# Date 2008-01-16 Time 01:56:46 PST -0800 (1200477406.21 s)
#phil __OFF__

Command line arguments: "../622.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22888
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 622

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.96301
Completeness in resolution range: 0.946374
Completeness with d_max=infinity: 0.943548

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   1.9630

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.96301
Completeness in resolution range: 0.946374
Completeness with d_max=infinity: 0.943548

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2012 [2174/2199]  1954   220  10.1%
  bin  2:  4.2012 -  3.3468 [2089/2109]  1884   205   9.8%
  bin  3:  3.3468 -  2.9273 [2072/2091]  1864   208  10.0%
  bin  4:  2.9273 -  2.6612 [2030/2060]  1824   206  10.1%
  bin  5:  2.6612 -  2.4714 [2025/2044]  1829   196   9.7%
  bin  6:  2.4714 -  2.3262 [2021/2046]  1814   207  10.2%
  bin  7:  2.3262 -  2.2101 [2010/2038]  1807   203  10.1%
  bin  8:  2.2101 -  2.1142 [1997/2033]  1798   199  10.0%
  bin  9:  2.1142 -  2.0330 [1993/2035]  1797   196   9.8%
  bin 10:  2.0330 -  1.9630 [1178/2044]  1059   119  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/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: 36
        2.42 -     3.04: 2218
        3.04 -     3.66: 4747
        3.66 -     4.28: 9107
        4.28 -     4.90: 12377
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.826 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.004 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28480 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_622/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.9914 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4739   r_free= 0.4671   ksol= 0.00   Bsol= 0.00   scale= 0.799    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.280639                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6862 0.99   1410  156 0.4047 0.3897      6.6049      6.6257|
|  2:  4.6862 -  3.7385 0.99   1361  153 0.3931 0.3585      6.7937       6.712|
|  3:  3.7385 -  3.2715 0.99   1329  142 0.4175 0.3691       6.654      6.6243|
|  4:  3.2715 -  2.9749 0.99   1329  152 0.4626 0.4517      6.5321      6.4958|
|  5:  2.9749 -  2.7631 0.99   1316  148 0.5049 0.5033      6.3595      6.3823|
|  6:  2.7631 -  2.6011 0.99   1313  144 0.5078 0.5484      6.2777      6.2235|
|  7:  2.6011 -  2.4714 0.99   1297  140 0.5106 0.5032      6.2446      6.1867|
|  8:  2.4714 -  2.3642 0.98   1288  146 0.5214 0.4890      6.1775      6.1879|
|  9:  2.3642 -  2.2735 0.98   1291  148 0.5173 0.5357      6.1155      6.1677|
| 10:  2.2735 -  2.1953 1.00   1290  144 0.5247 0.5261      6.1033      6.0717|
| 11:  2.1953 -  2.1269 0.98   1307  138 0.5013 0.4955      6.0341      6.0365|
| 12:  2.1269 -  2.0663 0.98   1262  142 0.5126 0.5547       5.954      6.0265|
| 13:  2.0663 -  2.0120 0.99   1284  141 0.5323 0.5261      5.8786      5.7965|
| 14:  2.0120 -  1.9630 0.42    553   65 0.5593 0.5275      5.8938       5.827|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.6862  1410   156  0.68  36.22   0.79     0.74      78673.64|
|  2:  4.6862 -  3.7385  1361   153  0.72  33.10   0.87     0.80      97894.80|
|  3:  3.7385 -  3.2715  1329   142  0.63  41.10   0.87     0.75     103235.85|
|  4:  3.2715 -  2.9749  1329   152  0.54  48.86   0.80     0.63      94580.28|
|  5:  2.9749 -  2.7631  1316   148  0.42  58.39   0.74     0.51      82621.01|
|  6:  2.7631 -  2.6011  1313   144  0.38  61.19   0.72     0.44      72782.45|
|  7:  2.6011 -  2.4714  1297   140  0.34  64.68   0.75     0.40      68664.46|
|  8:  2.4714 -  2.3642  1288   146  0.32  66.17   0.73     0.38      62251.31|
|  9:  2.3642 -  2.2735  1291   148  0.34  64.74   0.73     0.40      55584.91|
| 10:  2.2735 -  2.1953  1290   144  0.36  62.87   0.75     0.43      47439.00|
| 11:  2.1953 -  2.1269  1307   138  0.36  63.00   0.79     0.45      46209.80|
| 12:  2.1269 -  2.0663  1262   142  0.31  66.97   0.77     0.40      44165.60|
| 13:  2.0663 -  2.0120  1284   141  0.28  69.19   0.72     0.37      39519.41|
| 14:  2.0120 -  1.9630   553    65  0.33  65.41   0.71     0.38      30818.79|
|alpha:            min =        0.37 max =            0.80 mean =         0.51|
|beta:             min =    30818.79 max =       103235.85 mean =     67922.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.64|
|phase err.(test): min =        0.00 max =           89.97 mean =        56.90|
|-----------------------------------------------------------------------------|

============================== 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 = 14.665190             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.303   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.276773              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.100   (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:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1519 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2656 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3970 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5114 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6582 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7758 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.468 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.036 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4812   r_free= 0.4703   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.283017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4662   r_free= 0.4532   ksol= 0.38   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.49,10.05,7.95,0.00,0.00,0.00); trace/3= 8.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.275090                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.955295             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.624   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.154792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.715   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4662      final r-factor (work) = 0.3846          |
| start r-factor (free) = 0.4532      final r-factor (free) = 0.4067          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.9862 = 11.96 * 0.50 * 6.2765 + 1.00 * 53.4677                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1510 = 11.96 * 0.50 * 6.1919 + 1.00 * 0.1378                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3846      final r-factor (work) = 0.3367          |
| start r-factor (free) = 0.4067      final r-factor (free) = 0.3947          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1648 = 1.15 * 1.00 * 6.1919 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0720 = 1.15 * 1.00 * 6.1099 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.70   13.38    None  None   None       |
|    all(noH): 2823   0      0.00    77.70   13.38    None  None   None       |
|    Sol.    : 438    0      0.00    77.70   24.80    None  None   None       |
|    Mac.    : 2385   0      0.00    67.86   11.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.770: 1119   |   5:    38.850 -  46.620:   68        |
|      1:     7.770 -  15.540:  784   |   6:    46.620 -  54.390:   31        |
|      2:    15.540 -  23.310:  431   |   7:    54.390 -  62.160:   19        |
|      3:    23.310 -  31.080:  240   |   8:    62.160 -  69.930:    4        |
|      4:    31.080 -  38.850:  126   |   9:    69.930 -  77.700:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3367 r_free = 0.3947             target_work(ml) = 6.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3364 r_free = 0.3942             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3364   r_free= 0.3942   ksol= 0.38   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.49,10.05,7.95,0.00,0.00,0.00); trace/3= 8.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.094235                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3343   r_free= 0.3897   ksol= 0.37   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,6.12,4.96,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.095546                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.891351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.450  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.603082              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3343      final r-factor (work) = 0.2675          |
