# Date 2008-01-16 Time 03:18:15 PST -0800 (1200482295.25 s)
#phil __OFF__

Command line arguments: "../1184.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 = 19204
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1184

-------------------------------------------------------------------------------
  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, 47.6339, 87.2539, 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: 3.27, per 1000 atoms: 1.16


================================== 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, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02103
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2528
                             d_min =   2.0210

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, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2528 2.02103
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2532 -  4.3242 [2104/2128]  1894   210  10.0%
  bin  2:  4.3242 -  3.4453 [2037/2056]  1833   204  10.0%
  bin  3:  3.4453 -  3.0136 [2006/2025]  1803   203  10.1%
  bin  4:  3.0136 -  2.7398 [1988/2018]  1793   195   9.8%
  bin  5:  2.7398 -  2.5444 [1980/1999]  1782   198  10.0%
  bin  6:  2.5444 -  2.3950 [1940/1965]  1746   194  10.0%
  bin  7:  2.3950 -  2.2754 [1971/1999]  1770   201  10.2%
  bin  8:  2.2754 -  2.1767 [1946/1982]  1755   191   9.8%
  bin  9:  2.1767 -  2.0931 [1935/1977]  1743   192   9.9%
  bin 10:  2.0931 -  2.0210 [1682/1987]  1511   171  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/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:
        1.41 -     2.11: 2
        2.11 -     2.81: 745
        2.81 -     3.51: 4371
        3.51 -     4.20: 9111
        4.20 -     4.90: 13489
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.413 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 343 " - " O   HOH Z 277 "  2.134 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.134 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27713 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_1184/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 47.63395 87.2539 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: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4872   r_free= 0.4702   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.286138                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.3950 0.3699      6.5907      6.5017|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.4060 0.4394       6.808      6.8905|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.4494 0.4226      6.7024      6.6703|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.4794 0.4134      6.5561      6.4642|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.5077 0.4966      6.3802      6.4014|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.5216 0.5323      6.3051      6.2377|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.5232 0.4728      6.2421       6.226|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.5323 0.4709      6.2024      6.1484|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.5266 0.5837      6.1252      6.1715|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.5381 0.5087      6.1291      6.1661|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.5163 0.4962      6.0496      6.0578|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.5535 0.5094      6.0036      6.0207|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.5281 0.5104      5.8989      5.8563|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.5507 0.5281      5.8459      5.7599|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8228  1376   153  0.70  34.04   0.79     0.73      69900.39|
|  2:  4.8228 -  3.8483  1321   146  0.71  34.76   0.87     0.75     103099.63|
|  3:  3.8483 -  3.3678  1298   144  0.61  42.77   0.80     0.69     111451.04|
|  4:  3.3678 -  3.0626  1278   145  0.52  50.33   0.79     0.60      98799.63|
|  5:  3.0626 -  2.8446  1283   141  0.44  56.96   0.72     0.51      80729.21|
|  6:  2.8446 -  2.6778  1278   139  0.41  58.85   0.71     0.46      69744.64|
|  7:  2.6778 -  2.5444  1271   142  0.36  63.25   0.71     0.40      66463.62|
|  8:  2.5444 -  2.4341  1261   145  0.29  68.57   0.72     0.33      65141.04|
|  9:  2.4341 -  2.3407  1257   137  0.24  72.39   0.69     0.27      62193.66|
| 10:  2.3407 -  2.2602  1240   141  0.26  70.88   0.71     0.29      56338.03|
| 11:  2.2602 -  2.1897  1266   134  0.30  67.30   0.75     0.35      48245.01|
| 12:  2.1897 -  2.1273  1235   140  0.33  65.32   0.72     0.40      43190.18|
| 13:  2.1273 -  2.0715  1245   144  0.32  65.79   0.71     0.38      36728.20|
| 14:  2.0715 -  2.0210  1021   108  0.28  69.29   0.68     0.30      31559.80|
|alpha:            min =        0.27 max =            0.75 mean =         0.47|
|beta:             min =    31559.80 max =       111451.04 mean =     68238.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.15|
