# Date 2008-01-16 Time 03:09:50 PST -0800 (1200481790.35 s)
#phil __OFF__

Command line arguments: "../1130.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18429
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1130

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 87.6859, 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: 3.36, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 1.98357
Completeness in resolution range: 0.93898
Completeness with d_max=infinity: 0.936287

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2734
                             d_min =   1.9836

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 1.98357
Completeness in resolution range: 0.93898
Completeness with d_max=infinity: 0.936287

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2739 -  4.2458 [2196/2223]  1975   221  10.1%
  bin  2:  4.2458 -  3.3820 [2109/2129]  1900   209   9.9%
  bin  3:  3.3820 -  2.9580 [2073/2092]  1866   207  10.0%
  bin  4:  2.9580 -  2.6892 [2057/2087]  1848   209  10.2%
  bin  5:  2.6892 -  2.4973 [2040/2059]  1845   195   9.6%
  bin  6:  2.4973 -  2.3506 [2046/2071]  1832   214  10.5%
  bin  7:  2.3506 -  2.2333 [2026/2054]  1822   204  10.1%
  bin  8:  2.2333 -  2.1363 [2008/2044]  1807   201  10.0%
  bin  9:  2.1363 -  2.0543 [2017/2059]  1821   196   9.7%
  bin 10:  2.0543 -  1.9836 [1017/2044]   914   103  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2172
        3.04 -     3.66: 4645
        3.66 -     4.28: 8920
        4.28 -     4.90: 12249
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.252 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.283 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.287 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27999 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_1130/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/model_refine_001.geo

CPU time processing inputs: 8.97


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.4607 87.68585 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: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4837   r_free= 0.4681   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.283545                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.7361 0.99   1420  158 0.3999 0.3764      6.6034      6.5477|
|  2:  4.7361 -  3.7780 0.99   1373  155 0.3962 0.4038      6.7901      6.8203|
|  3:  3.7780 -  3.3059 0.99   1340  142 0.4398 0.4183      6.6585      6.6243|
|  4:  3.3059 -  3.0062 0.99   1331  154 0.4757 0.4419      6.5272      6.4841|
|  5:  3.0062 -  2.7921 0.99   1338  150 0.5142 0.4884      6.3745      6.3609|
|  6:  2.7921 -  2.6284 0.99   1320  146 0.5060 0.5091      6.2651      6.2205|
|  7:  2.6284 -  2.4973 0.99   1312  136 0.5398 0.4946      6.2514      6.1932|
|  8:  2.4973 -  2.3890 0.98   1302  152 0.5324 0.4945       6.172      6.1787|
|  9:  2.3890 -  2.2974 0.98   1303  149 0.5276 0.5692      6.1238      6.1881|
| 10:  2.2974 -  2.2183 1.00   1301  145 0.5320 0.4904       6.097      6.0729|
| 11:  2.2183 -  2.1492 0.98   1310  137 0.5190 0.4999      6.0408      6.0171|
| 12:  2.1492 -  2.0879 0.98   1287  145 0.5342 0.5158      5.9477       5.984|
| 13:  2.0879 -  2.0331 0.98   1274  141 0.5379 0.5052      5.8835      5.7874|
| 14:  2.0331 -  1.9836 0.32    419   49 0.5358 0.4696      5.8634      5.8466|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2739 -  4.7361  1420   158  0.70  34.37   0.78     0.74      72523.04|
|  2:  4.7361 -  3.7780  1373   155  0.72  33.68   0.86     0.78     101324.51|
|  3:  3.7780 -  3.3059  1340   142  0.61  42.58   0.84     0.73     107971.54|
|  4:  3.3059 -  3.0062  1331   154  0.53  49.15   0.77     0.64      95843.60|
|  5:  3.0062 -  2.7921  1338   150  0.45  55.65   0.73     0.55      78614.79|
|  6:  2.7921 -  2.6284  1320   146  0.42  58.62   0.72     0.48      69417.01|
|  7:  2.6284 -  2.4973  1312   136  0.36  63.00   0.73     0.41      65391.84|
|  8:  2.4973 -  2.3890  1302   152  0.32  66.13   0.70     0.37      61131.39|
|  9:  2.3890 -  2.2974  1303   149  0.31  66.72   0.72     0.36      56602.25|
| 10:  2.2974 -  2.2183  1301   145  0.32  65.89   0.73     0.38      50947.41|
| 11:  2.2183 -  2.1492  1310   137  0.32  66.02   0.78     0.40      47994.15|
| 12:  2.1492 -  2.0879  1287   145  0.34  64.79   0.72     0.42      42376.95|
| 13:  2.0879 -  2.0331  1274   141  0.34  64.33   0.70     0.44      35745.45|
| 14:  2.0331 -  1.9836   419    49  0.44  56.85   0.71     0.47      26451.12|
|alpha:            min =        0.36 max =            0.78 mean =         0.52|
|beta:             min =    26451.12 max =       107971.54 mean =     67534.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.95|
|phase err.(test): min =        0.00 max =           89.78 mean =        55.82|
|-----------------------------------------------------------------------------|