| start r-factor (free) = 0.3897      final r-factor (free) = 0.3278          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2347 = 7.89 * 0.50 * 6.1072 + 1.00 * 0.1378                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7487 = 7.89 * 0.50 * 5.9969 + 1.00 * 0.0868                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2675      final r-factor (work) = 0.2466          |
| start r-factor (free) = 0.3278      final r-factor (free) = 0.3150          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6329 = 0.60 * 1.00 * 5.9969 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5501 = 0.60 * 1.00 * 5.8651 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.78   13.39    None  None   None       |
|    all(noH): 2823   0      0.00    82.78   13.39    None  None   None       |
|    Sol.    : 438    0      0.00    82.78   30.39    None  None   None       |
|    Mac.    : 2385   0      0.00    67.18   10.27    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 -   8.278: 1281   |   5:    41.392 -  49.671:   53        |
|      1:     8.278 -  16.557:  745   |   6:    49.671 -  57.949:   35        |
|      2:    16.557 -  24.835:  337   |   7:    57.949 -  66.227:   11        |
|      3:    24.835 -  33.114:  218   |   8:    66.227 -  74.506:    2        |
|      4:    33.114 -  41.392:  140   |   9:    74.506 -  82.784:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2466 r_free = 0.3150             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2463 r_free = 0.3151             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2463   r_free= 0.3151   ksol= 0.37   Bsol= 50.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,6.12,4.96,0.00,0.00,0.00); trace/3= 4.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.843798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2446   r_free= 0.3126   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.21,3.54,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.842339                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.161052              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.872727              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.687  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2446      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3126      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2919 = 4.16 * 0.50 * 5.8664 + 1.00 * 0.0868                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9910 = 4.16 * 0.50 * 5.7294 + 1.00 * 0.0708                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1650          |
| start r-factor (free) = 0.2436      final r-factor (free) = 0.2255          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.4721 = 2.87 * 1.00 * 5.7294 + 1.00 * 0.0130                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9003 = 2.87 * 1.00 * 5.5289 + 1.00 * 0.0172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.59   14.59    None  None   None       |
|    all(noH): 2823   0      0.00    94.59   14.59    None  None   None       |
|    Sol.    : 438    0      1.76    93.00   40.49    None  None   None       |
|    Mac.    : 2385   0      0.00    94.59   9.83     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 -   9.459: 1561   |   5:    47.294 -  56.752:   98        |
|      1:     9.459 -  18.917:  623   |   6:    56.752 -  66.211:   50        |
|      2:    18.917 -  28.376:  192   |   7:    66.211 -  75.670:   30        |
|      3:    28.376 -  37.835:  136   |   8:    75.670 -  85.128:   11        |
|      4:    37.835 -  47.294:  116   |   9:    85.128 -  94.587:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1650 r_free = 0.2255             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1649 r_free = 0.2252             target_work(ml) = 5.488         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2252   ksol= 0.34   Bsol= 50.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.21,3.54,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.488167                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1647   r_free= 0.2246   ksol= 0.33   Bsol= 54.31   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.02,3.16,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.485868                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.547680              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680623              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.336  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2246      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8811 = 3.55 * 0.50 * 5.5305 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6609 = 3.55 * 0.50 * 5.4091 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6988 = 0.68 * 1.00 * 5.4091 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3866 = 0.68 * 1.00 * 5.3188 + 1.00 * 0.7665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.75   14.47    None  None   None       |
|    all(noH): 2823   0      0.00    94.75   14.47    None  None   None       |
|    Sol.    : 438    0      2.35    92.94   40.43    None  None   None       |
|    Mac.    : 2385   0      0.00    94.75   9.71     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 -   9.475: 1595   |   5:    47.376 -  56.852:   96        |
|      1:     9.475 -  18.951:  601   |   6:    56.852 -  66.327:   51        |
|      2:    18.951 -  28.426:  183   |   7:    66.327 -  75.802:   29        |
|      3:    28.426 -  37.901:  132   |   8:    75.802 -  85.278:   11        |
|      4:    37.901 -  47.376:  119   |   9:    85.278 -  94.753:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1323 r_free = 0.1891             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1322 r_free = 0.1890             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1322   r_free= 0.1890   ksol= 0.33   Bsol= 54.31   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.02,3.16,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305046                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1886   ksol= 0.32   Bsol= 49.42   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.78,3.18,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.304883                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.479198              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.847  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 11.872759             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.903   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1802          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3189 = 3.48 * 0.50 * 5.3190 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2523 = 3.48 * 0.50 * 5.2805 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1802      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 62.7129 = 11.87 * 1.00 * 5.2805 + 1.00 * 0.0187                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 62.1645 = 11.87 * 1.00 * 5.2345 + 1.00 * 0.0164                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.29  14.01    None  None   None       |
|    all(noH): 2823   0      0.00    105.29  14.01    None  None   None       |
|    Sol.    : 438    0      2.01    105.29  40.41    None  None   None       |
|    Mac.    : 2385   0      0.00    104.13  9.16     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 -  10.529: 1802   |   5:    52.645 -  63.174:   78        |
|      1:    10.529 -  21.058:  498   |   6:    63.174 -  73.703:   44        |
|      2:    21.058 -  31.587:  161   |   7:    73.703 -  84.232:   18        |
|      3:    31.587 -  42.116:  117   |   8:    84.232 -  94.761:    9        |
|      4:    42.116 -  52.645:   94   |   9:    94.761 - 105.290:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1723             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1722             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1722   ksol= 0.32   Bsol= 49.42   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.78,3.18,0.00,0.00,0.00); trace/3= 2.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209785                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6862 0.99   1410  156 0.0946 0.1296      5.3579      5.5787|
|  2:  4.6862 -  3.7385 0.99   1361  153 0.0849 0.1208      5.4459      5.6775|
|  3:  3.7385 -  3.2715 0.99   1329  142 0.1102 0.1538      5.5198      5.8722|