|phase err.(test): min =        0.00 max =           89.97 mean =        57.86|
|-----------------------------------------------------------------------------|

============================== 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 = 15.084605             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.534   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.514976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.457   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2571 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3820 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4961 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6451 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7599 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.615 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.650 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    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: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4914   r_free= 0.4745   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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.287034                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4803   r_free= 0.4632   ksol= 0.29   Bsol= 20.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,9.05,7.91,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.282287                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.479544             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.240788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.325   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4803      final r-factor (work) = 0.3933          |
| start r-factor (free) = 0.4632      final r-factor (free) = 0.4137          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.9830 = 13.48 * 0.50 * 6.2863 + 1.00 * 54.6145                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.8924 = 13.48 * 0.50 * 6.1927 + 1.00 * 0.1549                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3933      final r-factor (work) = 0.3503          |
| start r-factor (free) = 0.4137      final r-factor (free) = 0.3921          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6983 = 1.24 * 1.00 * 6.1927 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6029 = 1.24 * 1.00 * 6.1124 + 1.00 * 0.0187                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.78  13.19    None  None   None       |
|    all(noH): 2823   0      0.00    110.78  13.19    None  None   None       |
|    Sol.    : 438    0      0.00    110.78  27.34    None  None   None       |
|    Mac.    : 2385   0      0.00    75.75   10.60    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 -  11.078: 1589   |   5:    55.391 -  66.470:   28        |
|      1:    11.078 -  22.157:  741   |   6:    66.470 -  77.548:    9        |
|      2:    22.157 -  33.235:  269   |   7:    77.548 -  88.626:    0        |
|      3:    33.235 -  44.313:  108   |   8:    88.626 -  99.705:    2        |
|      4:    44.313 -  55.391:   75   |   9:    99.705 - 110.783:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3503 r_free = 0.3921             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3496 r_free = 0.3927             target_work(ml) = 6.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3496   r_free= 0.3927   ksol= 0.29   Bsol= 20.00   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,9.05,7.91,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.092853                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3486   r_free= 0.3898   ksol= 0.31   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.20,6.35,5.46,0.00,0.00,0.00); trace/3= 5.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.093982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.703230              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.312   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.568036              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.378  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3486      final r-factor (work) = 0.2696          |
| start r-factor (free) = 0.3898      final r-factor (free) = 0.3221          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5689 = 5.70 * 0.50 * 6.1067 + 1.00 * 0.1549                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1494 = 5.70 * 0.50 * 5.9861 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2696      final r-factor (work) = 0.2507          |
| start r-factor (free) = 0.3221      final r-factor (free) = 0.3021          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4201 = 0.57 * 1.00 * 5.9861 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3437 = 0.57 * 1.00 * 5.8575 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.43  12.92    None  None   None       |
|    all(noH): 2823   0      0.00    113.43  12.92    None  None   None       |
