# Date 2008-01-16 Time 00:57:14 PST -0800 (1200473834.27 s)
#phil __OFF__

Command line arguments: "../211.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24024
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 211

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.6339, 85.0941, 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: 3.26, 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: (68.845, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.96062
Completeness in resolution range: 0.949309
Completeness with d_max=infinity: 0.94642

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8759
                             d_min =   1.9606

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: (68.845, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.96062
Completeness in resolution range: 0.949309
Completeness with d_max=infinity: 0.94642

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8763 -  4.1954 [2170/2199]  1953   217  10.0%
  bin  2:  4.1954 -  3.3424 [2079/2102]  1873   206   9.9%
  bin  3:  3.3424 -  2.9236 [2063/2088]  1851   212  10.3%
  bin  4:  2.9236 -  2.6579 [2025/2041]  1830   195   9.6%
  bin  5:  2.6579 -  2.4683 [2004/2048]  1794   210  10.5%
  bin  6:  2.4683 -  2.3234 [2025/2053]  1835   190   9.4%
  bin  7:  2.3234 -  2.2074 [2002/2038]  1795   207  10.3%
  bin  8:  2.2074 -  2.1116 [1978/2020]  1786   192   9.7%
  bin  9:  2.1116 -  2.0305 [1987/2033]  1786   201  10.1%
  bin 10:  2.0305 -  1.9606 [1256/2013]  1127   129  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/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:
        1.26 -     1.99: 15
        1.99 -     2.72: 206
        2.72 -     3.44: 4652
        3.44 -     4.17: 9455
        4.17 -     4.90: 14332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.261 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.516 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.601 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.634 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.668 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28655 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_211/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/model_refine_001.geo

CPU time processing inputs: 9.45


============================ 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 = 68.845 47.63395 85.09415 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4970   r_free= 0.4861   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.294187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.4086 0.4031       6.611      6.6553|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.4248 0.4115       6.814      6.8233|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.4606 0.4309      6.6962      6.7339|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.4742 0.4614       6.524      6.4852|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.5298 0.5340      6.3932      6.4079|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.5193 0.5301      6.2779      6.2019|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.5322 0.4843      6.2782      6.1919|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.5369 0.5303      6.1866      6.1744|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.5453 0.5501      6.1257      6.1754|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.5370 0.5548      6.1219      6.1337|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.5495 0.5720      6.0348      6.0453|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.5449 0.5327        5.97      6.0053|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.5610 0.5288      5.8962      5.8826|
| 14:  2.0095 -  1.9606 0.50    635   76 0.5532 0.4623      5.9005      5.6991|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.65  38.50   0.80     0.66      84154.06|
|  2:  4.6794 -  3.7335  1350   151  0.66  39.08   0.88     0.72     121491.30|
|  3:  3.7335 -  3.2673  1331   146  0.56  47.35   0.84     0.68     128709.95|
|  4:  3.2673 -  2.9711  1324   139  0.47  54.15   0.80     0.57     109275.32|
|  5:  2.9711 -  2.7596  1306   148  0.37  62.29   0.73     0.46      91489.93|
|  6:  2.7596 -  2.5978  1303   147  0.33  65.00   0.72     0.39      76594.72|
|  7:  2.5978 -  2.4683  1282   151  0.33  65.34   0.73     0.38      69699.36|
|  8:  2.4683 -  2.3613  1310   133  0.33  65.45   0.72     0.39      60735.00|
|  9:  2.3613 -  2.2708  1298   149  0.30  67.46   0.72     0.37      58314.45|
| 10:  2.2708 -  2.1927  1278   142  0.26  70.29   0.77     0.32      54046.27|
| 11:  2.1927 -  2.1243  1281   149  0.20  75.30   0.73     0.26      53910.85|
| 12:  2.1243 -  2.0637  1273   141  0.20  75.28   0.74     0.26      49496.85|
| 13:  2.0637 -  2.0095  1254   129  0.27  70.17   0.73     0.34      39472.45|
| 14:  2.0095 -  1.9606   635    76  0.46  55.78   0.71     0.50      24485.35|
|alpha:            min =        0.26 max =            0.72 mean =         0.45|
|beta:             min =    24485.35 max =       128709.95 mean =     75344.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.70|
|phase err.(test): min =        0.00 max =           89.96 mean =        60.81|
|-----------------------------------------------------------------------------|

