6009  1305   142  0.90  15.84   0.99     0.97       6704.31|
|  7:  2.6009 -  2.4713  1287   139  0.91  15.26   1.00     0.96       5995.69|
|  8:  2.4713 -  2.3641  1289   146  0.91  15.10   1.00     0.98       5100.74|
|  9:  2.3641 -  2.2735  1269   146  0.91  15.02   1.01     0.97       4912.10|
| 10:  2.2735 -  2.1952  1303   142  0.90  15.58   1.01     0.98       4222.30|
| 11:  2.1952 -  2.1268  1281   139  0.90  15.91   1.00     0.95       4291.39|
| 12:  2.1268 -  2.0662  1262   147  0.91  15.15   1.01     1.01       3822.27|
| 13:  2.0662 -  2.0119  1289   135  0.90  16.40   1.01     0.99       3319.18|
| 14:  2.0119 -  1.9629   631    74  0.92  14.02   0.99     0.97       2678.88|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2678.88 max =        10263.01 mean =      6202.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.74 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.55   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    90.55   16.85    None  None   None       |
|    Sol.    : 438    0      5.74    87.62   40.10    None  None   None       |
|    Mac.    : 2385   0      0.00    90.55   12.58    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 -   9.058:  886   |   5:    45.276 -  54.331:   90        |
|      1:     9.058 -  18.112: 1231   |   6:    54.331 -  63.385:   62        |
|      2:    18.112 -  27.167:  249   |   7:    63.385 -  72.440:   35        |
|      3:    27.167 -  36.222:  139   |   8:    72.440 -  81.495:   10        |
|      4:    36.222 -  45.276:  116   |   9:    81.495 -  90.549:    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)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 4.657
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 305
   mapped sites are within: 0.761 - 4.657

peak=    6.527 closest distance to " NE2 GLN A  11 " =    1.303
peak=    5.745 closest distance to " O   HOH Z 144 " =    1.795
peak=    5.729 closest distance to " CG  PRO A  54 " =    1.332
peak=    5.497 closest distance to " O   HOH Z 126 " =    2.024
peak=    5.372 closest distance to " NH2 ARG A  56 " =    2.071
peak=    5.201 closest distance to " O   HOH Z 423 " =    1.807
peak=    5.094 closest distance to " O   HOH Z 427 " =    2.521
peak=    5.060 closest distance to " O   HOH Z 287 " =    1.920
peak=    5.003 closest distance to " O   HOH Z 417 " =    1.615
peak=    4.978 closest distance to " O   HOH Z  63 " =    1.639
peak=    4.952 closest distance to " CB  PRO A  54 " =    0.997
peak=    4.884 closest distance to " CB  SER A  63 " =    1.236
peak=    4.859 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.776 closest distance to " CB  GLN A 223 " =    1.494
peak=    4.770 closest distance to " O   HOH Z 232 " =    2.346
peak=    4.735 closest distance to " O   HOH Z 369 " =    2.217
peak=    4.718 closest distance to " O   HOH Z 298 " =    1.993
peak=    4.710 closest distance to " CG  PRO A 213 " =    1.297
peak=    4.664 closest distance to " O   HOH Z  78 " =    1.700
peak=    4.643 closest distance to " CG  PRO A  90 " =    1.200
peak=    4.573 closest distance to " CG  PRO A 198 " =    1.279
peak=    4.497 closest distance to " O   HOH Z 380 " =    1.762
peak=    4.492 closest distance to " ND2 ASN A 187 " =    1.547
peak=    4.466 closest distance to " CG2 VAL A 257 " =    0.888
peak=    4.449 closest distance to " CB  GLN A 183 " =    1.192
peak=    4.432 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.408 closest distance to " O   HOH Z 209 " =    2.228
peak=    4.407 closest distance to " O   HOH Z   9 " =    1.315
peak=    4.369 closest distance to " O   HOH Z  57 " =    2.202
peak=    4.362 closest distance to " CD  ARG A 159 " =    0.806
peak=    4.344 closest distance to " CB  GLU A 128 " =    0.998
peak=    4.336 closest distance to " O   HOH Z   1 " =    1.826
peak=    4.290 closest distance to " CG  TRP A 179 " =    2.124
peak=    4.271 closest distance to " CB  ARG A 190 " =    1.676
peak=    4.247 closest distance to " CB  ARG A  79 " =    1.389
peak=    4.243 closest distance to " O   HOH Z   1 " =    1.822
peak=    4.238 closest distance to " O   HOH Z 193 " =    1.817
peak=    4.236 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.229 closest distance to " O   HOH Z 236 " =    1.480
peak=    4.226 closest distance to " O   HOH Z   2 " =    1.584
peak=    4.192 closest distance to " O   HOH Z  78 " =    2.092
peak=    4.190 closest distance to " O   HOH Z 425 " =    1.377
peak=    4.185 closest distance to " O   HOH Z 316 " =    3.078
peak=    4.180 closest distance to " CB  GLU A 152 " =    1.321
peak=    4.168 closest distance to " CD  ARG A  66 " =    2.303
peak=    4.146 closest distance to " CB  ASN A 187 " =    1.139
peak=    4.130 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.113 closest distance to " O   HOH Z 371 " =    1.976
peak=    4.109 closest distance to " C   PRO A 198 " =    1.480
peak=    4.106 closest distance to " O   HOH Z 132 " =    2.402
peak=    4.095 closest distance to " O   HOH Z 214 " =    2.167
peak=    4.087 closest distance to " CB  VAL A 265 " =    1.313
peak=    4.065 closest distance to " O   HOH Z 368 " =    3.658
peak=    4.039 closest distance to " CB  SER A   3 " =    1.327
peak=    4.034 closest distance to " CG  PRO A 243 " =    1.106
peak=    4.007 closest distance to " O   HOH Z 234 " =    3.661
peak=    4.001 closest distance to " O   HOH Z 362 " =    2.101
peak=    3.983 closest distance to " O   HOH Z 146 " =    1.781
peak=    3.980 closest distance to " O   HOH Z 272 " =    1.770