|    Sol.    : 438    0      0.00    113.43  32.47    None  None   None       |
|    Mac.    : 2385   0      0.00    77.97   9.33     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 -  11.343: 1757   |   5:    56.714 -  68.056:   34        |
|      1:    11.343 -  22.685:  611   |   6:    68.056 -  79.399:   11        |
|      2:    22.685 -  34.028:  219   |   7:    79.399 -  90.742:    2        |
|      3:    34.028 -  45.371:  110   |   8:    90.742 - 102.084:    1        |
|      4:    45.371 -  56.714:   77   |   9:   102.084 - 113.427:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2507 r_free = 0.3021             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2505 r_free = 0.3024             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2505   r_free= 0.3024   ksol= 0.31   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.20,6.35,5.46,0.00,0.00,0.00); trace/3= 5.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.834250                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2495   r_free= 0.3009   ksol= 0.30   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,4.32,4.01,0.00,0.00,0.00); trace/3= 3.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.834901                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.858524              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.506419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.351  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2495      final r-factor (work) = 0.1815          |
| start r-factor (free) = 0.3009      final r-factor (free) = 0.2287          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3084 = 4.86 * 0.50 * 5.8573 + 1.00 * 0.0794                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9403 = 4.86 * 0.50 * 5.7061 + 1.00 * 0.0787                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1815      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2287      final r-factor (free) = 0.2116          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9122 = 0.51 * 1.00 * 5.7061 + 1.00 * 0.0225                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7989 = 0.51 * 1.00 * 5.5008 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.26  13.15    None  None   None       |
|    all(noH): 2823   0      0.00    108.26  13.15    None  None   None       |
|    Sol.    : 438    0      0.29    108.26  36.98    None  None   None       |
|    Mac.    : 2385   0      0.00    83.51   8.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.827: 1835   |   5:    54.132 -  64.959:   63        |
|      1:    10.827 -  21.653:  487   |   6:    64.959 -  75.785:   16        |
|      2:    21.653 -  32.479:  167   |   7:    75.785 -  86.612:    5        |
|      3:    32.479 -  43.306:  132   |   8:    86.612 -  97.438:    2        |
|      4:    43.306 -  54.132:  115   |   9:    97.438 - 108.265:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1644 r_free = 0.2116             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1641 r_free = 0.2118             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1641   r_free= 0.2118   ksol= 0.30   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,4.32,4.01,0.00,0.00,0.00); trace/3= 3.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.464444                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1639   r_free= 0.2115   ksol= 0.33   Bsol= 69.25   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,3.02,3.45,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.464450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.186715              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.837  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.547690              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.230  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1639      final r-factor (work) = 0.1423          |
| start r-factor (free) = 0.2115      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0965 = 2.19 * 0.50 * 5.5040 + 1.00 * 0.0787                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9728 = 2.19 * 0.50 * 5.4047 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.1902      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9732 = 0.55 * 1.00 * 5.4047 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9334 = 0.55 * 1.00 * 5.3305 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.59  13.13    None  None   None       |
|    all(noH): 2823   0      0.00    104.59  13.13    None  None   None       |
|    Sol.    : 438    0      0.94    104.59  37.91    None  None   None       |
|    Mac.    : 2385   0      0.00    85.05   8.57     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.460: 1817   |   5:    52.297 -  62.757:   78        |
|      1:    10.460 -  20.919:  495   |   6:    62.757 -  73.216:   26        |