============================== 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 = 18.834935             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.907   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.478626              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.670   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.960 -  1.354:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.354 -  1.748:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.748 -  2.142:       84 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.142 -  2.536:      495 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.536 -  2.930:     1279 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.930 -  3.324:     2426 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.324 -  3.718:     3982 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.718 -  4.112:     5281 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.112 -  4.506:     6886 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.506 -  4.900:     8268 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.198 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.960 |       2.647 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5012   r_free= 0.4926   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.294512                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4890   r_free= 0.4770   ksol= 0.37   Bsol= 20.00   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.28,9.91,7.68,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.288483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.724238             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.423   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.510423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.720   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4890      final r-factor (work) = 0.4124          |
| start r-factor (free) = 0.4770      final r-factor (free) = 0.4331          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 105.8288 = 16.72 * 0.50 * 6.2940 + 1.00 * 53.1980                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.1497 = 16.72 * 0.50 * 6.2160 + 1.00 * 0.1710                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4124      final r-factor (work) = 0.3685          |
| start r-factor (free) = 0.4331      final r-factor (free) = 0.4159          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4031 = 1.51 * 1.00 * 6.2160 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3047 = 1.51 * 1.00 * 6.1469 + 1.00 * 0.0202                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.02   14.49    None  None   None       |
|    all(noH): 2823   0      0.00    96.02   14.49    None  None   None       |
|    Sol.    : 438    0      0.00    96.02   27.24    None  None   None       |
|    Mac.    : 2385   0      0.00    74.08   12.15    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 -   9.602: 1284   |   5:    48.010 -  57.612:   42        |
|      1:     9.602 -  19.204:  766   |   6:    57.612 -  67.214:   23        |
|      2:    19.204 -  28.806:  385   |   7:    67.214 -  76.816:   13        |
|      3:    28.806 -  38.408:  208   |   8:    76.816 -  86.419:    3        |
|      4:    38.408 -  48.010:   98   |   9:    86.419 -  96.021:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3685 r_free = 0.4159             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3677 r_free = 0.4155             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3677   r_free= 0.4155   ksol= 0.37   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.28,9.91,7.68,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.127665                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3662   r_free= 0.4100   ksol= 0.33   Bsol= 34.88   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.10,6.19,5.11,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.128039                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.297428             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.147   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551139              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.973  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3662      final r-factor (work) = 0.2697          |
| start r-factor (free) = 0.4100      final r-factor (free) = 0.3224          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.9388 = 12.30 * 0.50 * 6.1424 + 1.00 * 0.1710                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.0797 = 12.30 * 0.50 * 6.0133 + 1.00 * 0.1056                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.2395          |
| start r-factor (free) = 0.3224      final r-factor (free) = 0.2961          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3348 = 0.55 * 1.00 * 6.0133 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2280 = 0.55 * 1.00 * 5.8313 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.65   13.81    None  None   None       |
|    all(noH): 2823   0      0.00    92.65   13.81    None  None   None       |
|    Sol.    : 438    0      2.01    92.65   32.96    None  None   None       |
|    Mac.    : 2385   0      0.00    81.32   10.29    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 -   9.265: 1436   |   5:    46.324 -  55.589:   56        |
|      1:     9.265 -  18.530:  721   |   6:    55.589 -  64.853:   33        |
|      2:    18.530 -  27.794:  265   |   7:    64.853 -  74.118:    9        |
|      3:    27.794 -  37.059:  169   |   8:    74.118 -  83.383:    5        |
|      4:    37.059 -  46.324:  127   |   9:    83.383 -  92.648:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2395 r_free = 0.2961             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2392 r_free = 0.2959             target_work(ml) = 5.786         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2392   r_free= 0.2959   ksol= 0.33   Bsol= 34.88   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.10,6.19,5.11,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.785812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2359   r_free= 0.2936   ksol= 0.33   Bsol= 39.57   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,3.56,3.10,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.782735                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.014470              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2359      final r-factor (work) = 0.1671          |
| start r-factor (free) = 0.2936      final r-factor (free) = 0.2140          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7400 = 5.01 * 0.50 * 5.8368 + 1.00 * 0.1056                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2558 = 5.01 * 0.50 * 5.6579 + 1.00 * 0.0702                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1536          |
| start r-factor (free) = 0.2140      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2110 = 0.21 * 1.00 * 5.6579 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1670 = 0.21 * 1.00 * 5.4408 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.71   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    85.71   13.57    None  None   None       |
|    Sol.    : 438    0      2.25    85.71   34.96    None  None   None       |
|    Mac.    : 2385   0      0.00    80.17   9.64     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 -   8.571: 1449   |   5:    42.854 -  51.425:  103        |
|      1:     8.571 -  17.142:  741   |   6:    51.425 -  59.996:   41        |
|      2:    17.142 -  25.713:  200   |   7:    59.996 -  68.567:   14        |
|      3:    25.713 -  34.283:  130   |   8:    68.567 -  77.138:    6        |
|      4:    34.283 -  42.854:  135   |   9:    77.138 -  85.709:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1536 r_free = 0.1955             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1533 r_free = 0.1955             target_work(ml) = 5.393         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.1955   ksol= 0.33   Bsol= 39.57   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,3.56,3.10,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.393195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1527   r_free= 0.1944   ksol= 0.32   Bsol= 39.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,2.10,1.95,0.00,0.00,0.00); trace/3= 1.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.393430                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.318994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.899  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.348   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1527      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1944      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1200 = 3.32 * 0.50 * 5.4534 + 1.00 * 0.0702                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8868 = 3.32 * 0.50 * 5.3123 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1982 = 0.22 * 1.00 * 5.3123 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1869 = 0.22 * 1.00 * 5.2195 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.99   13.61    None  None   None       |
|    all(noH): 2823   0      0.00    84.99   13.61    None  None   None       |
|    Sol.    : 438    0      2.61    82.26   35.51    None  None   None       |
|    Mac.    : 2385   0      0.00    84.99   9.59     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 -   8.499: 1437   |   5:    42.497 -  50.997:   98        |
|      1:     8.499 -  16.999:  771   |   6:    50.997 -  59.496:   58        |
|      2:    16.999 -  25.498:  178   |   7:    59.496 -  67.995:   14        |
|      3:    25.498 -  33.998:  123   |   8:    67.995 -  76.495:    5        |
|      4:    33.998 -  42.497:  134   |   9:    76.495 -  84.994:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1646             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1646             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1646   ksol= 0.32   Bsol= 39.57   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,2.10,1.95,0.00,0.00,0.00); trace/3= 1.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.208223                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1650   ksol= 0.32   Bsol= 39.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.30,1.72,1.76,0.00,0.00,0.00); trace/3= 1.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.209126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.019013              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.400  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.431095              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.464   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9493 = 3.02 * 0.50 * 5.2191 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8973 = 3.02 * 0.50 * 5.1824 + 1.00 * 0.0745                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2510 = 0.43 * 1.00 * 5.1824 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2322 = 0.43 * 1.00 * 5.1550 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.29   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    82.29   13.58    None  None   None       |
|    Sol.    : 438    0      2.01    75.52   35.98    None  None   None       |
|    Mac.    : 2385   0      0.00    82.29   9.46     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 -   8.229: 1397   |   5:    41.144 -  49.373:   97        |
|      1:     8.229 -  16.458:  803   |   6:    49.373 -  57.602:   77        |
|      2:    16.458 -  24.686:  187   |   7:    57.602 -  65.830:   22        |
|      3:    24.686 -  32.915:  123   |   8:    65.830 -  74.059:    8        |
|      4:    32.915 -  41.144:  102   |   9:    74.059 -  82.288:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1596             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1596             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1596   ksol= 0.32   Bsol= 39.57   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.30,1.72,1.76,0.00,0.00,0.00); trace/3= 1.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156679                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.0999 0.1308      5.3789      5.5489|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.0865 0.1106      5.4507       5.664|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.1064 0.1533      5.4858      5.8721|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.1220 0.1562      5.4547      5.6479|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.1353 0.1607      5.3396       5.472|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.1283 0.2104      5.2309      5.5266|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.1170 0.1589      5.1596      5.3662|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1175 0.1780      5.1006      5.3708|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.1190 0.1840      5.0458      5.3356|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1134 0.1787      4.9964      5.2317|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.1139 0.1798      4.9256      5.2389|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.1094 0.1762      4.8534      5.1558|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.1095 0.1733      4.7798      5.0427|
| 14:  2.0095 -  1.9606 0.50    635   76 0.1023 0.1627      4.6776      4.8989|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.94   8.83   0.98     0.97       7105.14|
|  2:  4.6794 -  3.7335  1350   151  0.95   8.32   1.02     1.01       9349.94|
|  3:  3.7335 -  3.2673  1331   146  0.93  11.75   1.03     1.02      11048.62|
|  4:  3.2673 -  2.9711  1324   139  0.92  14.19   1.01     1.00      10591.31|
|  5:  2.9711 -  2.7596  1306   148  0.90  16.23   0.99     0.96       8468.77|
|  6:  2.7596 -  2.5978  1303   147  0.90  16.52   0.98     0.95       7211.42|
|  7:  2.5978 -  2.4683  1282   151  0.90  15.66   0.98     0.95       6360.52|
|  8:  2.4683 -  2.3613  1310   133  0.91  15.79   1.00     0.98       5888.43|
|  9:  2.3613 -  2.2708  1298   149  0.89  16.87   1.01     0.98       5401.95|
| 10:  2.2708 -  2.1927  1278   142  0.90  16.13   1.00     0.97       4853.31|
| 11:  2.1927 -  2.1243  1281   149  0.90  16.45   1.00     0.98       4405.84|
| 12:  2.1243 -  2.0637  1273   141  0.91  15.07   1.00     0.97       3762.99|
| 13:  2.0637 -  2.0095  1254   129  0.90  16.08   1.00     1.00       3358.93|
| 14:  2.0095 -  1.9606   635    76  0.91  15.27   0.98     0.94       2691.20|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2691.20 max =        11048.62 mean =      6649.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.22 mean =        13.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1596   ksol= 0.32   Bsol= 42.72   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.41,0.53,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156643                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1596   ksol= 0.32   Bsol= 42.72   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.41,0.53,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156643                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.1000 0.1311      5.3794      5.5506|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.0867 0.1108      5.4526      5.6664|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.1065 0.1534       5.487      5.8728|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.1220 0.1561      5.4545      5.6477|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.1352 0.1606      5.3387      5.4714|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.1282 0.2099      5.2302      5.5253|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.1170 0.1591       5.159      5.3663|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1174 0.1777      5.1001      5.3697|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.1189 0.1841      5.0454      5.3357|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1134 0.1787      4.9962      5.2317|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.1138 0.1797      4.9254      5.2388|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.1094 0.1764      4.8534      5.1563|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.1096 0.1731      4.7797      5.0418|
| 14:  2.0095 -  1.9606 0.50    635   76 0.1022 0.1625      4.6768       4.898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.94   8.85   0.98     0.97       7118.83|
|  2:  4.6794 -  3.7335  1350   151  0.95   8.34   1.02     1.01       9383.40|
|  3:  3.7335 -  3.2673  1331   146  0.93  11.77   1.03     1.02      11086.53|
|  4:  3.2673 -  2.9711  1324   139  0.92  14.19   1.01     1.01      10587.63|
|  5:  2.9711 -  2.7596  1306   148  0.90  16.22   1.00     0.96       8452.96|
|  6:  2.7596 -  2.5978  1303   147  0.90  16.50   0.98     0.95       7198.48|
|  7:  2.5978 -  2.4683  1282   151  0.90  15.65   0.99     0.95       6353.30|
|  8:  2.4683 -  2.3613  1310   133  0.91  15.79   1.01     0.98       5883.28|
|  9:  2.3613 -  2.2708  1298   149  0.89  16.87   1.01     0.98       5398.70|
| 10:  2.2708 -  2.1927  1278   142  0.90  16.12   1.01     0.97       4851.29|
| 11:  2.1927 -  2.1243  1281   149  0.90  16.45   1.01     0.98       4406.11|
| 12:  2.1243 -  2.0637  1273   141  0.91  15.07   1.01     0.98       3763.57|
| 13:  2.0637 -  2.0095  1254   129  0.90  16.07   1.01     1.01       3355.39|
| 14:  2.0095 -  1.9606   635    76  0.91  15.25   0.99     0.95       2684.10|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2684.10 max =        11086.53 mean =      6651.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.46 mean =        13.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.32    83.60   14.89    None  None   None       |
|    all(noH): 2823   0      1.32    83.60   14.89    None  None   None       |
|    Sol.    : 438    0      3.33    76.83   37.30    None  None   None       |
|    Mac.    : 2385   0      1.32    83.60   10.78    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:     1.317 -   9.546: 1397   |   5:    42.461 -  50.690:   97        |
|      1:     9.546 -  17.775:  803   |   6:    50.690 -  58.918:   77        |
|      2:    17.775 -  26.003:  187   |   7:    58.918 -  67.147:   22        |
|      3:    26.003 -  34.232:  123   |   8:    67.147 -  75.376:    8        |
|      4:    34.232 -  42.461:  102   |   9:    75.376 -  83.605:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 4.862
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 331
   mapped sites are within: 0.702 - 4.862

