# Date 2008-01-16 Time 03:06:32 PST -0800 (1200481592.33 s)
#phil __OFF__

Command line arguments: "../1102.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13521
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1102

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.9914, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.96157
Completeness in resolution range: 0.944412
Completeness with d_max=infinity: 0.941688

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1461
                             d_min =   1.9616

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.96157
Completeness in resolution range: 0.944412
Completeness with d_max=infinity: 0.941688

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1465 -  4.1989 [2173/2200]  1959   214   9.8%
  bin  2:  4.1989 -  3.3446 [2092/2112]  1880   212  10.1%
  bin  3:  3.3446 -  2.9253 [2062/2081]  1856   206  10.0%
  bin  4:  2.9253 -  2.6594 [2035/2065]  1832   203  10.0%
  bin  5:  2.6594 -  2.4696 [2046/2065]  1845   201   9.8%
  bin  6:  2.4696 -  2.3246 [2026/2051]  1811   215  10.6%
  bin  7:  2.3246 -  2.2085 [2030/2058]  1831   199   9.8%
  bin  8:  2.2085 -  2.1127 [1985/2021]  1791   194   9.8%
  bin  9:  2.1127 -  2.0315 [1987/2040]  1796   191   9.6%
  bin 10:  2.0315 -  1.9616 [1153/2049]  1029   124  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/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: 0.14 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:
        1.54 -     2.21: 19
        2.21 -     2.88: 1310
        2.88 -     3.55: 4518
        3.55 -     4.23: 9312
        4.23 -     4.90: 13403
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.536 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.819 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.821 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
  ... (remaining 28557 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

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_1102/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/model_refine_001.geo

CPU time processing inputs: 9.32


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.9914 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5082   r_free= 0.5012   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.304572                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.4290 0.4587      6.6357      6.6999|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.4470 0.4302      6.8661       6.833|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.4800 0.4512      6.7135      6.7469|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.5078 0.4962      6.5715      6.5236|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.5267 0.5497      6.3861      6.3941|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.5419 0.5287      6.3007      6.2564|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.5509 0.4639      6.2667      6.1956|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.5460 0.5064      6.1845      6.1884|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.5416 0.4951      6.1494      6.1279|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.5382 0.5742      6.0916      6.1033|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.5330 0.5614      6.0516      6.0716|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.5235 0.5723      5.9602      5.9924|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.5603 0.5392      5.8831      5.8223|
| 14:  2.0105 -  1.9616 0.45    595   65 0.5741 0.4969      5.8465      5.8188|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.60  42.44   0.77     0.67     102053.96|
|  2:  4.6840 -  3.7362  1357   146  0.64  40.69   0.85     0.73     138363.61|
|  3:  3.7362 -  3.2693  1324   144  0.51  51.25   0.82     0.65     144709.98|
|  4:  3.2693 -  2.9729  1345   158  0.40  59.65   0.77     0.51     129357.55|
|  5:  2.9729 -  2.7612  1310   144  0.29  68.05   0.72     0.36     100883.79|
|  6:  2.7612 -  2.5992  1313   145  0.29  68.33   0.71     0.35      84210.90|
|  7:  2.5992 -  2.4696  1309   138  0.31  66.76   0.72     0.37      69708.30|
|  8:  2.4696 -  2.3625  1281   152  0.33  65.07   0.71     0.41      61535.11|
|  9:  2.3625 -  2.2719  1305   145  0.33  65.21   0.72     0.38      55254.37|
| 10:  2.2719 -  2.1937  1289   151  0.29  68.63   0.73     0.35      53212.57|
| 11:  2.1937 -  2.1253  1299   132  0.23  72.97   0.77     0.29      52666.66|
| 12:  2.1253 -  2.0647  1275   151  0.20  75.50   0.75     0.25      49232.91|
| 13:  2.0647 -  2.0105  1214   127  0.19  75.90   0.73     0.25      41645.69|
| 14:  2.0105 -  1.9616   595    65  0.26  70.90   0.69     0.31      33399.45|
|alpha:            min =        0.25 max =            0.73 mean =         0.43|
|beta:             min =    33399.45 max =       144709.98 mean =     82402.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.07|
|phase err.(test): min =        0.00 max =           89.96 mean =        63.20|
|-----------------------------------------------------------------------------|