|      2:    20.919 -  31.378:  160   |   7:    73.216 -  83.676:    7        |
|      3:    31.378 -  41.838:  121   |   8:    83.676 -  94.135:    3        |
|      4:    41.838 -  52.297:  115   |   9:    94.135 - 104.595:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1373 r_free = 0.1867             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1373 r_free = 0.1865             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1865   ksol= 0.33   Bsol= 69.25   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.50,3.02,3.45,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.320694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1867   ksol= 0.33   Bsol= 69.25   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.79,3.48,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.321326                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.490413              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.260  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616765              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.049  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1867      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7015 = 2.49 * 0.50 * 5.3308 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6553 = 2.49 * 0.50 * 5.2861 + 1.00 * 0.0730                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1744          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2740 = 0.62 * 1.00 * 5.2861 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2514 = 0.62 * 1.00 * 5.2490 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.66   12.98    None  None   None       |
|    all(noH): 2823   0      0.00    99.66   12.98    None  None   None       |
|    Sol.    : 438    0      1.32    99.66   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    86.52   8.40     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 -   9.966: 1789   |   5:    49.832 -  59.798:   88        |
|      1:     9.966 -  19.933:  519   |   6:    59.798 -  69.764:   42        |
|      2:    19.933 -  29.899:  147   |   7:    69.764 -  79.731:   12        |
|      3:    29.899 -  39.865:  124   |   8:    79.731 -  89.697:    6        |
|      4:    39.865 -  49.832:   95   |   9:    89.697 -  99.663:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1744             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1255 r_free = 0.1741             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1741   ksol= 0.33   Bsol= 69.25   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.79,3.48,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.245786                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.1052 0.1386      5.4248      5.5587|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.0895 0.1144      5.4824      5.6774|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.1145 0.1633      5.5516      5.9281|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.1335 0.1654      5.5434      5.6973|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.1538 0.1965       5.466      5.6551|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.1406 0.2068      5.3441      5.5705|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.1439 0.1896      5.2827       5.504|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.1361 0.1829      5.1938      5.4224|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.1344 0.2006      5.1478      5.3715|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.1306 0.1968      5.0887      5.3356|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.1337 0.2013      5.0688      5.3562|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.1258 0.1884      4.9758       5.315|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.1326 0.1916      4.9219      5.1539|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.1265 0.2036      4.8081      5.0739|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8228  1376   153  0.94   9.64   0.96     0.94       7943.98|
|  2:  4.8228 -  3.8483  1321   146  0.95   8.64   1.00     0.98       9829.67|
|  3:  3.8483 -  3.3678  1298   144  0.93  12.32   1.01     1.00      12132.38|
|  4:  3.3678 -  3.0626  1278   145  0.91  14.89   1.00     0.97      12010.80|
|  5:  3.0626 -  2.8446  1283   141  0.88  18.37   0.99     0.97      10884.61|
|  6:  2.8446 -  2.6778  1278   139  0.89  17.84   0.98     0.95       9007.28|
|  7:  2.6778 -  2.5444  1271   142  0.88  18.22   0.98     0.95       7896.31|
|  8:  2.5444 -  2.4341  1261   145  0.89  17.31   0.98     0.94       6645.52|
|  9:  2.4341 -  2.3407  1257   137  0.89  17.53   0.99     0.95       6255.64|
| 10:  2.3407 -  2.2602  1240   141  0.89  17.36   0.98     0.93       5368.36|
| 11:  2.2602 -  2.1897  1266   134  0.88  18.60   0.98     0.93       5471.17|
| 12:  2.1897 -  2.1273  1235   140  0.90  16.69   0.98     0.95       4724.82|