peak=   10.984 closest distance to " CB  VAL A 230 " =    1.396
peak=    6.437 closest distance to " CB  VAL A 296 " =    1.114
peak=    6.332 closest distance to " O   HOH Z 120 " =    1.161
peak=    6.024 closest distance to " CG  LEU A   5 " =    1.234
peak=    5.402 closest distance to " NH2 ARG A  56 " =    2.240
peak=    5.365 closest distance to " O   HOH Z 193 " =    1.888
peak=    5.327 closest distance to " O   HOH Z 402 " =    1.594
peak=    5.230 closest distance to " O   HOH Z 124 " =    1.598
peak=    5.180 closest distance to " O   HOH Z 272 " =    1.892
peak=    5.135 closest distance to " CB  ARG A 275 " =    0.962
peak=    5.067 closest distance to " CD1AILE A 234 " =    1.101
peak=    4.861 closest distance to " O   HOH Z  85 " =    1.811
peak=    4.843 closest distance to " CG  PRO A  54 " =    1.215
peak=    4.834 closest distance to " O   HOH Z 414 " =    1.995
peak=    4.789 closest distance to " CG2 VAL A 296 " =    1.028
peak=    4.782 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.777 closest distance to " O   HOH Z 142 " =    1.678
peak=    4.768 closest distance to " CB  GLN A 183 " =    1.317
peak=    4.752 closest distance to " CB  SER A  63 " =    1.091
peak=    4.742 closest distance to " O   HOH Z 126 " =    1.833
peak=    4.726 closest distance to " CG  LEU A 228 " =    1.171
peak=    4.680 closest distance to " O   HOH Z  54 " =    1.666
peak=    4.679 closest distance to " O   HOH Z  80 " =    1.945
peak=    4.645 closest distance to " O   HOH Z 209 " =    2.241
peak=    4.644 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.634 closest distance to " CB  GLN A 223 " =    1.411
peak=    4.628 closest distance to " O   SER A  87 " =    2.281
peak=    4.615 closest distance to " O   HOH Z 154 " =    1.641
peak=    4.539 closest distance to " CB  VAL A 230 " =    1.186
peak=    4.538 closest distance to " O   HOH Z 403 " =    1.809
peak=    4.534 closest distance to " C   PRO A 198 " =    1.480
peak=    4.527 closest distance to " O   HOH Z 236 " =    1.335
peak=    4.517 closest distance to " O   HOH Z 120 " =    2.098
peak=    4.473 closest distance to " O   HOH Z 327 " =    1.822
peak=    4.446 closest distance to " O   HOH Z 137 " =    1.569
peak=    4.435 closest distance to " NE2 GLN A  11 " =    1.032
peak=    4.435 closest distance to " O   HOH Z  47 " =    1.902
peak=    4.422 closest distance to " O   HOH Z 232 " =    2.327
peak=    4.394 closest distance to " O   HOH Z 278 " =    1.150
peak=    4.384 closest distance to " O   HOH Z 426 " =    1.458
peak=    4.379 closest distance to " CB  GLU A 152 " =    1.139
peak=    4.368 closest distance to " O   HOH Z 203 " =    1.735
peak=    4.359 closest distance to " CB  SER A   3 " =    1.259
peak=    4.351 closest distance to " O   HOH Z 234 " =    3.632
peak=    4.340 closest distance to " O   HOH Z 357 " =    2.049
peak=    4.336 closest distance to " O   HOH Z 423 " =    1.784
peak=    4.306 closest distance to " O   HOH Z 369 " =    2.324
peak=    4.282 closest distance to " CB  PRO A  54 " =    0.890
peak=    4.243 closest distance to " CB  TRP A 179 " =    1.125
peak=    4.236 closest distance to " O   HOH Z 419 " =    1.620
peak=    4.232 closest distance to " O   HOH Z 368 " =    2.170
peak=    4.218 closest distance to " O   HOH Z 247 " =    1.313
peak=    4.207 closest distance to " O   HOH Z 227 " =    1.644
peak=    4.151 closest distance to " O   HOH Z 128 " =    1.832
peak=    4.123 closest distance to " N   ASN A  39 " =    1.263
peak=    4.110 closest distance to " CD2 LEU A   5 " =    1.185
peak=    4.108 closest distance to " CG1 ILE A  33 " =    1.240
peak=    4.106 closest distance to " O   HOH Z 134 " =    1.734
peak=    4.076 closest distance to " O   HOH Z  97 " =    2.376
peak=    4.075 closest distance to " CG1 VAL A 296 " =    1.142
peak=    4.071 closest distance to " O   HOH Z 102 " =    1.346
peak=    4.065 closest distance to " O   HOH Z 303 " =    2.213
peak=    4.062 closest distance to " O   HOH Z  97 " =    1.948
peak=    4.055 closest distance to " O   HOH Z  63 " =    2.427
peak=    4.055 closest distance to " O   HOH Z 316 " =    2.808
peak=    4.052 closest distance to " NZ  LYS A 117 " =    3.018
peak=    4.049 closest distance to " O   HOH Z  43 " =    1.479
peak=    4.047 closest distance to " OE1 GLU A   2 " =    2.112
peak=    4.042 closest distance to " O   HOH Z 345 " =    1.814
peak=    4.011 closest distance to " CA  ALA A  21 " =    1.251
peak=    4.008 closest distance to " O   HOH Z 389 " =    1.831
peak=    4.007 closest distance to " O   HOH Z 346 " =    1.536
peak=    4.000 closest distance to " O   HOH Z 345 " =    2.489
peak=    3.960 closest distance to " O   HOH Z 245 " =    1.450
peak=    3.955 closest distance to " O   HOH Z  59 " =    2.159
peak=    3.950 closest distance to " O   HOH Z 156 " =    3.228
peak=    3.933 closest distance to " O   HOH Z  44 " =    2.040
peak=    3.924 closest distance to " CG  ARG A  66 " =    1.084
peak=    3.922 closest distance to " CB  SER A  26 " =    1.762
peak=    3.908 closest distance to " CB  ARG A  79 " =    1.450
peak=    3.906 closest distance to " CB  THR A  31 " =    1.488
peak=    3.905 closest distance to " CG  ARG A  66 " =    2.869
peak=    3.902 closest distance to " O   HOH Z 265 " =    2.460
peak=    3.899 closest distance to " CD2 TRP A 179 " =    1.388
peak=    3.884 closest distance to " O   HOH Z  47 " =    1.643
peak=    3.872 closest distance to " O   HOH Z  15 " =    2.187
peak=    3.868 closest distance to " CD2 LEU A 228 " =    1.179
peak=    3.868 closest distance to " O   HOH Z 197 " =    2.317
peak=    3.857 closest distance to " O   HOH Z 280 " =    2.643
peak=    3.851 closest distance to " CB  ARG A 139 " =    0.969
peak=    3.844 closest distance to " O   HOH Z 189 " =    2.428
peak=    3.837 closest distance to " O   HOH Z 126 " =    2.083
peak=    3.831 closest distance to " OG BSER A 164 " =    2.098
peak=    3.830 closest distance to " O   HOH Z 408 " =    1.658
peak=    3.827 closest distance to " CG2 ILE A  20 " =    1.422
peak=    3.827 closest distance to " O   HOH Z 411 " =    3.450
peak=    3.816 closest distance to " O   HOH Z 406 " =    1.598
peak=    3.811 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.809 closest distance to " O   HOH Z 322 " =    2.183
peak=    3.803 closest distance to " CA  VAL A  41 " =    0.787
peak=    3.800 closest distance to " O   TRP A 274 " =    1.911
peak=    3.799 closest distance to " CB  GLU A 128 " =    1.139
peak=    3.793 closest distance to " CG2 THR A 221 " =    1.215
peak=    3.782 closest distance to " CG2AVAL A 121 " =    2.066
peak=    3.770 closest distance to " CD  ARG A 269 " =    1.091
peak=    3.760 closest distance to " OD1 ASN A  69 " =    2.462
peak=    3.758 closest distance to " O   HOH Z 273 " =    2.812
peak=    3.751 closest distance to " CB  GLU A 277 " =    3.508