============================== 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 = 13.790419             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.455   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.180704              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.319   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2607 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3877 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6497 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7574 |
|-----------------------------------------------------------------------------|
|-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 |       54.296 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.690 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    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 = 12.167)------------------------------------------|
|    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: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4885   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.284923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4757   r_free= 0.4588   ksol= 0.35   Bsol= 50.00   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.36,7.36,9.23,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.278275                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.119586             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.589   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.119169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.030   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4757      final r-factor (work) = 0.3908          |
| start r-factor (free) = 0.4588      final r-factor (free) = 0.4051          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.3438 = 12.12 * 0.50 * 6.2788 + 1.00 * 54.2958                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6533 = 12.12 * 0.50 * 6.1899 + 1.00 * 0.1438                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3908      final r-factor (work) = 0.3416          |
| start r-factor (free) = 0.4051      final r-factor (free) = 0.3935          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9420 = 1.12 * 1.00 * 6.1899 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8386 = 1.12 * 1.00 * 6.0944 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.30   13.97    None  None   None       |
|    all(noH): 2823   0      0.00    83.30   13.97    None  None   None       |
|    Sol.    : 438    0      0.00    83.30   29.30    None  None   None       |
|    Mac.    : 2385   0      0.00    65.05   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.330: 1178   |   5:    41.649 -  49.979:   52        |
|      1:     8.330 -  16.660:  786   |   6:    49.979 -  58.309:   56        |
|      2:    16.660 -  24.989:  415   |   7:    58.309 -  66.638:   22        |
|      3:    24.989 -  33.319:  193   |   8:    66.638 -  74.968:    6        |
|      4:    33.319 -  41.649:  114   |   9:    74.968 -  83.298:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3416 r_free = 0.3935             target_work(ml) = 6.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3411 r_free = 0.3938             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3411   r_free= 0.3938   ksol= 0.35   Bsol= 50.00   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.36,7.36,9.23,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.075352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3387   r_free= 0.3905   ksol= 0.33   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,3.88,5.94,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.075803                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.779315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.480576              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.998  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3387      final r-factor (work) = 0.2343          |
| start r-factor (free) = 0.3905      final r-factor (free) = 0.2914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.9150 = 9.78 * 0.50 * 6.0886 + 1.00 * 0.1438                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1279 = 9.78 * 0.50 * 5.9388 + 1.00 * 0.0895                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2343      final r-factor (work) = 0.2051          |
| start r-factor (free) = 0.2914      final r-factor (free) = 0.2591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8722 = 0.48 * 1.00 * 5.9388 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7581 = 0.48 * 1.00 * 5.7138 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.98   13.31    None  None   None       |
|    all(noH): 2823   0      0.00    83.98   13.31    None  None   None       |
|    Sol.    : 438    0      0.00    83.98   34.75    None  None   None       |
|    Mac.    : 2385   0      0.00    66.85   9.37     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 -   8.398: 1414   |   5:    41.992 -  50.390:   90        |
|      1:     8.398 -  16.797:  742   |   6:    50.390 -  58.788:   50        |
|      2:    16.797 -  25.195:  223   |   7:    58.788 -  67.187:   23        |
|      3:    25.195 -  33.593:  144   |   8:    67.187 -  75.585:    6        |
|      4:    33.593 -  41.992:  130   |   9:    75.585 -  83.983:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2051 r_free = 0.2591             target_work(ml) = 5.660         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2048 r_free = 0.2593             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2048   r_free= 0.2593   ksol= 0.33   Bsol= 50.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,3.88,5.94,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.659317                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2027   r_free= 0.2578   ksol= 0.33   Bsol= 59.24   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.82,2.06,3.89,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.660832                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.024802              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.364732              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.712  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2027      final r-factor (work) = 0.1573          |
| start r-factor (free) = 0.2578      final r-factor (free) = 0.2050          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7455 = 3.02 * 0.50 * 5.7232 + 1.00 * 0.0898                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4751 = 3.02 * 0.50 * 5.5616 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1573      final r-factor (work) = 0.1451          |
| start r-factor (free) = 0.2050      final r-factor (free) = 0.1971          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6022 = 1.36 * 1.00 * 5.5616 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3796 = 1.36 * 1.00 * 5.3959 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   14.28    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   14.28    None  None   None       |
|    Sol.    : 438    0      1.59    90.51   40.63    None  None   None       |
|    Mac.    : 2385   0      0.00    80.53   9.45     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 -   9.051: 1540   |   5:    45.257 -  54.308:   95        |
|      1:     9.051 -  18.103:  671   |   6:    54.308 -  63.359:   76        |
|      2:    18.103 -  27.154:  175   |   7:    63.359 -  72.411:   35        |
|      3:    27.154 -  36.205:  117   |   8:    72.411 -  81.462:   20        |
|      4:    36.205 -  45.257:   91   |   9:    81.462 -  90.513:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1451 r_free = 0.1971             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1450 r_free = 0.1971             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1971   ksol= 0.33   Bsol= 59.24   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.82,2.06,3.89,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.379572                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.1969   ksol= 0.32   Bsol= 59.24   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,1.56,3.39,0.00,0.00,0.00); trace/3= 2.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.378588                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.448708              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.136  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.533  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1449      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1969      final r-factor (free) = 0.1788          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3708 = 3.45 * 0.50 * 5.3974 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2538 = 3.45 * 0.50 * 5.3226 + 1.00 * 0.0758                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1260      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1788      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2638 = 0.23 * 1.00 * 5.3226 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2457 = 0.23 * 1.00 * 5.2643 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.13   13.40    None  None   None       |
|    all(noH): 2823   0      0.00    83.13   13.40    None  None   None       |
|    Sol.    : 438    0      2.26    83.13   37.27    None  None   None       |
|    Mac.    : 2385   0      0.00    78.02   9.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.313: 1504   |   5:    41.565 -  49.878:   94        |
|      1:     8.313 -  16.626:  700   |   6:    49.878 -  58.191:   65        |
|      2:    16.626 -  24.939:  191   |   7:    58.191 -  66.504:   32        |
|      3:    24.939 -  33.252:  116   |   8:    66.504 -  74.817:   21        |
|      4:    33.252 -  41.565:   92   |   9:    74.817 -  83.130:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1716             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1714             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1714   ksol= 0.32   Bsol= 59.24   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,1.56,3.39,0.00,0.00,0.00); trace/3= 2.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.240478                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1714   ksol= 0.32   Bsol= 56.71   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,1.46,3.24,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.767339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.796  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.222  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1240          |
| start r-factor (free) = 0.1714      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7270 = 1.77 * 0.50 * 5.2636 + 1.00 * 0.0758                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6909 = 1.77 * 0.50 * 5.2406 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8698 = 0.16 * 1.00 * 5.2406 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8773 = 0.16 * 1.00 * 5.2388 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.49   13.20    None  None   None       |
|    all(noH): 2823   0      0.00    81.49   13.20    None  None   None       |
|    Sol.    : 438    0      2.60    81.49   36.36    None  None   None       |
|    Mac.    : 2385   0      0.00    77.45   8.94     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 -   8.150: 1476   |   5:    40.747 -  48.897:   89        |
|      1:     8.150 -  16.299:  741   |   6:    48.897 -  57.046:   64        |
|      2:    16.299 -  24.448:  181   |   7:    57.046 -  65.196:   32        |
|      3:    24.448 -  32.598:  110   |   8:    65.196 -  73.345:   20        |
|      4:    32.598 -  40.747:  101   |   9:    73.345 -  81.495:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1243 r_free = 0.1689             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1687             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1687   ksol= 0.32   Bsol= 56.71   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,1.46,3.24,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.234507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.7361 0.99   1420  158 0.1024 0.1407      5.4149      5.6114|
|  2:  4.7361 -  3.7780 0.99   1373  155 0.0925 0.1147       5.499      5.6645|
|  3:  3.7780 -  3.3059 0.99   1340  142 0.1151 0.1639      5.5399      5.8518|
|  4:  3.3059 -  3.0062 0.99   1331  154 0.1352 0.1773      5.5216      5.6868|
|  5:  3.0062 -  2.7921 0.99   1338  150 0.1515 0.1840      5.4249      5.6276|
|  6:  2.7921 -  2.6284 0.99   1320  146 0.1385 0.2131      5.2925      5.5492|
|  7:  2.6284 -  2.4973 0.99   1312  136 0.1431 0.1746      5.2738      5.3881|
|  8:  2.4973 -  2.3890 0.98   1302  152 0.1334 0.1797      5.1648      5.3865|
|  9:  2.3890 -  2.2974 0.98   1303  149 0.1375 0.2049      5.1475      5.4158|
| 10:  2.2974 -  2.2183 1.00   1301  145 0.1276 0.1632      5.0327      5.1845|
| 11:  2.2183 -  2.1492 0.98   1310  137 0.1249 0.2055      5.0213       5.416|
| 12:  2.1492 -  2.0879 0.98   1287  145 0.1282 0.1785      4.9367      5.1722|
| 13:  2.0879 -  2.0331 0.98   1274  141 0.1280 0.1764      4.8644      5.0694|
| 14:  2.0331 -  1.9836 0.32    419   49 0.1202 0.1499      4.7745      4.8928|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2739 -  4.7361  1420   158  0.94   9.36   0.97     0.95       7621.96|
|  2:  4.7361 -  3.7780  1373   155  0.95   8.51   1.00     0.99       9972.86|
|  3:  3.7780 -  3.3059  1340   142  0.93  12.23   1.02     1.02      11669.63|
|  4:  3.3059 -  3.0062  1331   154  0.91  15.00   1.00     0.98      11464.20|
|  5:  3.0062 -  2.7921  1338   150  0.89  17.47   0.99     0.98       9712.78|
|  6:  2.7921 -  2.6284  1320   146  0.89  17.64   0.98     0.95       8167.23|
|  7:  2.6284 -  2.4973  1312   136  0.89  17.07   0.99     0.96       7411.47|
|  8:  2.4973 -  2.3890  1302   152  0.89  17.27   0.98     0.96       6265.95|
|  9:  2.3890 -  2.2974  1303   149  0.89  17.27   1.00     0.95       6005.98|
| 10:  2.2974 -  2.2183  1301   145  0.89  16.91   1.00     0.97       4948.68|
| 11:  2.2183 -  2.1492  1310   137  0.90  16.76   1.00     0.94       4843.29|
| 12:  2.1492 -  2.0879  1287   145  0.90  16.86   1.01     1.01       4368.20|
| 13:  2.0879 -  2.0331  1274   141  0.89  17.88   0.99     0.97       3855.80|
| 14:  2.0331 -  1.9836   419    49  0.91  15.83   0.98     0.95       3076.78|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3076.78 max =        11669.63 mean =      7345.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.34|
|phase err.(test): min =        0.00 max =           88.33 mean =        14.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1676   ksol= 0.32   Bsol= 60.75   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.73,1.03,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233797                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1676   ksol= 0.32   Bsol= 60.75   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.73,1.03,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233797                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.7361 0.99   1420  158 0.1033 0.1313      5.4065      5.5747|
|  2:  4.7361 -  3.7780 0.99   1373  155 0.0930 0.1133       5.496      5.6622|
|  3:  3.7780 -  3.3059 0.99   1340  142 0.1156 0.1643      5.5401      5.8546|
|  4:  3.3059 -  3.0062 0.99   1331  154 0.1352 0.1785      5.5226      5.6916|
|  5:  3.0062 -  2.7921 0.99   1338  150 0.1516 0.1839      5.4265       5.627|
|  6:  2.7921 -  2.6284 0.99   1320  146 0.1385 0.2128      5.2924      5.5485|
|  7:  2.6284 -  2.4973 0.99   1312  136 0.1432 0.1754      5.2744      5.3896|
|  8:  2.4973 -  2.3890 0.98   1302  152 0.1334 0.1796       5.165      5.3863|
|  9:  2.3890 -  2.2974 0.98   1303  149 0.1375 0.2051       5.147      5.4162|
| 10:  2.2974 -  2.2183 1.00   1301  145 0.1275 0.1630      5.0323      5.1847|
| 11:  2.2183 -  2.1492 0.98   1310  137 0.1250 0.2053      5.0214      5.4158|
| 12:  2.1492 -  2.0879 0.98   1287  145 0.1282 0.1785      4.9369      5.1722|
| 13:  2.0879 -  2.0331 0.98   1274  141 0.1279 0.1763      4.8642      5.0693|
| 14:  2.0331 -  1.9836 0.32    419   49 0.1202 0.1497      4.7741      4.8918|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2739 -  4.7361  1420   158  0.94   9.19   0.97     0.94       7149.45|
|  2:  4.7361 -  3.7780  1373   155  0.95   8.27   1.00     0.98       9608.21|
|  3:  3.7780 -  3.3059  1340   142  0.93  12.16   1.01     1.01      11562.01|
|  4:  3.3059 -  3.0062  1331   154  0.91  15.03   1.00     0.98      11499.64|
|  5:  3.0062 -  2.7921  1338   150  0.89  17.48   0.98     0.97       9736.55|
|  6:  2.7921 -  2.6284  1320   146  0.89  17.64   0.97     0.94       8176.50|
|  7:  2.6284 -  2.4973  1312   136  0.89  17.08   0.98     0.95       7416.73|
|  8:  2.4973 -  2.3890  1302   152  0.89  17.26   0.98     0.95       6274.75|
|  9:  2.3890 -  2.2974  1303   149  0.89  17.26   0.99     0.94       5999.67|
| 10:  2.2974 -  2.2183  1301   145  0.89  16.91   0.99     0.96       4949.89|
| 11:  2.2183 -  2.1492  1310   137  0.90  16.76   0.98     0.93       4844.20|
| 12:  2.1492 -  2.0879  1287   145  0.90  16.86   1.00     1.00       4370.92|
| 13:  2.0879 -  2.0331  1274   141  0.89  17.87   0.98     0.96       3853.85|
| 14:  2.0331 -  1.9836   419    49  0.91  15.81   0.97     0.94       3069.44|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3069.44 max =        11562.01 mean =      7276.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.30|
|phase err.(test): min =        0.00 max =           87.70 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.167)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.00    83.50   15.20    None  None   None       |
|    all(noH): 2823   0      2.00    83.50   15.20    None  None   None       |
|    Sol.    : 438    0      4.61    83.50   38.37    None  None   None       |
|    Mac.    : 2385   0      2.00    79.45   10.95    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:     2.004 -  10.153: 1476   |   5:    42.751 -  50.901:   89        |
|      1:    10.153 -  18.303:  741   |   6:    50.901 -  59.050:   64        |
|      2:    18.303 -  26.452:  181   |   7:    59.050 -  67.200:   32        |
|      3:    26.452 -  34.602:  110   |   8:    67.200 -  75.349:   20        |
|      4:    34.602 -  42.751:  101   |   9:    75.349 -  83.499:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.420 - 4.794
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 337
   mapped sites are within: 0.730 - 4.794