============================== 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 = 24.731556             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.983   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.986660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.673   (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:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1543 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2662 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3971 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5104 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6608 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7801 |
|-----------------------------------------------------------------------------|
|-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 |       53.318 |
| 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 |       2.067 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    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 = 11.713)------------------------------------------|
|    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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5110   r_free= 0.5047   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.305245                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4991   r_free= 0.4879   ksol= 0.34   Bsol= 0.00   scale= 0.968    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.54,8.94,7.49,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.300760                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.818949             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.156   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.684301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.796   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4991      final r-factor (work) = 0.4400          |
| start r-factor (free) = 0.4879      final r-factor (free) = 0.4675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 115.7460 = 19.82 * 0.50 * 6.2998 + 1.00 * 53.3183                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 62.0953 = 19.82 * 0.50 * 6.2503 + 1.00 * 0.1584                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4400      final r-factor (work) = 0.4042          |
| start r-factor (free) = 0.4675      final r-factor (free) = 0.4632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5417 = 1.68 * 1.00 * 6.2503 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4672 = 1.68 * 1.00 * 6.2036 + 1.00 * 0.0186                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.61   15.46    None  None   None       |
|    all(noH): 2823   0      0.00    94.61   15.46    None  None   None       |
|    Sol.    : 438    0      0.00    89.85   23.15    None  None   None       |
|    Mac.    : 2385   0      0.00    94.61   14.05    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 -   9.461: 1068   |   5:    47.303 -  56.763:   39        |
|      1:     9.461 -  18.921:  890   |   6:    56.763 -  66.224:   18        |
|      2:    18.921 -  28.382:  474   |   7:    66.224 -  75.684:   12        |
|      3:    28.382 -  37.842:  217   |   8:    75.684 -  85.145:    1        |
|      4:    37.842 -  47.303:  100   |   9:    85.145 -  94.605:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4042 r_free = 0.4632             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4040 r_free = 0.4635             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4040   r_free= 0.4635   ksol= 0.34   Bsol= 0.00   scale= 1.104    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.54,8.94,7.49,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.196672                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4023   r_free= 0.4616   ksol= 0.34   Bsol= 34.81   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.61,4.98,4.54,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.197976                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.099770             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.371  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.804258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.524  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4023      final r-factor (work) = 0.3291          |
| start r-factor (free) = 0.4616      final r-factor (free) = 0.3904          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.9715 = 15.10 * 0.50 * 6.2005 + 1.00 * 0.1584                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.3993 = 15.10 * 0.50 * 6.1303 + 1.00 * 0.1162                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3291      final r-factor (work) = 0.3050          |
| start r-factor (free) = 0.3904      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9490 = 0.80 * 1.00 * 6.1303 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8546 = 0.80 * 1.00 * 6.0187 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.14   15.57    None  None   None       |
|    all(noH): 2823   0      0.00    97.14   15.57    None  None   None       |
|    Sol.    : 438    0      0.00    84.34   29.81    None  None   None       |
|    Mac.    : 2385   0      0.00    97.14   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.714: 1176   |   5:    48.568 -  58.282:   45        |
|      1:     9.714 -  19.427:  833   |   6:    58.282 -  67.996:   16        |
|      2:    19.427 -  29.141:  416   |   7:    67.996 -  77.709:    5        |
|      3:    29.141 -  38.855:  222   |   8:    77.709 -  87.423:    3        |
|      4:    38.855 -  48.568:  104   |   9:    87.423 -  97.137:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3050 r_free = 0.3794             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3047 r_free = 0.3792             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3047   r_free= 0.3792   ksol= 0.34   Bsol= 34.81   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.61,4.98,4.54,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.000414                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3030   r_free= 0.3765   ksol= 0.33   Bsol= 45.75   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.34,2.65,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.000179                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.735622              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.550  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.339780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.666  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3030      final r-factor (work) = 0.2303          |
| start r-factor (free) = 0.3765      final r-factor (free) = 0.2962          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3946 = 7.74 * 0.50 * 6.0185 + 1.00 * 0.1163                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9350 = 7.74 * 0.50 * 5.9036 + 1.00 * 0.1010                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2303      final r-factor (work) = 0.2074          |
| start r-factor (free) = 0.2962      final r-factor (free) = 0.2704          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0198 = 0.34 * 1.00 * 5.9036 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9536 = 0.34 * 1.00 * 5.7217 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.43   14.97    None  None   None       |
|    all(noH): 2823   0      0.00    92.43   14.97    None  None   None       |
|    Sol.    : 438    0      2.38    83.52   35.73    None  None   None       |
|    Mac.    : 2385   0      0.00    92.43   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.243: 1250   |   5:    46.217 -  55.460:   78        |
|      1:     9.243 -  18.487:  886   |   6:    55.460 -  64.703:   32        |
|      2:    18.487 -  27.730:  250   |   7:    64.703 -  73.947:    2        |
|      3:    27.730 -  36.973:  177   |   8:    73.947 -  83.190:    4        |
|      4:    36.973 -  46.217:  140   |   9:    83.190 -  92.433:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2074 r_free = 0.2704             target_work(ml) = 5.674         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2069 r_free = 0.2694             target_work(ml) = 5.671         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2069   r_free= 0.2694   ksol= 0.33   Bsol= 45.75   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.34,2.65,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.671176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2058   r_free= 0.2666   ksol= 0.34   Bsol= 50.57   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,0.46,1.44,0.00,0.00,0.00); trace/3= 0.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.670196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.777717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.100   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.944  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2058      final r-factor (work) = 0.1604          |
| start r-factor (free) = 0.2666      final r-factor (free) = 0.2135          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9203 = 3.78 * 0.50 * 5.7279 + 1.00 * 0.1010                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5828 = 3.78 * 0.50 * 5.5676 + 1.00 * 0.0664                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1604      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2135      final r-factor (free) = 0.2036          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1980 = 0.21 * 1.00 * 5.5676 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1669 = 0.21 * 1.00 * 5.4264 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.59   14.83    None  None   None       |
|    all(noH): 2823   0      0.00    90.59   14.83    None  None   None       |