peak=    3.747 closest distance to " O   HOH Z 421 " =    1.990
peak=    3.743 closest distance to " CA  ALA A  51 " =    1.022
peak=    3.740 closest distance to " ND2 ASN A 187 " =    1.601
peak=    3.738 closest distance to " O   HOH Z 417 " =    3.309
peak=    3.738 closest distance to " O   HOH Z 253 " =    1.646
peak=    3.738 closest distance to " O   HOH Z 147 " =    1.821
peak=    3.733 closest distance to " CG  PRO A 243 " =    1.231
peak=    3.717 closest distance to " CE  LYS A 119 " =    0.987
peak=    3.700 closest distance to " O   HOH Z 315 " =    1.872
peak=    3.688 closest distance to " O   HOH Z 261 " =    2.003
peak=    3.683 closest distance to " O   HOH Z  68 " =    1.929
peak=    3.682 closest distance to " O   HOH Z 248 " =    1.709
peak=    3.676 closest distance to " O   HOH Z 130 " =    2.457
peak=    3.673 closest distance to " O   HOH Z 361 " =    3.124
peak=    3.663 closest distance to " O   HOH Z 394 " =    1.538
peak=    3.652 closest distance to " CG1BVAL A  72 " =    1.602
peak=    3.649 closest distance to " O   HOH Z 250 " =    1.564
peak=    3.646 closest distance to " CB  ALA A 100 " =    1.161
peak=    3.644 closest distance to " O   HOH Z 344 " =    1.897
peak=    3.637 closest distance to " O   HOH Z 193 " =    2.123
peak=    3.635 closest distance to " CB  TRP A 266 " =    1.151
peak=    3.633 closest distance to " O   HOH Z 298 " =    1.834
peak=    3.627 closest distance to " O   HOH Z 271 " =    2.442
peak=    3.626 closest distance to " O   HOH Z 284 " =    2.818
peak=    3.624 closest distance to " O   HOH Z  66 " =    2.140
peak=    3.623 closest distance to " O   HOH Z 380 " =    2.128
peak=    3.619 closest distance to " O   HOH Z 163 " =    1.324
peak=    3.613 closest distance to " CA  ASN A 176 " =    1.018
peak=    3.612 closest distance to " OD2 ASP A 298 " =    3.945
peak=    3.608 closest distance to " O   HOH Z 420 " =    2.122
peak=    3.604 closest distance to " O   HOH Z 334 " =    1.438
peak=    3.601 closest distance to " O   HOH Z 367 " =    3.437
peak=    3.597 closest distance to " O   GLY A  23 " =    2.337
peak=    3.591 closest distance to " CB  ASN A 148 " =    1.379
peak=    3.590 closest distance to " CB  ALA A 248 " =    1.408
peak=    3.590 closest distance to " O   HOH Z 365 " =    2.967
peak=    3.587 closest distance to " CD  LYS A 166 " =    1.325
peak=    3.584 closest distance to " CB  ASN A  39 " =    0.770
peak=    3.583 closest distance to " OD2 ASP A 286 " =    2.659
peak=    3.572 closest distance to " O   HOH Z  78 " =    1.680
peak=    3.571 closest distance to " O   HOH Z 295 " =    1.518
peak=    3.566 closest distance to " O   HOH Z 286 " =    2.260
peak=    3.565 closest distance to " O   ASP A 124 " =    1.560
peak=    3.556 closest distance to " O   HOH Z 155 " =    1.573
peak=    3.553 closest distance to " O   HOH Z 109 " =    2.087
peak=    3.541 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.541 closest distance to " O   HOH Z 416 " =    2.723
peak=    3.540 closest distance to " O   HOH Z 364 " =    2.319
peak=    3.535 closest distance to " O   HOH Z  19 " =    2.151
peak=    3.531 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.530 closest distance to " NH2BARG A 145 " =    2.304
peak=    3.526 closest distance to " CA  LYS A 117 " =    1.358
peak=    3.523 closest distance to " O   HOH Z 132 " =    1.024
peak=    3.520 closest distance to " OD1 ASP A 286 " =    1.715
peak=    3.517 closest distance to " O   HOH Z 214 " =    2.511
peak=    3.515 closest distance to " O   HOH Z 406 " =    1.113
peak=    3.507 closest distance to " OG1 THR A 294 " =    2.297
peak=    3.494 closest distance to " CG  PRO A 198 " =    1.360
peak=    3.494 closest distance to " O   HOH Z 261 " =    1.966
peak=    3.483 closest distance to " O   HOH Z 383 " =    1.871
peak=    3.469 closest distance to " CD  ARG A 159 " =    0.791
peak=    3.468 closest distance to " CG  GLN A  77 " =    2.218
peak=    3.468 closest distance to " CA  ARG A 195 " =    1.272
peak=    3.467 closest distance to " CG2 ILE A 120 " =    1.296
peak=    3.462 closest distance to " CE1 HIS A 108 " =    1.132
peak=    3.460 closest distance to " O   HOH Z 422 " =    2.601
peak=    3.455 closest distance to " CB  GLN A 278 " =    0.768
peak=    3.453 closest distance to " CG  GLN A  58 " =    2.553
peak=    3.451 closest distance to " O   HOH Z 344 " =    2.781
peak=    3.450 closest distance to " CB  VAL A 202 " =    1.477
peak=    3.441 closest distance to " O   HOH Z 425 " =    1.387
peak=    3.436 closest distance to " O   HOH Z  88 " =    3.659
peak=    3.433 closest distance to " OG  SER A 276 " =    1.482
peak=    3.433 closest distance to " O   HOH Z 374 " =    2.502
peak=    3.425 closest distance to " CA  ALA A 295 " =    0.994
peak=    3.423 closest distance to " O   HOH Z 435 " =    1.837
peak=    3.421 closest distance to " O   HOH Z  40 " =    1.682
peak=    3.415 closest distance to " O   HOH Z 251 " =    1.651
peak=    3.412 closest distance to " O   HOH Z 425 " =    2.050
peak=    3.410 closest distance to " NH2AARG A 145 " =    2.242
peak=    3.410 closest distance to " CB  SER A 141 " =    0.990
peak=    3.409 closest distance to " O   HOH Z 337 " =    3.644
peak=    3.402 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.402 closest distance to " O   HOH Z 215 " =    1.442
peak=    3.402 closest distance to " CA  ARG A  66 " =    0.923
peak=    3.384 closest distance to " O   HOH Z 409 " =    1.867
peak=    3.384 closest distance to " O   HOH Z 411 " =    1.758
peak=    3.382 closest distance to " O   HOH Z 234 " =    1.746
peak=    3.381 closest distance to " CG2 ILE A 234 " =    2.002
peak=    3.379 closest distance to " O   HOH Z 132 " =    2.587
peak=    3.378 closest distance to " CG2 THR A 294 " =    1.578
peak=    3.378 closest distance to " O   HOH Z 112 " =    1.757
peak=    3.372 closest distance to " CB  ALA A 295 " =    1.156
peak=    3.361 closest distance to " CB  PRO A 198 " =    1.038
peak=    3.360 closest distance to " O   HOH Z 214 " =    2.366
peak=    3.357 closest distance to " O   HOH Z 162 " =    2.108
peak=    3.356 closest distance to " CB  VAL A 265 " =    1.197
peak=    3.356 closest distance to " CD  PRO A  54 " =    1.005
peak=    3.345 closest distance to " O   HOH Z 427 " =    2.465
peak=    3.344 closest distance to " CA  ASP A 191 " =    1.037
peak=    3.342 closest distance to " CB  ALA A   1 " =    1.249
peak=    3.342 closest distance to " CG AARG A 275 " =    1.268
peak=    3.341 closest distance to " O   HOH Z 287 " =    1.774
peak=    3.339 closest distance to " O   HOH Z 261 " =    1.877
peak=    3.339 closest distance to " O   HOH Z 298 " =    4.862
peak=    3.339 closest distance to " CB  ILE A 120 " =    1.625
peak=    3.337 closest distance to " O   HOH Z 158 " =    2.879
peak=    3.334 closest distance to " O   HOH Z 355 " =    1.859