peak=    3.970 closest distance to " O   HOH Z 158 " =    2.899
peak=    3.961 closest distance to " CB  TRP A 266 " =    1.051
peak=    3.954 closest distance to " NZ  LYS A 117 " =    3.022
peak=    3.929 closest distance to " O   HOH Z 144 " =    2.275
peak=    3.928 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.914 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.913 closest distance to " O   HOH Z 352 " =    1.714
peak=    3.900 closest distance to " CB  SER A 216 " =    0.807
peak=    3.892 closest distance to " O   HOH Z 250 " =    1.525
peak=    3.884 closest distance to " O   HOH Z   9 " =    1.932
peak=    3.866 closest distance to " ND1 HIS A  86 " =    1.792
peak=    3.859 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.837 closest distance to " O   HOH Z  66 " =    2.114
peak=    3.833 closest distance to " CB  THR A 157 " =    1.154
peak=    3.824 closest distance to " NZ  LYS A 119 " =    2.562
peak=    3.814 closest distance to " O   HOH Z  61 " =    1.526
peak=    3.814 closest distance to " O   HOH Z 391 " =    2.856
peak=    3.807 closest distance to " O   HOH Z 392 " =    1.237
peak=    3.804 closest distance to " O   HOH Z   3 " =    1.969
peak=    3.802 closest distance to " CG  LEU A 167 " =    1.222
peak=    3.801 closest distance to " O   SER A  87 " =    2.199
peak=    3.800 closest distance to " CG  PRO A 280 " =    0.789
peak=    3.785 closest distance to " O   HOH Z 425 " =    1.989
peak=    3.781 closest distance to " O   HOH Z 327 " =    1.707
peak=    3.777 closest distance to " OD1 ASN A  69 " =    2.677
peak=    3.776 closest distance to " OG BSER A 164 " =    2.307
peak=    3.770 closest distance to " CB  GLU A 277 " =    3.555
peak=    3.768 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.765 closest distance to " O   HOH Z 365 " =    2.739
peak=    3.760 closest distance to " N   PHE A 130 " =    1.218
peak=    3.746 closest distance to " O   HOH Z 389 " =    1.813
peak=    3.737 closest distance to " N   GLN A 278 " =    1.137
peak=    3.730 closest distance to " O   HOH Z 437 " =    1.832
peak=    3.729 closest distance to " CB  TRP A 179 " =    1.399
peak=    3.729 closest distance to " CA  ASN A 215 " =    1.132
peak=    3.728 closest distance to " O   HOH Z 116 " =    2.936
peak=    3.718 closest distance to " O   HOH Z   7 " =    1.281
peak=    3.715 closest distance to " O   HOH Z 405 " =    1.381
peak=    3.703 closest distance to " CB  ARG A 139 " =    1.001
peak=    3.702 closest distance to " CZ  PHE A 218 " =    1.027
peak=    3.702 closest distance to " CG1 ILE A  33 " =    1.292
peak=    3.682 closest distance to " O   HOH Z 394 " =    1.676
peak=    3.681 closest distance to " O   HOH Z 346 " =    1.748
peak=    3.665 closest distance to " O   HOH Z 386 " =    2.997
peak=    3.664 closest distance to " O   HOH Z 175 " =    2.150
peak=    3.660 closest distance to " CB  ILE A 120 " =    1.321
peak=    3.648 closest distance to " CD2 LEU A 297 " =    1.011
peak=    3.644 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.642 closest distance to " CD  ARG A 138 " =    0.761
peak=    3.638 closest distance to " OD1BASN A 224 " =    2.241
peak=    3.634 closest distance to " NH1AARG A 145 " =    1.200
peak=    3.624 closest distance to " O   HOH Z 426 " =    1.936
peak=    3.615 closest distance to " CB  LEU A 143 " =    1.106
peak=    3.605 closest distance to " CD  PRO A 243 " =    1.680
peak=    3.604 closest distance to " O   HOH Z 257 " =    2.210
peak=    3.602 closest distance to " CB  SER A 212 " =    1.177
peak=    3.602 closest distance to " O   HOH Z  40 " =    2.198
peak=    3.598 closest distance to " O   HOH Z 222 " =    2.492
peak=    3.594 closest distance to " CB  LYS A 117 " =    1.219
peak=    3.588 closest distance to " CA  ALA A 233 " =    1.002
peak=    3.588 closest distance to " O   HOH Z 112 " =    1.088
peak=    3.582 closest distance to " CA  ALA A 299 " =    0.889
peak=    3.569 closest distance to " O   HOH Z  44 " =    1.661
peak=    3.565 closest distance to " O   HOH Z 390 " =    2.469
peak=    3.563 closest distance to " O   HOH Z 371 " =    2.988
peak=    3.563 closest distance to " OG  SER A  62 " =    2.980
peak=    3.559 closest distance to " CB  THR A  31 " =    1.699
peak=    3.559 closest distance to " O   HOH Z 245 " =    1.308
peak=    3.559 closest distance to " O   HOH Z 286 " =    2.268
peak=    3.556 closest distance to " CB  ALA A   1 " =    4.657
peak=    3.553 closest distance to " CB  SER A  62 " =    1.179
peak=    3.552 closest distance to " O   HOH Z  10 " =    1.764
peak=    3.551 closest distance to " CB  ASN A 142 " =    0.955
peak=    3.546 closest distance to " O   HOH Z 357 " =    1.962
peak=    3.545 closest distance to " CA  TYR A 116 " =    1.323
peak=    3.544 closest distance to " O   HOH Z  21 " =    1.666
peak=    3.540 closest distance to " CD2 TRP A 179 " =    1.289
peak=    3.524 closest distance to " CB  ALA A 114 " =    1.435
peak=    3.521 closest distance to " O   HOH Z 213 " =    2.230
peak=    3.513 closest distance to " N   GLU A   2 " =    1.397
peak=    3.512 closest distance to " NE2 GLN A  73 " =    3.651
peak=    3.505 closest distance to " CD BLYS A 290 " =    1.099
peak=    3.503 closest distance to " CE1 TYR A 186 " =    1.352
peak=    3.502 closest distance to " CG  MET A 113 " =    1.111
peak=    3.497 closest distance to " O   HOH Z 344 " =    3.150
peak=    3.496 closest distance to " O   HOH Z  44 " =    2.849