peak=   10.704 closest distance to " CB  VAL A 230 " =    1.481
peak=    7.208 closest distance to " CG2 VAL A 296 " =    1.206
peak=    6.704 closest distance to " CG  ARG A 138 " =    1.210
peak=    6.418 closest distance to " CD2 LEU A   5 " =    1.279
peak=    6.245 closest distance to " NH1 ARG A 138 " =    1.062
peak=    5.611 closest distance to " O   HOH Z 232 " =    2.260
peak=    5.545 closest distance to " CG  PRO A  54 " =    1.472
peak=    5.473 closest distance to " CG  LEU A   5 " =    1.271
peak=    5.399 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.274 closest distance to " NE2 GLN A  11 " =    1.148
peak=    5.124 closest distance to " O   HOH Z 142 " =    2.098
peak=    5.053 closest distance to " CG  PRO A 198 " =    1.339
peak=    4.900 closest distance to " CD  ARG A 138 " =    1.156
peak=    4.897 closest distance to " O   HOH Z 222 " =    1.308
peak=    4.869 closest distance to " CB  ASN A 148 " =    1.304
peak=    4.821 closest distance to " O   HOH Z 111 " =    1.860
peak=    4.782 closest distance to " CD1AILE A 234 " =    1.067
peak=    4.728 closest distance to " CB  PRO A  54 " =    1.064
peak=    4.720 closest distance to " O   HOH Z 369 " =    1.993
peak=    4.720 closest distance to " O   HOH Z 102 " =    1.057
peak=    4.717 closest distance to " CB  ASP A 124 " =    0.811
peak=    4.660 closest distance to " CG  LEU A 228 " =    1.213
peak=    4.604 closest distance to " CB  SER A  63 " =    1.275
peak=    4.571 closest distance to " CZ  PHE A 218 " =    1.093
peak=    4.545 closest distance to " O   HOH Z 287 " =    2.188
peak=    4.544 closest distance to " CG  LEU A 167 " =    1.267
peak=    4.516 closest distance to " CG  PRO A 243 " =    1.143
peak=    4.502 closest distance to " CB  GLN A 183 " =    1.176
peak=    4.494 closest distance to " O   HOH Z   7 " =    1.361
peak=    4.452 closest distance to " O   HOH Z 265 " =    2.102
peak=    4.448 closest distance to " O   HOH Z 298 " =    2.007
peak=    4.441 closest distance to " CB  VAL A 230 " =    1.301
peak=    4.415 closest distance to " CB  ASN A 142 " =    0.936
peak=    4.404 closest distance to " ND2 ASN A 187 " =    1.602
peak=    4.402 closest distance to " CB  VAL A 265 " =    1.365
peak=    4.347 closest distance to " O   HOH Z 183 " =    1.318
peak=    4.340 closest distance to " CD2 LEU A 228 " =    1.216
peak=    4.330 closest distance to " O   HOH Z   9 " =    1.757
peak=    4.324 closest distance to " O   PRO A 198 " =    1.574
peak=    4.312 closest distance to " CB  ASN A  39 " =    0.903
peak=    4.307 closest distance to " O   HOH Z 303 " =    2.238
peak=    4.297 closest distance to " O   HOH Z 272 " =    1.883
peak=    4.284 closest distance to " CG  PRO A 213 " =    1.347
peak=    4.274 closest distance to " O   HOH Z 427 " =    2.948
peak=    4.255 closest distance to " CA  VAL A 296 " =    1.111
peak=    4.237 closest distance to " CA  SER A  87 " =    0.870
peak=    4.213 closest distance to " CB  TRP A 266 " =    0.940
peak=    4.211 closest distance to " CB  SER A 210 " =    0.841
peak=    4.179 closest distance to " NH1AARG A 145 " =    1.201
peak=    4.139 closest distance to " O   HOH Z 368 " =    2.108
peak=    4.104 closest distance to " O   HOH Z 425 " =    1.505
peak=    4.082 closest distance to " CD  ARG A  66 " =    2.225
peak=    4.058 closest distance to " CD  ARG A 159 " =    0.759
peak=    4.058 closest distance to " CB  ARG A 275 " =    0.940
peak=    4.047 closest distance to " CB  VAL A 202 " =    1.555
peak=    4.024 closest distance to " O   HOH Z 410 " =    1.444
peak=    3.994 closest distance to " NH1 ARG A  56 " =    0.964
peak=    3.979 closest distance to " CB  SER A   3 " =    1.530
peak=    3.976 closest distance to " O   HOH Z 126 " =    1.991
peak=    3.964 closest distance to " O   HOH Z 184 " =    1.527
peak=    3.961 closest distance to " O   HOH Z 346 " =    1.605
peak=    3.961 closest distance to " O   HOH Z 261 " =    2.117
peak=    3.959 closest distance to " CD  ARG A 269 " =    0.947
peak=    3.941 closest distance to " CG1 ILE A 151 " =    1.245
peak=    3.923 closest distance to " O   TYR A 116 " =    1.202
peak=    3.905 closest distance to " O   HOH Z 316 " =    3.029
peak=    3.895 closest distance to " O   HOH Z 188 " =    3.078
peak=    3.891 closest distance to " CB  SER A 216 " =    0.906
peak=    3.887 closest distance to " O   HOH Z 423 " =    1.627
peak=    3.885 closest distance to " O   ASP A 132 " =    3.944
peak=    3.879 closest distance to " NE2 HIS A 207 " =    1.075
peak=    3.870 closest distance to " CA  ALA A  51 " =    1.016
peak=    3.868 closest distance to " NH2AARG A 190 " =    1.803
peak=    3.857 closest distance to " CB  ALA A 104 " =    0.796
peak=    3.845 closest distance to " CD1 LEU A 300 " =    1.134
peak=    3.837 closest distance to " O   HOH Z 353 " =    2.565
peak=    3.835 closest distance to " CA  ILE A 234 " =    0.967
peak=    3.816 closest distance to " O   HOH Z  88 " =    3.142
peak=    3.812 closest distance to " O   HOH Z 411 " =    3.332
peak=    3.789 closest distance to " ND1 HIS A  86 " =    1.758
peak=    3.788 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.782 closest distance to " O   HOH Z 126 " =    1.556
peak=    3.778 closest distance to " N   PHE A 130 " =    1.286
peak=    3.770 closest distance to " O   HOH Z 156 " =    2.850
peak=    3.762 closest distance to " O   HOH Z 158 " =    3.128
peak=    3.759 closest distance to " O   HOH Z 389 " =    1.954
peak=    3.752 closest distance to " CB  ARG A 138 " =    1.426
peak=    3.748 closest distance to " CA  PRO A  54 " =    1.374
peak=    3.747 closest distance to " CD  LYS A 166 " =    1.242
peak=    3.745 closest distance to " NH1 ARG A  14 " =    0.925
peak=    3.742 closest distance to " CG  GLN A  88 " =    1.012
peak=    3.740 closest distance to " O   HOH Z  44 " =    2.085
peak=    3.738 closest distance to " CB  GLU A  46 " =    0.948
peak=    3.736 closest distance to " CB  ARG A  79 " =    1.451
peak=    3.735 closest distance to " CZ  PHE A 192 " =    1.044
peak=    3.731 closest distance to " CB  ARG A 190 " =    1.618
peak=    3.718 closest distance to " O   HOH Z 290 " =    1.285
peak=    3.707 closest distance to " CB  SER A 212 " =    1.337
peak=    3.703 closest distance to " CG2 THR A 221 " =    1.011
peak=    3.701 closest distance to " O   HOH Z 294 " =    1.577
peak=    3.695 closest distance to " CB  ILE A 120 " =    1.207
peak=    3.693 closest distance to " N   SER A 271 " =    0.975
peak=    3.686 closest distance to " CZ3 TRP A 266 " =    1.090
peak=    3.683 closest distance to " CB AVAL A  41 " =    1.280
peak=    3.682 closest distance to " O   HOH Z   2 " =    1.698
peak=    3.676 closest distance to " CG BARG A 102 " =    1.930
peak=    3.675 closest distance to " O   HOH Z   1 " =    1.953
peak=    3.672 closest distance to " CB  GLN A 103 " =    1.059
peak=    3.672 closest distance to " O   HOH Z 258 " =    2.230
peak=    3.670 closest distance to " CB  LEU A 228 " =    1.183
peak=    3.647 closest distance to " CB  LEU A 143 " =    1.233