|    Sol.    : 438    0      4.14    80.78   37.52    None  None   None       |
|    Mac.    : 2385   0      0.00    90.59   10.66    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 -   9.059: 1325   |   5:    45.296 -  54.355:  106        |
|      1:     9.059 -  18.118:  863   |   6:    54.355 -  63.414:   49        |
|      2:    18.118 -  27.178:  200   |   7:    63.414 -  72.474:    9        |
|      3:    27.178 -  36.237:  142   |   8:    72.474 -  81.533:    4        |
|      4:    36.237 -  45.296:  121   |   9:    81.533 -  90.592:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1514 r_free = 0.2036             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1512 r_free = 0.2027             target_work(ml) = 5.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.2027   ksol= 0.34   Bsol= 50.57   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,0.46,1.44,0.00,0.00,0.00); trace/3= 0.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.397501                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.2023   ksol= 0.32   Bsol= 44.33   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.43,-0.37,0.82,-0.00,0.00,0.00); trace/3= 0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.397550                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.130173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.828  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170672              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.653  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1345          |
| start r-factor (free) = 0.2023      final r-factor (free) = 0.1816          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8490 = 2.13 * 0.50 * 5.4292 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7564 = 2.13 * 0.50 * 5.3502 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1345      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1816      final r-factor (free) = 0.1788          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9216 = 0.17 * 1.00 * 5.3502 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9095 = 0.17 * 1.00 * 5.2820 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    90.00   14.73    None  None   None       |
|    all(noH): 2823   0      0.37    90.00   14.73    None  None   None       |
|    Sol.    : 438    0      4.71    83.39   37.28    None  None   None       |
|    Mac.    : 2385   0      0.37    90.00   10.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.365 -   9.328: 1379   |   5:    45.180 -  54.143:  106        |
|      1:     9.328 -  18.291:  833   |   6:    54.143 -  63.106:   49        |
|      2:    18.291 -  27.254:  198   |   7:    63.106 -  72.069:   12        |
|      3:    27.254 -  36.217:  134   |   8:    72.069 -  81.033:    4        |
|      4:    36.217 -  45.180:  103   |   9:    81.033 -  89.996:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1317 r_free = 0.1788             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1784             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1784   ksol= 0.32   Bsol= 44.33   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.43,-0.37,0.82,-0.00,0.00,0.00); trace/3= 0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273249                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.1066 0.1397      5.4339      5.6272|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.0980 0.1354      5.5539      5.8114|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.1293 0.1678      5.6271      5.9247|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.1477 0.1859      5.6183      5.7179|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.1597 0.2110      5.4612      5.7136|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.1455 0.1931      5.3312      5.5387|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.1521 0.1945       5.308      5.4612|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.1402 0.2050      5.1927      5.4883|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.1388 0.1988      5.1592      5.3941|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.1324 0.1913      5.0672       5.298|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.1329 0.1969      5.0651      5.3963|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.1297 0.1935      4.9919      5.2237|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.1361 0.1886      4.9064      5.1627|
| 14:  2.0105 -  1.9616 0.45    595   65 0.1149 0.1541      4.7416       4.928|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.93   9.82   0.98     0.96       8033.42|
|  2:  4.6840 -  3.7362  1357   146  0.94   9.34   1.02     1.01      11282.33|
|  3:  3.7362 -  3.2693  1324   144  0.91  14.13   1.03     1.03      13942.71|
|  4:  3.2693 -  2.9729  1345   158  0.89  17.17   1.01     0.97      14015.06|
|  5:  2.9729 -  2.7612  1310   144  0.89  17.56   0.99     0.97      10056.39|
|  6:  2.7612 -  2.5992  1313   145  0.88  18.38   0.98     0.96       8785.57|
|  7:  2.5992 -  2.4696  1309   138  0.88  18.15   1.00     0.98       8014.51|
|  8:  2.4696 -  2.3625  1281   152  0.88  18.16   0.99     0.96       6636.09|
|  9:  2.3625 -  2.2719  1305   145  0.89  17.75   1.02     0.98       6225.20|
| 10:  2.2719 -  2.1937  1289   151  0.89  17.23   1.01     0.99       5345.18|
| 11:  2.1937 -  2.1253  1299   132  0.88  18.58   1.01     0.97       5528.52|
| 12:  2.1253 -  2.0647  1275   151  0.89  17.90   1.01     1.00       5005.13|
| 13:  2.0647 -  2.0105  1214   127  0.88  18.54   1.02     1.00       4162.64|
| 14:  2.0105 -  1.9616   595    65  0.90  16.44   1.00     0.97       3089.54|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     3089.54 max =        14015.06 mean =      8119.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.29|
|phase err.(test): min =        0.00 max =           89.84 mean =        15.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1783   ksol= 0.32   Bsol= 44.47   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.62,0.51,-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: 5.272979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1783   ksol= 0.32   Bsol= 44.47   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,-0.62,0.51,-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: 5.272979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.6840 0.99   1414  161 0.1063 0.1394      5.4303      5.6258|
|  2:  4.6840 -  3.7362 0.99   1357  146 0.0981 0.1356      5.5541      5.8133|
|  3:  3.7362 -  3.2693 0.99   1324  144 0.1293 0.1679      5.6276      5.9251|
|  4:  3.2693 -  2.9729 0.99   1345  158 0.1477 0.1859      5.6183       5.718|
|  5:  2.9729 -  2.7612 0.99   1310  144 0.1597 0.2109      5.4613      5.7137|
|  6:  2.7612 -  2.5992 0.99   1313  145 0.1455 0.1932      5.3312       5.539|
|  7:  2.5992 -  2.4696 0.99   1309  138 0.1521 0.1944      5.3078      5.4608|
|  8:  2.4696 -  2.3625 0.98   1281  152 0.1401 0.2048      5.1924      5.4878|
|  9:  2.3625 -  2.2719 0.98   1305  145 0.1388 0.1989       5.159      5.3945|
| 10:  2.2719 -  2.1937 1.00   1289  151 0.1324 0.1912      5.0671      5.2974|
| 11:  2.1937 -  2.1253 0.98   1299  132 0.1329 0.1969      5.0648       5.396|
| 12:  2.1253 -  2.0647 0.98   1275  151 0.1297 0.1936       4.992      5.2236|
| 13:  2.0647 -  2.0105 0.93   1214  127 0.1361 0.1888      4.9065      5.1633|
| 14:  2.0105 -  1.9616 0.45    595   65 0.1150 0.1542      4.7421      4.9282|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1465 -  4.6840  1414   161  0.93   9.79   0.98     0.96       7980.82|
|  2:  4.6840 -  3.7362  1357   146  0.94   9.32   1.02     1.00      11264.78|
|  3:  3.7362 -  3.2693  1324   144  0.91  14.14   1.03     1.03      13967.12|
|  4:  3.2693 -  2.9729  1345   158  0.89  17.17   1.00     0.97      14022.49|
|  5:  2.9729 -  2.7612  1310   144  0.89  17.56   0.99     0.96      10062.15|
|  6:  2.7612 -  2.5992  1313   145  0.88  18.37   0.98     0.95       8786.74|
|  7:  2.5992 -  2.4696  1309   138  0.88  18.15   0.99     0.97       8012.69|
|  8:  2.4696 -  2.3625  1281   152  0.88  18.15   0.98     0.95       6633.01|
|  9:  2.3625 -  2.2719  1305   145  0.89  17.74   1.01     0.97       6221.59|
| 10:  2.2719 -  2.1937  1289   151  0.89  17.22   1.00     0.98       5340.71|
| 11:  2.1937 -  2.1253  1299   132  0.88  18.56   1.01     0.96       5523.90|
| 12:  2.1253 -  2.0647  1275   151  0.89  17.89   1.00     1.00       5003.51|
| 13:  2.0647 -  2.0105  1214   127  0.88  18.54   1.01     0.99       4163.73|
| 14:  2.0105 -  1.9616   595    65  0.90  16.45   0.99     0.96       3093.30|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3093.30 max =        14022.49 mean =      8115.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.28|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.713)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    90.13   14.87    None  None   None       |
|    all(noH): 2823   0      0.50    90.13   14.87    None  None   None       |
|    Sol.    : 438    0      4.85    83.53   37.42    None  None   None       |
|    Mac.    : 2385   0      0.50    90.13   10.73    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:     0.503 -   9.466: 1379   |   5:    45.318 -  54.281:  106        |
|      1:     9.466 -  18.429:  833   |   6:    54.281 -  63.244:   49        |
|      2:    18.429 -  27.392:  198   |   7:    63.244 -  72.207:   12        |
|      3:    27.392 -  36.355:  134   |   8:    72.207 -  81.170:    4        |
|      4:    36.355 -  45.318:  103   |   9:    81.170 -  90.134:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.843
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 318
   mapped sites are within: 0.729 - 5.843