peak=    3.493 closest distance to " O   HOH Z 128 " =    2.035
peak=    3.490 closest distance to " O   HOH Z 109 " =    2.510
peak=    3.485 closest distance to " CB  TYR A 169 " =    0.828
peak=    3.484 closest distance to " O   HOH Z 343 " =    3.307
peak=    3.482 closest distance to " NH2BARG A 145 " =    2.016
peak=    3.481 closest distance to " O   HOH Z 126 " =    1.433
peak=    3.478 closest distance to " O   HOH Z 180 " =    2.127
peak=    3.476 closest distance to " O   HOH Z 368 " =    1.873
peak=    3.464 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.461 closest distance to " O   HOH Z 411 " =    3.747
peak=    3.455 closest distance to " CA  SER A  87 " =    1.022
peak=    3.453 closest distance to " O   HOH Z 219 " =    2.274
peak=    3.452 closest distance to " CA  THR A 264 " =    0.847
peak=    3.451 closest distance to " O   HOH Z  59 " =    2.029
peak=    3.445 closest distance to " O   HOH Z 403 " =    1.376
peak=    3.445 closest distance to " O   HOH Z 423 " =    1.899
peak=    3.442 closest distance to " O   TYR A 116 " =    1.365
peak=    3.439 closest distance to " O   HOH Z  88 " =    3.959
peak=    3.438 closest distance to " O   HOH Z  88 " =    2.866
peak=    3.428 closest distance to " CG1BVAL A  72 " =    1.378
peak=    3.424 closest distance to " NH1BARG A 145 " =    1.227
peak=    3.422 closest distance to " O   HOH Z 145 " =    2.347
peak=    3.422 closest distance to " OD2 ASP A 286 " =    2.737
peak=    3.420 closest distance to " CD1 LEU A 300 " =    1.149
peak=    3.418 closest distance to " N   CYS A 260 " =    0.761
peak=    3.417 closest distance to " CA  ALA A  84 " =    1.331
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.642
peak=    3.412 closest distance to " CA  ARG A 195 " =    1.288
peak=    3.404 closest distance to " CA  MET A 105 " =    0.877
peak=    3.394 closest distance to " O   HOH Z 195 " =    1.249
peak=    3.391 closest distance to " O   HOH Z 305 " =    3.546
peak=    3.387 closest distance to " O   HOH Z 272 " =    2.061
peak=    3.384 closest distance to " N   ASN A 127 " =    1.369
peak=    3.378 closest distance to " O   HOH Z 298 " =    2.480
peak=    3.374 closest distance to " NH2AARG A 190 " =    1.736
peak=    3.373 closest distance to " O   HOH Z 189 " =    2.318
peak=    3.371 closest distance to " CA  ASN A 127 " =    1.003
peak=    3.370 closest distance to " O   HOH Z 172 " =    2.728
peak=    3.361 closest distance to " N   SER A  97 " =    0.856
peak=    3.361 closest distance to " O   HOH Z  88 " =    2.732
peak=    3.359 closest distance to " OG BSER A  99 " =    2.277
peak=    3.358 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.358 closest distance to " CB  ALA A 114 " =    0.887
peak=    3.354 closest distance to " CE3 TRP A 274 " =    1.279
peak=    3.350 closest distance to " O   HOH Z  24 " =    1.815
peak=    3.348 closest distance to " CB  ASP A 140 " =    0.853
peak=    3.345 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.344 closest distance to " CB  ASP A 124 " =    0.881
peak=    3.341 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.335 closest distance to " O   HOH Z 193 " =    1.628
peak=    3.332 closest distance to " O   HOH Z  59 " =    1.448
peak=    3.330 closest distance to " O   HOH Z 291 " =    1.525
peak=    3.328 closest distance to " O   HOH Z 421 " =    2.123
peak=    3.320 closest distance to " CB  SER A 276 " =    1.220
peak=    3.315 closest distance to " O   HOH Z  97 " =    2.096
peak=    3.314 closest distance to " CA  ALA A 158 " =    1.092
peak=    3.314 closest distance to " CB  GLN A  89 " =    1.309
peak=    3.313 closest distance to " O   ASN A  74 " =    1.528
peak=    3.307 closest distance to " N   ALA A   1 " =    2.231
peak=    3.301 closest distance to " O   HOH Z 207 " =    2.133
peak=    3.301 closest distance to " CG1 ILE A 151 " =    1.077
peak=    3.301 closest distance to " CG2 ILE A 120 " =    1.071
peak=    3.299 closest distance to " O   HOH Z 132 " =    3.021
peak=    3.298 closest distance to " O   HOH Z 435 " =    1.935
peak=    3.298 closest distance to " O   HOH Z 345 " =    1.732
peak=    3.293 closest distance to " ND2 ASN A 249 " =    0.803
peak=    3.289 closest distance to " O   HOH Z  43 " =    2.189
peak=    3.289 closest distance to " CB  TYR A 116 " =    0.887
peak=    3.288 closest distance to " O   HOH Z  17 " =    1.771
peak=    3.286 closest distance to " CA  LEU A 101 " =    1.653
peak=    3.279 closest distance to " O   HOH Z  55 " =    2.072
peak=    3.277 closest distance to " CB  LYS A 290 " =    1.454
peak=    3.274 closest distance to " O   ASN A 209 " =    1.440
peak=    3.273 closest distance to " NE  ARG A  56 " =    3.425
peak=    3.272 closest distance to " O   HOH Z  59 " =    2.434
peak=    3.271 closest distance to " O   HOH Z 193 " =    2.016
peak=    3.270 closest distance to " CB  MET A  47 " =    1.079
peak=    3.269 closest distance to " NE2 GLN A  58 " =    3.820
peak=    3.268 closest distance to " O   HOH Z 329 " =    3.789
peak=    3.266 closest distance to " CG  LEU A 101 " =    1.192
peak=    3.264 closest distance to " CA  ILE A 234 " =    1.006
peak=    3.255 closest distance to " O   HOH Z 290 " =    1.047
peak=    3.255 closest distance to " CG  GLN A  89 " =    1.490
peak=    3.252 closest distance to " CA  SER A  95 " =    1.044
peak=    3.243 closest distance to " O   HOH Z 302 " =    1.603
peak=    3.240 closest distance to " CA  ALA A 233 " =    1.027
peak=    3.239 closest distance to " O   HOH Z 207 " =    1.716