peak=    3.647 closest distance to " O   HOH Z 214 " =    2.064
peak=    3.639 closest distance to " O   HOH Z 193 " =    1.689
peak=    3.638 closest distance to " O   HOH Z 185 " =    1.912
peak=    3.634 closest distance to " O   HOH Z  30 " =    1.744
peak=    3.634 closest distance to " CG1 VAL A 153 " =    0.952
peak=    3.631 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.631 closest distance to " CB  ASN A 187 " =    1.079
peak=    3.627 closest distance to " O   HOH Z 193 " =    1.961
peak=    3.624 closest distance to " O   HOH Z  78 " =    1.587
peak=    3.620 closest distance to " O   HOH Z  10 " =    1.833
peak=    3.610 closest distance to " CB  LEU A  83 " =    0.781
peak=    3.607 closest distance to " CG1 ILE A  49 " =    1.587
peak=    3.604 closest distance to " CA  ALA A 295 " =    1.128
peak=    3.603 closest distance to " CB  GLU A 128 " =    1.038
peak=    3.603 closest distance to " O   HOH Z  57 " =    1.405
peak=    3.602 closest distance to " CA  ARG A 195 " =    1.205
peak=    3.599 closest distance to " CD1 ILE A  33 " =    1.878
peak=    3.597 closest distance to " CE  LYS A  76 " =    0.903
peak=    3.593 closest distance to " CE3 TRP A  85 " =    1.204
peak=    3.588 closest distance to " ND2 ASN A 249 " =    0.872
peak=    3.569 closest distance to " CD BLYS A 290 " =    1.034
peak=    3.566 closest distance to " CB  GLU A 277 " =    3.655
peak=    3.556 closest distance to " CZ  PHE A  38 " =    1.220
peak=    3.554 closest distance to " CA  ASP A 162 " =    0.863
peak=    3.545 closest distance to " CB  MET A  40 " =    0.807
peak=    3.544 closest distance to " CB  ASP A 140 " =    0.871
peak=    3.539 closest distance to " CE3 TRP A 274 " =    1.335
peak=    3.537 closest distance to " OG  SER A  62 " =    2.816
peak=    3.535 closest distance to " CG2 VAL A 257 " =    0.940
peak=    3.526 closest distance to " O   PRO A 198 " =    1.374
peak=    3.525 closest distance to " CA  LEU A 282 " =    0.953
peak=    3.523 closest distance to " NE AARG A 275 " =    1.470
peak=    3.522 closest distance to " CB  PRO A 243 " =    1.264
peak=    3.516 closest distance to " O   HOH Z 148 " =    2.328
peak=    3.513 closest distance to " NZ  LYS A 117 " =    3.155
peak=    3.511 closest distance to " CA  TYR A 116 " =    1.489
peak=    3.506 closest distance to " OE2 GLU A   2 " =    1.937
peak=    3.501 closest distance to " N   SER A 135 " =    1.265
peak=    3.497 closest distance to " O   HOH Z 171 " =    4.130
peak=    3.497 closest distance to " CG1 ILE A  33 " =    1.290
peak=    3.495 closest distance to " CB  LEU A 237 " =    0.852
peak=    3.492 closest distance to " O   HOH Z 285 " =    2.331
peak=    3.491 closest distance to " O   HOH Z 128 " =    2.183
peak=    3.483 closest distance to " O   HOH Z 437 " =    1.738
peak=    3.472 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.470 closest distance to " O   ASN A 209 " =    1.398
peak=    3.465 closest distance to " CA  ARG A 102 " =    1.178
peak=    3.465 closest distance to " O   HOH Z 406 " =    1.573
peak=    3.462 closest distance to " CD  GLN A 240 " =    1.660
peak=    3.461 closest distance to " CA  ARG A  36 " =    1.178
peak=    3.461 closest distance to " O   HOH Z 291 " =    1.655
peak=    3.459 closest distance to " NH2AARG A 145 " =    1.144
peak=    3.455 closest distance to " NE  ARG A  56 " =    3.604
peak=    3.447 closest distance to " CA  MET A  40 " =    1.108
peak=    3.446 closest distance to " O   HOH Z 359 " =    1.451
peak=    3.445 closest distance to " OH  TYR A 247 " =    1.114
peak=    3.443 closest distance to " CA  THR A 264 " =    0.785
peak=    3.442 closest distance to " O   HOH Z 180 " =    2.099
peak=    3.441 closest distance to " CD1 LEU A   5 " =    1.352
peak=    3.433 closest distance to " CA  ALA A 184 " =    1.078
peak=    3.433 closest distance to " O   HOH Z  68 " =    1.944
peak=    3.432 closest distance to " CB  ALA A  34 " =    1.047
peak=    3.431 closest distance to " O   HOH Z 332 " =    1.573
peak=    3.430 closest distance to " CA  TYR A  30 " =    0.985
peak=    3.429 closest distance to " OG  SER A 135 " =    1.272
peak=    3.425 closest distance to " O   HOH Z 380 " =    1.763
peak=    3.424 closest distance to " O   HOH Z 173 " =    1.784
peak=    3.424 closest distance to " CB  THR A  82 " =    1.317
peak=    3.423 closest distance to " CB  ASN A 173 " =    0.974
peak=    3.422 closest distance to " CA  ASN A 127 " =    1.116
peak=    3.418 closest distance to " CE1 TYR A 186 " =    1.422
peak=    3.415 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.412 closest distance to " CB  ASN A 110 " =    1.113
peak=    3.406 closest distance to " OH  TYR A 186 " =    1.008
peak=    3.401 closest distance to " CA  GLY A 267 " =    1.024
peak=    3.398 closest distance to " O   HOH Z 350 " =    1.718
peak=    3.394 closest distance to " CA  ILE A 106 " =    0.786
peak=    3.393 closest distance to " CA  ALA A  21 " =    1.148
peak=    3.390 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.388 closest distance to " CB  ALA A 242 " =    0.779
peak=    3.385 closest distance to " O   HOH Z  78 " =    2.524
peak=    3.384 closest distance to " O   SER A  87 " =    2.409
peak=    3.381 closest distance to " CB  ALA A 248 " =    1.085
peak=    3.381 closest distance to " OG  SER A 276 " =    1.177
peak=    3.381 closest distance to " O   HOH Z 148 " =    1.439
peak=    3.378 closest distance to " CA  ALA A 154 " =    1.084
peak=    3.375 closest distance to " O   HOH Z  80 " =    1.617
peak=    3.375 closest distance to " CG1 VAL A 296 " =    1.277
peak=    3.372 closest distance to " CA  ASN A 215 " =    1.157
peak=    3.370 closest distance to " N   ALA A 256 " =    1.172
peak=    3.365 closest distance to " CB  ALA A 160 " =    1.363
peak=    3.362 closest distance to " NH2BARG A 190 " =    1.499
peak=    3.360 closest distance to " CB  MET A  47 " =    0.986
peak=    3.351 closest distance to " CA  ALA A 160 " =    1.123
peak=    3.351 closest distance to " CD  ARG A  24 " =    1.199
peak=    3.350 closest distance to " O   HOH Z 109 " =    2.634
peak=    3.346 closest distance to " O   HOH Z  61 " =    1.645
peak=    3.346 closest distance to " O   HOH Z 172 " =    3.019
peak=    3.345 closest distance to " O   HOH Z   1 " =    1.948
peak=    3.344 closest distance to " O   HOH Z 435 " =    2.113
peak=    3.342 closest distance to " C   GLN A  88 " =    1.569
peak=    3.340 closest distance to " CA  ASN A 284 " =    0.801
peak=    3.339 closest distance to " CG  GLN A  89 " =    1.516
peak=    3.336 closest distance to " O   HOH Z 133 " =    2.546
peak=    3.336 closest distance to " O   HOH Z 211 " =    1.012
peak=    3.334 closest distance to " O   HOH Z 215 " =    1.414
peak=    3.330 closest distance to " CB  GLN A  89 " =    1.238
peak=    3.330 closest distance to " CA  ARG A 159 " =    1.269
peak=    3.329 closest distance to " O   HOH Z 313 " =    1.631
peak=    3.328 closest distance to " O   HOH Z 284 " =    3.141
peak=    3.324 closest distance to " O   ASP A 200 " =    1.561