peak=    3.333 closest distance to " O   HOH Z  49 " =    2.512
peak=    3.325 closest distance to " CB  THR A  52 " =    0.970
peak=    3.322 closest distance to " OD1 ASN A  60 " =    1.625
peak=    3.321 closest distance to " O   HOH Z 197 " =    2.044
peak=    3.317 closest distance to " O   HOH Z 353 " =    2.881
peak=    3.317 closest distance to " O   HOH Z 359 " =    1.577
peak=    3.313 closest distance to " CB  ARG A 190 " =    1.669
peak=    3.307 closest distance to " O   HOH Z 438 " =    2.490
peak=    3.307 closest distance to " CZ2 TRP A 150 " =    1.069
peak=    3.303 closest distance to " O   HOH Z  88 " =    2.653
peak=    3.300 closest distance to " O   HOH Z 299 " =    2.241
peak=    3.299 closest distance to " O   HOH Z 362 " =    3.357
peak=    3.298 closest distance to " O   GLY A  91 " =    1.413
peak=    3.298 closest distance to " O   HOH Z 412 " =    3.728
peak=    3.296 closest distance to " O   HOH Z 227 " =    2.164
peak=    3.296 closest distance to " CD  ARG A 195 " =    0.858
peak=    3.292 closest distance to " CE  MET A 105 " =    2.271
peak=    3.292 closest distance to " CD2 HIS A  81 " =    1.161
peak=    3.291 closest distance to " O   HOH Z 281 " =    4.174
peak=    3.290 closest distance to " CB  MET A  47 " =    1.268
peak=    3.290 closest distance to " O   HOH Z 380 " =    1.906
peak=    3.286 closest distance to " NZ  LYS A  76 " =    1.820
peak=    3.284 closest distance to " O   HOH Z 291 " =    1.666
peak=    3.279 closest distance to " O   HOH Z 148 " =    3.157
peak=    3.278 closest distance to " CB  TYR A 247 " =    0.972
peak=    3.276 closest distance to " N   SER A 135 " =    1.232
peak=    3.276 closest distance to " CD  GLN A 194 " =    1.498
peak=    3.276 closest distance to " CA  ARG A  36 " =    1.014
peak=    3.275 closest distance to " CZ AARG A 102 " =    1.695
peak=    3.274 closest distance to " CD1 LEU A 228 " =    1.586
peak=    3.271 closest distance to " CA  TYR A 116 " =    1.482
peak=    3.270 closest distance to " O   HOH Z 130 " =    1.083
peak=    3.260 closest distance to " CG2 ILE A 106 " =    0.702
peak=    3.260 closest distance to " NH2 ARG A  79 " =    1.292
peak=    3.258 closest distance to " OG  SER A  22 " =    2.650
peak=    3.258 closest distance to " O   HOH Z 194 " =    2.199
peak=    3.254 closest distance to " OH  TYR A 116 " =    1.180
peak=    3.254 closest distance to " O  BHOH Z  74 " =    1.470
peak=    3.251 closest distance to " CD  LYS A 119 " =    1.786
peak=    3.250 closest distance to " O   HOH Z 423 " =    3.162
peak=    3.249 closest distance to " OG BSER A 210 " =    1.380
peak=    3.246 closest distance to " CB  ARG A 259 " =    1.896
peak=    3.246 closest distance to " O   ALA A 165 " =    1.378
peak=    3.246 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.244 closest distance to " OG  SER A 245 " =    1.427
peak=    3.243 closest distance to " CD2 TYR A  30 " =    0.827
peak=    3.241 closest distance to " OE1 GLN A  11 " =    1.740
peak=    3.237 closest distance to " CB  SER A 273 " =    0.854
peak=    3.235 closest distance to " O   HOH Z 381 " =    1.537
peak=    3.235 closest distance to " O   HOH Z  71 " =    1.913
peak=    3.230 closest distance to " O   HOH Z 185 " =    1.618
peak=    3.227 closest distance to " CB  ASN A 215 " =    1.092
peak=    3.226 closest distance to " NH1AARG A 145 " =    1.196
peak=    3.224 closest distance to " CH2 TRP A 274 " =    2.102
peak=    3.223 closest distance to " CG1 ILE A  49 " =    1.526
peak=    3.222 closest distance to " N   ASP A 162 " =    1.270
peak=    3.213 closest distance to " O   HOH Z  61 " =    1.426
peak=    3.213 closest distance to " O   HOH Z 162 " =    1.705
peak=    3.211 closest distance to " CZ2 TRP A 274 " =    1.680
peak=    3.211 closest distance to " CA  ASP A 140 " =    1.142
peak=    3.210 closest distance to " O   HOH Z 326 " =    1.419
peak=    3.210 closest distance to " O   ALA A 158 " =    1.279
peak=    3.204 closest distance to " O   THR A  82 " =    2.002
peak=    3.199 closest distance to " O   HOH Z 257 " =    2.233
peak=    3.198 closest distance to " O   HOH Z 244 " =    1.571
peak=    3.194 closest distance to " CZ  PHE A  38 " =    1.377
peak=    3.194 closest distance to " O   HOH Z 428 " =    3.860
peak=    3.187 closest distance to " O   HOH Z  66 " =    1.711
peak=    3.186 closest distance to " O   HOH Z 189 " =    2.720
peak=    3.180 closest distance to " C   ALA A 299 " =    0.895
peak=    3.173 closest distance to " CA  ALA A  84 " =    1.292
peak=    3.172 closest distance to " O   HOH Z 250 " =    1.386
peak=    3.172 closest distance to " O   HOH Z 387 " =    1.983
peak=    3.168 closest distance to " NZ  LYS A  48 " =    1.430
peak=    3.163 closest distance to " CG  MET A 113 " =    1.361
peak=    3.161 closest distance to " O   HOH Z  96 " =    2.023
peak=    3.161 closest distance to " CZ2 TRP A 179 " =    1.850
peak=    3.160 closest distance to " O   ALA A   1 " =    1.647
peak=    3.153 closest distance to " O   HOH Z 166 " =    1.447
peak=    3.152 closest distance to " O   HOH Z  39 " =    2.575
peak=    3.148 closest distance to " O   HOH Z 155 " =    2.953
peak=    3.147 closest distance to " SD  MET A 185 " =    1.159
peak=    3.146 closest distance to " NH2BARG A 190 " =    1.695
peak=    3.146 closest distance to " CB  LYS A 290 " =    1.087
peak=    3.145 closest distance to " CA  LEU A  83 " =    1.386
peak=    3.144 closest distance to " O   HOH Z 213 " =    1.732
peak=    3.142 closest distance to " CB  LEU A   5 " =    1.207
peak=    3.135 closest distance to " CA  ASP A 162 " =    1.151
peak=    3.135 closest distance to " OG BSER A 258 " =    3.312
peak=    3.129 closest distance to " CD1 LEU A 101 " =    1.200
peak=    3.121 closest distance to " CA  LYS A 290 " =    1.033
peak=    3.119 closest distance to " O   HOH Z  83 " =    1.560
peak=    3.118 closest distance to " N   SER A 146 " =    1.958
peak=    3.114 closest distance to " CG  PRO A  90 " =    1.170
peak=    3.112 closest distance to " O   HOH Z 192 " =    1.836
peak=    3.110 closest distance to " O   HOH Z 110 " =    1.279
peak=    3.107 closest distance to " O   HOH Z 279 " =    2.029
peak=    3.105 closest distance to " CB  ALA A  71 " =    1.294
peak=    3.103 closest distance to " O   ILE A  33 " =    1.292
peak=    3.094 closest distance to " OD2 ASP A 298 " =    3.817
peak=    3.093 closest distance to " O   HOH Z  38 " =    1.442
peak=    3.086 closest distance to " O   HOH Z  40 " =    2.012
peak=    3.073 closest distance to " CA  ALA A 158 " =    1.176
peak=    3.067 closest distance to " O   HOH Z 156 " =    2.373
peak=    3.066 closest distance to " O   HOH Z  78 " =    2.127
peak=    3.061 closest distance to " OG1 THR A 221 " =    1.228
peak=    3.040 closest distance to " O   HOH Z 215 " =    1.536
peak=    3.002 closest distance to " O   HOH Z  88 " =    2.982