peak=    3.238 closest distance to " CA  ILE A 263 " =    1.064
peak=    3.235 closest distance to " O   HOH Z 130 " =    2.160
peak=    3.235 closest distance to " CB  ALA A  34 " =    1.092
peak=    3.233 closest distance to " CA  MET A  40 " =    1.128
peak=    3.229 closest distance to " CD1 ILE A 263 " =    1.356
peak=    3.229 closest distance to " O   HOH Z 336 " =    1.927
peak=    3.227 closest distance to " O   HOH Z 407 " =    2.131
peak=    3.225 closest distance to " CH2 TRP A  92 " =    2.119
peak=    3.221 closest distance to " O   HOH Z 409 " =    2.215
peak=    3.220 closest distance to " CG  GLN A 278 " =    1.263
peak=    3.220 closest distance to " O  BHOH Z 338 " =    2.442
peak=    3.215 closest distance to " O   HOH Z 213 " =    1.795
peak=    3.214 closest distance to " O   ARG A 145 " =    1.653
peak=    3.214 closest distance to " O   HOH Z  66 " =    2.089
peak=    3.212 closest distance to " O   HOH Z 244 " =    1.697
peak=    3.210 closest distance to " CA  ALA A 233 " =    1.660
peak=    3.202 closest distance to " O   HOH Z 183 " =    1.374
peak=    3.201 closest distance to " CB  ALA A  21 " =    1.916
peak=    3.196 closest distance to " CA  ALA A  21 " =    1.172
peak=    3.196 closest distance to " C   GLU A 277 " =    1.310
peak=    3.191 closest distance to " CD2 LEU A 255 " =    1.624
peak=    3.189 closest distance to " O   HOH Z  93 " =    2.315
peak=    3.188 closest distance to " O   HOH Z  90 " =    2.062
peak=    3.187 closest distance to " O   HOH Z 139 " =    1.110
peak=    3.186 closest distance to " CB  PRO A 243 " =    1.200
peak=    3.186 closest distance to " N   ARG A 156 " =    1.291
peak=    3.184 closest distance to " CB  LEU A 300 " =    0.923
peak=    3.184 closest distance to " CG1 VAL A 189 " =    1.785
peak=    3.184 closest distance to " NE AARG A 275 " =    1.339
peak=    3.183 closest distance to " O   HOH Z 124 " =    2.518
peak=    3.178 closest distance to " CA  ALA A 291 " =    0.862
peak=    3.178 closest distance to " O   HOH Z 135 " =    1.695
peak=    3.176 closest distance to " NZ  LYS A 117 " =    1.290
peak=    3.176 closest distance to " O   HOH Z 368 " =    4.282
peak=    3.176 closest distance to " OG  SER A  62 " =    2.912
peak=    3.175 closest distance to " O   HOH Z 130 " =    3.672
peak=    3.174 closest distance to " O   HOH Z 432 " =    1.844
peak=    3.172 closest distance to " O   HOH Z 373 " =    1.466
peak=    3.168 closest distance to " CZ3 TRP A 266 " =    1.134
peak=    3.165 closest distance to " CG BARG A 102 " =    1.832
peak=    3.163 closest distance to " CD  LYS A 166 " =    1.330
peak=    3.162 closest distance to " O   HOH Z 225 " =    1.438
peak=    3.161 closest distance to " O   HOH Z 375 " =    0.993
peak=    3.160 closest distance to " CG2BVAL A  41 " =    0.765
peak=    3.159 closest distance to " O   HOH Z 266 " =    3.375
peak=    3.156 closest distance to " CD  ARG A  79 " =    2.256
peak=    3.154 closest distance to " O   HOH Z 273 " =    2.895
peak=    3.142 closest distance to " O   HOH Z 271 " =    2.501
peak=    3.136 closest distance to " CB  VAL A 265 " =    2.318
peak=    3.118 closest distance to " CG  GLU A 277 " =    1.977
peak=    3.117 closest distance to " O   HOH Z 325 " =    3.736
peak=    3.111 closest distance to " O   HOH Z  47 " =    1.839
peak=    3.108 closest distance to " CB  SER A  26 " =    1.631
peak=    3.103 closest distance to " ND1 HIS A  81 " =    1.632
peak=    3.102 closest distance to " CG2 VAL A 197 " =    1.036
peak=    3.097 closest distance to " O   HOH Z 403 " =    1.574
peak=    3.093 closest distance to " O   HOH Z 217 " =    1.605
peak=    3.091 closest distance to " CB  MET A 188 " =    1.673
peak=    3.084 closest distance to " O   PRO A 198 " =    1.219
peak=    3.083 closest distance to " O   PRO A  90 " =    1.635
peak=    3.082 closest distance to " O   HOH Z  89 " =    2.081
peak=    3.071 closest distance to " OG BSER A 134 " =    3.209
peak=    3.069 closest distance to " CB  ASN A 215 " =    1.046
peak=    3.068 closest distance to " O   HOH Z 419 " =    1.524
peak=    3.067 closest distance to " CB  GLU A 152 " =    1.293
peak=    3.056 closest distance to " CB  ARG A 138 " =    0.906
peak=    3.024 closest distance to " O   HOH Z 238 " =    3.713

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 5.747
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.777 - 5.747

peak=   -4.653 closest distance to " O   HOH Z 377 " =    1.924
peak=   -4.537 closest distance to " CB  PRO A 243 " =    2.558
peak=   -4.321 closest distance to " C   HIS A 108 " =    1.182
peak=   -4.253 closest distance to " O   HOH Z 351 " =    1.645
peak=   -4.223 closest distance to " O   PRO A 198 " =    1.262
peak=   -4.211 closest distance to " CD  ARG A 156 " =    2.086
peak=   -4.179 closest distance to " OG BSER A 134 " =    1.296
peak=   -4.139 closest distance to " O   HOH Z 266 " =    4.834
peak=   -4.136 closest distance to " CD  ARG A  14 " =    3.417
peak=   -4.131 closest distance to " CD1 LEU A 255 " =    2.918
peak=   -4.108 closest distance to " O   HOH Z  65 " =    1.048
peak=   -4.072 closest distance to " O   HOH Z 185 " =    2.114
peak=   -4.063 closest distance to " O   HOH Z 389 " =    1.914
peak=   -3.987 closest distance to " O   HOH Z 231 " =    2.046
peak=   -3.942 closest distance to " CG  GLN A 223 " =    1.824
peak=   -3.934 closest distance to " CA  GLY A  98 " =    1.727
peak=   -3.916 closest distance to " CB  ALA A 291 " =    2.169