peak=    9.449 closest distance to " CB  VAL A 230 " =    1.471
peak=    7.075 closest distance to " CG2 VAL A 296 " =    1.201
peak=    7.015 closest distance to " O   HOH Z 130 " =    1.379
peak=    6.912 closest distance to " CG  ARG A 138 " =    1.210
peak=    6.154 closest distance to " O   HOH Z  15 " =    1.082
peak=    5.984 closest distance to " O   HOH Z  65 " =    1.518
peak=    5.833 closest distance to " CD2 LEU A   5 " =    1.362
peak=    5.760 closest distance to " O   HOH Z 390 " =    1.172
peak=    5.755 closest distance to " O   HOH Z   7 " =    2.070
peak=    5.632 closest distance to " O   HOH Z 222 " =    1.463
peak=    5.565 closest distance to " NH2 ARG A  56 " =    2.261
peak=    5.564 closest distance to " O   HOH Z 183 " =    1.663
peak=    5.403 closest distance to " O   HOH Z 214 " =    1.673
peak=    5.237 closest distance to " O   HOH Z 410 " =    1.748
peak=    5.180 closest distance to " NE2 GLN A  11 " =    1.229
peak=    5.096 closest distance to " O   HOH Z 385 " =    1.009
peak=    5.092 closest distance to " NH1 ARG A  56 " =    1.193
peak=    5.002 closest distance to " CD1AILE A 234 " =    0.986
peak=    4.958 closest distance to " CB  VAL A 230 " =    1.194
peak=    4.944 closest distance to " O   HOH Z 403 " =    1.522
peak=    4.927 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.914 closest distance to " O   HOH Z 239 " =    1.773
peak=    4.901 closest distance to " O   HOH Z 132 " =    1.342
peak=    4.876 closest distance to " O   HOH Z 350 " =    1.407
peak=    4.858 closest distance to " O   HOH Z 427 " =    1.421
peak=    4.803 closest distance to " O   HOH Z 186 " =    1.528
peak=    4.789 closest distance to " O   HOH Z 232 " =    2.097
peak=    4.771 closest distance to " O   HOH Z 133 " =    1.772
peak=    4.749 closest distance to " O   HOH Z 424 " =    1.329
peak=    4.746 closest distance to " O   HOH Z 147 " =    1.558
peak=    4.742 closest distance to " O   HOH Z 369 " =    1.957
peak=    4.670 closest distance to " CG  PRO A 198 " =    1.412
peak=    4.652 closest distance to " NH1 ARG A 138 " =    1.035
peak=    4.641 closest distance to " CB  SER A   3 " =    1.466
peak=    4.636 closest distance to " O   HOH Z  63 " =    1.502
peak=    4.615 closest distance to " O   HOH Z 126 " =    1.827
peak=    4.598 closest distance to " O   HOH Z 124 " =    1.490
peak=    4.568 closest distance to " O   HOH Z 316 " =    2.992
peak=    4.560 closest distance to " CG  LEU A   5 " =    1.247
peak=    4.531 closest distance to " CG  LEU A 228 " =    1.150
peak=    4.499 closest distance to " O   HOH Z  37 " =    1.385
peak=    4.496 closest distance to " O   HOH Z 182 " =    1.384
peak=    4.458 closest distance to " CB  GLN A 223 " =    1.330
peak=    4.407 closest distance to " O   HOH Z 117 " =    1.438
peak=    4.386 closest distance to " O   HOH Z 373 " =    1.980
peak=    4.380 closest distance to " O   HOH Z 127 " =    1.116
peak=    4.377 closest distance to " O   HOH Z 225 " =    1.535
peak=    4.338 closest distance to " CA  SER A  87 " =    0.914
peak=    4.309 closest distance to " O   HOH Z 193 " =    1.847
peak=    4.302 closest distance to " O   HOH Z 144 " =    1.645
peak=    4.277 closest distance to " CB  SER A  63 " =    1.301
peak=    4.274 closest distance to " CB  ASN A 187 " =    1.043
peak=    4.261 closest distance to " O   HOH Z 414 " =    1.509
peak=    4.245 closest distance to " O   HOH Z  48 " =    1.743
peak=    4.245 closest distance to " CB  ASN A 148 " =    1.276
peak=    4.237 closest distance to " O   HOH Z 236 " =    1.816
peak=    4.229 closest distance to " O   PRO A 198 " =    1.347
peak=    4.227 closest distance to " CG  LEU A 167 " =    1.240
peak=    4.213 closest distance to " O   HOH Z 344 " =    1.266
peak=    4.209 closest distance to " O   HOH Z 116 " =    1.312
peak=    4.207 closest distance to " NH2BARG A 102 " =    0.979
peak=    4.178 closest distance to " O   HOH Z 427 " =    2.605
peak=    4.174 closest distance to " O   HOH Z 108 " =    1.902
peak=    4.173 closest distance to " NZ BLYS A 290 " =    1.053
peak=    4.143 closest distance to " O   HOH Z 236 " =    1.835
peak=    4.141 closest distance to " CB  TYR A 169 " =    0.877
peak=    4.134 closest distance to " CD  ARG A 138 " =    0.981
peak=    4.125 closest distance to " O   HOH Z 148 " =    1.913
peak=    4.123 closest distance to " CB  ARG A 275 " =    0.964
peak=    4.117 closest distance to " O   HOH Z 334 " =    2.822
peak=    4.111 closest distance to " O   HOH Z 126 " =    1.546
peak=    4.106 closest distance to " CB  ASP A 124 " =    0.872
peak=    4.094 closest distance to " CD2 LEU A 228 " =    1.318
peak=    4.090 closest distance to " OD2 ASP A 286 " =    2.696
peak=    4.082 closest distance to " CD2 TRP A 179 " =    2.150
peak=    4.077 closest distance to " O   HOH Z  49 " =    1.411
peak=    4.072 closest distance to " CB  SER A 216 " =    0.973
peak=    4.069 closest distance to " O   HOH Z 357 " =    1.564
peak=    4.057 closest distance to " O   HOH Z  59 " =    2.285
peak=    4.051 closest distance to " CB  PRO A  54 " =    1.048
peak=    4.042 closest distance to " CB  VAL A 296 " =    1.209
peak=    4.042 closest distance to " CE3 TRP A 274 " =    2.290
peak=    4.032 closest distance to " OD1 ASN A 217 " =    1.689
peak=    4.031 closest distance to " O   HOH Z 217 " =    1.831
peak=    4.018 closest distance to " OE1 GLU A   2 " =    2.085
peak=    4.010 closest distance to " CD BLYS A 290 " =    1.095
peak=    4.006 closest distance to " O   HOH Z  57 " =    1.178
peak=    3.997 closest distance to " CG  GLN A  88 " =    1.047
peak=    3.992 closest distance to " NH2BARG A 190 " =    1.629
peak=    3.987 closest distance to " O   HOH Z 143 " =    1.461
peak=    3.984 closest distance to " O   HOH Z 134 " =    1.599
peak=    3.982 closest distance to " O   HOH Z 298 " =    2.022
peak=    3.980 closest distance to " O   HOH Z 411 " =    3.430
peak=    3.974 closest distance to " CA  ILE A 234 " =    0.960
peak=    3.967 closest distance to " O   HOH Z 258 " =    2.357
peak=    3.967 closest distance to " O   HOH Z 139 " =    1.475
peak=    3.922 closest distance to " NZ  LYS A 117 " =    1.444
peak=    3.919 closest distance to " O   HOH Z 184 " =    1.478
peak=    3.908 closest distance to " CB  MET A  40 " =    0.877
peak=    3.902 closest distance to " O   HOH Z 380 " =    1.915
peak=    3.901 closest distance to " O   HOH Z 361 " =    1.495
peak=    3.899 closest distance to " O   HOH Z 171 " =    2.514
peak=    3.894 closest distance to " CA  LEU A 282 " =    1.064
peak=    3.873 closest distance to " CB  GLU A 128 " =    1.016
peak=    3.857 closest distance to " O   HOH Z 222 " =    1.935
peak=    3.827 closest distance to " O   HOH Z 371 " =    2.690