|  4:  3.2715 -  2.9749 0.99   1329  152 0.1298 0.1918      5.5127      5.7015|
|  5:  2.9749 -  2.7631 0.99   1316  148 0.1380 0.1866      5.3755      5.6392|
|  6:  2.7631 -  2.6011 0.99   1313  144 0.1278 0.2067      5.2564      5.5589|
|  7:  2.6011 -  2.4714 0.99   1297  140 0.1340 0.1784      5.2272      5.3868|
|  8:  2.4714 -  2.3642 0.98   1288  146 0.1283 0.1803      5.1583      5.4058|
|  9:  2.3642 -  2.2735 0.98   1291  148 0.1290 0.1934       5.117       5.401|
| 10:  2.2735 -  2.1953 1.00   1290  144 0.1210 0.1930      5.0339      5.3006|
| 11:  2.1953 -  2.1269 0.98   1307  138 0.1217 0.2062      5.0374      5.3823|
| 12:  2.1269 -  2.0663 0.98   1262  142 0.1237 0.1913      4.9638      5.2863|
| 13:  2.0663 -  2.0120 0.99   1284  141 0.1208 0.1883      4.8648      5.0995|
| 14:  2.0120 -  1.9630 0.42    553   65 0.1094 0.1554      4.7488      4.9159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.6862  1410   156  0.94   9.42   0.98     0.95       7392.56|
|  2:  4.6862 -  3.7385  1361   153  0.95   8.46   1.03     1.01       9765.26|
|  3:  3.7385 -  3.2715  1329   142  0.92  12.46   1.05     1.04      11756.19|
|  4:  3.2715 -  2.9749  1329   152  0.90  15.69   1.03     1.00      12206.95|
|  5:  2.9749 -  2.7631  1316   148  0.89  17.22   1.01     0.99       9572.27|
|  6:  2.7631 -  2.6011  1313   144  0.88  17.95   0.99     0.95       8091.28|
|  7:  2.6011 -  2.4714  1297   140  0.89  16.96   1.00     0.96       7194.17|
|  8:  2.4714 -  2.3642  1288   146  0.89  17.41   1.00     0.98       6580.62|
|  9:  2.3642 -  2.2735  1291   148  0.89  17.46   1.00     0.95       6085.99|
| 10:  2.2735 -  2.1953  1290   144  0.88  18.21   1.01     0.96       5409.76|
| 11:  2.1953 -  2.1269  1307   138  0.88  18.40   1.00     0.95       5520.31|
| 12:  2.1269 -  2.0663  1262   142  0.88  18.26   1.01     1.00       4964.72|
| 13:  2.0663 -  2.0120  1284   141  0.88  18.87   1.01     0.98       4111.28|
| 14:  2.0120 -  1.9630   553    65  0.91  15.40   0.99     0.96       3103.63|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3103.63 max =        12206.95 mean =      7481.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.81|
|phase err.(test): min =        0.00 max =           89.30 mean =        15.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1722   ksol= 0.32   Bsol= 51.69   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.56,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1722   ksol= 0.32   Bsol= 51.69   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.46,-0.56,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209629                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.6862 0.99   1410  156 0.0946 0.1297      5.3584      5.5797|
|  2:  4.6862 -  3.7385 0.99   1361  153 0.0850 0.1208      5.4465      5.6778|
|  3:  3.7385 -  3.2715 0.99   1329  142 0.1102 0.1538      5.5201      5.8726|
|  4:  3.2715 -  2.9749 0.99   1329  152 0.1298 0.1917      5.5125      5.7012|
|  5:  2.9749 -  2.7631 0.99   1316  148 0.1380 0.1865       5.375      5.6384|
|  6:  2.7631 -  2.6011 0.99   1313  144 0.1277 0.2066      5.2558      5.5582|
|  7:  2.6011 -  2.4714 0.99   1297  140 0.1340 0.1787       5.227      5.3878|
|  8:  2.4714 -  2.3642 0.98   1288  146 0.1283 0.1801      5.1582      5.4048|
|  9:  2.3642 -  2.2735 0.98   1291  148 0.1290 0.1928      5.1166      5.4001|
| 10:  2.2735 -  2.1953 1.00   1290  144 0.1210 0.1931      5.0338      5.3021|
| 11:  2.1953 -  2.1269 0.98   1307  138 0.1216 0.2064      5.0376      5.3831|
| 12:  2.1269 -  2.0663 0.98   1262  142 0.1236 0.1911      4.9637      5.2865|
| 13:  2.0663 -  2.0120 0.99   1284  141 0.1207 0.1876      4.8639      5.0971|
| 14:  2.0120 -  1.9630 0.42    553   65 0.1092 0.1551      4.7468       4.914|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.6862  1410   156  0.94   9.43   0.98     0.95       7400.79|
|  2:  4.6862 -  3.7385  1361   153  0.95   8.47   1.03     1.01       9777.29|
|  3:  3.7385 -  3.2715  1329   142  0.92  12.47   1.05     1.04      11770.91|
|  4:  3.2715 -  2.9749  1329   152  0.90  15.69   1.03     1.01      12197.72|
|  5:  2.9749 -  2.7631  1316   148  0.89  17.20   1.01     0.99       9555.91|
|  6:  2.7631 -  2.6011  1313   144  0.88  17.94   0.99     0.95       8083.52|
|  7:  2.6011 -  2.4714  1297   140  0.89  16.96   1.00     0.97       7190.30|
|  8:  2.4714 -  2.3642  1288   146  0.89  17.41   1.00     0.99       6577.99|
|  9:  2.3642 -  2.2735  1291   148  0.89  17.45   1.00     0.95       6082.50|
| 10:  2.2735 -  2.1953  1290   144  0.88  18.22   1.01     0.96       5414.99|
| 11:  2.1953 -  2.1269  1307   138  0.88  18.43   1.00     0.95       5530.97|
| 12:  2.1269 -  2.0663  1262   142  0.88  18.27   1.02     1.01       4967.41|
| 13:  2.0663 -  2.0120  1284   141  0.88  18.85   1.01     0.98       4101.79|
| 14:  2.0120 -  1.9630   553    65  0.91  15.34   0.99     0.97       3085.90|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3085.90 max =        12197.72 mean =      7481.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.81|
|phase err.(test): min =        0.00 max =           89.31 mean =        15.16|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.699)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.27    107.56  16.28    None  None   None       |
|    all(noH): 2823   0      2.27    107.56  16.28    None  None   None       |
|    Sol.    : 438    0      4.28    107.56  42.68    None  None   None       |
|    Mac.    : 2385   0      2.27    106.41  11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.273 -  12.802: 1802   |   5:    54.918 -  65.447:   78        |
|      1:    12.802 -  23.331:  498   |   6:    65.447 -  75.976:   44        |
|      2:    23.331 -  33.860:  161   |   7:    75.976 -  86.505:   18        |
|      3:    33.860 -  44.389:  117   |   8:    86.505 -  97.034:    9        |
|      4:    44.389 -  54.918:   94   |   9:    97.034 - 107.563:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.279 - 5.180
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 332
   mapped sites are within: 0.724 - 5.180

peak=    9.928 closest distance to " CB  VAL A 230 " =    1.436
peak=    8.462 closest distance to " CG2 VAL A 296 " =    1.320
peak=    8.279 closest distance to " O   HOH Z 130 " =    1.770
peak=    6.520 closest distance to " CD2 LEU A   5 " =    1.270
peak=    6.237 closest distance to " NE2 GLN A  11 " =    1.163
peak=    6.189 closest distance to " CG  ARG A 138 " =    1.055
peak=    6.161 closest distance to " O   HOH Z  65 " =    1.510
peak=    5.566 closest distance to " CG  PRO A  54 " =    1.399
peak=    5.521 closest distance to " NH2 ARG A  56 " =    2.088
peak=    5.385 closest distance to " O   HOH Z 142 " =    2.009
peak=    5.365 closest distance to " O   HOH Z   9 " =    1.815
peak=    5.146 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.130 closest distance to " O   HOH Z 427 " =    2.434
peak=    5.051 closest distance to " CB  VAL A 230 " =    1.163
peak=    4.985 closest distance to " CB  PRO A  54 " =    1.064
peak=    4.985 closest distance to " O   HOH Z 232 " =    2.255
peak=    4.922 closest distance to " CD1AILE A 234 " =    1.004
peak=    4.914 closest distance to " O   HOH Z 424 " =    1.177
peak=    4.902 closest distance to " NH1 ARG A 138 " =    1.017
peak=    4.808 closest distance to " O   HOH Z 417 " =    1.587
peak=    4.796 closest distance to " CG  LEU A   5 " =    1.152
peak=    4.744 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.706 closest distance to " O   HOH Z 425 " =    1.586
peak=    4.670 closest distance to " O   HOH Z 375 " =    1.033
peak=    4.651 closest distance to " O   HOH Z   7 " =    1.505
peak=    4.646 closest distance to " O   HOH Z   2 " =    1.766
peak=    4.627 closest distance to " O   HOH Z 222 " =    1.241
peak=    4.586 closest distance to " O   HOH Z 126 " =    2.066
peak=    4.549 closest distance to " O   HOH Z 369 " =    2.119
peak=    4.499 closest distance to " O   HOH Z 112 " =    1.143
peak=    4.446 closest distance to " O   HOH Z 127 " =    1.089
peak=    4.431 closest distance to " O   HOH Z  91 " =    2.441
peak=    4.414 closest distance to " O   HOH Z 209 " =    2.345
peak=    4.376 closest distance to " O   HOH Z 124 " =    1.382
peak=    4.325 closest distance to " O   HOH Z  78 " =    1.633
peak=    4.320 closest distance to " O   HOH Z 380 " =    2.091
peak=    4.310 closest distance to " O   HOH Z 316 " =    2.972