peak=    3.319 closest distance to " O   HOH Z 368 " =    3.577
peak=    3.319 closest distance to " NE1 TRP A 274 " =    0.960
peak=    3.317 closest distance to " CB  ALA A 291 " =    1.063
peak=    3.316 closest distance to " O   HOH Z 215 " =    2.787
peak=    3.313 closest distance to " O   HOH Z 263 " =    1.644
peak=    3.311 closest distance to " CG2 ILE A 151 " =    0.737
peak=    3.311 closest distance to " CB  TRP A 150 " =    1.416
peak=    3.304 closest distance to " O   HOH Z 175 " =    3.740
peak=    3.304 closest distance to " O   HOH Z 235 " =    1.683
peak=    3.302 closest distance to " OG  SER A  62 " =    3.132
peak=    3.302 closest distance to " O   HOH Z  21 " =    1.801
peak=    3.302 closest distance to " CE3 TRP A 150 " =    0.979
peak=    3.301 closest distance to " O   HOH Z 326 " =    2.139
peak=    3.300 closest distance to " O   HOH Z 153 " =    3.761
peak=    3.296 closest distance to " CD  ARG A  14 " =    1.293
peak=    3.294 closest distance to " O   HOH Z 147 " =    1.674
peak=    3.287 closest distance to " O   HOH Z 409 " =    2.502
peak=    3.284 closest distance to " CB  TRP A 179 " =    1.364
peak=    3.283 closest distance to " CB  ALA A  10 " =    0.877
peak=    3.280 closest distance to " CB  SER A  62 " =    1.058
peak=    3.280 closest distance to " O   MET A 105 " =    1.729
peak=    3.280 closest distance to " CB  ALA A 114 " =    0.827
peak=    3.279 closest distance to " O   HOH Z 302 " =    1.806
peak=    3.277 closest distance to " O   HOH Z 185 " =    2.215
peak=    3.277 closest distance to " CG  PHE A 204 " =    1.029
peak=    3.276 closest distance to " O   THR A 294 " =    1.096
peak=    3.274 closest distance to " O   HOH Z 248 " =    1.778
peak=    3.271 closest distance to " O   HOH Z 130 " =    3.619
peak=    3.270 closest distance to " CG  MET A 185 " =    1.125
peak=    3.268 closest distance to " O   GLY A 203 " =    1.472
peak=    3.266 closest distance to " CD2 TRP A 179 " =    1.267
peak=    3.263 closest distance to " CG  GLU A  37 " =    0.826
peak=    3.251 closest distance to " O   HOH Z 196 " =    1.253
peak=    3.250 closest distance to " CB  SER A 273 " =    0.944
peak=    3.245 closest distance to " O   HOH Z  59 " =    1.824
peak=    3.244 closest distance to " CD1 ILE A 106 " =    0.900
peak=    3.243 closest distance to " CZ3 TRP A  92 " =    1.343
peak=    3.238 closest distance to " OD2 ASP A 286 " =    2.851
peak=    3.237 closest distance to " CA  TYR A 186 " =    1.574
peak=    3.236 closest distance to " CA  ALA A 291 " =    0.939
peak=    3.234 closest distance to " O   HOH Z 170 " =    1.119
peak=    3.230 closest distance to " OD1 ASN A 217 " =    1.518
peak=    3.229 closest distance to " CD1 LEU A 101 " =    1.141
peak=    3.228 closest distance to " O   PHE A 192 " =    1.358
peak=    3.226 closest distance to " O   HOH Z 424 " =    2.908
peak=    3.222 closest distance to " CB  VAL A 250 " =    1.093
peak=    3.219 closest distance to " O   HOH Z 124 " =    1.871
peak=    3.205 closest distance to " CG  ARG A 269 " =    1.708
peak=    3.205 closest distance to " CE2 PHE A  16 " =    1.083
peak=    3.205 closest distance to " CB  ALA A   1 " =    4.794
peak=    3.203 closest distance to " CA  GLU A 152 " =    0.972
peak=    3.203 closest distance to " CG2 ILE A 234 " =    1.095
peak=    3.201 closest distance to " O   HOH Z 200 " =    3.129
peak=    3.200 closest distance to " N   SER A  12 " =    1.588
peak=    3.198 closest distance to " ND1 HIS A  81 " =    1.834
peak=    3.195 closest distance to " CG AARG A 275 " =    1.291
peak=    3.191 closest distance to " N   ARG A 190 " =    1.074
peak=    3.191 closest distance to " O   ASN A  74 " =    1.598
peak=    3.185 closest distance to " O   HOH Z 392 " =    1.288
peak=    3.184 closest distance to " N   TYR A  15 " =    0.851
peak=    3.183 closest distance to " CG  MET A 113 " =    1.427
peak=    3.181 closest distance to " N   ALA A 291 " =    1.325
peak=    3.171 closest distance to " CD1 LEU A  96 " =    0.780
peak=    3.169 closest distance to " O   HOH Z 135 " =    2.010
peak=    3.169 closest distance to " O  BHOH Z  74 " =    1.369
peak=    3.169 closest distance to " CA  ALA A 158 " =    1.171
peak=    3.167 closest distance to " O   HOH Z 340 " =    2.123
peak=    3.166 closest distance to " CD1 LEU A 261 " =    1.259
peak=    3.162 closest distance to " CG  ARG A 159 " =    1.052
peak=    3.160 closest distance to " O   HOH Z  20 " =    1.867
peak=    3.157 closest distance to " OE2 GLU A  53 " =    2.131
peak=    3.156 closest distance to " CD  LYS A  76 " =    1.854
peak=    3.154 closest distance to " O   HOH Z 403 " =    1.566
peak=    3.150 closest distance to " CG2 VAL A 268 " =    0.976
peak=    3.150 closest distance to " CD2 TYR A 186 " =    1.183
peak=    3.149 closest distance to " CB  ALA A  43 " =    0.986
peak=    3.147 closest distance to " N   ASN A 127 " =    1.257
peak=    3.146 closest distance to " O   HOH Z 403 " =    1.327
peak=    3.145 closest distance to " OG1 THR A 279 " =    1.468
peak=    3.143 closest distance to " CB  LYS A 117 " =    1.225
peak=    3.142 closest distance to " O   HOH Z 273 " =    2.702
peak=    3.140 closest distance to " OG  SER A 206 " =    1.130
peak=    3.138 closest distance to " O   HOH Z 238 " =    3.586
peak=    3.136 closest distance to " OH  TYR A 214 " =    1.296
peak=    3.134 closest distance to " CE2 TYR A 186 " =    0.943
peak=    3.133 closest distance to " O   HOH Z  85 " =    2.040
peak=    3.133 closest distance to " O   HOH Z 126 " =    1.738
peak=    3.132 closest distance to " O   HOH Z 345 " =    3.496
peak=    3.129 closest distance to " O   HOH Z 352 " =    1.807
peak=    3.123 closest distance to " O   HOH Z 260 " =    1.490
peak=    3.122 closest distance to " N   ARG A 156 " =    1.366
peak=    3.121 closest distance to " O   HOH Z 110 " =    1.591
peak=    3.120 closest distance to " O   HOH Z 244 " =    1.759
peak=    3.117 closest distance to " OD1 ASN A  69 " =    2.544
peak=    3.116 closest distance to " CB  GLU A 175 " =    0.975
peak=    3.113 closest distance to " O   HOH Z 166 " =    3.724
peak=    3.107 closest distance to " CB  LEU A 300 " =    0.921
peak=    3.105 closest distance to " CB  LYS A 193 " =    1.141
peak=    3.102 closest distance to " N   ASN A  39 " =    1.149
peak=    3.099 closest distance to " O   CYS A 168 " =    1.315
peak=    3.090 closest distance to " CA  THR A 221 " =    0.867
peak=    3.087 closest distance to " CD2 LEU A 167 " =    1.028
peak=    3.082 closest distance to " CA  ARG A 139 " =    1.089
peak=    3.075 closest distance to " CG1AVAL A 121 " =    0.730
peak=    3.066 closest distance to " OG BSER A 212 " =    2.781
peak=    3.065 closest distance to " CE2 TYR A 293 " =    0.959
peak=    3.062 closest distance to " OG BSER A 134 " =    2.853
peak=    3.060 closest distance to " CE  MET A  93 " =    1.550
peak=    3.057 closest distance to " O   HOH Z 128 " =    1.449
peak=    3.032 closest distance to " O   PHE A  61 " =    1.431