peak=    3.820 closest distance to " O   HOH Z  51 " =    1.961
peak=    3.806 closest distance to " NE AARG A 275 " =    1.512
peak=    3.803 closest distance to " CG2 THR A 221 " =    1.358
peak=    3.792 closest distance to " ND2 ASN A 249 " =    1.885
peak=    3.780 closest distance to " CB  SER A 210 " =    0.898
peak=    3.770 closest distance to " O   HOH Z 260 " =    1.289
peak=    3.757 closest distance to " CB  MET A  47 " =    1.050
peak=    3.755 closest distance to " CA  ASP A  50 " =    1.113
peak=    3.741 closest distance to " O   HOH Z 207 " =    2.269
peak=    3.739 closest distance to " CB  ASN A  39 " =    0.799
peak=    3.737 closest distance to " N   GLN A 278 " =    0.879
peak=    3.722 closest distance to " O   HOH Z 234 " =    3.638
peak=    3.721 closest distance to " O   HOH Z  61 " =    1.738
peak=    3.721 closest distance to " NH2BARG A 145 " =    1.959
peak=    3.719 closest distance to " O   HOH Z  78 " =    1.607
peak=    3.705 closest distance to " CA  GLU A 152 " =    1.052
peak=    3.700 closest distance to " O   HOH Z 368 " =    2.075
peak=    3.698 closest distance to " CD BARG A 102 " =    1.318
peak=    3.692 closest distance to " O   HOH Z   6 " =    2.016
peak=    3.691 closest distance to " CA  ALA A  51 " =    1.149
peak=    3.688 closest distance to " CB  ILE A 234 " =    0.849
peak=    3.672 closest distance to " CG2 VAL A 257 " =    0.944
peak=    3.662 closest distance to " CG  ARG A 159 " =    0.911
peak=    3.648 closest distance to " N   ARG A 156 " =    1.339
peak=    3.643 closest distance to " O   HOH Z 193 " =    1.719
peak=    3.642 closest distance to " O   PRO A 198 " =    1.548
peak=    3.639 closest distance to " O   HOH Z 419 " =    2.031
peak=    3.636 closest distance to " CZ  PHE A 192 " =    0.986
peak=    3.631 closest distance to " CG1 ILE A 120 " =    1.387
peak=    3.623 closest distance to " CZ3 TRP A 123 " =    1.407
peak=    3.619 closest distance to " O   SER A  87 " =    2.365
peak=    3.614 closest distance to " OG BSER A 212 " =    2.725
peak=    3.612 closest distance to " O   HOH Z 227 " =    1.578
peak=    3.607 closest distance to " O   HOH Z  32 " =    2.409
peak=    3.607 closest distance to " ND1 HIS A  86 " =    1.787
peak=    3.605 closest distance to " O   HOH Z 116 " =    2.684
peak=    3.602 closest distance to " O   HOH Z 217 " =    2.317
peak=    3.602 closest distance to " ND2 ASN A  60 " =    3.051
peak=    3.601 closest distance to " CG  LYS A 166 " =    1.276
peak=    3.597 closest distance to " CB  GLU A 152 " =    1.354
peak=    3.596 closest distance to " O   HOH Z 272 " =    1.933
peak=    3.592 closest distance to " O   HOH Z 155 " =    1.604
peak=    3.591 closest distance to " O   ASN A 301 " =    2.315
peak=    3.587 closest distance to " CB  VAL A 265 " =    1.258
peak=    3.581 closest distance to " O   HOH Z   9 " =    1.931
peak=    3.580 closest distance to " O   HOH Z  61 " =    1.487
peak=    3.580 closest distance to " NH1BARG A 275 " =    1.523
peak=    3.577 closest distance to " CG2 ILE A 234 " =    0.927
peak=    3.572 closest distance to " CD1 ILE A  33 " =    1.699
peak=    3.570 closest distance to " CB  VAL A 202 " =    1.558
peak=    3.567 closest distance to " O   HOH Z 384 " =    1.743
peak=    3.551 closest distance to " OE2 GLU A   2 " =    1.877
peak=    3.549 closest distance to " O   HOH Z 263 " =    2.203
peak=    3.548 closest distance to " N   TYR A  15 " =    0.959
peak=    3.535 closest distance to " CB  ALA A  34 " =    1.016
peak=    3.534 closest distance to " NE2 GLN A  58 " =    5.288
peak=    3.534 closest distance to " O   HOH Z 105 " =    1.306
peak=    3.533 closest distance to " O   HOH Z 281 " =    4.573
peak=    3.533 closest distance to " NH1AARG A 145 " =    1.071
peak=    3.531 closest distance to " CB  ALA A 161 " =    0.914
peak=    3.531 closest distance to " CB  LEU A 300 " =    1.010
peak=    3.526 closest distance to " OG  SER A 276 " =    0.932
peak=    3.524 closest distance to " O   HOH Z 271 " =    2.062
peak=    3.518 closest distance to " CB  ASN A 142 " =    0.815
peak=    3.515 closest distance to " NH1 ARG A  66 " =    1.685
peak=    3.514 closest distance to " OE1 GLN A 240 " =    1.613
peak=    3.513 closest distance to " NE2 GLN A  58 " =    3.158
peak=    3.508 closest distance to " O   HOH Z 383 " =    2.519
peak=    3.502 closest distance to " O   HOH Z 120 " =    1.145
peak=    3.495 closest distance to " O   HOH Z 220 " =    1.515
peak=    3.493 closest distance to " O   HOH Z 438 " =    2.622
peak=    3.492 closest distance to " O   HOH Z 119 " =    1.465
peak=    3.490 closest distance to " N   ALA A   1 " =    1.241
peak=    3.488 closest distance to " OG  SER A  62 " =    2.818
peak=    3.484 closest distance to " O   HOH Z   7 " =    3.251
peak=    3.483 closest distance to " CA  ASN A 127 " =    0.989
peak=    3.483 closest distance to " O   HOH Z  97 " =    1.312
peak=    3.477 closest distance to " O   HOH Z 132 " =    2.058
peak=    3.475 closest distance to " CB  LEU A 237 " =    0.909
peak=    3.471 closest distance to " O   HOH Z 145 " =    2.540
peak=    3.471 closest distance to " ND2 ASN A 187 " =    1.694
peak=    3.470 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.465 closest distance to " O   HOH Z 302 " =    1.693
peak=    3.460 closest distance to " CD1 LEU A 300 " =    1.227
peak=    3.455 closest distance to " CB  ASN A 148 " =    1.920
peak=    3.449 closest distance to " O   HOH Z 329 " =    3.654
peak=    3.430 closest distance to " O   HOH Z 133 " =    2.225
peak=    3.429 closest distance to " O   HOH Z 371 " =    1.796
peak=    3.429 closest distance to " OD1 ASP A 231 " =    1.758
peak=    3.427 closest distance to " O   CYS A 168 " =    1.474
peak=    3.425 closest distance to " O   HOH Z 247 " =    1.406
peak=    3.419 closest distance to " NH1 ARG A  14 " =    0.954
peak=    3.418 closest distance to " O   HOH Z 434 " =    1.547
peak=    3.416 closest distance to " O   HOH Z  40 " =    2.556
peak=    3.413 closest distance to " CG  PRO A 280 " =    0.978
peak=    3.410 closest distance to " O   HOH Z  69 " =    2.378
peak=    3.409 closest distance to " NH2 ARG A 219 " =    1.724
peak=    3.394 closest distance to " O   HOH Z 263 " =    1.481
peak=    3.392 closest distance to " CB  GLN A 183 " =    1.122
peak=    3.390 closest distance to " CH2 TRP A 150 " =    1.020
peak=    3.388 closest distance to " O   HOH Z 412 " =    4.612
peak=    3.383 closest distance to " CB  TRP A 266 " =    1.003
peak=    3.383 closest distance to " O   HOH Z 281 " =    2.260
peak=    3.383 closest distance to " N   PHE A 130 " =    1.268
peak=    3.381 closest distance to " CB  THR A 157 " =    1.050