peak=    4.288 closest distance to " CB  ARG A 275 " =    1.012
peak=    4.257 closest distance to " O   HOH Z  63 " =    1.554
peak=    4.242 closest distance to " CG  LEU A 167 " =    1.299
peak=    4.232 closest distance to " O   HOH Z 298 " =    1.776
peak=    4.205 closest distance to " CB  SER A   3 " =    1.419
peak=    4.202 closest distance to " O   HOH Z 287 " =    1.879
peak=    4.179 closest distance to " O   HOH Z  59 " =    1.617
peak=    4.176 closest distance to " O   HOH Z 418 " =    0.959
peak=    4.150 closest distance to " O   HOH Z 133 " =    1.426
peak=    4.149 closest distance to " CB  SER A  63 " =    1.281
peak=    4.141 closest distance to " CB  GLN A 223 " =    1.553
peak=    4.139 closest distance to " O   HOH Z  24 " =    1.905
peak=    4.129 closest distance to " CD2 LEU A 228 " =    1.302
peak=    4.125 closest distance to " O   HOH Z  61 " =    1.613
peak=    4.121 closest distance to " O   HOH Z 423 " =    1.692
peak=    4.096 closest distance to " O   HOH Z 214 " =    2.183
peak=    4.070 closest distance to " O   HOH Z 346 " =    1.623
peak=    4.069 closest distance to " O   HOH Z 272 " =    1.796
peak=    4.068 closest distance to " CB  ASN A 148 " =    1.405
peak=    4.019 closest distance to " CH2 TRP A 266 " =    1.037
peak=    4.008 closest distance to " O   HOH Z 225 " =    1.568
peak=    4.002 closest distance to " CG  LYS A  76 " =    1.722
peak=    3.999 closest distance to " O   HOH Z 419 " =    2.125
peak=    3.990 closest distance to " O   HOH Z   1 " =    1.814
peak=    3.987 closest distance to " O   HOH Z 389 " =    1.332
peak=    3.980 closest distance to " O   HOH Z 371 " =    2.785
peak=    3.964 closest distance to " CB  VAL A 202 " =    1.672
peak=    3.950 closest distance to " CB  ASN A  39 " =    1.008
peak=    3.949 closest distance to " O   HOH Z 422 " =    2.569
peak=    3.946 closest distance to " O   HOH Z 425 " =    2.056
peak=    3.940 closest distance to " CB  GLU A 128 " =    1.121
peak=    3.938 closest distance to " O   HOH Z 410 " =    1.465
peak=    3.937 closest distance to " O   HOH Z 193 " =    1.797
peak=    3.927 closest distance to " CB  GLU A 277 " =    3.536
peak=    3.922 closest distance to " O   HOH Z 158 " =    3.030
peak=    3.918 closest distance to " O   HOH Z 290 " =    0.989
peak=    3.904 closest distance to " O   HOH Z 368 " =    3.658
peak=    3.899 closest distance to " O   HOH Z 352 " =    1.705
peak=    3.899 closest distance to " CB  SER A 216 " =    0.952
peak=    3.887 closest distance to " O   HOH Z 366 " =    3.121
peak=    3.880 closest distance to " O   HOH Z 139 " =    1.140
peak=    3.874 closest distance to " CA  PHE A 283 " =    1.425
peak=    3.869 closest distance to " CB  TRP A 266 " =    1.087
peak=    3.866 closest distance to " O   HOH Z 234 " =    3.624
peak=    3.862 closest distance to " OG  SER A  62 " =    3.043
peak=    3.834 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.824 closest distance to " CB  VAL A 296 " =    1.111
peak=    3.811 closest distance to " O   HOH Z 405 " =    1.419
peak=    3.808 closest distance to " O   HOH Z  68 " =    2.097
peak=    3.807 closest distance to " O   HOH Z 327 " =    1.570
peak=    3.807 closest distance to " CG  TRP A 179 " =    2.304
peak=    3.796 closest distance to " CB  LEU A 228 " =    1.298
peak=    3.795 closest distance to " CB BVAL A  41 " =    1.195
peak=    3.784 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.778 closest distance to " CG  PRO A 213 " =    1.202
peak=    3.777 closest distance to " CB  TRP A 179 " =    1.428
peak=    3.765 closest distance to " NH1AARG A 145 " =    1.123
peak=    3.760 closest distance to " CG BARG A 102 " =    1.977
peak=    3.751 closest distance to " O   HOH Z  39 " =    1.267
peak=    3.746 closest distance to " O   PRO A 198 " =    1.253
peak=    3.731 closest distance to " CA  ASN A 127 " =    1.115
peak=    3.720 closest distance to " O   PRO A 198 " =    1.521
peak=    3.718 closest distance to " O   HOH Z 392 " =    1.247
peak=    3.718 closest distance to " O   HOH Z  78 " =    1.861
peak=    3.712 closest distance to " N   GLN A 278 " =    1.266
peak=    3.709 closest distance to " O   HOH Z 133 " =    2.538
peak=    3.708 closest distance to " O   HOH Z 195 " =    1.404
peak=    3.702 closest distance to " O   HOH Z 361 " =    1.257
peak=    3.698 closest distance to " O   HOH Z 130 " =    2.364
peak=    3.698 closest distance to " CB  SER A 276 " =    1.163
peak=    3.688 closest distance to " OG  SER A  62 " =    2.746
peak=    3.671 closest distance to " CG  GLN A  89 " =    1.381
peak=    3.665 closest distance to " O   HOH Z 145 " =    2.563
peak=    3.664 closest distance to " CA  ASN A 215 " =    1.207
peak=    3.664 closest distance to " N   ASN A 127 " =    1.394
peak=    3.654 closest distance to " OE1 GLN A 240 " =    1.535
peak=    3.651 closest distance to " O   HOH Z  59 " =    2.076
peak=    3.642 closest distance to " O   HOH Z 222 " =    1.978
peak=    3.634 closest distance to " O   HOH Z 146 " =    1.635
peak=    3.630 closest distance to " O   HOH Z 359 " =    1.130
peak=    3.628 closest distance to " CA  TYR A  30 " =    0.976
peak=    3.626 closest distance to " O   HOH Z 411 " =    3.633
peak=    3.620 closest distance to " CB  ASP A 124 " =    0.924
peak=    3.611 closest distance to " CE3 TRP A 150 " =    1.042
peak=    3.599 closest distance to " O   HOH Z 167 " =    1.864
peak=    3.595 closest distance to " O   HOH Z 362 " =    2.024
peak=    3.591 closest distance to " O   HOH Z 375 " =    2.412
peak=    3.589 closest distance to " O   HOH Z  88 " =    3.480
peak=    3.587 closest distance to " CD1 LEU A   5 " =    1.487
peak=    3.582 closest distance to " N   TYR A  15 " =    1.031
peak=    3.577 closest distance to " CB  VAL A 265 " =    1.335
peak=    3.572 closest distance to " O   HOH Z  97 " =    1.968
peak=    3.563 closest distance to " O   HOH Z 384 " =    1.308
peak=    3.555 closest distance to " CB  MET A  40 " =    0.941
peak=    3.555 closest distance to " CB  ALA A 114 " =    1.497
peak=    3.554 closest distance to " NZ  LYS A 117 " =    3.020
peak=    3.552 closest distance to " CB  LEU A 237 " =    0.855
peak=    3.548 closest distance to " O   HOH Z   1 " =    1.699
peak=    3.546 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.542 closest distance to " O   HOH Z 145 " =    1.998
peak=    3.539 closest distance to " O   HOH Z  55 " =    1.999
peak=    3.538 closest distance to " NE2 GLN A  58 " =    3.920
peak=    3.535 closest distance to " O   HOH Z  10 " =    1.731
peak=    3.533 closest distance to " O   HOH Z  88 " =    2.961
peak=    3.529 closest distance to " O   HOH Z 236 " =    1.651
peak=    3.529 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.524 closest distance to " CA  ARG A 195 " =    1.366
peak=    3.522 closest distance to " CG2 VAL A 257 " =    0.861
peak=    3.520 closest distance to " O   HOH Z 133 " =    2.539
peak=    3.517 closest distance to " O   HOH Z  51 " =    1.356
peak=    3.517 closest distance to " OG BSER A  99 " =    2.145
peak=    3.515 closest distance to " O   HOH Z 184 " =    1.424
peak=    3.514 closest distance to " O   HOH Z 189 " =    2.709
peak=    3.509 closest distance to " O   HOH Z 438 " =    2.090
peak=    3.505 closest distance to " O   HOH Z 258 " =    2.112
peak=    3.504 closest distance to " CB  GLU A 152 " =    1.358
peak=    3.501 closest distance to " CG  PRO A 198 " =    1.203
peak=    3.500 closest distance to " CG2 THR A 221 " =    1.214
peak=    3.499 closest distance to " O   HOH Z  76 " =    0.962
peak=    3.497 closest distance to " O   HOH Z 122 " =    2.069
peak=    3.496 closest distance to " CB  GLN A  88 " =    1.370
peak=    3.491 closest distance to " ND2 ASN A 110 " =    1.803
peak=    3.491 closest distance to " N   PHE A 130 " =    1.282
peak=    3.488 closest distance to " OG BSER A 212 " =    2.921
peak=    3.483 closest distance to " O   HOH Z 368 " =    1.909
peak=    3.481 closest distance to " O   HOH Z 233 " =    1.786
peak=    3.478 closest distance to " N   GLU A   2 " =    1.384
peak=    3.478 closest distance to " CB  GLU A 236 " =    1.237
peak=    3.478 closest distance to " O   HOH Z  22 " =    2.118
peak=    3.476 closest distance to " O   HOH Z 424 " =    2.320
peak=    3.470 closest distance to " CD  ARG A 159 " =    0.738
peak=    3.468 closest distance to " CB  ASN A 215 " =    1.219
peak=    3.466 closest distance to " CE  LYS A  76 " =    0.874
peak=    3.465 closest distance to " O   HOH Z 128 " =    1.865