| 13:  2.1273 -  2.0715  1245   144  0.88  18.36   0.98     0.96       4359.88|
| 14:  2.0715 -  2.0210  1021   108  0.89  17.31   0.94     0.90       3292.12|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     3292.12 max =        12132.38 mean =      7656.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.84|
|phase err.(test): min =        0.00 max =           89.96 mean =        15.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1741   ksol= 0.32   Bsol= 68.34   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.19,0.64,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.245615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.25 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1741   ksol= 0.32   Bsol= 68.34   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.19,0.64,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.245615                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2532 -  4.8228 0.99   1376  153 0.1048 0.1384      5.4222      5.5583|
|  2:  4.8228 -  3.8483 0.99   1321  146 0.0894 0.1141      5.4819      5.6757|
|  3:  3.8483 -  3.3678 0.99   1298  144 0.1145 0.1633      5.5513      5.9282|
|  4:  3.3678 -  3.0626 0.99   1278  145 0.1336 0.1654      5.5438      5.6976|
|  5:  3.0626 -  2.8446 0.99   1283  141 0.1540 0.1968      5.4666      5.6554|
|  6:  2.8446 -  2.6778 0.99   1278  139 0.1406 0.2067      5.3445      5.5701|
|  7:  2.6778 -  2.5444 0.99   1271  142 0.1440 0.1899       5.283       5.505|
|  8:  2.5444 -  2.4341 0.98   1261  145 0.1362 0.1829      5.1939       5.422|
|  9:  2.4341 -  2.3407 0.98   1257  137 0.1343 0.2006      5.1475      5.3712|
| 10:  2.3407 -  2.2602 0.99   1240  141 0.1307 0.1970      5.0888      5.3361|
| 11:  2.2602 -  2.1897 0.98   1266  134 0.1337 0.2014      5.0687      5.3565|
| 12:  2.1897 -  2.1273 0.97   1235  140 0.1258 0.1885      4.9758      5.3153|
| 13:  2.1273 -  2.0715 1.00   1245  144 0.1326 0.1915      4.9218      5.1536|
| 14:  2.0715 -  2.0210 0.79   1021  108 0.1265 0.2032      4.8077       5.073|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2532 -  4.8228  1376   153  0.94   9.66   0.96     0.94       7945.48|
|  2:  4.8228 -  3.8483  1321   146  0.95   8.63   1.00     0.98       9822.60|
|  3:  3.8483 -  3.3678  1298   144  0.93  12.31   1.01     1.00      12121.04|
|  4:  3.3678 -  3.0626  1278   145  0.91  14.89   1.00     0.98      12011.43|
|  5:  3.0626 -  2.8446  1283   141  0.88  18.37   0.99     0.97      10889.01|
|  6:  2.8446 -  2.6778  1278   139  0.89  17.85   0.98     0.95       9012.19|
|  7:  2.6778 -  2.5444  1271   142  0.88  18.22   0.99     0.96       7897.13|
|  8:  2.5444 -  2.4341  1261   145  0.89  17.31   0.98     0.94       6641.96|
|  9:  2.4341 -  2.3407  1257   137  0.89  17.53   0.99     0.95       6254.92|
| 10:  2.3407 -  2.2602  1240   141  0.89  17.35   0.99     0.94       5364.18|
| 11:  2.2602 -  2.1897  1266   134  0.88  18.61   0.98     0.93       5475.45|
| 12:  2.1897 -  2.1273  1235   140  0.90  16.69   0.98     0.96       4724.73|
| 13:  2.1273 -  2.0715  1245   144  0.88  18.35   0.99     0.97       4358.72|
| 14:  2.0715 -  2.0210  1021   108  0.89  17.29   0.95     0.90       3286.44|
|alpha:            min =        0.90 max =            1.00 mean =         0.96|
|beta:             min =     3286.44 max =        12121.04 mean =      7654.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.84|
|phase err.(test): min =        0.00 max =           90.00 mean =        15.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.432)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.98    102.65  15.97    None  None   None       |
|    all(noH): 2823   0      2.98    102.65  15.97    None  None   None       |
|    Sol.    : 438    0      4.30    102.65  40.91    None  None   None       |
|    Mac.    : 2385   0      2.98    89.51   11.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.985 -  12.951: 1789   |   5:    52.816 -  62.783:   88        |
|      1:    12.951 -  22.917:  519   |   6:    62.783 -  72.749:   42        |
|      2:    22.917 -  32.884:  147   |   7:    72.749 -  82.715:   12        |
|      3:    32.884 -  42.850:  124   |   8:    82.715 -  92.682:    6        |
|      4:    42.850 -  52.816:   95   |   9:    92.682 - 102.648:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.311 - 4.913
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 345
   mapped sites are within: 0.720 - 4.913

peak=    9.317 closest distance to " CG2 VAL A 230 " =    1.458
peak=    7.200 closest distance to " CG2 VAL A 296 " =    1.164
peak=    6.423 closest distance to " CG  ARG A 138 " =    1.212
peak=    6.042 closest distance to " CD1AILE A 234 " =    1.170
peak=    5.671 closest distance to " CG  LEU A   5 " =    1.229
peak=    5.378 closest distance to " O   HOH Z 210 " =    1.257
peak=    5.313 closest distance to " O   HOH Z 111 " =    2.118
peak=    5.212 closest distance to " CB  GLN A 223 " =    1.430