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.507 - 5.531
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.719 - 5.531

peak=   -5.733 closest distance to " CG2 VAL A 230 " =    0.719
peak=   -5.247 closest distance to " CD  ARG A 138 " =    1.104
peak=   -4.372 closest distance to " O   HOH Z 231 " =    0.741
peak=   -4.337 closest distance to " O   PRO A 198 " =    1.184
peak=   -4.335 closest distance to " O   HOH Z 211 " =    0.876
peak=   -4.220 closest distance to " CG  ARG A 138 " =    0.851
peak=   -4.139 closest distance to " O   HOH Z 290 " =    1.147
peak=   -4.065 closest distance to " OE1 GLN A  88 " =    1.079
peak=   -4.054 closest distance to " O   HOH Z 231 " =    1.807
peak=   -4.053 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -4.050 closest distance to " CD  ARG A  14 " =    3.095
peak=   -3.971 closest distance to " CZ2 TRP A  92 " =    2.885
peak=   -3.963 closest distance to " CD  ARG A 156 " =    2.105
peak=   -3.949 closest distance to " CA  GLY A 241 " =    2.378
peak=   -3.945 closest distance to " CG  TRP A 266 " =    1.881
peak=   -3.907 closest distance to " N   THR A 157 " =    1.591
peak=   -3.894 closest distance to " O   HOH Z 102 " =    1.359
peak=   -3.882 closest distance to " CG  GLN A  88 " =    0.857
peak=   -3.877 closest distance to " O   GLY A 203 " =    2.485
peak=   -3.849 closest distance to " O   HOH Z 162 " =    2.607
peak=   -3.834 closest distance to " CG1 VAL A 296 " =    1.371
peak=   -3.832 closest distance to " OG  SER A  97 " =    2.286
peak=   -3.824 closest distance to " O   HOH Z 351 " =    1.396
peak=   -3.797 closest distance to " CD1 TYR A 247 " =    2.839
peak=   -3.796 closest distance to " O   HOH Z 394 " =    1.534
peak=   -3.780 closest distance to " OG BSER A 134 " =    1.462
peak=   -3.769 closest distance to " CB  TRP A  85 " =    2.558
peak=   -3.764 closest distance to " CG2 VAL A 296 " =    0.849
peak=   -3.755 closest distance to " CG2BVAL A  41 " =    2.535
peak=   -3.746 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.739 closest distance to " CB  ALA A  43 " =    2.587
peak=   -3.736 closest distance to " CA  ASP A  27 " =    2.448
peak=   -3.718 closest distance to " O   HOH Z 435 " =    2.871
peak=   -3.709 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.699 closest distance to " CD  GLN A 223 " =    2.343
peak=   -3.684 closest distance to " O   HOH Z 377 " =    0.757
peak=   -3.672 closest distance to " O   HOH Z  44 " =    2.333
peak=   -3.656 closest distance to " C   LEU A 222 " =    0.932
peak=   -3.637 closest distance to " CD2 LEU A   5 " =    0.980
peak=   -3.628 closest distance to " CA  GLY A 241 " =    3.128
peak=   -3.625 closest distance to " O   HOH Z 275 " =    1.848
peak=   -3.624 closest distance to " CZ  PHE A  38 " =    2.599
peak=   -3.621 closest distance to " CB  VAL A 230 " =    1.033
peak=   -3.612 closest distance to " O   HOH Z 166 " =    2.008
peak=   -3.611 closest distance to " O   PRO A 163 " =    1.958
peak=   -3.599 closest distance to " O   VAL A 189 " =    2.485
peak=   -3.599 closest distance to " O   HOH Z 108 " =    1.365
peak=   -3.594 closest distance to " O   HOH Z 166 " =    2.239
peak=   -3.594 closest distance to " CB  PRO A 163 " =    2.458
peak=   -3.590 closest distance to " O   GLY A  17 " =    1.356
peak=   -3.577 closest distance to " CB  ALA A 161 " =    2.665
peak=   -3.567 closest distance to " O   HOH Z  38 " =    1.362
peak=   -3.564 closest distance to " OG BSER A 134 " =    1.969
peak=   -3.555 closest distance to " CB  ALA A 248 " =    2.116
peak=   -3.554 closest distance to " N   ALA A  43 " =    2.461
peak=   -3.553 closest distance to " O   HOH Z 111 " =    1.821
peak=   -3.552 closest distance to " O   HOH Z 411 " =    5.211
peak=   -3.529 closest distance to " CB  PHE A 130 " =    1.287
peak=   -3.526 closest distance to " CE2 TYR A  30 " =    2.829
peak=   -3.523 closest distance to " CZ3 TRP A 179 " =    1.139
peak=   -3.522 closest distance to " O   GLU A  53 " =    1.563
peak=   -3.519 closest distance to " O   HOH Z 185 " =    2.235
peak=   -3.514 closest distance to " CD1 LEU A 228 " =    2.417
peak=   -3.513 closest distance to " C   ALA A 158 " =    1.426
peak=   -3.509 closest distance to " OE1 GLU A  44 " =    0.821
peak=   -3.508 closest distance to " CE3 TRP A 150 " =    2.332
peak=   -3.505 closest distance to " CG  LEU A   5 " =    0.914
peak=   -3.490 closest distance to " O   GLY A 211 " =    1.272
peak=   -3.488 closest distance to " CD2 TYR A 293 " =    1.861
peak=   -3.482 closest distance to " CG1 VAL A 265 " =    2.472
peak=   -3.481 closest distance to " CG1 VAL A 112 " =    2.593
peak=   -3.480 closest distance to " CB  VAL A 296 " =    1.016
peak=   -3.474 closest distance to " CA  GLY A  98 " =    1.995
peak=   -3.455 closest distance to " ND2 ASN A  60 " =    1.641
peak=   -3.452 closest distance to " CD  GLN A  58 " =    0.792
peak=   -3.440 closest distance to " O   HOH Z  60 " =    2.525
peak=   -3.438 closest distance to " O   HOH Z 359 " =    3.110
peak=   -3.433 closest distance to " O   LEU A 101 " =    2.900
peak=   -3.429 closest distance to " CD  LYS A 289 " =    2.457
peak=   -3.429 closest distance to " O   HOH Z 241 " =    1.252
peak=   -3.421 closest distance to " O   HOH Z  51 " =    1.011
peak=   -3.416 closest distance to " O   ASP A  27 " =    1.777
peak=   -3.416 closest distance to " CB  ALA A   9 " =    2.545
peak=   -3.414 closest distance to " O   HOH Z 216 " =    1.297
peak=   -3.412 closest distance to " O   ILE A  49 " =    1.741
peak=   -3.411 closest distance to " O   HOH Z 407 " =    3.175
peak=   -3.410 closest distance to " OG  SER A  87 " =    1.514
peak=   -3.406 closest distance to " OH  TYR A 172 " =    1.768
peak=   -3.403 closest distance to " O   HOH Z  43 " =    1.646
peak=   -3.397 closest distance to " CE1 TYR A 169 " =    2.626
peak=   -3.394 closest distance to " O   HOH Z 118 " =    1.392
peak=   -3.392 closest distance to " CB  PHE A 192 " =    1.766
peak=   -3.389 closest distance to " CG2AVAL A  41 " =    2.848
peak=   -3.382 closest distance to " CG1 VAL A 250 " =    2.755
peak=   -3.382 closest distance to " O   HOH Z 118 " =    1.229
peak=   -3.381 closest distance to " O   HOH Z 201 " =    1.654
peak=   -3.373 closest distance to " C   ASN A 285 " =    2.470
peak=   -3.370 closest distance to " CG  GLU A  53 " =    1.353
peak=   -3.364 closest distance to " OG  SER A  63 " =    1.034
peak=   -3.364 closest distance to " O   HOH Z 281 " =    2.703
peak=   -3.364 closest distance to " O   HOH Z 389 " =    2.158
peak=   -3.364 closest distance to " CB  ALA A 248 " =    2.484
peak=   -3.361 closest distance to " O   HOH Z 359 " =    1.600