peak=    3.381 closest distance to " CG1 ILE A  33 " =    1.341
peak=    3.380 closest distance to " O   HOH Z 146 " =    1.775
peak=    3.380 closest distance to " O   HOH Z 282 " =    1.521
peak=    3.378 closest distance to " CA  ALA A 295 " =    0.945
peak=    3.374 closest distance to " O   HOH Z 145 " =    1.934
peak=    3.374 closest distance to " CG  LYS A  76 " =    1.509
peak=    3.370 closest distance to " O   HOH Z  59 " =    2.032
peak=    3.369 closest distance to " O   HOH Z  64 " =    1.864
peak=    3.367 closest distance to " CB  GLU A 236 " =    1.320
peak=    3.360 closest distance to " O   HOH Z 278 " =    1.074
peak=    3.360 closest distance to " CA  ALA A 154 " =    1.022
peak=    3.358 closest distance to " CB  SER A 276 " =    1.170
peak=    3.347 closest distance to " O   HOH Z  18 " =    2.036
peak=    3.343 closest distance to " O   ALA A 291 " =    1.466
peak=    3.341 closest distance to " O   GLY A 302 " =    2.242
peak=    3.335 closest distance to " O   HOH Z   1 " =    1.898
peak=    3.334 closest distance to " O   HOH Z 424 " =    3.140
peak=    3.331 closest distance to " C   GLN A  88 " =    1.438
peak=    3.328 closest distance to " O   HOH Z 358 " =    1.405
peak=    3.320 closest distance to " CG  GLN A  55 " =    1.785
peak=    3.320 closest distance to " CG1 ILE A 151 " =    1.093
peak=    3.313 closest distance to " O   HOH Z 260 " =    1.306
peak=    3.296 closest distance to " O   HOH Z  59 " =    1.576
peak=    3.294 closest distance to " CG  GLU A   2 " =    1.309
peak=    3.292 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.290 closest distance to " CA  THR A 221 " =    0.854
peak=    3.290 closest distance to " O   HOH Z 392 " =    1.364
peak=    3.284 closest distance to " CD  ARG A 269 " =    1.017
peak=    3.283 closest distance to " O   HOH Z 139 " =    2.067
peak=    3.281 closest distance to " O   HOH Z 200 " =    5.576
peak=    3.277 closest distance to " CG1 VAL A 197 " =    0.910
peak=    3.268 closest distance to " CA  ALA A  21 " =    1.024
peak=    3.266 closest distance to " O   ALA A  10 " =    1.616
peak=    3.265 closest distance to " N   VAL A 126 " =    1.202
peak=    3.264 closest distance to " O   HOH Z 108 " =    1.740
peak=    3.260 closest distance to " CA  ALA A 158 " =    1.026
peak=    3.258 closest distance to " CB  LEU A 143 " =    1.064
peak=    3.258 closest distance to " O   HOH Z  22 " =    1.978
peak=    3.251 closest distance to " CB  THR A  82 " =    1.208
peak=    3.238 closest distance to " OH  TYR A 186 " =    0.969
peak=    3.237 closest distance to " CA  VAL A  41 " =    0.910
peak=    3.236 closest distance to " O   HOH Z 233 " =    1.372
peak=    3.233 closest distance to " CG1BVAL A  72 " =    1.145
peak=    3.230 closest distance to " CB  TRP A 179 " =    1.506
peak=    3.226 closest distance to " O   HOH Z  80 " =    1.648
peak=    3.221 closest distance to " CB  PHE A  16 " =    1.179
peak=    3.217 closest distance to " O  BHOH Z 338 " =    2.382
peak=    3.216 closest distance to " O   HOH Z 344 " =    2.799
peak=    3.216 closest distance to " O   HOH Z 227 " =    2.027
peak=    3.216 closest distance to " CA  MET A  47 " =    1.137
peak=    3.213 closest distance to " CG  LYS A 119 " =    1.326
peak=    3.212 closest distance to " O   HOH Z 193 " =    1.862
peak=    3.212 closest distance to " O   HOH Z 415 " =    5.843
peak=    3.209 closest distance to " CA  ASN A  74 " =    1.165
peak=    3.207 closest distance to " CA  ILE A 106 " =    0.829
peak=    3.207 closest distance to " SD  MET A  93 " =    1.411
peak=    3.203 closest distance to " O   HOH Z 374 " =    1.102
peak=    3.203 closest distance to " O   HOH Z 152 " =    2.272
peak=    3.202 closest distance to " O   HOH Z  71 " =    1.211
peak=    3.200 closest distance to " O   ALA A 165 " =    1.227
peak=    3.194 closest distance to " O   HOH Z 332 " =    1.593
peak=    3.191 closest distance to " O   HOH Z 122 " =    1.896
peak=    3.190 closest distance to " C   ASP A 298 " =    1.506
peak=    3.189 closest distance to " CB  TRP A 150 " =    1.391
peak=    3.188 closest distance to " CA  GLN A 223 " =    0.945
peak=    3.182 closest distance to " O   HOH Z 326 " =    3.799
peak=    3.179 closest distance to " CB  ALA A  10 " =    0.956
peak=    3.178 closest distance to " O   HOH Z  76 " =    1.517
peak=    3.177 closest distance to " CA  TYR A 186 " =    1.498
peak=    3.175 closest distance to " CB  GLU A 152 " =    1.393
peak=    3.175 closest distance to " O   HOH Z 282 " =    2.434
peak=    3.173 closest distance to " NH2 ARG A 269 " =    0.945
peak=    3.166 closest distance to " CB  ARG A 138 " =    1.565
peak=    3.166 closest distance to " O   HOH Z 261 " =    1.810
peak=    3.165 closest distance to " CD2 LEU A 143 " =    1.679
peak=    3.163 closest distance to " O   HOH Z 282 " =    2.247
peak=    3.161 closest distance to " CZ2 TRP A 266 " =    1.010
peak=    3.155 closest distance to " CE3 TRP A 274 " =    1.423
peak=    3.153 closest distance to " CB  ALA A 104 " =    0.734
peak=    3.152 closest distance to " CA  GLY A 267 " =    1.293
peak=    3.147 closest distance to " O   HOH Z 367 " =    2.188
peak=    3.146 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.145 closest distance to " NE2 GLN A 223 " =    1.615
peak=    3.144 closest distance to " O   HOH Z 158 " =    2.323
peak=    3.143 closest distance to " CA  ALA A 160 " =    1.257
peak=    3.142 closest distance to " O   HOH Z 204 " =    1.562
peak=    3.142 closest distance to " O   HOH Z 251 " =    1.893
peak=    3.136 closest distance to " O   HOH Z 181 " =    2.211
peak=    3.136 closest distance to " O   HOH Z 166 " =    1.414
peak=    3.132 closest distance to " CG  GLN A 278 " =    3.890
peak=    3.131 closest distance to " O   HOH Z 271 " =    2.238
peak=    3.128 closest distance to " O   HOH Z  57 " =    1.561
peak=    3.127 closest distance to " O   HOH Z 135 " =    1.944
peak=    3.127 closest distance to " N   SER A 271 " =    1.070
peak=    3.126 closest distance to " O   ASN A 209 " =    1.785
peak=    3.121 closest distance to " CG1 ILE A  49 " =    1.191
peak=    3.097 closest distance to " O   HOH Z 189 " =    2.656
peak=    3.083 closest distance to " CB  PHE A 225 " =    1.345
peak=    3.082 closest distance to " N   CYS A 260 " =    0.916
peak=    3.079 closest distance to " CB  PRO A  54 " =    1.400
peak=    3.070 closest distance to " NH2AARG A 190 " =    1.412
peak=    3.070 closest distance to " O   HOH Z 213 " =    2.589
peak=    3.069 closest distance to " O   HOH Z 345 " =    1.851
peak=    3.066 closest distance to " O   HOH Z  47 " =    1.669
peak=    3.056 closest distance to " O   HOH Z  40 " =    2.162
peak=    3.044 closest distance to " CD  LYS A 166 " =    1.354