peak=    3.465 closest distance to " CD1 LEU A 281 " =    1.050
peak=    3.463 closest distance to " O   HOH Z 414 " =    1.091
peak=    3.462 closest distance to " CB  MET A  47 " =    1.195
peak=    3.451 closest distance to " O   HOH Z 323 " =    1.591
peak=    3.448 closest distance to " CZ3 TRP A  92 " =    1.158
peak=    3.447 closest distance to " O   HOH Z 175 " =    2.127
peak=    3.445 closest distance to " NH2AARG A 190 " =    1.725
peak=    3.444 closest distance to " O   HOH Z 213 " =    2.159
peak=    3.444 closest distance to " CB  ILE A 234 " =    1.161
peak=    3.428 closest distance to " CG  GLN A  88 " =    1.139
peak=    3.428 closest distance to " O   HOH Z   3 " =    2.131
peak=    3.425 closest distance to " O   HOH Z 154 " =    1.895
peak=    3.424 closest distance to " O   HOH Z 126 " =    1.604
peak=    3.424 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.417 closest distance to " NH2BARG A 145 " =    1.964
peak=    3.413 closest distance to " O   HOH Z 193 " =    1.560
peak=    3.405 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.401 closest distance to " O   THR A 294 " =    1.027
peak=    3.397 closest distance to " ND2 ASN A 249 " =    0.779
peak=    3.395 closest distance to " OE2 GLU A  53 " =    1.833
peak=    3.394 closest distance to " CG2 ILE A 234 " =    0.978
peak=    3.394 closest distance to " CE AMET A  47 " =    1.407
peak=    3.394 closest distance to " O   ASN A 209 " =    1.565
peak=    3.391 closest distance to " O   HOH Z   6 " =    1.975
peak=    3.389 closest distance to " O   HOH Z 250 " =    1.253
peak=    3.389 closest distance to " O   HOH Z 209 " =    2.488
peak=    3.388 closest distance to " CA  THR A 221 " =    1.013
peak=    3.387 closest distance to " O   HOH Z 259 " =    2.243
peak=    3.385 closest distance to " CG1BVAL A  72 " =    1.072
peak=    3.365 closest distance to " CB  ASN A 142 " =    1.023
peak=    3.362 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.361 closest distance to " CB  PHE A 225 " =    1.432
peak=    3.353 closest distance to " OD2 ASP A 286 " =    2.612
peak=    3.349 closest distance to " O   HOH Z 145 " =    3.641
peak=    3.348 closest distance to " CG BARG A 190 " =    1.237
peak=    3.347 closest distance to " O   HOH Z 373 " =    1.490
peak=    3.343 closest distance to " O   MET A 105 " =    1.752
peak=    3.342 closest distance to " CA  LYS A 117 " =    1.125
peak=    3.340 closest distance to " CB  ASN A 187 " =    1.089
peak=    3.337 closest distance to " ND2 ASN A 187 " =    1.603
peak=    3.334 closest distance to " O   HOH Z 109 " =    2.273
peak=    3.329 closest distance to " CB  ARG A 190 " =    1.709
peak=    3.329 closest distance to " O   HOH Z 329 " =    3.949
peak=    3.329 closest distance to " CE3 TRP A 274 " =    1.262
peak=    3.328 closest distance to " NE AARG A 275 " =    1.331
peak=    3.324 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.318 closest distance to " CG1 VAL A 202 " =    1.884
peak=    3.318 closest distance to " NZ  LYS A 117 " =    1.219
peak=    3.317 closest distance to " CB  GLN A  89 " =    1.189
peak=    3.312 closest distance to " CB  THR A 157 " =    1.124
peak=    3.310 closest distance to " OG BSER A 164 " =    2.080
peak=    3.309 closest distance to " CA  ALA A  51 " =    1.137
peak=    3.306 closest distance to " CA  GLY A 267 " =    1.074
peak=    3.305 closest distance to " O   HOH Z 410 " =    2.106
peak=    3.299 closest distance to " O   HOH Z 389 " =    2.952
peak=    3.298 closest distance to " O   HOH Z 423 " =    1.201
peak=    3.296 closest distance to " OG1 THR A 221 " =    1.310
peak=    3.294 closest distance to " CA  ASN A  74 " =    1.208
peak=    3.293 closest distance to " CD1 ILE A  33 " =    1.793
peak=    3.290 closest distance to " CD  ARG A 138 " =    1.134
peak=    3.290 closest distance to " CG  GLN A 278 " =    3.663
peak=    3.288 closest distance to " NH2 ARG A 269 " =    0.850
peak=    3.288 closest distance to " N   SER A 271 " =    0.988
peak=    3.286 closest distance to " O   HOH Z 303 " =    2.585
peak=    3.286 closest distance to " CB  ARG A 219 " =    0.866
peak=    3.286 closest distance to " CB  LEU A 300 " =    0.856
peak=    3.284 closest distance to " O   HOH Z  88 " =    3.671
peak=    3.283 closest distance to " CB  TRP A 150 " =    1.200
peak=    3.281 closest distance to " CA  MET A 105 " =    0.915
peak=    3.280 closest distance to " O  BHOH Z 338 " =    2.452
peak=    3.278 closest distance to " CG2 VAL A 197 " =    1.148
peak=    3.277 closest distance to " O   HOH Z 148 " =    2.282
peak=    3.277 closest distance to " O   HOH Z 145 " =    1.870
peak=    3.273 closest distance to " O   HOH Z 153 " =    3.702
peak=    3.273 closest distance to " O   HOH Z 371 " =    3.130
peak=    3.273 closest distance to " CE  MET A  93 " =    1.516
peak=    3.271 closest distance to " CZ  PHE A 218 " =    1.109
peak=    3.270 closest distance to " O   HOH Z 336 " =    1.932
peak=    3.267 closest distance to " CB  ARG A 139 " =    0.996
peak=    3.266 closest distance to " O   HOH Z  93 " =    2.461
peak=    3.266 closest distance to " O   HOH Z 345 " =    3.215
peak=    3.265 closest distance to " O   HOH Z 130 " =    2.614
peak=    3.261 closest distance to " CE1 HIS A 115 " =    3.658
peak=    3.261 closest distance to " CB  SER A 212 " =    1.295
peak=    3.260 closest distance to " CG AARG A 275 " =    1.044
peak=    3.259 closest distance to " O   HOH Z  20 " =    1.337
peak=    3.254 closest distance to " O   HOH Z 305 " =    3.473
peak=    3.247 closest distance to " CG2 ILE A 106 " =    0.944
peak=    3.247 closest distance to " CD2 PHE A  59 " =    1.861
peak=    3.244 closest distance to " N   ALA A 256 " =    0.896
peak=    3.244 closest distance to " CD2 HIS A  81 " =    0.847
peak=    3.241 closest distance to " O   HOH Z 334 " =    1.389
peak=    3.240 closest distance to " O   HOH Z 356 " =    1.280
peak=    3.240 closest distance to " CG1 ILE A 151 " =    1.143
peak=    3.239 closest distance to " CA  ALA A  21 " =    1.209
peak=    3.236 closest distance to " O   HOH Z 302 " =    1.525
peak=    3.235 closest distance to " CE3 TRP A  85 " =    1.240
peak=    3.233 closest distance to " CB  HIS A 108 " =    0.845
peak=    3.230 closest distance to " O   HOH Z  44 " =    2.567
peak=    3.225 closest distance to " O   HOH Z 272 " =    2.213
peak=    3.222 closest distance to " OE2 GLU A   2 " =    1.988
peak=    3.221 closest distance to " O   HOH Z 207 " =    2.343
peak=    3.219 closest distance to " CG  ARG A 159 " =    0.890
peak=    3.214 closest distance to " O   HOH Z 344 " =    2.894
peak=    3.213 closest distance to " CA  ILE A 106 " =    0.724
peak=    3.213 closest distance to " O   HOH Z 357 " =    2.068
peak=    3.209 closest distance to " O   HOH Z 402 " =    1.340
peak=    3.206 closest distance to " CG2 ILE A  20 " =    1.838
peak=    3.206 closest distance to " O   HOH Z 403 " =    1.542
peak=    3.203 closest distance to " CB  ALA A 248 " =    1.400
peak=    3.201 closest distance to " NH1BARG A 145 " =    1.256
peak=    3.199 closest distance to " N   ARG A 156 " =    1.280
peak=    3.199 closest distance to " O   HOH Z 273 " =    2.883
peak=    3.196 closest distance to " O   HOH Z  58 " =    1.799
peak=    3.191 closest distance to " ND2BASN A 224 " =    0.834
peak=    3.190 closest distance to " CA  LYS A 290 " =    1.353
peak=    3.181 closest distance to " O  BHOH Z  74 " =    1.395
peak=    3.175 closest distance to " O   HOH Z 371 " =    1.919
peak=    3.169 closest distance to " O   ILE A  20 " =    1.938
peak=    3.167 closest distance to " CG  MET A 185 " =    1.224
peak=    3.165 closest distance to " O   HOH Z  40 " =    2.125
peak=    3.164 closest distance to " N   ALA A 154 " =    0.773
peak=    3.164 closest distance to " NH2BARG A 190 " =    1.436
peak=    3.162 closest distance to " CA  ALA A 158 " =    1.191
peak=    3.161 closest distance to " CB  ASN A 148 " =    1.935
peak=    3.161 closest distance to " O   HOH Z 383 " =    2.481
peak=    3.147 closest distance to " O   HOH Z 172 " =    2.785
peak=    3.144 closest distance to " CD  LYS A 166 " =    1.394
peak=    3.136 closest distance to " O   HOH Z 143 " =    1.371
peak=    3.129 closest distance to " NE2 GLN A  73 " =    1.560
peak=    3.124 closest distance to " O   HOH Z 148 " =    3.507
peak=    3.118 closest distance to " O   GLY A 302 " =    2.132
peak=    3.117 closest distance to " CA  ALA A 291 " =    0.881