peak=   -3.357 closest distance to " CG  ASP A 231 " =    0.739
peak=   -3.354 closest distance to " CA  GLY A 203 " =    2.520
peak=   -3.350 closest distance to " C   SER A  22 " =    2.337
peak=   -3.346 closest distance to " O   HOH Z 380 " =    1.123
peak=   -3.344 closest distance to " CG2 VAL A 202 " =    2.817
peak=   -3.343 closest distance to " CE BMET A  47 " =    1.566
peak=   -3.340 closest distance to " CD1 ILE A  33 " =    2.548
peak=   -3.339 closest distance to " O   HOH Z 377 " =    1.275
peak=   -3.335 closest distance to " CG2 VAL A 296 " =    1.639
peak=   -3.331 closest distance to " NH2AARG A 275 " =    5.531
peak=   -3.328 closest distance to " O   GLY A  80 " =    2.569
peak=   -3.321 closest distance to " O   HOH Z 100 " =    1.024
peak=   -3.321 closest distance to " CD  GLU A 277 " =    1.272
peak=   -3.319 closest distance to " O   HOH Z 251 " =    4.845
peak=   -3.317 closest distance to " C   MET A 188 " =    1.441
peak=   -3.316 closest distance to " C   GLU A 236 " =    0.891
peak=   -3.311 closest distance to " O   HOH Z 390 " =    2.288
peak=   -3.310 closest distance to " O   SER A 271 " =    2.309
peak=   -3.309 closest distance to " CG  LEU A 228 " =    0.896
peak=   -3.304 closest distance to " C   PHE A  59 " =    1.124
peak=   -3.303 closest distance to " C   LYS A  76 " =    1.320
peak=   -3.302 closest distance to " CB  TYR A  15 " =    2.158
peak=   -3.292 closest distance to " O   HOH Z  60 " =    1.670
peak=   -3.290 closest distance to " C   GLY A  13 " =    0.857
peak=   -3.289 closest distance to " O   HOH Z  63 " =    1.751
peak=   -3.287 closest distance to " O   HOH Z 353 " =    2.043
peak=   -3.277 closest distance to " O   HOH Z 350 " =    1.679
peak=   -3.272 closest distance to " O   HOH Z 412 " =    4.527
peak=   -3.272 closest distance to " CD  PRO A 213 " =    2.076
peak=   -3.268 closest distance to " O   HOH Z  73 " =    1.993
peak=   -3.266 closest distance to " OG1 THR A 246 " =    1.430
peak=   -3.263 closest distance to " CG  LEU A 101 " =    2.562
peak=   -3.261 closest distance to " N   ASP A 270 " =    1.504
peak=   -3.259 closest distance to " O   HOH Z 295 " =    1.548
peak=   -3.258 closest distance to " O   HOH Z 131 " =    4.077
peak=   -3.255 closest distance to " CB  ALA A 114 " =    2.451
peak=   -3.247 closest distance to " OG  SER A 206 " =    1.739
peak=   -3.245 closest distance to " CE2 TRP A  70 " =    2.395
peak=   -3.242 closest distance to " NZ  LYS A 166 " =    1.123
peak=   -3.242 closest distance to " NE2 GLN A  88 " =    0.901
peak=   -3.239 closest distance to " N   ALA A 226 " =    2.094
peak=   -3.236 closest distance to " CA  VAL A 296 " =    1.043
peak=   -3.230 closest distance to " CA  SER A 135 " =    1.325
peak=   -3.228 closest distance to " CG1 VAL A 112 " =    3.175
peak=   -3.223 closest distance to " CD  GLN A  77 " =    1.099
peak=   -3.221 closest distance to " O   HOH Z 133 " =    1.427
peak=   -3.221 closest distance to " O   HOH Z 177 " =    1.913
peak=   -3.219 closest distance to " CG1 VAL A 125 " =    1.792
peak=   -3.217 closest distance to " OD2 ASP A  50 " =    2.070
peak=   -3.217 closest distance to " O   HOH Z 275 " =    1.499
peak=   -3.216 closest distance to " CB  ASP A 132 " =    2.383
peak=   -3.214 closest distance to " O   HOH Z  11 " =    1.895
peak=   -3.213 closest distance to " CZ  PHE A 130 " =    1.079
peak=   -3.212 closest distance to " O   HOH Z  52 " =    1.625
peak=   -3.205 closest distance to " O   HOH Z 286 " =    1.661
peak=   -3.202 closest distance to " CD  PRO A 243 " =    1.991
peak=   -3.199 closest distance to " CB  ASP A 200 " =    2.722
peak=   -3.199 closest distance to " N   ASP A 191 " =    1.143
peak=   -3.192 closest distance to " CB  CYS A 254 " =    2.016
peak=   -3.192 closest distance to " CB  HIS A  86 " =    1.107
peak=   -3.192 closest distance to " CE  LYS A  76 " =    2.657
peak=   -3.191 closest distance to " CB  ALA A 227 " =    2.435
peak=   -3.191 closest distance to " ND2 ASN A  45 " =    1.168
peak=   -3.191 closest distance to " O   HOH Z 282 " =    4.945
peak=   -3.188 closest distance to " N   SER A 212 " =    1.858
peak=   -3.187 closest distance to " CD1 ILE A 239 " =    2.217
peak=   -3.186 closest distance to " O   ARG A 145 " =    1.435
peak=   -3.178 closest distance to " O   HOH Z 144 " =    1.526
peak=   -3.173 closest distance to " O   HOH Z 112 " =    1.351
peak=   -3.171 closest distance to " O   GLY A 196 " =    1.272
peak=   -3.168 closest distance to " O   HOH Z 145 " =    1.565
peak=   -3.167 closest distance to " OG ASER A 134 " =    1.583
peak=   -3.163 closest distance to " O   SER A  22 " =    2.269
peak=   -3.157 closest distance to " O   HOH Z 389 " =    1.513
peak=   -3.153 closest distance to " CG  LEU A 167 " =    0.809
peak=   -3.152 closest distance to " CG2 VAL A 112 " =    2.528
peak=   -3.145 closest distance to " O   HOH Z  65 " =    1.165
peak=   -3.143 closest distance to " O   HOH Z 114 " =    1.783
peak=   -3.138 closest distance to " CB  PRO A  54 " =    2.563
peak=   -3.136 closest distance to " CE3 TRP A  70 " =    1.737
peak=   -3.130 closest distance to " CG  PRO A 163 " =    2.598
peak=   -3.129 closest distance to " O   SER A 164 " =    1.867
peak=   -3.128 closest distance to " O   TYR A  30 " =    2.489
peak=   -3.124 closest distance to " O   HOH Z 313 " =    1.454
peak=   -3.123 closest distance to " O   HOH Z 389 " =    4.726
peak=   -3.120 closest distance to " CD2 HIS A 207 " =    2.422
peak=   -3.118 closest distance to " O   HOH Z 371 " =    1.402
peak=   -3.116 closest distance to " OD1 ASN A  60 " =    0.825
peak=   -3.110 closest distance to " CG1 VAL A  67 " =    2.908
peak=   -3.105 closest distance to " CB  HIS A  81 " =    1.039
peak=   -3.105 closest distance to " O   HOH Z   2 " =    2.032
peak=   -3.094 closest distance to " O   HOH Z 166 " =    1.374
peak=   -3.093 closest distance to " O   VAL A 121 " =    1.126
peak=   -3.085 closest distance to " O   HOH Z  32 " =    1.922
peak=   -3.084 closest distance to " CE2 PHE A 218 " =    2.533
peak=   -3.083 closest distance to " OH  TYR A 247 " =    2.139
peak=   -3.074 closest distance to " CD1 PHE A  61 " =    1.431
peak=   -3.071 closest distance to " CD2 TYR A 169 " =    2.090
peak=   -3.064 closest distance to " O   HOH Z 118 " =    1.212
peak=   -3.063 closest distance to " NE2 GLN A 240 " =    1.586
peak=   -3.061 closest distance to " NH2 ARG A 219 " =    1.794
peak=   -3.061 closest distance to " CA  GLY A 133 " =    2.225
peak=   -3.059 closest distance to " CD1 ILE A 199 " =    2.667
peak=   -3.050 closest distance to " OD2 ASP A 140 " =    1.131