peak=   -3.916 closest distance to " O   HOH Z 198 " =    1.858
peak=   -3.903 closest distance to " O   SER A 135 " =    1.448
peak=   -3.901 closest distance to " O   HOH Z 290 " =    1.089
peak=   -3.863 closest distance to " CG1 VAL A 112 " =    2.931
peak=   -3.859 closest distance to " O   HOH Z 372 " =    2.509
peak=   -3.859 closest distance to " O   VAL A  67 " =    2.566
peak=   -3.854 closest distance to " O   HOH Z 407 " =    3.141
peak=   -3.850 closest distance to " CG  PHE A 283 " =    2.602
peak=   -3.827 closest distance to " CZ3 TRP A 179 " =    1.249
peak=   -3.824 closest distance to " O   PRO A 243 " =    2.432
peak=   -3.811 closest distance to " OD1 ASP A 191 " =    1.901
peak=   -3.769 closest distance to " N   THR A 157 " =    1.558
peak=   -3.766 closest distance to " CB  ALA A  43 " =    2.393
peak=   -3.766 closest distance to " CG  GLN A  58 " =    1.072
peak=   -3.755 closest distance to " O   HOH Z  52 " =    1.249
peak=   -3.742 closest distance to " CB  ALA A 248 " =    2.029
peak=   -3.738 closest distance to " O   HOH Z 152 " =    4.902
peak=   -3.723 closest distance to " O   HOH Z  13 " =    1.688
peak=   -3.707 closest distance to " CZ  PHE A  59 " =    1.491
peak=   -3.703 closest distance to " OE1 GLN A  88 " =    1.124
peak=   -3.685 closest distance to " O   ARG A 145 " =    1.440
peak=   -3.679 closest distance to " O   SER A  22 " =    2.544
peak=   -3.661 closest distance to " ND2 ASN A  45 " =    1.959
peak=   -3.660 closest distance to " O   HOH Z 317 " =    1.441
peak=   -3.656 closest distance to " O   HOH Z 131 " =    4.083
peak=   -3.650 closest distance to " O   HOH Z 313 " =    1.745
peak=   -3.640 closest distance to " O   VAL A 189 " =    2.516
peak=   -3.639 closest distance to " O   HOH Z  60 " =    2.389
peak=   -3.633 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.630 closest distance to " CB  PHE A 192 " =    1.949
peak=   -3.630 closest distance to " OG  SER A  87 " =    1.293
peak=   -3.618 closest distance to " O   PHE A 218 " =    1.424
peak=   -3.608 closest distance to " CB  CYS A 254 " =    2.145
peak=   -3.604 closest distance to " O   HOH Z 140 " =    1.483
peak=   -3.597 closest distance to " ND2 ASN A  45 " =    1.116
peak=   -3.592 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.592 closest distance to " O   HOH Z 298 " =    1.107
peak=   -3.581 closest distance to " CB  ASP A  27 " =    2.340
peak=   -3.577 closest distance to " CB  TYR A  15 " =    2.131
peak=   -3.571 closest distance to " CE  MET A 105 " =    2.416
peak=   -3.568 closest distance to " O   SER A  95 " =    1.410
peak=   -3.562 closest distance to " CE3 TRP A 123 " =    1.356
peak=   -3.561 closest distance to " N   GLN A  58 " =    1.577
peak=   -3.554 closest distance to " O   HOH Z 298 " =    2.422
peak=   -3.549 closest distance to " O   HOH Z  90 " =    2.489
peak=   -3.538 closest distance to " O   HOH Z 211 " =    1.528
peak=   -3.538 closest distance to " NH1AARG A 275 " =    1.859
peak=   -3.532 closest distance to " O   VAL A  67 " =    2.861
peak=   -3.518 closest distance to " CD2 TYR A 293 " =    1.870
peak=   -3.515 closest distance to " O   HOH Z 377 " =    1.065
peak=   -3.508 closest distance to " CA  GLY A 133 " =    1.983
peak=   -3.505 closest distance to " CZ2 TRP A 274 " =    0.940
peak=   -3.502 closest distance to " O   HOH Z  63 " =    2.316
peak=   -3.501 closest distance to " CB  ASN A  39 " =    2.341
peak=   -3.492 closest distance to " OD1 ASN A 187 " =    1.609
peak=   -3.482 closest distance to " C   ALA A 158 " =    1.487
peak=   -3.481 closest distance to " OD2 ASP A 171 " =    2.023
peak=   -3.473 closest distance to " O   HOH Z 384 " =    2.898
peak=   -3.472 closest distance to " O   ALA A  10 " =    1.717
peak=   -3.472 closest distance to " O   HOH Z 250 " =    1.375
peak=   -3.471 closest distance to " N   ALA A  43 " =    2.528
peak=   -3.465 closest distance to " O   HOH Z  43 " =    1.765
peak=   -3.464 closest distance to " O   HOH Z   9 " =    1.646
peak=   -3.458 closest distance to " CD1 LEU A 101 " =    2.221
peak=   -3.454 closest distance to " O   PRO A 163 " =    1.923
peak=   -3.453 closest distance to " O   HOH Z 191 " =    5.524
peak=   -3.447 closest distance to " O   VAL A 197 " =    1.694
peak=   -3.444 closest distance to " O   HOH Z 385 " =    2.036
peak=   -3.442 closest distance to " CD1 ILE A 239 " =    2.298
peak=   -3.439 closest distance to " ND2 ASN A 285 " =    2.075
peak=   -3.438 closest distance to " O   HOH Z 166 " =    1.263
peak=   -3.434 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.430 closest distance to " OD1 ASP A 171 " =    1.586
peak=   -3.421 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.419 closest distance to " CD2 PHE A 225 " =    1.159
peak=   -3.418 closest distance to " CB  ALA A 161 " =    2.521
peak=   -3.417 closest distance to " OG BSER A 134 " =    1.644
peak=   -3.417 closest distance to " ND2 ASN A 249 " =    2.366
peak=   -3.415 closest distance to " OD2 ASP A 191 " =    1.419
peak=   -3.413 closest distance to " CB  PRO A 163 " =    2.419
peak=   -3.406 closest distance to " O   HOH Z 102 " =    1.602
peak=   -3.403 closest distance to " O   HOH Z 345 " =    2.024
peak=   -3.399 closest distance to " CE3 TRP A 274 " =    2.340
peak=   -3.398 closest distance to " O   HOH Z  11 " =    1.826
peak=   -3.397 closest distance to " CE2 TYR A  30 " =    2.615
peak=   -3.381 closest distance to " OD1 ASN A 148 " =    1.577