peak=    3.117 closest distance to " OE1 GLU A  53 " =    1.473
peak=    3.116 closest distance to " CB  PHE A 204 " =    1.013
peak=    3.108 closest distance to " N   THR A 246 " =    1.373
peak=    3.103 closest distance to " O   HOH Z 421 " =    3.257
peak=    3.100 closest distance to " O   CYS A 168 " =    1.283
peak=    3.097 closest distance to " O   HOH Z 423 " =    1.647
peak=    3.095 closest distance to " CB  TYR A  30 " =    1.916
peak=    3.092 closest distance to " O   HOH Z 118 " =    1.386
peak=    3.091 closest distance to " CA  ASP A 149 " =    1.223
peak=    3.089 closest distance to " O   HOH Z 412 " =    5.180
peak=    3.087 closest distance to " CA  ALA A 299 " =    0.987
peak=    3.087 closest distance to " O   PRO A  90 " =    1.559
peak=    3.087 closest distance to " O   HOH Z  94 " =    2.472
peak=    3.083 closest distance to " O   HOH Z   9 " =    1.686
peak=    3.081 closest distance to " NZ  LYS A  48 " =    1.202
peak=    3.078 closest distance to " CB  SER A 210 " =    0.925
peak=    3.076 closest distance to " CA  LEU A 282 " =    1.057
peak=    3.070 closest distance to " O   HOH Z 417 " =    1.827
peak=    3.052 closest distance to " O   HOH Z 298 " =    2.885
peak=    3.039 closest distance to " CG  GLU A 277 " =    4.201
peak=    3.026 closest distance to " OG BSER A 164 " =    2.506
peak=    3.016 closest distance to " OE1 GLU A   2 " =    1.386
peak=    3.013 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.007 closest distance to " O   HOH Z  43 " =    2.195

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.715 - 5.990
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.715 - 5.990

peak=   -4.826 closest distance to " OG BSER A 134 " =    1.476
peak=   -4.506 closest distance to " CG2 VAL A 230 " =    0.824
peak=   -4.331 closest distance to " CE2 PHE A 218 " =    2.460
peak=   -4.265 closest distance to " O   HOH Z 266 " =    4.914
peak=   -4.261 closest distance to " CG  ARG A 138 " =    0.968
peak=   -4.253 closest distance to " CD  ARG A  14 " =    3.147
peak=   -4.128 closest distance to " CA  ASP A  27 " =    2.366
peak=   -4.068 closest distance to " CB  ALA A  43 " =    2.518
peak=   -4.061 closest distance to " O   HOH Z 185 " =    2.056
peak=   -4.044 closest distance to " CD1 LEU A 255 " =    2.905
peak=   -4.027 closest distance to " O   HOH Z 350 " =    1.899
peak=   -4.014 closest distance to " O   HOH Z 131 " =    3.975
peak=   -3.945 closest distance to " CA  GLY A  98 " =    1.841
peak=   -3.915 closest distance to " N   THR A 157 " =    1.438
peak=   -3.901 closest distance to " OG  SER A  87 " =    1.308
peak=   -3.898 closest distance to " O   SER A 135 " =    1.466
peak=   -3.895 closest distance to " O   PRO A 198 " =    1.210
peak=   -3.886 closest distance to " CB  ASP A 132 " =    2.369
peak=   -3.877 closest distance to " O   HOH Z  43 " =    1.833
peak=   -3.874 closest distance to " O   HOH Z 407 " =    3.143
peak=   -3.869 closest distance to " C   HIS A 108 " =    1.206
peak=   -3.853 closest distance to " CD  ARG A 156 " =    1.949
peak=   -3.852 closest distance to " CA  ASN A 127 " =    1.167
peak=   -3.835 closest distance to " O   HOH Z 359 " =    1.736
peak=   -3.818 closest distance to " CB  PRO A 243 " =    2.634
peak=   -3.817 closest distance to " CG2 VAL A 296 " =    1.799
peak=   -3.804 closest distance to " CD  LYS A 289 " =    2.392
peak=   -3.790 closest distance to " N   PRO A 163 " =    1.536
peak=   -3.785 closest distance to " CZ2 TRP A 274 " =    0.910
peak=   -3.775 closest distance to " O   PRO A 243 " =    2.493
peak=   -3.760 closest distance to " O   SER A  22 " =    2.453
peak=   -3.724 closest distance to " O   HOH Z 211 " =    1.372
peak=   -3.724 closest distance to " CE2 TYR A  30 " =    2.590
peak=   -3.722 closest distance to " CA  GLY A 133 " =    1.970
peak=   -3.719 closest distance to " O   PRO A 163 " =    1.921
peak=   -3.709 closest distance to " CD  GLN A 223 " =    2.331
peak=   -3.695 closest distance to " O   HOH Z 435 " =    2.324
peak=   -3.689 closest distance to " O   HOH Z 389 " =    1.413
peak=   -3.688 closest distance to " O   ALA A  84 " =    1.618
peak=   -3.681 closest distance to " O   HOH Z 389 " =    2.098
peak=   -3.677 closest distance to " O   MET A  40 " =    2.812
peak=   -3.671 closest distance to " O   HOH Z 377 " =    2.052
peak=   -3.661 closest distance to " CB  VAL A 230 " =    0.987
peak=   -3.656 closest distance to " CD2 TYR A 293 " =    1.818
peak=   -3.655 closest distance to " CB  TYR A  15 " =    2.127
peak=   -3.636 closest distance to " O   HOH Z 216 " =    1.648
peak=   -3.632 closest distance to " CB  ASN A  39 " =    2.256
peak=   -3.626 closest distance to " O   HOH Z 292 " =    1.562
peak=   -3.623 closest distance to " CA  GLY A 203 " =    2.357
peak=   -3.621 closest distance to " ND2 ASN A 187 " =    1.474
peak=   -3.620 closest distance to " CB  ALA A 248 " =    2.025
peak=   -3.614 closest distance to " ND2 ASN A 285 " =    1.978
peak=   -3.608 closest distance to " CG  PRO A 163 " =    2.582
peak=   -3.599 closest distance to " NH2 ARG A  79 " =    2.132
peak=   -3.591 closest distance to " N   VAL A  72 " =    1.714
peak=   -3.587 closest distance to " CD1 LEU A 101 " =    2.169
peak=   -3.586 closest distance to " O   HOH Z 111 " =    2.145
peak=   -3.577 closest distance to " OE1 GLU A 277 " =    2.237
peak=   -3.570 closest distance to " CG1 VAL A 112 " =    3.027
peak=   -3.554 closest distance to " CD2 LEU A   5 " =    0.990
peak=   -3.542 closest distance to " O   HOH Z  51 " =    0.715
peak=   -3.538 closest distance to " OE2 GLU A 152 " =    1.154
peak=   -3.536 closest distance to " O   HOH Z 191 " =    5.551
peak=   -3.535 closest distance to " O   HOH Z 134 " =    3.751
peak=   -3.525 closest distance to " N   ALA A  43 " =    2.629
peak=   -3.524 closest distance to " OG  SER A  63 " =    1.305
peak=   -3.520 closest distance to " CE  MET A 105 " =    2.363
peak=   -3.519 closest distance to " CE1 PHE A  59 " =    1.963
peak=   -3.518 closest distance to " CD  ARG A 138 " =    1.507
peak=   -3.513 closest distance to " O   HOH Z 100 " =    1.154
peak=   -3.504 closest distance to " CZ  TYR A 169 " =    1.726
peak=   -3.493 closest distance to " O   HOH Z 359 " =    3.421
peak=   -3.492 closest distance to " O   HOH Z 351 " =    1.553
peak=   -3.491 closest distance to " O   VAL A  67 " =    2.602
peak=   -3.477 closest distance to " ND2 ASN A 249 " =    2.288
peak=   -3.476 closest distance to " O   ASP A 191 " =    1.980
peak=   -3.470 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.469 closest distance to " O   ARG A 145 " =    1.408
peak=   -3.467 closest distance to " CB  GLN A  55 " =    1.223
peak=   -3.466 closest distance to " CB  ALA A   7 " =    1.954
peak=   -3.459 closest distance to " NH2 ARG A 219 " =    1.746
peak=   -3.459 closest distance to " CB  ALA A   9 " =    2.373
peak=   -3.459 closest distance to " CG  GLN A  58 " =    1.073
peak=   -3.458 closest distance to " OG  SER A 141 " =    1.836
peak=   -3.456 closest distance to " OG  SER A 206 " =    1.794
peak=   -3.447 closest distance to " O   HOH Z 231 " =    1.945
peak=   -3.446 closest distance to " O   HOH Z 114 " =    2.986
peak=   -3.434 closest distance to " O   HOH Z  39 " =    1.156
peak=   -3.416 closest distance to " O   GLN A  11 " =    1.476
peak=   -3.409 closest distance to " CE2 TRP A  70 " =    2.295
peak=   -3.406 closest distance to " O   HOH Z  60 " =    2.346
peak=   -3.401 closest distance to " OG  SER A 245 " =    1.352
peak=   -3.400 closest distance to " N   SER A 276 " =    1.301
peak=   -3.399 closest distance to " O   HOH Z 166 " =    1.798
peak=   -3.389 closest distance to " CD2 LEU A 237 " =    2.617
peak=   -3.388 closest distance to " CG2 VAL A 296 " =    1.171
peak=   -3.385 closest distance to " O   HOH Z 377 " =    1.325
peak=   -3.372 closest distance to " O   HOH Z  67 " =    3.012
peak=   -3.366 closest distance to " O   GLU A 152 " =    1.583
peak=   -3.366 closest distance to " OG  SER A  62 " =    4.347
peak=   -3.364 closest distance to " O   HOH Z 348 " =    1.760
peak=   -3.364 closest distance to " N   ARG A 138 " =    1.501
peak=   -3.352 closest distance to " CB  PHE A 130 " =    1.215
peak=   -3.349 closest distance to " O   HOH Z 385 " =    1.727
peak=   -3.349 closest distance to " O   HOH Z 427 " =    1.728
peak=   -3.344 closest distance to " O   HOH Z 313 " =    1.437
peak=   -3.343 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.343 closest distance to " CA  ALA A 227 " =    2.395