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.214 - 5.775
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 182 from: 192
   mapped sites are within: 0.708 - 5.775

peak=   -5.697 closest distance to " CG2 VAL A 230 " =    0.801
peak=   -4.953 closest distance to " OE1 GLN A  88 " =    0.827
peak=   -4.688 closest distance to " O   HOH Z 290 " =    1.095
peak=   -4.594 closest distance to " O   PRO A 198 " =    1.271
peak=   -4.369 closest distance to " O   HOH Z 298 " =    0.937
peak=   -4.327 closest distance to " O   HOH Z 385 " =    0.788
peak=   -4.207 closest distance to " O   HOH Z 198 " =    2.384
peak=   -4.169 closest distance to " CG  MET A 105 " =    0.938
peak=   -4.146 closest distance to " CD  ARG A 138 " =    1.094
peak=   -4.126 closest distance to " O   HOH Z  71 " =    0.920
peak=   -4.084 closest distance to " C   ASN A 285 " =    2.265
peak=   -4.035 closest distance to " OG ASER A 134 " =    1.125
peak=   -4.034 closest distance to " O   HOH Z  51 " =    0.953
peak=   -4.002 closest distance to " O   ALA A   1 " =    1.131
peak=   -3.991 closest distance to " O   HOH Z  43 " =    1.545
peak=   -3.953 closest distance to " CG  ARG A 138 " =    0.976
peak=   -3.909 closest distance to " C   ALA A 158 " =    1.267
peak=   -3.886 closest distance to " CD2 LEU A   5 " =    0.881
peak=   -3.884 closest distance to " OE1 GLU A 277 " =    2.398
peak=   -3.872 closest distance to " CE2 TYR A  30 " =    2.842
peak=   -3.871 closest distance to " CG  PRO A 163 " =    2.463
peak=   -3.863 closest distance to " O   HOH Z  61 " =    1.056
peak=   -3.851 closest distance to " CD  ARG A  14 " =    3.012
peak=   -3.851 closest distance to " CD  LYS A 289 " =    2.472
peak=   -3.823 closest distance to " O   HOH Z 207 " =    1.874
peak=   -3.791 closest distance to " OD1 ASN A  60 " =    0.883
peak=   -3.788 closest distance to " O   HOH Z 388 " =    1.835
peak=   -3.734 closest distance to " NH2AARG A 275 " =    5.650
peak=   -3.733 closest distance to " NH2 ARG A  79 " =    1.894
peak=   -3.731 closest distance to " CG  GLN A  88 " =    0.910
peak=   -3.730 closest distance to " O   HOH Z  15 " =    0.799
peak=   -3.724 closest distance to " OG BSER A 134 " =    1.552
peak=   -3.709 closest distance to " OG  SER A  87 " =    1.295
peak=   -3.704 closest distance to " CD  GLN A  58 " =    0.864
peak=   -3.685 closest distance to " CD  GLU A 277 " =    0.834
peak=   -3.675 closest distance to " CA  ASP A  27 " =    2.361
peak=   -3.672 closest distance to " O   HOH Z 134 " =    2.411
peak=   -3.668 closest distance to " CA  GLY A 133 " =    1.979
peak=   -3.668 closest distance to " O   HOH Z 377 " =    1.264
peak=   -3.665 closest distance to " CB  PRO A 243 " =    2.595
peak=   -3.661 closest distance to " CG  ASP A 231 " =    0.758
peak=   -3.631 closest distance to " CB  ALA A 248 " =    1.904
peak=   -3.630 closest distance to " CG  GLU A 152 " =    0.758
peak=   -3.612 closest distance to " O   ALA A  51 " =    1.465
peak=   -3.593 closest distance to " O   HOH Z 389 " =    4.589
peak=   -3.591 closest distance to " CB  ALA A   9 " =    2.574
peak=   -3.590 closest distance to " O   HOH Z 415 " =    0.918
peak=   -3.582 closest distance to " O   HOH Z 266 " =    4.645
peak=   -3.578 closest distance to " CB  TYR A  15 " =    2.063
peak=   -3.570 closest distance to " O   HOH Z  13 " =    1.513
peak=   -3.562 closest distance to " N   ALA A 292 " =    2.305
peak=   -3.559 closest distance to " O   HOH Z  39 " =    1.196
peak=   -3.555 closest distance to " CD1 LEU A 101 " =    2.397
peak=   -3.549 closest distance to " OD1 ASN A 301 " =    1.925
peak=   -3.539 closest distance to " O   HOH Z 103 " =    1.637
peak=   -3.536 closest distance to " O   HOH Z 166 " =    1.527
peak=   -3.532 closest distance to " O   HOH Z 359 " =    1.747
peak=   -3.530 closest distance to " O   HOH Z  28 " =    1.312
peak=   -3.519 closest distance to " N   SER A  12 " =    1.223
peak=   -3.501 closest distance to " O   HOH Z  60 " =    1.457
peak=   -3.493 closest distance to " O   GLY A  98 " =    2.031
peak=   -3.489 closest distance to " CD1 TRP A 179 " =    0.796
peak=   -3.488 closest distance to " O   HOH Z 102 " =    1.337
peak=   -3.479 closest distance to " O   HOH Z 124 " =    3.039
peak=   -3.471 closest distance to " O   HOH Z 117 " =    0.768
peak=   -3.462 closest distance to " CB  ALA A 100 " =    2.483
peak=   -3.462 closest distance to " O   HOH Z 185 " =    2.307
peak=   -3.454 closest distance to " O   HOH Z 211 " =    1.226
peak=   -3.450 closest distance to " CD  LYS A 166 " =    2.410
peak=   -3.449 closest distance to " O   PRO A 163 " =    1.932
peak=   -3.447 closest distance to " O   HOH Z  76 " =    1.146
peak=   -3.437 closest distance to " OG  SER A  97 " =    2.101
peak=   -3.437 closest distance to " CB  ALA A 227 " =    2.298
peak=   -3.436 closest distance to " O   HOH Z 198 " =    2.090
peak=   -3.434 closest distance to " CG2 ILE A 151 " =    2.414
peak=   -3.427 closest distance to " CA  GLY A  23 " =    1.878
peak=   -3.424 closest distance to " N   GLN A  88 " =    1.719
peak=   -3.418 closest distance to " CD2 LEU A 237 " =    2.345
peak=   -3.415 closest distance to " O   HOH Z 184 " =    1.472
peak=   -3.413 closest distance to " O   HOH Z 412 " =    5.775
peak=   -3.409 closest distance to " C   ARG A 269 " =    1.399
peak=   -3.401 closest distance to " O   ILE A  49 " =    1.741
peak=   -3.398 closest distance to " CD  ARG A 156 " =    1.935
peak=   -3.396 closest distance to " OG  SER A   3 " =    1.217
peak=   -3.396 closest distance to " O   HOH Z  53 " =    1.811
peak=   -3.388 closest distance to " O   HOH Z 111 " =    0.745
peak=   -3.386 closest distance to " CE1 PHE A  59 " =    1.482
peak=   -3.381 closest distance to " O   HOH Z 433 " =    1.258
peak=   -3.381 closest distance to " O   TYR A 247 " =    2.834
peak=   -3.374 closest distance to " CB  PRO A 163 " =    2.470
peak=   -3.371 closest distance to " ND2 ASN A  60 " =    1.719
peak=   -3.371 closest distance to " O   HOH Z 350 " =    2.052
peak=   -3.363 closest distance to " CA  GLY A  98 " =    1.932
peak=   -3.361 closest distance to " O   HOH Z 198 " =    0.877
peak=   -3.359 closest distance to " CB  CYS A 254 " =    1.704
peak=   -3.351 closest distance to " N   THR A 157 " =    1.696
peak=   -3.349 closest distance to " O   HOH Z 139 " =    1.117
peak=   -3.343 closest distance to " O   PRO A 243 " =    2.481
peak=   -3.342 closest distance to " O   ALA A 226 " =    1.524
peak=   -3.342 closest distance to " CZ  TYR A 172 " =    1.742
peak=   -3.339 closest distance to " OE1 GLU A   2 " =    1.694
peak=   -3.332 closest distance to " O   VAL A 197 " =    1.568
peak=   -3.330 closest distance to " O   HOH Z 427 " =    0.749
peak=   -3.326 closest distance to " O   HOH Z 130 " =    0.710
peak=   -3.323 closest distance to " O   HOH Z 139 " =    2.805
peak=   -3.322 closest distance to " O   HOH Z 365 " =    1.095
peak=   -3.322 closest distance to " O   HOH Z 189 " =    2.833
peak=   -3.318 closest distance to " N   HIS A 115 " =    2.089
peak=   -3.314 closest distance to " CZ  ARG A  24 " =    1.868
peak=   -3.314 closest distance to " CB  TYR A 172 " =    2.249
peak=   -3.312 closest distance to " CB  ASN A  39 " =    2.145
peak=   -3.302 closest distance to " CD1 TRP A 274 " =    1.362
peak=   -3.300 closest distance to " CB  GLN A  55 " =    1.243
peak=   -3.299 closest distance to " OE1 GLN A  11 " =    0.948
peak=   -3.294 closest distance to " O   HOH Z  40 " =    3.984
peak=   -3.288 closest distance to " CB  PHE A 283 " =    2.518
peak=   -3.272 closest distance to " CG1 VAL A 268 " =    2.607
peak=   -3.271 closest distance to " O   HOH Z 125 " =    3.159
peak=   -3.266 closest distance to " O   HOH Z  56 " =    0.744
peak=   -3.262 closest distance to " O   HOH Z 231 " =    1.577
peak=   -3.261 closest distance to " CE  MET A 188 " =    2.257
peak=   -3.260 closest distance to " CA  GLY A 241 " =    2.177
peak=   -3.258 closest distance to " CG  TRP A 266 " =    1.677
peak=   -3.254 closest distance to " O   TRP A 179 " =    1.488
peak=   -3.251 closest distance to " O   ARG A 159 " =    1.648
peak=   -3.236 closest distance to " CG2 VAL A 296 " =    0.784
peak=   -3.231 closest distance to " O   HOH Z 426 " =    1.924
peak=   -3.228 closest distance to " O   HOH Z 171 " =    2.875
peak=   -3.227 closest distance to " O   HOH Z 241 " =    1.204
peak=   -3.227 closest distance to " OG  SER A 245 " =    1.113
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.470
peak=   -3.226 closest distance to " OG1 THR A 178 " =    1.164
peak=   -3.226 closest distance to " O   HOH Z  20 " =    2.487
peak=   -3.225 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.225 closest distance to " O   HOH Z 414 " =    2.027
peak=   -3.221 closest distance to " O   HOH Z 176 " =    0.708
peak=   -3.221 closest distance to " O   GLN A 194 " =    1.328
peak=   -3.217 closest distance to " CB  ALA A 100 " =    2.216
peak=   -3.208 closest distance to " CB  PRO A  54 " =    2.390
peak=   -3.206 closest distance to " O   VAL A  67 " =    2.713
peak=   -3.205 closest distance to " O   GLN A  11 " =    1.644
peak=   -3.205 closest distance to " CD1 PHE A  59 " =    2.005
peak=   -3.202 closest distance to " N   GLN A  58 " =    1.784
peak=   -3.192 closest distance to " O   HOH Z 132 " =    0.787
peak=   -3.189 closest distance to " O   HOH Z 281 " =    4.349
peak=   -3.185 closest distance to " O   HOH Z 331 " =    1.330
peak=   -3.184 closest distance to " CG2 VAL A 296 " =    1.936
peak=   -3.184 closest distance to " O   THR A  18 " =    1.632
peak=   -3.183 closest distance to " O   GLY A  80 " =    2.434
peak=   -3.175 closest distance to " O   ALA A 256 " =    2.166
peak=   -3.172 closest distance to " NH2 ARG A  66 " =    3.314
peak=   -3.170 closest distance to " CD  ARG A 139 " =    1.810
peak=   -3.167 closest distance to " O   HOH Z 192 " =    2.485
peak=   -3.155 closest distance to " O   HOH Z 351 " =    1.360
peak=   -3.151 closest distance to " C   ASP A 124 " =    1.203
peak=   -3.150 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.147 closest distance to " CB  TRP A  85 " =    2.580
peak=   -3.146 closest distance to " O   HOH Z  97 " =    1.054
peak=   -3.142 closest distance to " CB  ALA A   7 " =    2.066
peak=   -3.142 closest distance to " O   HOH Z 285 " =    2.866
peak=   -3.139 closest distance to " N   PHE A  59 " =    2.061
peak=   -3.137 closest distance to " C   MET A 188 " =    1.691
peak=   -3.133 closest distance to " C   ASP A 231 " =    2.392
peak=   -3.127 closest distance to " CG1 ILE A  20 " =    2.353
peak=   -3.122 closest distance to " CE  LYS A  76 " =    2.903
peak=   -3.121 closest distance to " CB  ALA A 248 " =    2.403
peak=   -3.120 closest distance to " O   HOH Z 306 " =    3.148
peak=   -3.107 closest distance to " N   PHE A 225 " =    2.514
peak=   -3.107 closest distance to " O   HOH Z 390 " =    2.317
peak=   -3.105 closest distance to " CZ  ARG A 259 " =    0.790
peak=   -3.099 closest distance to " O   HOH Z  44 " =    2.100
peak=   -3.088 closest distance to " N   ASP A 171 " =    2.754
peak=   -3.080 closest distance to " CG  ARG A 219 " =    2.376
peak=   -3.059 closest distance to " O   HOH Z 165 " =    2.344
peak=   -3.058 closest distance to " CA  ASN A 217 " =    1.601
peak=   -3.056 closest distance to " O   HOH Z 221 " =    1.170
peak=   -3.053 closest distance to " CD2 TRP A 150 " =    1.112
peak=   -3.048 closest distance to " CA  THR A 157 " =    1.210
peak=   -3.045 closest distance to " O   HOH Z 409 " =    2.923
peak=   -3.039 closest distance to " O   HOH Z  60 " =    2.502
peak=   -3.033 closest distance to " CD2 LEU A 237 " =    2.369
peak=   -3.027 closest distance to " CZ3 TRP A 123 " =    1.666