peak=   -3.377 closest distance to " ND2 ASN A 187 " =    1.473
peak=   -3.372 closest distance to " CE BMET A  47 " =    1.333
peak=   -3.357 closest distance to " CB  PRO A  54 " =    2.400
peak=   -3.356 closest distance to " NE  ARG A  36 " =    1.979
peak=   -3.353 closest distance to " OG  SER A 245 " =    1.298
peak=   -3.351 closest distance to " O   ILE A  49 " =    1.685
peak=   -3.348 closest distance to " O   HOH Z  60 " =    1.929
peak=   -3.347 closest distance to " ND2 ASN A  60 " =    4.165
peak=   -3.345 closest distance to " CG  ASN A  39 " =    1.715
peak=   -3.344 closest distance to " O   ALA A   7 " =    1.578
peak=   -3.343 closest distance to " O   HOH Z  24 " =    1.193
peak=   -3.343 closest distance to " O   HOH Z  28 " =    1.851
peak=   -3.342 closest distance to " NH2AARG A 275 " =    5.296
peak=   -3.339 closest distance to " CZ  TYR A 169 " =    1.648
peak=   -3.338 closest distance to " CB  TRP A  85 " =    2.353
peak=   -3.338 closest distance to " CG1 VAL A 230 " =    2.037
peak=   -3.337 closest distance to " CB  ALA A 131 " =    1.986
peak=   -3.331 closest distance to " CG1 VAL A 268 " =    2.387
peak=   -3.330 closest distance to " C   LEU A 143 " =    1.162
peak=   -3.326 closest distance to " CA  GLY A 203 " =    2.295
peak=   -3.323 closest distance to " O   HOH Z 111 " =    2.135
peak=   -3.308 closest distance to " ND2BASN A 224 " =    1.709
peak=   -3.307 closest distance to " O   ASP A 162 " =    2.195
peak=   -3.306 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.302 closest distance to " N   ASN A 127 " =    1.527
peak=   -3.299 closest distance to " OG  SER A  97 " =    2.170
peak=   -3.299 closest distance to " O   HOH Z 409 " =    5.747
peak=   -3.290 closest distance to " NH2 ARG A  79 " =    2.028
peak=   -3.290 closest distance to " O   HOH Z  38 " =    1.727
peak=   -3.288 closest distance to " O   TYR A 247 " =    2.842
peak=   -3.287 closest distance to " O   HOH Z 253 " =    3.847
peak=   -3.286 closest distance to " CG2 ILE A 263 " =    2.323
peak=   -3.284 closest distance to " O   HOH Z 359 " =    3.325
peak=   -3.284 closest distance to " N   MET A 188 " =    1.920
peak=   -3.280 closest distance to " NE2 GLN A 278 " =    1.736
peak=   -3.276 closest distance to " OE1 GLN A 183 " =    1.505
peak=   -3.273 closest distance to " O   VAL A 174 " =    2.232
peak=   -3.271 closest distance to " O   ALA A  34 " =    2.547
peak=   -3.270 closest distance to " CA  GLY A  57 " =    2.118
peak=   -3.270 closest distance to " O   HOH Z 348 " =    1.835
peak=   -3.259 closest distance to " CG1 VAL A 197 " =    2.170
peak=   -3.256 closest distance to " CD  ARG A 139 " =    1.551
peak=   -3.254 closest distance to " CG2 THR A  18 " =    2.742
peak=   -3.254 closest distance to " CB  ALA A 291 " =    2.014
peak=   -3.252 closest distance to " CE  LYS A  76 " =    2.757
peak=   -3.249 closest distance to " O   ALA A 161 " =    1.600
peak=   -3.247 closest distance to " O   GLN A 240 " =    1.878
peak=   -3.246 closest distance to " CD  GLU A 277 " =    1.129
peak=   -3.242 closest distance to " CB  ALA A 248 " =    2.312
peak=   -3.240 closest distance to " CE2 PHE A 218 " =    2.389
peak=   -3.238 closest distance to " O   HOH Z  51 " =    1.066
peak=   -3.237 closest distance to " CG  PRO A 243 " =    1.692
peak=   -3.226 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.219 closest distance to " O   HOH Z 352 " =    2.182
peak=   -3.218 closest distance to " OE2 GLU A 152 " =    1.070
peak=   -3.218 closest distance to " CG  ARG A 269 " =    2.376
peak=   -3.210 closest distance to " O   GLY A  80 " =    2.412
peak=   -3.210 closest distance to " O   HOH Z 266 " =    4.612
peak=   -3.205 closest distance to " O   HOH Z 432 " =    3.614
peak=   -3.198 closest distance to " O   HOH Z   1 " =    1.490
peak=   -3.196 closest distance to " CB  ILE A  33 " =    2.839
peak=   -3.195 closest distance to " CD2 PHE A  61 " =    2.049
peak=   -3.193 closest distance to " O   HOH Z 281 " =    2.795
peak=   -3.191 closest distance to " O   HOH Z 418 " =    1.631
peak=   -3.187 closest distance to " O   ALA A 180 " =    1.163
peak=   -3.185 closest distance to " O   HOH Z 174 " =    2.668
peak=   -3.184 closest distance to " O   TRP A  70 " =    1.417
peak=   -3.178 closest distance to " O   HOH Z 383 " =    0.915
peak=   -3.177 closest distance to " N   SER A 212 " =    1.889
peak=   -3.172 closest distance to " O   HOH Z 263 " =    3.098
peak=   -3.167 closest distance to " CE1 TYR A 169 " =    2.590
peak=   -3.159 closest distance to " O   GLY A  17 " =    1.150
peak=   -3.156 closest distance to " O   HOH Z 218 " =    3.652
peak=   -3.153 closest distance to " OG  SER A  87 " =    1.596
peak=   -3.152 closest distance to " O   HOH Z 198 " =    1.695
peak=   -3.150 closest distance to " O   HOH Z 282 " =    1.175
peak=   -3.138 closest distance to " O   HOH Z 348 " =    2.242
peak=   -3.131 closest distance to " CB  ALA A 114 " =    2.574
peak=   -3.130 closest distance to " CG2BVAL A  41 " =    1.119
peak=   -3.127 closest distance to " O   HOH Z 292 " =    1.510
peak=   -3.123 closest distance to " CD1 LEU A   5 " =    2.476
peak=   -3.115 closest distance to " OD1 ASP A 200 " =    1.423
peak=   -3.108 closest distance to " CB  ALA A 100 " =    2.063
peak=   -3.104 closest distance to " OG  SER A  63 " =    1.147
peak=   -3.103 closest distance to " O   HOH Z 318 " =    1.776
peak=   -3.103 closest distance to " CD  LYS A 289 " =    2.350
peak=   -3.098 closest distance to " OG1 THR A  82 " =    1.840