peak=   -3.342 closest distance to " O   HOH Z 337 " =    1.747
peak=   -3.339 closest distance to " O   HOH Z  64 " =    2.417
peak=   -3.337 closest distance to " C   ARG A 269 " =    1.361
peak=   -3.327 closest distance to " O   HOH Z 166 " =    1.693
peak=   -3.323 closest distance to " CA  GLY A  35 " =    1.986
peak=   -3.315 closest distance to " O   HOH Z 231 " =    0.886
peak=   -3.313 closest distance to " O   HOH Z 298 " =    2.782
peak=   -3.310 closest distance to " CB  PRO A 163 " =    2.331
peak=   -3.309 closest distance to " CB  ALA A 161 " =    2.434
peak=   -3.306 closest distance to " N   ALA A 248 " =    1.549
peak=   -3.300 closest distance to " O   HOH Z 208 " =    2.110
peak=   -3.299 closest distance to " CG2 VAL A 202 " =    2.635
peak=   -3.294 closest distance to " CB  PRO A  90 " =    1.671
peak=   -3.291 closest distance to " CB  PHE A 192 " =    1.714
peak=   -3.291 closest distance to " ND2 ASN A 252 " =    2.000
peak=   -3.290 closest distance to " O   HOH Z 352 " =    1.591
peak=   -3.287 closest distance to " O   HOH Z  52 " =    1.712
peak=   -3.286 closest distance to " ND2 ASN A  69 " =    1.659
peak=   -3.285 closest distance to " CG2 ILE A  20 " =    2.971
peak=   -3.284 closest distance to " OE1 GLN A  88 " =    1.090
peak=   -3.282 closest distance to " O   HOH Z 368 " =    2.408
peak=   -3.280 closest distance to " O   HOH Z 286 " =    1.895
peak=   -3.277 closest distance to " CG  TRP A 266 " =    1.833
peak=   -3.276 closest distance to " CZ2 TRP A  92 " =    2.772
peak=   -3.271 closest distance to " O   HOH Z 353 " =    1.422
peak=   -3.267 closest distance to " N   ALA A 226 " =    2.043
peak=   -3.267 closest distance to " O   HOH Z 385 " =    0.891
peak=   -3.264 closest distance to " CA  HIS A 207 " =    1.172
peak=   -3.262 closest distance to " OG  SER A  26 " =    1.098
peak=   -3.261 closest distance to " O   ALA A  10 " =    1.777
peak=   -3.261 closest distance to " CG  ASN A 301 " =    1.963
peak=   -3.258 closest distance to " CE BMET A  47 " =    1.137
peak=   -3.257 closest distance to " C   ASN A 187 " =    1.885
peak=   -3.256 closest distance to " CB  ALA A 131 " =    1.969
peak=   -3.256 closest distance to " O   PRO A 198 " =    1.442
peak=   -3.256 closest distance to " O   HOH Z 198 " =    1.710
peak=   -3.256 closest distance to " O   HOH Z 404 " =    1.350
peak=   -3.247 closest distance to " O   VAL A 189 " =    2.441
peak=   -3.245 closest distance to " O   SER A 271 " =    2.001
peak=   -3.243 closest distance to " O   HOH Z 198 " =    2.114
peak=   -3.243 closest distance to " O   TYR A  30 " =    2.793
peak=   -3.242 closest distance to " OG  SER A   3 " =    1.535
peak=   -3.229 closest distance to " O   HOH Z 394 " =    1.483
peak=   -3.228 closest distance to " CD2 LEU A   5 " =    2.601
peak=   -3.227 closest distance to " OG BSER A 134 " =    1.835
peak=   -3.227 closest distance to " CB  TRP A  85 " =    2.528
peak=   -3.226 closest distance to " O   HOH Z 345 " =    1.987
peak=   -3.220 closest distance to " C   MET A 188 " =    1.530
peak=   -3.215 closest distance to " O   HOH Z 111 " =    1.233
peak=   -3.212 closest distance to " OG ASER A 134 " =    1.227
peak=   -3.211 closest distance to " C   ARG A  79 " =    2.518
peak=   -3.208 closest distance to " O   HOH Z 426 " =    1.579
peak=   -3.199 closest distance to " O   PHE A 218 " =    1.531
peak=   -3.194 closest distance to " CZ  PHE A  59 " =    1.577
peak=   -3.192 closest distance to " O   HOH Z 352 " =    2.011
peak=   -3.191 closest distance to " CA  GLY A  57 " =    2.190
peak=   -3.190 closest distance to " O   GLY A  80 " =    2.475
peak=   -3.187 closest distance to " CG  ARG A 259 " =    2.434
peak=   -3.182 closest distance to " O   HOH Z  63 " =    2.268
peak=   -3.180 closest distance to " O   ASN A 301 " =    1.506
peak=   -3.180 closest distance to " O   HOH Z 423 " =    2.530
peak=   -3.177 closest distance to " NH2AARG A 275 " =    5.258
peak=   -3.175 closest distance to " CG  LEU A 228 " =    0.944
peak=   -3.172 closest distance to " O   HOH Z 197 " =    3.103
peak=   -3.169 closest distance to " OG1 THR A 178 " =    1.192
peak=   -3.169 closest distance to " N   ALA A   1 " =    1.566
peak=   -3.167 closest distance to " C   ILE A 151 " =    0.892
peak=   -3.165 closest distance to " O   ALA A   1 " =    1.349
peak=   -3.156 closest distance to " CG1 VAL A 250 " =    2.641
peak=   -3.156 closest distance to " O   HOH Z  68 " =    1.328
peak=   -3.152 closest distance to " O   HOH Z 207 " =    1.928
peak=   -3.148 closest distance to " O   HOH Z 111 " =    4.546
peak=   -3.148 closest distance to " O   HOH Z 426 " =    2.221
peak=   -3.147 closest distance to " O   HOH Z  60 " =    1.949
peak=   -3.144 closest distance to " O   HOH Z 414 " =    1.992
peak=   -3.142 closest distance to " C   ALA A 158 " =    1.358
peak=   -3.133 closest distance to " O   HOH Z 421 " =    3.225
peak=   -3.132 closest distance to " N   ASP A 171 " =    2.546
peak=   -3.130 closest distance to " OG  SER A  97 " =    2.173
peak=   -3.127 closest distance to " O   HOH Z 336 " =    5.990
peak=   -3.117 closest distance to " O   HOH Z 197 " =    4.192
peak=   -3.111 closest distance to " CG  PHE A 283 " =    2.531
peak=   -3.106 closest distance to " O   HOH Z 415 " =    1.313
peak=   -3.105 closest distance to " O   HOH Z 290 " =    1.225
peak=   -3.102 closest distance to " CG1 VAL A 296 " =    1.407
peak=   -3.102 closest distance to " CD2 HIS A 207 " =    2.305
peak=   -3.099 closest distance to " CD2 PHE A  61 " =    1.981
peak=   -3.098 closest distance to " O   HOH Z 221 " =    1.254
peak=   -3.098 closest distance to " O   HOH Z 414 " =    1.908
peak=   -3.093 closest distance to " CD  LYS A 166 " =    2.327
peak=   -3.088 closest distance to " O   HOH Z 128 " =    2.286
peak=   -3.070 closest distance to " OD1 ASP A 171 " =    1.583
peak=   -3.068 closest distance to " O   HOH Z  96 " =    4.012
peak=   -3.065 closest distance to " O   HOH Z 189 " =    1.739
peak=   -3.065 closest distance to " O   HOH Z 262 " =    2.482
peak=   -3.051 closest distance to " CB  ALA A 114 " =    2.388
peak=   -3.049 closest distance to " O   LYS A 289 " =    2.956
peak=   -3.045 closest distance to " CB  TYR A  68 " =    1.707
peak=   -3.040 closest distance to " O   HOH Z  56 " =    1.164
peak=   -3.020 closest distance to " O   HOH Z 393 " =    4.205
peak=   -3.019 closest distance to " NH1 ARG A  66 " =    3.733
peak=   -3.016 closest distance to " O   HOH Z 377 " =    1.627

================= 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    :  0.4739 0.4671   6.280639e+00   6.263863e+00
   1_bss:  0.4662 0.4532   6.275090e+00   6.252727e+00
   1_xyz:  0.3846 0.4067   6.167519e+00   6.197980e+00
   1_adp:  0.3367 0.3947   6.094668e+00   6.184900e+00
   1_occ:  0.3364 0.3942   6.094235e+00   6.185277e+00
   2_bss:  0.3343 0.3897   6.095546e+00   6.184505e+00
   2_xyz:  0.2675 0.3278   5.900970e+00   6.038567e+00
   2_adp:  0.2466 0.3150   5.843761e+00   6.002982e+00
   2_occ:  0.2463 0.3151   5.843798e+00   6.003460e+00
   3_bss:  0.2446 0.3126   5.842339e+00   6.000742e+00
   3_xyz:  0.1858 0.2436   5.588588e+00   5.787337e+00
   3_adp:  0.1650 0.2255   5.488927e+00   5.718880e+00
   3_occ:  0.1649 0.2252   5.488167e+00   5.717814e+00
   4_bss:  0.1647 0.2246   5.485868e+00   5.715251e+00
   4_xyz:  0.1362 0.1937   5.330161e+00   5.579633e+00
   4_adp:  0.1323 0.1891   5.305421e+00   5.556463e+00
   4_occ:  0.1322 0.1890   5.305046e+00   5.555917e+00
   5_bss:  0.1326 0.1886   5.304883e+00   5.554283e+00
   5_xyz:  0.1241 0.1802   5.253473e+00   5.512652e+00
   5_adp:  0.1176 0.1723   5.210219e+00   5.468911e+00
   5_occ:  0.1176 0.1722   5.209785e+00   5.468361e+00
   5_bss:  0.1175 0.1722   5.209629e+00   5.468221e+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:  0.383  20.000   6.489  10.046   7.950   0.000   0.000   0.000
   1_xyz:  0.383  20.000   6.489  10.046   7.950   0.000   0.000   0.000
   1_adp:  0.383  20.000   6.489  10.046   7.950   0.000   0.000   0.000
   1_occ:  0.383  20.000   6.489  10.046   7.950   0.000   0.000   0.000
   2_bss:  0.368  50.000   3.683   6.123   4.964   0.000   0.000   0.000
   2_xyz:  0.368  50.000   3.683   6.123   4.964   0.000   0.000   0.000
   2_adp:  0.368  50.000   3.683   6.123   4.964   0.000   0.000   0.000
   2_occ:  0.368  50.000   3.683   6.123   4.964   0.000   0.000   0.000