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.539 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.772 - 5.939

peak=   -4.787 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.713 closest distance to " CG2 VAL A 230 " =    0.772
peak=   -4.665 closest distance to " O   VAL A  67 " =    2.656
peak=   -4.407 closest distance to " O   PRO A 163 " =    2.037
peak=   -4.360 closest distance to " C   HIS A 108 " =    1.160
peak=   -4.359 closest distance to " O   HOH Z 155 " =    1.709
peak=   -4.315 closest distance to " SG  CYS A 254 " =    3.194
peak=   -4.283 closest distance to " O   HOH Z 266 " =    4.430
peak=   -4.238 closest distance to " CD1 LEU A 101 " =    2.513
peak=   -4.160 closest distance to " OXT GLY A 302 " =    2.749
peak=   -4.091 closest distance to " CB  ALA A 161 " =    2.432
peak=   -4.071 closest distance to " O   HOH Z 166 " =    1.764
peak=   -4.062 closest distance to " N   ALA A 248 " =    1.872
peak=   -3.957 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.920 closest distance to " O   HOH Z 377 " =    1.739
peak=   -3.915 closest distance to " CZ  TYR A 169 " =    1.832
peak=   -3.914 closest distance to " OG BSER A 134 " =    1.439
peak=   -3.913 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.910 closest distance to " O   HOH Z 362 " =    5.939
peak=   -3.907 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.873 closest distance to " CD2 TYR A  30 " =    2.662
peak=   -3.851 closest distance to " CD  GLN A  58 " =    1.298
peak=   -3.851 closest distance to " O   HOH Z  37 " =    1.750
peak=   -3.842 closest distance to " O   HOH Z 414 " =    1.737
peak=   -3.839 closest distance to " CB  ALA A 291 " =    2.400
peak=   -3.815 closest distance to " NH2 ARG A  79 " =    1.964
peak=   -3.800 closest distance to " C   THR A 279 " =    1.144
peak=   -3.796 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.792 closest distance to " O   VAL A  67 " =    2.687
peak=   -3.788 closest distance to " O   HOH Z 290 " =    0.949
peak=   -3.778 closest distance to " O   ALA A   1 " =    1.883
peak=   -3.777 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.770 closest distance to " O   HOH Z 196 " =    2.120
peak=   -3.764 closest distance to " CH2 TRP A 179 " =    1.349
peak=   -3.754 closest distance to " ND2 ASN A  69 " =    1.551
peak=   -3.748 closest distance to " O   ASN A  45 " =    1.805
peak=   -3.736 closest distance to " CD1 PHE A 130 " =    2.240
peak=   -3.727 closest distance to " CB  ALA A 248 " =    1.910
peak=   -3.684 closest distance to " CD1 LEU A 255 " =    2.595
peak=   -3.668 closest distance to " OG  SER A  97 " =    2.295
peak=   -3.666 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.664 closest distance to " OG BSER A 134 " =    1.614
peak=   -3.662 closest distance to " NE2 GLN A  88 " =    1.057
peak=   -3.655 closest distance to " N   GLN A  58 " =    1.955
peak=   -3.648 closest distance to " O   HOH Z 114 " =    3.396
peak=   -3.643 closest distance to " ND2 ASN A 187 " =    1.544
peak=   -3.640 closest distance to " O   HOH Z  71 " =    1.422
peak=   -3.636 closest distance to " CD  LYS A 289 " =    2.442
peak=   -3.634 closest distance to " CG  GLN A 223 " =    2.335
peak=   -3.633 closest distance to " CG  ASP A 231 " =    0.856
peak=   -3.631 closest distance to " O   HOH Z 407 " =    2.937
peak=   -3.626 closest distance to " O   HOH Z 165 " =    2.007
peak=   -3.622 closest distance to " O   HOH Z 136 " =    2.002
peak=   -3.602 closest distance to " ND2 ASN A  39 " =    1.100
peak=   -3.600 closest distance to " O   HOH Z 423 " =    2.273
peak=   -3.595 closest distance to " O   ALA A 160 " =    1.394
peak=   -3.593 closest distance to " N   ALA A 226 " =    1.902
peak=   -3.585 closest distance to " CD2 LEU A 300 " =    2.630
peak=   -3.575 closest distance to " O   VAL A 174 " =    2.027
peak=   -3.553 closest distance to " CG2 THR A 221 " =    2.320
peak=   -3.553 closest distance to " O   HOH Z 120 " =    1.109
peak=   -3.551 closest distance to " CE BMET A  47 " =    1.422
peak=   -3.547 closest distance to " O   HOH Z 389 " =    1.616
peak=   -3.547 closest distance to " N   THR A 157 " =    1.513
peak=   -3.543 closest distance to " O   ALA A 256 " =    1.450
peak=   -3.531 closest distance to " CD2 PHE A 192 " =    1.994
peak=   -3.529 closest distance to " C   ALA A 158 " =    1.221
peak=   -3.529 closest distance to " N   SER A 276 " =    1.331
peak=   -3.527 closest distance to " O   ASN A 187 " =    1.466
peak=   -3.521 closest distance to " O   HOH Z 313 " =    1.280
peak=   -3.517 closest distance to " O   MET A  40 " =    2.826
peak=   -3.506 closest distance to " NE2 GLN A 194 " =    1.766
peak=   -3.498 closest distance to " CG1 VAL A 296 " =    1.050
peak=   -3.497 closest distance to " CG  GLU A  53 " =    1.429
peak=   -3.490 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.487 closest distance to " CG2 VAL A 197 " =    2.192
peak=   -3.485 closest distance to " OG  SER A  26 " =    1.297
peak=   -3.474 closest distance to " O   HOH Z 353 " =    2.186
peak=   -3.464 closest distance to " CB  ALA A 248 " =    2.259
peak=   -3.463 closest distance to " O   HOH Z 191 " =    5.540
peak=   -3.461 closest distance to " CG  ASP A  50 " =    2.509
peak=   -3.461 closest distance to " CD  GLN A 103 " =    1.377
peak=   -3.460 closest distance to " OXT GLY A 302 " =    3.468
peak=   -3.447 closest distance to " O   HOH Z 174 " =    4.270
peak=   -3.444 closest distance to " O   HOH Z 422 " =    1.564
peak=   -3.442 closest distance to " N   THR A 235 " =    1.330
peak=   -3.435 closest distance to " O   GLY A  80 " =    2.678
peak=   -3.433 closest distance to " O   HOH Z 388 " =    1.969
peak=   -3.430 closest distance to " O   HOH Z 126 " =    1.816
peak=   -3.429 closest distance to " OD2 ASP A 191 " =    1.467
peak=   -3.428 closest distance to " CD  ARG A 195 " =    5.127
peak=   -3.428 closest distance to " N   VAL A 189 " =    1.594
peak=   -3.427 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.410 closest distance to " CD1 PHE A  59 " =    2.129
peak=   -3.409 closest distance to " NE2 GLN A  88 " =    1.916
peak=   -3.408 closest distance to " O   HOH Z 166 " =    1.467
peak=   -3.405 closest distance to " O   SER A 210 " =    1.913
peak=   -3.404 closest distance to " O   HOH Z  17 " =    1.125
peak=   -3.403 closest distance to " O   HOH Z  60 " =    2.016
peak=   -3.396 closest distance to " CG  MET A 105 " =    0.882
peak=   -3.391 closest distance to " O   HOH Z  92 " =    1.693