================= 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    :  0.5082 0.5012   6.304572e+00   6.297202e+00
   1_bss:  0.4991 0.4879   6.300760e+00   6.291707e+00
   1_xyz:  0.4400 0.4675   6.235868e+00   6.262182e+00
   1_adp:  0.4042 0.4632   6.197220e+00   6.260650e+00
   1_occ:  0.4040 0.4635   6.196672e+00   6.260322e+00
   2_bss:  0.4023 0.4616   6.197976e+00   6.258987e+00
   2_xyz:  0.3291 0.3904   6.045012e+00   6.165186e+00
   2_adp:  0.3050 0.3794   6.001141e+00   6.138676e+00
   2_occ:  0.3047 0.3792   6.000414e+00   6.138490e+00
   3_bss:  0.3030 0.3765   6.000179e+00   6.136059e+00
   3_xyz:  0.2303 0.2962   5.769179e+00   5.949602e+00
   3_adp:  0.2074 0.2704   5.673739e+00   5.866220e+00
   3_occ:  0.2069 0.2694   5.671176e+00   5.863804e+00
   4_bss:  0.2058 0.2666   5.670196e+00   5.861461e+00
   4_xyz:  0.1604 0.2135   5.451847e+00   5.676378e+00
   4_adp:  0.1514 0.2036   5.399519e+00   5.625943e+00
   4_occ:  0.1512 0.2027   5.397501e+00   5.622969e+00
   5_bss:  0.1512 0.2023   5.397550e+00   5.622404e+00
   5_xyz:  0.1345 0.1816   5.290957e+00   5.521113e+00
   5_adp:  0.1317 0.1788   5.274553e+00   5.507019e+00
   5_occ:  0.1316 0.1784   5.273249e+00   5.504853e+00
   5_bss:  0.1316 0.1783   5.272979e+00   5.504853e+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:  0.336   0.000   8.542   8.945   7.494   0.000   0.000   0.000
   1_xyz:  0.336   0.000   8.542   8.945   7.494   0.000   0.000   0.000
   1_adp:  0.336   0.000   8.542   8.945   7.494   0.000   0.000   0.000
   1_occ:  0.336   0.000   8.542   8.945   7.494   0.000   0.000   0.000
   2_bss:  0.341  34.812   4.609   4.984   4.539   0.000   0.000   0.000
   2_xyz:  0.341  34.812   4.609   4.984   4.539   0.000   0.000   0.000
   2_adp:  0.341  34.812   4.609   4.984   4.539   0.000   0.000   0.000
   2_occ:  0.341  34.812   4.609   4.984   4.539   0.000   0.000   0.000
   3_bss:  0.329  45.750   2.646   2.342   2.650   0.000   0.000   0.000
   3_xyz:  0.329  45.750   2.646   2.342   2.650   0.000   0.000   0.000
   3_adp:  0.329  45.750   2.646   2.342   2.650   0.000   0.000   0.000
   3_occ:  0.329  45.750   2.646   2.342   2.650   0.000   0.000   0.000
   4_bss:  0.338  50.568   1.066   0.464   1.440   0.000   0.000   0.000
   4_xyz:  0.338  50.568   1.066   0.464   1.440   0.000   0.000   0.000
   4_adp:  0.338  50.568   1.066   0.464   1.440   0.000   0.000   0.000
   4_occ:  0.338  50.568   1.066   0.464   1.440   0.000   0.000   0.000
   5_bss:  0.325  44.334   0.434  -0.375   0.822  -0.000   0.000   0.000
   5_xyz:  0.325  44.334   0.434  -0.375   0.822  -0.000   0.000   0.000
   5_adp:  0.325  44.334   0.434  -0.375   0.822  -0.000   0.000   0.000
   5_occ:  0.325  44.334   0.434  -0.375   0.822  -0.000   0.000   0.000
   5_bss:  0.319  44.472   0.111  -0.624   0.514  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.080 0.3544  0.4292    82407.165
   1_bss:  63.469 0.3481  0.5301    80809.831
   1_xyz:  57.780 0.4204  0.6295    68452.359
   1_adp:  56.837 0.4323  0.7069    67410.050
   1_occ:  56.888 0.4317  0.7052    67492.763
   2_bss:  56.734 0.4335  0.6329    67180.731
   2_xyz:  44.580 0.5852  0.8464    44820.708
   2_adp:  41.864 0.6189  0.9015    40880.843
   2_occ:  41.846 0.6191  0.9013    40805.648
   3_bss:  41.599 0.6218  0.8382    40395.914
   3_xyz:  30.257 0.7542  0.9759    23158.260
   3_adp:  26.486 0.7961  1.0041    18898.153
   3_occ:  26.385 0.7971  1.0042    18724.151
   4_bss:  26.304 0.7978  0.9503    18598.917
   4_xyz:  20.651 0.8550  0.9870    11825.882
   4_adp:  19.234 0.8693  0.9922    10670.690
   4_occ:  19.164 0.8699  0.9921    10571.583
   5_bss:  19.147 0.8700  0.9670    10545.662
   5_xyz:  16.649 0.8928  0.9798     8389.043
   5_adp:  16.261 0.8965  0.9814     8161.964
   5_occ:  16.218 0.8969  0.9814     8120.567
   5_bss:  16.212 0.8969  0.9759     8116.696
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3318e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3318e+01
   1_xyz:   1.782  0.014  0.110 18.689  0.007  4.107   1.5840e-01
   1_adp:   1.782  0.014  0.110 18.689  0.007  4.107   1.5840e-01
   1_occ:   1.782  0.014  0.110 18.689  0.007  4.107   1.5840e-01
   2_bss:   1.782  0.014  0.110 18.689  0.007  4.107   1.5840e-01
   2_xyz:   1.299  0.011  0.093 17.320  0.006  4.101   1.1623e-01
   2_adp:   1.299  0.011  0.093 17.320  0.006  4.101   1.1623e-01
   2_occ:   1.299  0.011  0.093 17.320  0.006  4.101   1.1623e-01
   3_bss:   1.299  0.011  0.093 17.320  0.006  4.101   1.1623e-01
   3_xyz:   1.195  0.010  0.081 16.154  0.005  4.104   1.0104e-01
   3_adp:   1.195  0.010  0.081 16.154  0.005  4.104   1.0104e-01
   3_occ:   1.195  0.010  0.081 16.154  0.005  4.104   1.0104e-01
   4_bss:   1.195  0.010  0.081 16.154  0.005  4.104   1.0104e-01
   4_xyz:   1.013  0.007  0.075 15.706  0.004  4.114   6.6416e-02
   4_adp:   1.013  0.007  0.075 15.706  0.004  4.114   6.6416e-02
   4_occ:   1.013  0.007  0.075 15.706  0.004  4.114   6.6416e-02
   5_bss:   1.013  0.007  0.075 15.706  0.004  4.114   6.6416e-02
   5_xyz:   0.955  0.006  0.072 15.490  0.003  4.109   5.7993e-02
   5_adp:   0.955  0.006  0.072 15.490  0.003  4.109   5.7993e-02
   5_occ:   0.955  0.006  0.072 15.490  0.003  4.109   5.7993e-02
   5_bss:   0.955  0.006  0.072 15.490  0.003  4.109   5.7993e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9104e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9104e+00
   1_xyz:  14.271  0.177  0.474 88.678  0.044  2.163   1.0696e-01
   1_adp:  14.271  0.177  0.474 88.678  0.044  2.163   1.0696e-01
   1_occ:  14.271  0.177  0.474 88.678  0.044  2.163   1.0696e-01
   2_bss:  14.271  0.177  0.474 88.678  0.044  2.163   1.0696e-01
   2_xyz:   8.612  0.122  0.306 84.604  0.047  2.068   8.5107e-02
   2_adp:   8.612  0.122  0.306 84.604  0.047  2.068   8.5107e-02
   2_occ:   8.612  0.122  0.306 84.604  0.047  2.068   8.5107e-02
   3_bss:   8.612  0.122  0.306 84.604  0.047  2.068   8.5107e-02
   3_xyz:   8.980  0.096  0.326 73.523  0.037  2.186   2.5124e-01
   3_adp:   8.980  0.096  0.326 73.523  0.037  2.186   2.5124e-01
   3_occ:   8.980  0.096  0.326 73.523  0.037  2.186   2.5124e-01
   4_bss:   8.980  0.096  0.326 73.523  0.037  2.186   2.5124e-01
   4_xyz:   8.294  0.054  0.374 80.586  0.034  2.331   6.0403e-02
   4_adp:   8.294  0.054  0.374 80.586  0.034  2.331   6.0403e-02
   4_occ:   8.294  0.054  0.374 80.586  0.034  2.331   6.0403e-02
   5_bss:   8.294  0.054  0.374 80.586  0.034  2.331   6.0403e-02
   5_xyz:   7.874  0.053  0.397 83.639  0.028  2.313   4.0524e-02
   5_adp:   7.874  0.053  0.397 83.639  0.028  2.313   4.0524e-02
   5_occ:   7.874  0.053  0.397 83.639  0.028  2.313   4.0524e-02
   5_bss:   7.874  0.053  0.397 83.639  0.028  2.313   4.0524e-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:  94.61   0.00  15.46  94.61   0.00  14.05  89.85   0.00  23.15
   1_occ:  94.61   0.00  15.46  94.61   0.00  14.05  89.85   0.00  23.15
   2_bss:  94.61   0.00  15.46  94.61   0.00  14.05  89.85   0.00  23.15
   2_xyz:  94.61   0.00  15.46  94.61   0.00  14.05  89.85   0.00  23.15
   2_adp:  97.14   0.00  15.57  97.14   0.00  12.95  84.34   0.00  29.81
   2_occ:  97.14   0.00  15.57  97.14   0.00  12.95  84.34   0.00  29.81
   3_bss:  97.14   0.00  15.57  97.14   0.00  12.95  84.34   0.00  29.81
   3_xyz:  97.14   0.00  15.57  97.14   0.00  12.95  84.34   0.00  29.81
   3_adp:  92.43   0.00  14.97  92.43   0.00  11.16  83.52   2.38  35.73
   3_occ:  92.43   0.00  14.97  92.43   0.00  11.16  83.52   2.38  35.73
   4_bss:  92.43   0.00  14.97  92.43   0.00  11.16  83.52   2.38  35.73
   4_xyz:  92.43   0.00  14.97  92.43   0.00  11.16  83.52   2.38  35.73
   4_adp:  90.59   0.00  14.83  90.59   0.00  10.66  80.78   4.14  37.52
   4_occ:  90.59   0.00  14.83  90.59   0.00  10.66  80.78   4.14  37.52
   5_bss:  90.59   0.00  14.83  90.59   0.00  10.66  80.78   4.14  37.52
   5_xyz:  90.59   0.00  14.83  90.59   0.00  10.66  80.78   4.14  37.52
   5_adp:  90.00   0.37  14.73  90.00   0.37  10.59  83.39   4.71  37.28
   5_occ:  90.00   0.37  14.73  90.00   0.37  10.59  83.39   4.71  37.28
   5_bss:  90.13   0.50  14.87  90.13   0.50  10.73  83.53   4.85  37.42
------------------------------------------------------------------------
 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:    1.280    0.032    0.416
   1_adp:    1.280    0.032    0.416
   1_occ:    1.280    0.032    0.416
   2_bss:    1.280    0.032    0.416
   2_xyz:    1.591    0.048    0.622
   2_adp:    1.591    0.048    0.622
   2_occ:    1.591    0.048    0.622
   3_bss:    1.591    0.048    0.622
   3_xyz:    1.840    0.048    0.765
   3_adp:    1.840    0.048    0.765
   3_occ:    1.840    0.048    0.765
   4_bss:    1.840    0.048    0.765
   4_xyz:    2.166    0.063    0.845
   4_adp:    2.166    0.063    0.845
   4_occ:    2.166    0.063    0.845
   5_bss:    2.166    0.063    0.845
   5_xyz:    2.332    0.048    0.875
   5_adp:    2.332    0.048    0.875
   5_occ:    2.332    0.048    0.875
   5_bss:    2.332    0.048    0.875
------------------------------------------------------------------------

CPU time actual refinement: 345.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/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_1102/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1102/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.37 
  Macro-tasks:
    bulk solvent and scale       = 38.91  
    individual site refinement   = 149.46 
    weights calculation          = 32.47  
    collect and process          = 6.28   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 227.27 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 110.05 
    alpha_beta                      = 7.98   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 120.13 
    fmodel                         = 6.72   
    r_factors                      = 0.19   
    phase_errors                   = 10.10  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 258.96 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.844 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    638 calls, 109.65 s
gradients_fft:          584 calls, 106.64 s

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

# Date 2008-01-16 Time 03:12:30 PST -0800 (1200481950.36 s)
Start R-work = 0.5082, R-free = 0.5012 (no bulk solvent and anisotropic scale)
Final R-work = 0.1476, R-free = 0.1949 (no bulk solvent and anisotropic scale)

Start R-work = 0.4991, R-free = 0.4879
Final R-work = 0.1316, R-free = 0.1783