   3_bss:  0.341  50.000   2.244   3.207   3.540   0.000   0.000   0.000
   3_xyz:  0.341  50.000   2.244   3.207   3.540   0.000   0.000   0.000
   3_adp:  0.341  50.000   2.244   3.207   3.540   0.000   0.000   0.000
   3_occ:  0.341  50.000   2.244   3.207   3.540   0.000   0.000   0.000
   4_bss:  0.331  54.306   1.717   2.022   3.160   0.000   0.000   0.000
   4_xyz:  0.331  54.306   1.717   2.022   3.160   0.000   0.000   0.000
   4_adp:  0.331  54.306   1.717   2.022   3.160   0.000   0.000   0.000
   4_occ:  0.331  54.306   1.717   2.022   3.160   0.000   0.000   0.000
   5_bss:  0.321  49.417   1.681   1.783   3.176   0.000   0.000   0.000
   5_xyz:  0.321  49.417   1.681   1.783   3.176   0.000   0.000   0.000
   5_adp:  0.321  49.417   1.681   1.783   3.176   0.000   0.000   0.000
   5_occ:  0.321  49.417   1.681   1.783   3.176   0.000   0.000   0.000
   5_bss:  0.321  51.690  -0.459  -0.555   1.014   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.663 0.4365  0.5137    67918.037
   1_bss:  56.084 0.4425  0.6586    65022.126
   1_xyz:  48.081 0.5428  0.7906    50621.769
   1_adp:  45.394 0.5765  0.8848    47393.310
   1_occ:  45.485 0.5754  0.8823    47493.520
   2_bss:  45.098 0.5801  0.7954    46960.692
   2_xyz:  34.875 0.7023  0.9417    29776.142
   2_adp:  32.508 0.7299  0.9738    26920.386
   2_occ:  32.547 0.7295  0.9732    26981.442
   3_bss:  32.310 0.7320  0.9105    26683.021
   3_xyz:  23.944 0.8218  0.9858    15268.374
   3_adp:  21.654 0.8452  0.9903    12836.576
   3_occ:  21.622 0.8455  0.9902    12796.046
   4_bss:  21.541 0.8462  0.9661    12698.207
   4_xyz:  18.445 0.8757  0.9818     9470.627
   4_adp:  17.841 0.8815  0.9838     9080.739
   4_occ:  17.837 0.8815  0.9835     9059.382
   5_bss:  17.804 0.8817  0.9800     9010.887
   5_xyz:  16.721 0.8916  0.9846     8160.429
   5_adp:  15.754 0.9003  0.9791     7495.561
   5_occ:  15.746 0.9003  0.9790     7481.236
   5_bss:  15.744 0.9004  0.9812     7480.810
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3468e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3468e+01
   1_xyz:   1.660  0.013  0.105 18.264  0.006  4.107   1.3777e-01
   1_adp:   1.660  0.013  0.105 18.264  0.006  4.107   1.3777e-01
   1_occ:   1.660  0.013  0.105 18.264  0.006  4.107   1.3777e-01
   2_bss:   1.660  0.013  0.105 18.264  0.006  4.107   1.3777e-01
   2_xyz:   1.169  0.009  0.085 16.284  0.005  4.106   8.6820e-02
   2_adp:   1.169  0.009  0.085 16.284  0.005  4.106   8.6820e-02
   2_occ:   1.169  0.009  0.085 16.284  0.005  4.106   8.6820e-02
   3_bss:   1.169  0.009  0.085 16.284  0.005  4.106   8.6820e-02
   3_xyz:   1.089  0.008  0.080 15.926  0.004  4.119   7.0813e-02
   3_adp:   1.089  0.008  0.080 15.926  0.004  4.119   7.0813e-02
   3_occ:   1.089  0.008  0.080 15.926  0.004  4.119   7.0813e-02
   4_bss:   1.089  0.008  0.080 15.926  0.004  4.119   7.0813e-02
   4_xyz:   1.018  0.007  0.077 15.796  0.004  4.108   6.6090e-02
   4_adp:   1.018  0.007  0.077 15.796  0.004  4.108   6.6090e-02
   4_occ:   1.018  0.007  0.077 15.796  0.004  4.108   6.6090e-02
   5_bss:   1.018  0.007  0.077 15.796  0.004  4.108   6.6090e-02
   5_xyz:   1.042  0.007  0.081 15.763  0.004  4.112   6.6370e-02
   5_adp:   1.042  0.007  0.081 15.763  0.004  4.112   6.6370e-02
   5_occ:   1.042  0.007  0.081 15.763  0.004  4.112   6.6370e-02
   5_bss:   1.042  0.007  0.081 15.763  0.004  4.112   6.6370e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_xyz:  13.011  0.183  0.405 87.545  0.034  2.115   9.6338e-02
   1_adp:  13.011  0.183  0.405 87.545  0.034  2.115   9.6338e-02
   1_occ:  13.011  0.183  0.405 87.545  0.034  2.115   9.6338e-02
   2_bss:  13.011  0.183  0.405 87.545  0.034  2.115   9.6338e-02
   2_xyz:   6.912  0.082  0.315 86.753  0.040  2.139   6.1625e-02
   2_adp:   6.912  0.082  0.315 86.753  0.040  2.139   6.1625e-02
   2_occ:   6.912  0.082  0.315 86.753  0.040  2.139   6.1625e-02
   3_bss:   6.912  0.082  0.315 86.753  0.040  2.139   6.1625e-02
   3_xyz:   7.276  0.050  0.382 89.763  0.030  2.304   6.8370e-02
   3_adp:   7.276  0.050  0.382 89.763  0.030  2.304   6.8370e-02
   3_occ:   7.276  0.050  0.382 89.763  0.030  2.304   6.8370e-02
   4_bss:   7.276  0.050  0.382 89.763  0.030  2.304   6.8370e-02
   4_xyz:   6.905  0.054  0.351 81.768  0.034  2.297   7.9074e-02
   4_adp:   6.905  0.054  0.351 81.768  0.034  2.297   7.9074e-02
   4_occ:   6.905  0.054  0.351 81.768  0.034  2.297   7.9074e-02
   5_bss:   6.905  0.054  0.351 81.768  0.034  2.297   7.9074e-02
   5_xyz:   8.461  0.055  0.432 82.965  0.038  2.296   4.9751e-02
   5_adp:   8.461  0.055  0.432 82.965  0.038  2.296   4.9751e-02
   5_occ:   8.461  0.055  0.432 82.965  0.038  2.296   4.9751e-02
   5_bss:   8.461  0.055  0.432 82.965  0.038  2.296   4.9751e-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:  77.70   0.00  13.38  67.86   0.00  11.29  77.70   0.00  24.80
   1_occ:  77.70   0.00  13.38  67.86   0.00  11.29  77.70   0.00  24.80
   2_bss:  77.70   0.00  13.38  67.86   0.00  11.29  77.70   0.00  24.80
   2_xyz:  77.70   0.00  13.38  67.86   0.00  11.29  77.70   0.00  24.80
   2_adp:  82.78   0.00  13.39  67.18   0.00  10.27  82.78   0.00  30.39
   2_occ:  82.78   0.00  13.39  67.18   0.00  10.27  82.78   0.00  30.39
   3_bss:  82.78   0.00  13.39  67.18   0.00  10.27  82.78   0.00  30.39
   3_xyz:  82.78   0.00  13.39  67.18   0.00  10.27  82.78   0.00  30.39
   3_adp:  94.59   0.00  14.59  94.59   0.00   9.83  93.00   1.76  40.49
   3_occ:  94.59   0.00  14.59  94.59   0.00   9.83  93.00   1.76  40.49
   4_bss:  94.59   0.00  14.59  94.59   0.00   9.83  93.00   1.76  40.49
   4_xyz:  94.59   0.00  14.59  94.59   0.00   9.83  93.00   1.76  40.49
   4_adp:  94.75   0.00  14.47  94.75   0.00   9.71  92.94   2.35  40.43
   4_occ:  94.75   0.00  14.47  94.75   0.00   9.71  92.94   2.35  40.43
   5_bss:  94.75   0.00  14.47  94.75   0.00   9.71  92.94   2.35  40.43
   5_xyz:  94.75   0.00  14.47  94.75   0.00   9.71  92.94   2.35  40.43
   5_adp: 105.29   0.00  14.01 104.13   0.00   9.16 105.29   2.01  40.41
   5_occ: 105.29   0.00  14.01 104.13   0.00   9.16 105.29   2.01  40.41
   5_bss: 107.56   2.27  16.28 106.41   2.27  11.44 107.56   4.28  42.68
------------------------------------------------------------------------
 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    0.023    0.408
   1_adp:    1.240    0.023    0.408
   1_occ:    1.240    0.023    0.408
   2_bss:    1.240    0.023    0.408
   2_xyz:    1.467    0.021    0.573
   2_adp:    1.467    0.021    0.573
   2_occ:    1.467    0.021    0.573
   3_bss:    1.467    0.021    0.573
   3_xyz:    1.669    0.030    0.668
   3_adp:    1.669    0.030    0.668
   3_occ:    1.669    0.030    0.668
   4_bss:    1.669    0.030    0.668
   4_xyz:    1.824    0.022    0.726
   4_adp:    1.824    0.022    0.726
   4_occ:    1.824    0.022    0.726
   5_bss:    1.824    0.022    0.726
   5_xyz:    1.837    0.029    0.742
   5_adp:    1.837    0.029    0.742
   5_occ:    1.837    0.029    0.742
   5_bss:    1.837    0.029    0.742
------------------------------------------------------------------------

CPU time actual refinement: 317.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/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_622/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_622/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.06 
  Macro-tasks:
    bulk solvent and scale       = 41.44  
    individual site refinement   = 126.28 
    weights calculation          = 30.89  
    collect and process          = 6.36   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.08 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 96.11  
    alpha_beta                      = 8.20   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 105.20 
    fmodel                         = 6.87   
    r_factors                      = 0.23   
    phase_errors                   = 10.43  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 230.82 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.552 micro seconds
Total CPU time: 5.51 minutes
from_scatterers_fft:    620 calls, 95.86 s
gradients_fft:          566 calls, 92.88 s

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

# Date 2008-01-16 Time 02:02:15 PST -0800 (1200477735.42 s)
Start R-work = 0.4739, R-free = 0.4671 (no bulk solvent and anisotropic scale)
Final R-work = 0.1342, R-free = 0.1859 (no bulk solvent and anisotropic scale)

Start R-work = 0.4662, R-free = 0.4532
Final R-work = 0.1175, R-free = 0.1722