peak=   -3.390 closest distance to " CD1 LEU A 228 " =    2.181
peak=   -3.390 closest distance to " OD1 ASP A 191 " =    1.516
peak=   -3.389 closest distance to " O   HOH Z 283 " =    1.717
peak=   -3.381 closest distance to " CD1 TYR A 247 " =    2.332
peak=   -3.379 closest distance to " NH2 ARG A  66 " =    1.478
peak=   -3.374 closest distance to " CG1 VAL A 112 " =    2.636
peak=   -3.373 closest distance to " CB  PRO A 163 " =    2.779
peak=   -3.367 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.367 closest distance to " CB  GLN A  11 " =    1.852
peak=   -3.367 closest distance to " C   GLY A  80 " =    2.455
peak=   -3.361 closest distance to " O   GLY A 196 " =    1.074
peak=   -3.355 closest distance to " CD2 LEU A 237 " =    2.663
peak=   -3.347 closest distance to " OG1 THR A  82 " =    1.217
peak=   -3.344 closest distance to " OD2 ASP A  50 " =    1.305
peak=   -3.344 closest distance to " CB  PHE A 208 " =    2.265
peak=   -3.337 closest distance to " O   ALA A 161 " =    1.646
peak=   -3.331 closest distance to " N   ARG A  66 " =    1.741
peak=   -3.330 closest distance to " N   SER A 210 " =    1.427
peak=   -3.326 closest distance to " CB  ALA A  43 " =    2.334
peak=   -3.323 closest distance to " C   LEU A 143 " =    1.027
peak=   -3.321 closest distance to " N   ALA A 248 " =    2.250
peak=   -3.318 closest distance to " OD1 ASN A 148 " =    1.561
peak=   -3.313 closest distance to " CB  ASN A  39 " =    2.271
peak=   -3.311 closest distance to " CG2 THR A 178 " =    2.220
peak=   -3.309 closest distance to " O   SER A  95 " =    1.580
peak=   -3.305 closest distance to " O   HOH Z 171 " =    1.957
peak=   -3.303 closest distance to " O   TRP A  92 " =    1.969
peak=   -3.300 closest distance to " N   SER A 206 " =    1.808
peak=   -3.296 closest distance to " NH2 ARG A  66 " =    4.826
peak=   -3.294 closest distance to " CE  LYS A 166 " =    3.047
peak=   -3.294 closest distance to " O   HOH Z  56 " =    2.370
peak=   -3.286 closest distance to " OG ASER A 134 " =    1.139
peak=   -3.286 closest distance to " O   HOH Z 250 " =    1.316
peak=   -3.285 closest distance to " O   HOH Z 361 " =    3.480
peak=   -3.279 closest distance to " O   HOH Z  11 " =    1.761
peak=   -3.279 closest distance to " N   HIS A 115 " =    2.032
peak=   -3.277 closest distance to " O   HOH Z  61 " =    1.552
peak=   -3.273 closest distance to " CG  GLU A   2 " =    1.773
peak=   -3.271 closest distance to " O   HOH Z 414 " =    2.371
peak=   -3.271 closest distance to " CD  GLN A 223 " =    0.858
peak=   -3.269 closest distance to " CA  VAL A 296 " =    1.019
peak=   -3.269 closest distance to " O   HOH Z 198 " =    2.171
peak=   -3.266 closest distance to " O   HOH Z 313 " =    1.905
peak=   -3.258 closest distance to " O   SER A 146 " =    0.973
peak=   -3.257 closest distance to " OG  SER A  62 " =    1.230
peak=   -3.256 closest distance to " O   HOH Z 234 " =    4.087
peak=   -3.254 closest distance to " CE3 TRP A 150 " =    2.197
peak=   -3.251 closest distance to " NH2AARG A 275 " =    4.777
peak=   -3.240 closest distance to " O   VAL A 197 " =    1.287
peak=   -3.235 closest distance to " OD1 ASN A  39 " =    2.143
peak=   -3.232 closest distance to " O   HOH Z 174 " =    2.191
peak=   -3.231 closest distance to " O   HOH Z 193 " =    1.738
peak=   -3.230 closest distance to " O   PRO A 198 " =    1.197
peak=   -3.230 closest distance to " O   HOH Z   6 " =    1.827
peak=   -3.226 closest distance to " CG2 VAL A 189 " =    1.990
peak=   -3.226 closest distance to " O   HOH Z 310 " =    3.436
peak=   -3.225 closest distance to " O   HOH Z 285 " =    3.722
peak=   -3.224 closest distance to " O   HOH Z 431 " =    2.137
peak=   -3.219 closest distance to " CD2 LEU A 237 " =    2.705
peak=   -3.214 closest distance to " CG  LYS A 193 " =    2.293
peak=   -3.213 closest distance to " O   ALA A  51 " =    1.439
peak=   -3.209 closest distance to " CB  ASP A 132 " =    2.276
peak=   -3.208 closest distance to " OG  SER A   3 " =    1.328
peak=   -3.197 closest distance to " O   HOH Z 172 " =    4.980
peak=   -3.197 closest distance to " C   VAL A 189 " =    1.850
peak=   -3.194 closest distance to " O   SER A 273 " =    1.382
peak=   -3.191 closest distance to " CD  ARG A 139 " =    1.635
peak=   -3.190 closest distance to " O   HOH Z 193 " =    1.615
peak=   -3.189 closest distance to " O   HOH Z 340 " =    1.150
peak=   -3.184 closest distance to " N   SER A 271 " =    1.491
peak=   -3.177 closest distance to " OD2 ASP A 171 " =    2.398
peak=   -3.176 closest distance to " CE  MET A 105 " =    1.949
peak=   -3.170 closest distance to " C   GLY A  91 " =    1.299
peak=   -3.169 closest distance to " CG2 ILE A 263 " =    2.191
peak=   -3.167 closest distance to " CG  GLU A 152 " =    1.122
peak=   -3.164 closest distance to " CA  GLY A 133 " =    1.916
peak=   -3.160 closest distance to " CD1 LEU A  25 " =    2.481
peak=   -3.158 closest distance to " CA  ALA A 137 " =    2.563
peak=   -3.158 closest distance to " OD1 ASN A 249 " =    1.910
peak=   -3.149 closest distance to " O   ARG A 219 " =    1.793
peak=   -3.144 closest distance to " O   HOH Z  97 " =    1.385
peak=   -3.139 closest distance to " CA  GLY A 203 " =    2.226
peak=   -3.138 closest distance to " O   HOH Z 297 " =    2.722
peak=   -3.136 closest distance to " O   HOH Z  48 " =    1.286
peak=   -3.134 closest distance to " CG  ARG A 269 " =    2.205
peak=   -3.134 closest distance to " O   HOH Z  90 " =    2.783
peak=   -3.132 closest distance to " O   HOH Z 211 " =    1.542
peak=   -3.131 closest distance to " NH2 ARG A  79 " =    1.779
peak=   -3.127 closest distance to " CA  GLY A 241 " =    2.417
peak=   -3.123 closest distance to " OG  SER A  63 " =    1.154
peak=   -3.123 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.122 closest distance to " O   SER A  22 " =    2.159
peak=   -3.112 closest distance to " O   HOH Z 131 " =    4.042
peak=   -3.109 closest distance to " O   HOH Z  55 " =    2.423
peak=   -3.106 closest distance to " O   HOH Z 154 " =    1.412
peak=   -3.097 closest distance to " CD  GLU A 152 " =    2.141
peak=   -3.092 closest distance to " O   HOH Z 292 " =    2.726
peak=   -3.085 closest distance to " CD  ARG A 259 " =    2.499
peak=   -3.069 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.038 closest distance to " CB  ALA A 291 " =    2.108
peak=   -3.024 closest distance to " O   HOH Z  93 " =    2.372
peak=   -3.014 closest distance to " O   HOH Z 424 " =    2.892