peak=   -3.083 closest distance to " O   HOH Z 282 " =    4.725
peak=   -3.076 closest distance to " CB  ASP A 132 " =    2.357
peak=   -3.066 closest distance to " OG  SER A 206 " =    1.810
peak=   -3.063 closest distance to " O   ASN A 127 " =    1.777
peak=   -3.056 closest distance to " C   ALA A 114 " =    2.231
peak=   -3.052 closest distance to " ND2 ASN A  39 " =    1.946
peak=   -3.051 closest distance to " O   HOH Z 414 " =    2.018
peak=   -3.037 closest distance to " CE  MET A 105 " =    2.288

================= 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    :  0.3758 0.3705   6.185290e+00   6.174125e+00
   1_bss:  0.3587 0.3568   6.166264e+00   6.154322e+00
   1_xyz:  0.2729 0.3090   5.914296e+00   5.993875e+00
   1_adp:  0.2488 0.3231   5.868227e+00   6.021311e+00
   1_occ:  0.2485 0.3230   5.867620e+00   6.020845e+00
   2_bss:  0.2466 0.3177   5.858981e+00   6.011433e+00
   2_xyz:  0.1822 0.2338   5.572586e+00   5.757415e+00
   2_adp:  0.1673 0.2164   5.497199e+00   5.696175e+00
   2_occ:  0.1673 0.2163   5.496636e+00   5.695958e+00
   3_bss:  0.1666 0.2148   5.490076e+00   5.688147e+00
   3_xyz:  0.1338 0.1801   5.292746e+00   5.515443e+00
   3_adp:  0.1278 0.1739   5.254020e+00   5.479416e+00
   3_occ:  0.1277 0.1738   5.253789e+00   5.479210e+00
   4_bss:  0.1278 0.1734   5.252808e+00   5.477409e+00
   4_xyz:  0.1162 0.1605   5.167076e+00   5.401030e+00
   4_adp:  0.1126 0.1597   5.150538e+00   5.394043e+00
   4_occ:  0.1126 0.1596   5.150261e+00   5.393733e+00
   5_bss:  0.1125 0.1595   5.149256e+00   5.392986e+00
   5_xyz:  0.1109 0.1576   5.139357e+00   5.384861e+00
   5_adp:  0.1106 0.1560   5.135564e+00   5.380153e+00
   5_occ:  0.1105 0.1561   5.135378e+00   5.379986e+00
   5_bss:  0.1104 0.1560   5.135349e+00   5.379881e+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:  0.355  50.000  -3.276   3.732  -1.864   0.000  -0.000  -0.000
   1_xyz:  0.355  50.000  -3.276   3.732  -1.864   0.000  -0.000  -0.000
   1_adp:  0.355  50.000  -3.276   3.732  -1.864   0.000  -0.000  -0.000
   1_occ:  0.355  50.000  -3.276   3.732  -1.864   0.000  -0.000  -0.000
   2_bss:  0.336  52.777  -2.325   0.087  -1.075   0.000  -0.000  -0.000
   2_xyz:  0.336  52.777  -2.325   0.087  -1.075   0.000  -0.000  -0.000
   2_adp:  0.336  52.777  -2.325   0.087  -1.075   0.000  -0.000  -0.000
   2_occ:  0.336  52.777  -2.325   0.087  -1.075   0.000  -0.000  -0.000
   3_bss:  0.336  52.777  -2.324  -1.580  -0.959  -0.000  -0.000  -0.000
   3_xyz:  0.336  52.777  -2.324  -1.580  -0.959  -0.000  -0.000  -0.000
   3_adp:  0.336  52.777  -2.324  -1.580  -0.959  -0.000  -0.000  -0.000
   3_occ:  0.336  52.777  -2.324  -1.580  -0.959  -0.000  -0.000  -0.000
   4_bss:  0.336  52.777  -2.502  -2.339  -1.153  -0.000  -0.000  -0.000
   4_xyz:  0.336  52.777  -2.502  -2.339  -1.153  -0.000  -0.000  -0.000
   4_adp:  0.336  52.777  -2.502  -2.339  -1.153  -0.000  -0.000  -0.000
   4_occ:  0.336  52.777  -2.502  -2.339  -1.153  -0.000  -0.000  -0.000
   5_bss:  0.325  52.777  -2.329  -2.367  -1.007  -0.000  -0.000  -0.000
   5_xyz:  0.325  52.777  -2.329  -2.367  -1.007  -0.000  -0.000  -0.000
   5_adp:  0.325  52.777  -2.329  -2.367  -1.007  -0.000  -0.000  -0.000
   5_occ:  0.325  52.777  -2.329  -2.367  -1.007  -0.000  -0.000  -0.000
   5_bss:  0.325  52.780  -2.155  -2.282  -0.812  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.391 0.6166  0.8100    45737.607
   1_bss:  41.628 0.6241  0.8050    42793.781
   1_xyz:  31.975 0.7369  0.9181    26128.041
   1_adp:  33.538 0.7181  0.8977    28177.876
   1_occ:  33.572 0.7177  0.8970    28185.065
   2_bss:  32.721 0.7274  0.8915    27106.577
   2_xyz:  23.035 0.8311  0.9812    13995.184
   2_adp:  20.863 0.8537  0.9913    12113.075
   2_occ:  20.860 0.8536  0.9908    12093.284
   3_bss:  20.584 0.8562  0.9750    11801.786
   3_xyz:  16.829 0.8906  0.9922     8216.351
   3_adp:  15.979 0.8985  0.9900     7743.911
   3_occ:  15.977 0.8985  0.9898     7733.316
   4_bss:  15.928 0.8989  0.9771     7695.235
   4_xyz:  14.274 0.9125  0.9842     6515.738
   4_adp:  14.106 0.9141  0.9797     6400.852
   4_occ:  14.100 0.9141  0.9796     6394.764
   5_bss:  14.079 0.9143  0.9832     6376.993
   5_xyz:  13.927 0.9157  0.9823     6270.861
   5_adp:  13.809 0.9167  0.9769     6206.989
   5_occ:  13.805 0.9167  0.9769     6202.729
   5_bss:  13.805 0.9167  0.9824     6202.941
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7083e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7083e-01
   1_xyz:   1.420  0.011  0.093 15.492  0.006  4.105   1.0953e-01
   1_adp:   1.420  0.011  0.093 15.492  0.006  4.105   1.0953e-01
   1_occ:   1.420  0.011  0.093 15.492  0.006  4.105   1.0953e-01
   2_bss:   1.420  0.011  0.093 15.492  0.006  4.105   1.0953e-01
   2_xyz:   1.132  0.007  0.078 14.616  0.004  4.108   6.7635e-02
   2_adp:   1.132  0.007  0.078 14.616  0.004  4.108   6.7635e-02
   2_occ:   1.132  0.007  0.078 14.616  0.004  4.108   6.7635e-02
   3_bss:   1.132  0.007  0.078 14.616  0.004  4.108   6.7635e-02
   3_xyz:   0.929  0.006  0.068 14.437  0.004  4.110   5.2645e-02
   3_adp:   0.929  0.006  0.068 14.437  0.004  4.110   5.2645e-02
   3_occ:   0.929  0.006  0.068 14.437  0.004  4.110   5.2645e-02
   4_bss:   0.929  0.006  0.068 14.437  0.004  4.110   5.2645e-02
   4_xyz:   0.965  0.006  0.072 14.406  0.004  4.113   5.5081e-02
   4_adp:   0.965  0.006  0.072 14.406  0.004  4.113   5.5081e-02
   4_occ:   0.965  0.006  0.072 14.406  0.004  4.113   5.5081e-02