================= 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    :  0.4837 0.4681   6.283545e+00   6.264302e+00
   1_bss:  0.4757 0.4588   6.278275e+00   6.258170e+00
   1_xyz:  0.3908 0.4051   6.161265e+00   6.184915e+00
   1_adp:  0.3416 0.3935   6.076030e+00   6.161148e+00
   1_occ:  0.3411 0.3938   6.075352e+00   6.161537e+00
   2_bss:  0.3387 0.3905   6.075803e+00   6.160094e+00
   2_xyz:  0.2343 0.2914   5.773124e+00   5.934713e+00
   2_adp:  0.2051 0.2591   5.659892e+00   5.837191e+00
   2_occ:  0.2048 0.2593   5.659317e+00   5.837053e+00
   3_bss:  0.2027 0.2578   5.660832e+00   5.836960e+00
   3_xyz:  0.1573 0.2050   5.432509e+00   5.633864e+00
   3_adp:  0.1451 0.1971   5.379807e+00   5.598678e+00
   3_occ:  0.1450 0.1971   5.379572e+00   5.598534e+00
   4_bss:  0.1449 0.1969   5.378588e+00   5.597515e+00
   4_xyz:  0.1260 0.1788   5.265454e+00   5.505199e+00
   4_adp:  0.1247 0.1716   5.241126e+00   5.467034e+00
   4_occ:  0.1246 0.1714   5.240478e+00   5.466605e+00
   5_bss:  0.1246 0.1714   5.240450e+00   5.466621e+00
   5_xyz:  0.1240 0.1694   5.236168e+00   5.458616e+00
   5_adp:  0.1243 0.1689   5.235117e+00   5.453666e+00
   5_occ:  0.1242 0.1687   5.234507e+00   5.452981e+00
   5_bss:  0.1245 0.1676   5.233797e+00   5.450405e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.350  50.000   8.357   7.356   9.231   0.000   0.000   0.000
   1_xyz:  0.350  50.000   8.357   7.356   9.231   0.000   0.000   0.000
   1_adp:  0.350  50.000   8.357   7.356   9.231   0.000   0.000   0.000
   1_occ:  0.350  50.000   8.357   7.356   9.231   0.000   0.000   0.000
   2_bss:  0.332  50.000   5.138   3.880   5.939   0.000   0.000   0.000
   2_xyz:  0.332  50.000   5.138   3.880   5.939   0.000   0.000   0.000
   2_adp:  0.332  50.000   5.138   3.880   5.939   0.000   0.000   0.000
   2_occ:  0.332  50.000   5.138   3.880   5.939   0.000   0.000   0.000
   3_bss:  0.332  59.244   2.817   2.058   3.893   0.000   0.000   0.000
   3_xyz:  0.332  59.244   2.817   2.058   3.893   0.000   0.000   0.000
   3_adp:  0.332  59.244   2.817   2.058   3.893   0.000   0.000   0.000
   3_occ:  0.332  59.244   2.817   2.058   3.893   0.000   0.000   0.000
   4_bss:  0.325  59.244   2.117   1.563   3.391   0.000   0.000   0.000
   4_xyz:  0.325  59.244   2.117   1.563   3.391   0.000   0.000   0.000
   4_adp:  0.325  59.244   2.117   1.563   3.391   0.000   0.000   0.000
   4_occ:  0.325  59.244   2.117   1.563   3.391   0.000   0.000   0.000
   5_bss:  0.322  56.710   1.940   1.461   3.243   0.000   0.000   0.000
   5_xyz:  0.322  56.710   1.940   1.461   3.243   0.000   0.000   0.000
   5_adp:  0.322  56.710   1.940   1.461   3.243   0.000   0.000   0.000
   5_occ:  0.322  56.710   1.940   1.461   3.243   0.000   0.000   0.000
   5_bss:  0.323  60.754  -0.299  -0.731   1.030   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.938 0.4459  0.5181    67531.270
   1_bss:  56.118 0.4426  0.6567    66530.355
   1_xyz:  46.895 0.5577  0.7985    48255.044
   1_adp:  43.735 0.5970  0.9043    44400.945
   1_occ:  43.803 0.5961  0.9020    44473.595
   2_bss:  43.597 0.5984  0.8073    44147.168
   2_xyz:  30.317 0.7528  0.9759    22444.225
   2_adp:  26.104 0.7998  1.0062    17596.748
   2_occ:  26.100 0.7998  1.0056    17562.647
   3_bss:  26.080 0.8002  0.9354    17620.741
   3_xyz:  19.706 0.8643  0.9827    10776.018
   3_adp:  18.871 0.8724  0.9831    10082.219
   3_occ:  18.868 0.8724  0.9829    10077.205
   4_bss:  18.850 0.8725  0.9629    10046.084
   4_xyz:  16.701 0.8918  0.9727     8116.466
   4_adp:  15.760 0.9004  0.9742     7573.256
   4_occ:  15.760 0.9004  0.9741     7551.699
   5_bss:  15.760 0.9004  0.9692     7550.235
   5_xyz:  15.456 0.9034  0.9694     7410.218
   5_adp:  15.300 0.9050  0.9694     7361.196
   5_occ:  15.287 0.9051  0.9695     7345.392
   5_bss:  15.245 0.9053  0.9623     7276.540
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4296e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4296e+01
   1_xyz:   1.708  0.014  0.109 18.264  0.006  4.110   1.4377e-01
   1_adp:   1.708  0.014  0.109 18.264  0.006  4.110   1.4377e-01
   1_occ:   1.708  0.014  0.109 18.264  0.006  4.110   1.4377e-01
   2_bss:   1.708  0.014  0.109 18.264  0.006  4.110   1.4377e-01
   2_xyz:   1.228  0.010  0.089 16.681  0.005  4.132   8.9460e-02
   2_adp:   1.228  0.010  0.089 16.681  0.005  4.132   8.9460e-02
   2_occ:   1.228  0.010  0.089 16.681  0.005  4.132   8.9460e-02
   3_bss:   1.228  0.010  0.089 16.681  0.005  4.132   8.9460e-02
   3_xyz:   1.020  0.007  0.078 15.832  0.003  4.129   6.3732e-02
   3_adp:   1.020  0.007  0.078 15.832  0.003  4.129   6.3732e-02
   3_occ:   1.020  0.007  0.078 15.832  0.003  4.129   6.3732e-02
   4_bss:   1.020  0.007  0.078 15.832  0.003  4.129   6.3732e-02
   4_xyz:   1.112  0.010  0.086 15.745  0.004  4.114   7.5756e-02
   4_adp:   1.112  0.010  0.086 15.745  0.004  4.114   7.5756e-02
   4_occ:   1.112  0.010  0.086 15.745  0.004  4.114   7.5756e-02
   5_bss:   1.112  0.010  0.086 15.745  0.004  4.114   7.5756e-02
   5_xyz:   0.972  0.007  0.076 15.426  0.003  4.115   6.0000e-02
   5_adp:   0.972  0.007  0.076 15.426  0.003  4.115   6.0000e-02
   5_occ:   0.972  0.007  0.076 15.426  0.003  4.115   6.0000e-02
   5_bss:   0.972  0.007  0.076 15.426  0.003  4.115   6.0000e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0399e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0399e+00
   1_xyz:  14.283  0.173  0.433 85.554  0.039  2.274   1.0518e-01
   1_adp:  14.283  0.173  0.433 85.554  0.039  2.274   1.0518e-01
   1_occ:  14.283  0.173  0.433 85.554  0.039  2.274   1.0518e-01
   2_bss:  14.283  0.173  0.433 85.554  0.039  2.274   1.0518e-01
   2_xyz:   7.067  0.081  0.274 86.796  0.045  2.122   5.9127e-02
   2_adp:   7.067  0.081  0.274 86.796  0.045  2.122   5.9127e-02
   2_occ:   7.067  0.081  0.274 86.796  0.045  2.122   5.9127e-02
   3_bss:   7.067  0.081  0.274 86.796  0.045  2.122   5.9127e-02
   3_xyz:   8.486  0.055  0.365 86.263  0.027  2.379   4.7389e-02
   3_adp:   8.486  0.055  0.365 86.263  0.027  2.379   4.7389e-02
   3_occ:   8.486  0.055  0.365 86.263  0.027  2.379   4.7389e-02
   4_bss:   8.486  0.055  0.365 86.263  0.027  2.379   4.7389e-02
   4_xyz:   8.603  0.073  0.492 82.968  0.040  2.319   5.6030e-02
   4_adp:   8.603  0.073  0.492 82.968  0.040  2.319   5.6030e-02
   4_occ:   8.603  0.073  0.492 82.968  0.040  2.319   5.6030e-02
   5_bss:   8.603  0.073  0.492 82.968  0.040  2.319   5.6030e-02
   5_xyz:   8.240  0.051  0.383 83.703  0.039  2.391   3.6261e-02
   5_adp:   8.240  0.051  0.383 83.703  0.039  2.391   3.6261e-02
   5_occ:   8.240  0.051  0.383 83.703  0.039  2.391   3.6261e-02
   5_bss:   8.240  0.051  0.383 83.703  0.039  2.391   3.6261e-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:  83.30   0.00  13.97  65.05   0.00  11.16  83.30   0.00  29.30
   1_occ:  83.30   0.00  13.97  65.05   0.00  11.16  83.30   0.00  29.30
   2_bss:  83.30   0.00  13.97  65.05   0.00  11.16  83.30   0.00  29.30
   2_xyz:  83.30   0.00  13.97  65.05   0.00  11.16  83.30   0.00  29.30
   2_adp:  83.98   0.00  13.31  66.85   0.00   9.37  83.98   0.00  34.75
   2_occ:  83.98   0.00  13.31  66.85   0.00   9.37  83.98   0.00  34.75
   3_bss:  83.98   0.00  13.31  66.85   0.00   9.37  83.98   0.00  34.75
   3_xyz:  83.98   0.00  13.31  66.85   0.00   9.37  83.98   0.00  34.75
   3_adp:  90.51   0.00  14.28  80.53   0.00   9.45  90.51   1.59  40.63
   3_occ:  90.51   0.00  14.28  80.53   0.00   9.45  90.51   1.59  40.63
   4_bss:  90.51   0.00  14.28  80.53   0.00   9.45  90.51   1.59  40.63
   4_xyz:  90.51   0.00  14.28  80.53   0.00   9.45  90.51   1.59  40.63
   4_adp:  83.13   0.00  13.40  78.02   0.00   9.01  83.13   2.26  37.27
   4_occ:  83.13   0.00  13.40  78.02   0.00   9.01  83.13   2.26  37.27
   5_bss:  83.13   0.00  13.40  78.02   0.00   9.01  83.13   2.26  37.27
   5_xyz:  83.13   0.00  13.40  78.02   0.00   9.01  83.13   2.26  37.27
   5_adp:  81.49   0.00  13.20  77.45   0.00   8.94  81.49   2.60  36.36
   5_occ:  81.49   0.00  13.20  77.45   0.00   8.94  81.49   2.60  36.36
   5_bss:  83.50   2.00  15.20  79.45   2.00  10.95  83.50   4.61  38.37
------------------------------------------------------------------------
 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:    1.240    0.016    0.411
   1_adp:    1.240    0.016    0.411
   1_occ:    1.240    0.016    0.411
   2_bss:    1.240    0.016    0.411
   2_xyz:    1.495    0.046    0.601
   2_adp:    1.495    0.046    0.601
   2_occ:    1.495    0.046    0.601
   3_bss:    1.495    0.046    0.601
   3_xyz:    1.541    0.045    0.660
   3_adp:    1.541    0.045    0.660
   3_occ:    1.541    0.045    0.660
   4_bss:    1.541    0.045    0.660
   4_xyz:    1.700    0.018    0.698
   4_adp:    1.700    0.018    0.698
   4_occ:    1.700    0.018    0.698
   5_bss:    1.700    0.018    0.698
   5_xyz:    1.811    0.073    0.709
   5_adp:    1.811    0.073    0.709
   5_occ:    1.811    0.073    0.709
   5_bss:    1.811    0.073    0.709
------------------------------------------------------------------------

CPU time actual refinement: 353.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/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_1130/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1130/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.77 
  Macro-tasks:
    bulk solvent and scale       = 37.59  
    individual site refinement   = 146.97 
    weights calculation          = 32.81  
    collect and process          = 6.65   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 224.12 
  Micro-tasks:
    mask                            = 2.28   
    f_calc                          = 115.98 
    alpha_beta                      = 8.64   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 120.80 
    fmodel                         = 6.86   
    r_factors                      = 0.23   
    phase_errors                   = 11.48  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 267.74 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.971 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    665 calls, 115.61 s
gradients_fft:          610 calls, 109.35 s

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

# Date 2008-01-16 Time 03:15:57 PST -0800 (1200482157.84 s)
Start R-work = 0.4837, R-free = 0.4681 (no bulk solvent and anisotropic scale)
Final R-work = 0.1410, R-free = 0.1853 (no bulk solvent and anisotropic scale)

Start R-work = 0.4757, R-free = 0.4588
Final R-work = 0.1245, R-free = 0.1676