================= 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    :  0.4970 0.4861   6.294187e+00   6.285496e+00
   1_bss:  0.4890 0.4770   6.288483e+00   6.279129e+00
   1_xyz:  0.4124 0.4331   6.193742e+00   6.227966e+00
   1_adp:  0.3685 0.4159   6.128996e+00   6.206172e+00
   1_occ:  0.3677 0.4155   6.127665e+00   6.205643e+00
   2_bss:  0.3662 0.4100   6.128039e+00   6.204563e+00
   2_xyz:  0.2697 0.3224   5.881440e+00   6.029177e+00
   2_adp:  0.2395 0.2961   5.786687e+00   5.950282e+00
   2_occ:  0.2392 0.2959   5.785812e+00   5.949567e+00
   3_bss:  0.2359 0.2936   5.782735e+00   5.946613e+00
   3_xyz:  0.1671 0.2140   5.482412e+00   5.684677e+00
   3_adp:  0.1536 0.1955   5.394221e+00   5.590271e+00
   3_occ:  0.1533 0.1955   5.393195e+00   5.589878e+00
   4_bss:  0.1527 0.1944   5.393430e+00   5.587280e+00
   4_xyz:  0.1264 0.1678   5.236213e+00   5.452808e+00
   4_adp:  0.1221 0.1646   5.209620e+00   5.433569e+00
   4_occ:  0.1219 0.1646   5.208223e+00   5.432569e+00
   5_bss:  0.1221 0.1650   5.209126e+00   5.433761e+00
   5_xyz:  0.1141 0.1593   5.163012e+00   5.403750e+00
   5_adp:  0.1122 0.1596   5.156794e+00   5.405361e+00
   5_occ:  0.1121 0.1596   5.156679e+00   5.405600e+00
   5_bss:  0.1121 0.1596   5.156643e+00   5.405686e+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:  0.367  20.001   7.278   9.911   7.680   0.000   0.000   0.000
   1_xyz:  0.367  20.001   7.278   9.911   7.680   0.000   0.000   0.000
   1_adp:  0.367  20.001   7.278   9.911   7.680   0.000   0.000   0.000
   1_occ:  0.367  20.001   7.278   9.911   7.680   0.000   0.000   0.000
   2_bss:  0.334  34.876   4.103   6.186   5.112   0.000   0.000   0.000
   2_xyz:  0.334  34.876   4.103   6.186   5.112   0.000   0.000   0.000
   2_adp:  0.334  34.876   4.103   6.186   5.112   0.000   0.000   0.000
   2_occ:  0.334  34.876   4.103   6.186   5.112   0.000   0.000   0.000
   3_bss:  0.326  39.573   1.736   3.562   3.102   0.000   0.000   0.000
   3_xyz:  0.326  39.573   1.736   3.562   3.102   0.000   0.000   0.000
   3_adp:  0.326  39.573   1.736   3.562   3.102   0.000   0.000   0.000
   3_occ:  0.326  39.573   1.736   3.562   3.102   0.000   0.000   0.000
   4_bss:  0.324  39.573   0.482   2.100   1.950   0.000   0.000   0.000
   4_xyz:  0.324  39.573   0.482   2.100   1.950   0.000   0.000   0.000
   4_adp:  0.324  39.573   0.482   2.100   1.950   0.000   0.000   0.000
   4_occ:  0.324  39.573   0.482   2.100   1.950   0.000   0.000   0.000
   5_bss:  0.323  39.573   0.296   1.718   1.757   0.000   0.000   0.000
   5_xyz:  0.323  39.573   0.296   1.718   1.757   0.000   0.000   0.000
   5_adp:  0.323  39.573   0.296   1.718   1.757   0.000   0.000   0.000
   5_occ:  0.323  39.573   0.296   1.718   1.757   0.000   0.000   0.000
   5_bss:  0.324  42.720  -0.945   0.414   0.531   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.713 0.3848  0.4514    75332.144
   1_bss:  60.817 0.3815  0.5679    73130.104
   1_xyz:  52.926 0.4813  0.7049    57111.763
   1_adp:  48.592 0.5367  0.8434    51817.435
   1_occ:  48.456 0.5384  0.8445    51588.200
   2_bss:  48.141 0.5421  0.7631    50944.868
   2_xyz:  35.158 0.6978  0.9621    28797.241
   2_adp:  30.682 0.7498  1.0133    23337.376
   2_occ:  30.636 0.7503  1.0138    23281.715
   3_bss:  30.448 0.7521  0.9329    22974.307
   3_xyz:  21.066 0.8507  1.0094    11944.220
   3_adp:  18.571 0.8755  1.0254     9928.148
   3_occ:  18.559 0.8757  1.0256     9923.373
   4_bss:  18.479 0.8763  0.9784     9843.837
   4_xyz:  15.478 0.9028  0.9891     7362.344
   4_adp:  15.010 0.9070  0.9902     7136.662
   4_occ:  14.990 0.9072  0.9901     7126.864
   5_bss:  15.023 0.9069  0.9809     7179.274
   5_xyz:  14.314 0.9128  0.9821     6685.770
   5_adp:  14.353 0.9125  0.9779     6644.783
   5_occ:  14.354 0.9125  0.9778     6647.794
   5_bss:  14.354 0.9125  0.9800     6650.164
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3198e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3198e+01
   1_xyz:   1.881  0.015  0.116 18.418  0.008  4.106   1.7099e-01
   1_adp:   1.881  0.015  0.116 18.418  0.008  4.106   1.7099e-01
   1_occ:   1.881  0.015  0.116 18.418  0.008  4.106   1.7099e-01
   2_bss:   1.881  0.015  0.116 18.418  0.008  4.106   1.7099e-01
   2_xyz:   1.369  0.011  0.091 16.785  0.006  4.107   1.0561e-01
   2_adp:   1.369  0.011  0.091 16.785  0.006  4.107   1.0561e-01
   2_occ:   1.369  0.011  0.091 16.785  0.006  4.107   1.0561e-01
   3_bss:   1.369  0.011  0.091 16.785  0.006  4.107   1.0561e-01
   3_xyz:   1.103  0.008  0.077 15.585  0.005  4.125   7.0200e-02
   3_adp:   1.103  0.008  0.077 15.585  0.005  4.125   7.0200e-02
   3_occ:   1.103  0.008  0.077 15.585  0.005  4.125   7.0200e-02
   4_bss:   1.103  0.008  0.077 15.585  0.005  4.125   7.0200e-02
   4_xyz:   1.122  0.008  0.084 15.510  0.005  4.120   7.1074e-02
   4_adp:   1.122  0.008  0.084 15.510  0.005  4.120   7.1074e-02
   4_occ:   1.122  0.008  0.084 15.510  0.005  4.120   7.1074e-02
   5_bss:   1.122  0.008  0.084 15.510  0.005  4.120   7.1074e-02
   5_xyz:   1.137  0.009  0.087 15.494  0.005  4.123   7.4495e-02
   5_adp:   1.137  0.009  0.087 15.494  0.005  4.123   7.4495e-02
   5_occ:   1.137  0.009  0.087 15.494  0.005  4.123   7.4495e-02
   5_bss:   1.137  0.009  0.087 15.494  0.005  4.123   7.4495e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.960   6.8903e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.960   6.8903e+00
   1_xyz:  17.218  0.190  0.586 86.991  0.050  2.069   1.1605e-01
   1_adp:  17.218  0.190  0.586 86.991  0.050  2.069   1.1605e-01
   1_occ:  17.218  0.190  0.586 86.991  0.050  2.069   1.1605e-01
   2_bss:  17.218  0.190  0.586 86.991  0.050  2.069   1.1605e-01
   2_xyz:  10.151  0.139  0.379 82.637  0.059  2.195   9.0224e-02
   2_adp:  10.151  0.139  0.379 82.637  0.059  2.195   9.0224e-02
   2_occ:  10.151  0.139  0.379 82.637  0.059  2.195   9.0224e-02
   3_bss:  10.151  0.139  0.379 82.637  0.059  2.195   9.0224e-02
   3_xyz:   6.783  0.053  0.297 81.759  0.042  2.248   4.9353e-02
   3_adp:   6.783  0.053  0.297 81.759  0.042  2.248   4.9353e-02
   3_occ:   6.783  0.053  0.297 81.759  0.042  2.248   4.9353e-02
   4_bss:   6.783  0.053  0.297 81.759  0.042  2.248   4.9353e-02
   4_xyz:   7.439  0.046  0.513 84.258  0.042  2.182   4.8412e-02
   4_adp:   7.439  0.046  0.513 84.258  0.042  2.182   4.8412e-02
   4_occ:   7.439  0.046  0.513 84.258  0.042  2.182   4.8412e-02
   5_bss:   7.439  0.046  0.513 84.258  0.042  2.182   4.8412e-02
   5_xyz:   7.656  0.051  0.538 81.301  0.040  2.275   7.8569e-02
   5_adp:   7.656  0.051  0.538 81.301  0.040  2.275   7.8569e-02
   5_occ:   7.656  0.051  0.538 81.301  0.040  2.275   7.8569e-02
   5_bss:   7.656  0.051  0.538 81.301  0.040  2.275   7.8569e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  96.02   0.00  14.49  74.08   0.00  12.15  96.02   0.00  27.24
   1_occ:  96.02   0.00  14.49  74.08   0.00  12.15  96.02   0.00  27.24
   2_bss:  96.02   0.00  14.49  74.08   0.00  12.15  96.02   0.00  27.24
   2_xyz:  96.02   0.00  14.49  74.08   0.00  12.15  96.02   0.00  27.24
   2_adp:  92.65   0.00  13.81  81.32   0.00  10.29  92.65   2.01  32.96
   2_occ:  92.65   0.00  13.81  81.32   0.00  10.29  92.65   2.01  32.96
   3_bss:  92.65   0.00  13.81  81.32   0.00  10.29  92.65   2.01  32.96
   3_xyz:  92.65   0.00  13.81  81.32   0.00  10.29  92.65   2.01  32.96
   3_adp:  85.71   0.00  13.57  80.17   0.00   9.64  85.71   2.25  34.96
   3_occ:  85.71   0.00  13.57  80.17   0.00   9.64  85.71   2.25  34.96
   4_bss:  85.71   0.00  13.57  80.17   0.00   9.64  85.71   2.25  34.96
   4_xyz:  85.71   0.00  13.57  80.17   0.00   9.64  85.71   2.25  34.96
   4_adp:  84.99   0.00  13.61  84.99   0.00   9.59  82.26   2.61  35.51
   4_occ:  84.99   0.00  13.61  84.99   0.00   9.59  82.26   2.61  35.51
   5_bss:  84.99   0.00  13.61  84.99   0.00   9.59  82.26   2.61  35.51
   5_xyz:  84.99   0.00  13.61  84.99   0.00   9.59  82.26   2.61  35.51
   5_adp:  82.29   0.00  13.58  82.29   0.00   9.46  75.52   2.01  35.98
   5_occ:  82.29   0.00  13.58  82.29   0.00   9.46  75.52   2.01  35.98
   5_bss:  83.60   1.32  14.89  83.60   1.32  10.78  76.83   3.33  37.30
------------------------------------------------------------------------
 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:    1.187    0.026    0.429
   1_adp:    1.187    0.026    0.429
   1_occ:    1.187    0.026    0.429
   2_bss:    1.187    0.026    0.429
   2_xyz:    1.630    0.058    0.650
   2_adp:    1.630    0.058    0.650
   2_occ:    1.630    0.058    0.650
   3_bss:    1.630    0.058    0.650
   3_xyz:    1.735    0.028    0.734
   3_adp:    1.735    0.028    0.734
   3_occ:    1.735    0.028    0.734
   4_bss:    1.735    0.028    0.734
   4_xyz:    1.782    0.063    0.790
   4_adp:    1.782    0.063    0.790
   4_occ:    1.782    0.063    0.790
   5_bss:    1.782    0.063    0.790
   5_xyz:    1.827    0.061    0.807
   5_adp:    1.827    0.061    0.807
   5_occ:    1.827    0.061    0.807
   5_bss:    1.827    0.061    0.807
------------------------------------------------------------------------

CPU time actual refinement: 340.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/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/trial/run_211/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_211/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.09 
  Macro-tasks:
    bulk solvent and scale       = 40.41  
    individual site refinement   = 142.43 
    weights calculation          = 32.46  
    collect and process          = 6.45   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 221.91 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.36 
    alpha_beta                      = 7.94   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 116.39 
    fmodel                         = 7.63   
    r_factors                      = 0.26   
    phase_errors                   = 10.40  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 251.77 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.770 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    651 calls, 105.02 s
gradients_fft:          597 calls, 102.99 s

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

# Date 2008-01-16 Time 01:03:06 PST -0800 (1200474186.66 s)
Start R-work = 0.4970, R-free = 0.4861 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.4890, R-free = 0.4770
Final R-work = 0.1121, R-free = 0.1596