   5_bss:   0.965  0.006  0.072 14.406  0.004  4.113   5.5081e-02
   5_xyz:   0.912  0.005  0.069 14.315  0.004  4.109   5.0796e-02
   5_adp:   0.912  0.005  0.069 14.315  0.004  4.109   5.0796e-02
   5_occ:   0.912  0.005  0.069 14.315  0.004  4.109   5.0796e-02
   5_bss:   0.912  0.005  0.069 14.315  0.004  4.109   5.0796e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3939e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3939e-01
   1_xyz:   8.145  0.067  0.352 84.061  0.047  2.048   1.0405e-01
   1_adp:   8.145  0.067  0.352 84.061  0.047  2.048   1.0405e-01
   1_occ:   8.145  0.067  0.352 84.061  0.047  2.048   1.0405e-01
   2_bss:   8.145  0.067  0.352 84.061  0.047  2.048   1.0405e-01
   2_xyz:   7.180  0.037  0.213 82.590  0.038  2.318   6.8471e-02
   2_adp:   7.180  0.037  0.213 82.590  0.038  2.318   6.8471e-02
   2_occ:   7.180  0.037  0.213 82.590  0.038  2.318   6.8471e-02
   3_bss:   7.180  0.037  0.213 82.590  0.038  2.318   6.8471e-02
   3_xyz:   6.875  0.049  0.206 82.210  0.033  2.321   4.4336e-02
   3_adp:   6.875  0.049  0.206 82.210  0.033  2.321   4.4336e-02
   3_occ:   6.875  0.049  0.206 82.210  0.033  2.321   4.4336e-02
   4_bss:   6.875  0.049  0.206 82.210  0.033  2.321   4.4336e-02
   4_xyz:   6.623  0.037  0.220 84.403  0.033  2.330   3.9484e-02
   4_adp:   6.623  0.037  0.220 84.403  0.033  2.330   3.9484e-02
   4_occ:   6.623  0.037  0.220 84.403  0.033  2.330   3.9484e-02
   5_bss:   6.623  0.037  0.220 84.403  0.033  2.330   3.9484e-02
   5_xyz:   6.461  0.042  0.210 84.387  0.033  2.328   3.5322e-02
   5_adp:   6.461  0.042  0.210 84.387  0.033  2.328   3.5322e-02
   5_occ:   6.461  0.042  0.210 84.387  0.033  2.328   3.5322e-02
   5_bss:   6.461  0.042  0.210 84.387  0.033  2.328   3.5322e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  93.43   0.00  17.44  68.33   0.00  13.63  93.43   3.81  38.20
   1_occ:  93.43   0.00  17.44  68.33   0.00  13.63  93.43   3.81  38.20
   2_bss:  93.43   0.00  17.44  68.33   0.00  13.63  93.43   3.81  38.20
   2_xyz:  93.43   0.00  17.44  68.33   0.00  13.63  93.43   3.81  38.20
   2_adp:  85.97   0.00  17.06  75.56   0.00  13.11  85.97   5.77  38.57
   2_occ:  85.97   0.00  17.06  75.56   0.00  13.11  85.97   5.77  38.57
   3_bss:  85.97   0.00  17.06  75.56   0.00  13.11  85.97   5.77  38.57
   3_xyz:  85.97   0.00  17.06  75.56   0.00  13.11  85.97   5.77  38.57
   3_adp:  83.98   1.15  16.76  75.50   1.15  12.74  83.98   4.40  38.62
   3_occ:  83.98   1.15  16.76  75.50   1.15  12.74  83.98   4.40  38.62
   4_bss:  83.98   1.15  16.76  75.50   1.15  12.74  83.98   4.40  38.62
   4_xyz:  83.98   1.15  16.76  75.50   1.15  12.74  83.98   4.40  38.62
   4_adp:  89.49   0.00  17.22  88.06   0.00  12.79  89.49   4.31  41.38
   4_occ:  89.49   0.00  17.22  88.06   0.00  12.79  89.49   4.31  41.38
   5_bss:  89.49   0.00  17.22  88.06   0.00  12.79  89.49   4.31  41.38
   5_xyz:  89.49   0.00  17.22  88.06   0.00  12.79  89.49   4.31  41.38
   5_adp:  90.55   0.00  16.85  90.55   0.00  12.58  87.62   5.74  40.10
   5_occ:  90.55   0.00  16.85  90.55   0.00  12.58  87.62   5.74  40.10
   5_bss:  90.55   0.00  16.85  90.55   0.00  12.58  87.62   5.74  40.10
------------------------------------------------------------------------
 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:    1.647    0.015    0.338
   1_adp:    1.647    0.015    0.338
   1_occ:    1.647    0.015    0.338
   2_bss:    1.647    0.015    0.338
   2_xyz:    1.349    0.033    0.472
   2_adp:    1.349    0.033    0.472
   2_occ:    1.349    0.033    0.472
   3_bss:    1.349    0.033    0.472
   3_xyz:    1.200    0.023    0.560
   3_adp:    1.200    0.023    0.560
   3_occ:    1.200    0.023    0.560
   4_bss:    1.200    0.023    0.560
   4_xyz:    1.240    0.046    0.589
   4_adp:    1.240    0.046    0.589
   4_occ:    1.240    0.046    0.589
   5_bss:    1.240    0.046    0.589
   5_xyz:    1.314    0.050    0.601
   5_adp:    1.314    0.050    0.601
   5_occ:    1.314    0.050    0.601
   5_bss:    1.314    0.050    0.601
------------------------------------------------------------------------

CPU time actual refinement: 349.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/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_621/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_621/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.34 
  Macro-tasks:
    bulk solvent and scale       = 40.25  
    individual site refinement   = 152.82 
    weights calculation          = 29.76  
    collect and process          = 6.76   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 229.67 
  Micro-tasks:
    mask                            = 1.66   
    f_calc                          = 113.61 
    alpha_beta                      = 8.65   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 119.37 
    fmodel                         = 7.03   
    r_factors                      = 0.20   
    phase_errors                   = 11.83  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 263.84 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.791 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    678 calls, 113.13 s
gradients_fft:          623 calls, 106.43 s

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

# Date 2008-01-16 Time 05:16:19 PST -0800 (1200489379.75 s)
Start R-work = 0.3758, R-free = 0.3705 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.3587, R-free = 0.3568
Final R-work = 0.1104, R-free = 0.1560