peak=    5.185 closest distance to " CB  SER A  63 " =    1.337
peak=    5.079 closest distance to " NH1 ARG A 138 " =    1.038
peak=    4.970 closest distance to " CG  PRO A  54 " =    1.369
peak=    4.944 closest distance to " CG  LEU A 228 " =    1.241
peak=    4.863 closest distance to " CG  PRO A 280 " =    0.893
peak=    4.777 closest distance to " O   HOH Z 232 " =    2.177
peak=    4.738 closest distance to " O   HOH Z 102 " =    1.544
peak=    4.678 closest distance to " CA  VAL A 230 " =    1.255
peak=    4.672 closest distance to " CG  PRO A 198 " =    1.204
peak=    4.596 closest distance to " CZ  PHE A 218 " =    1.140
peak=    4.571 closest distance to " O   PRO A 198 " =    1.537
peak=    4.483 closest distance to " O   HOH Z 411 " =    3.621
peak=    4.481 closest distance to " CB  PRO A  54 " =    0.943
peak=    4.467 closest distance to " CB  TRP A 266 " =    1.016
peak=    4.400 closest distance to " CG  PRO A 243 " =    1.178
peak=    4.400 closest distance to " O   HOH Z 369 " =    2.039
peak=    4.390 closest distance to " O   HOH Z 425 " =    1.567
peak=    4.384 closest distance to " O   HOH Z 265 " =    2.096
peak=    4.382 closest distance to " CD2 LEU A 228 " =    1.245
peak=    4.377 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.295 closest distance to " CD2 LEU A   5 " =    1.023
peak=    4.242 closest distance to " O   HOH Z 368 " =    2.275
peak=    4.238 closest distance to " CG2 THR A 221 " =    1.055
peak=    4.227 closest distance to " CB  ASP A 124 " =    0.752
peak=    4.225 closest distance to " O   HOH Z 433 " =    1.818
peak=    4.131 closest distance to " O   HOH Z 184 " =    1.784
peak=    4.129 closest distance to " CG  PRO A 213 " =    1.284
peak=    4.124 closest distance to " NH1AARG A 145 " =    1.182
peak=    4.092 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.084 closest distance to " O   HOH Z 303 " =    2.341
peak=    4.075 closest distance to " O   HOH Z 261 " =    1.654
peak=    4.070 closest distance to " O   HOH Z  48 " =    1.753
peak=    4.067 closest distance to " O   SER A  87 " =    2.374
peak=    4.064 closest distance to " CB  TYR A 169 " =    0.720
peak=    4.047 closest distance to " NE2 GLN A  11 " =    1.112
peak=    4.036 closest distance to " O   HOH Z  63 " =    2.014
peak=    4.014 closest distance to " O   HOH Z   4 " =    1.733
peak=    4.013 closest distance to " O   HOH Z 120 " =    1.160
peak=    4.007 closest distance to " O   HOH Z  49 " =    1.335
peak=    4.006 closest distance to " CD  ARG A 138 " =    1.218
peak=    4.000 closest distance to " CD  ARG A  66 " =    2.520
peak=    3.995 closest distance to " CZ  PHE A 192 " =    1.081
peak=    3.991 closest distance to " CB  ARG A 275 " =    0.846
peak=    3.985 closest distance to " O   HOH Z 236 " =    1.996
peak=    3.981 closest distance to " CB  GLU A 277 " =    3.821
peak=    3.974 closest distance to " OD1 ASN A 217 " =    1.610
peak=    3.967 closest distance to " CB  ARG A 190 " =    1.726
peak=    3.967 closest distance to " CB  ASN A 142 " =    1.004
peak=    3.958 closest distance to " CB  VAL A 296 " =    1.056
peak=    3.957 closest distance to " O   HOH Z 247 " =    1.566
peak=    3.938 closest distance to " O   ASP A 124 " =    1.178
peak=    3.933 closest distance to " CG2 ILE A 234 " =    0.933
peak=    3.920 closest distance to " O   HOH Z 131 " =    2.303
peak=    3.880 closest distance to " CG1 VAL A 153 " =    1.114
peak=    3.870 closest distance to " O   HOH Z 234 " =    3.771
peak=    3.858 closest distance to " CB  GLU A 128 " =    1.139
peak=    3.851 closest distance to " CB AVAL A  41 " =    1.194
peak=    3.847 closest distance to " CG  MET A 185 " =    1.392
peak=    3.839 closest distance to " O   HOH Z  80 " =    1.916
peak=    3.836 closest distance to " CB  ASN A 148 " =    1.364
peak=    3.833 closest distance to " NH1 ARG A  56 " =    1.040
peak=    3.832 closest distance to " O   HOH Z 359 " =    1.611
peak=    3.826 closest distance to " O   HOH Z 316 " =    3.129
peak=    3.821 closest distance to " CB  VAL A 202 " =    1.518
peak=    3.818 closest distance to " CB  LEU A 143 " =    1.278
peak=    3.812 closest distance to " CD  ARG A 269 " =    0.950
peak=    3.807 closest distance to " CA  PRO A  54 " =    1.405
peak=    3.805 closest distance to " CB  ASP A 140 " =    0.850
peak=    3.800 closest distance to " CA  ARG A 195 " =    1.256
peak=    3.792 closest distance to " CA  ILE A 106 " =    0.784
peak=    3.787 closest distance to " O   HOH Z   9 " =    2.140
peak=    3.782 closest distance to " O   HOH Z  32 " =    1.993
peak=    3.781 closest distance to " CB  ASN A  39 " =    0.811
peak=    3.778 closest distance to " CD  LYS A 166 " =    1.325
peak=    3.773 closest distance to " O   HOH Z 134 " =    1.645
peak=    3.768 closest distance to " O   HOH Z 126 " =    1.675
peak=    3.767 closest distance to " O   HOH Z 394 " =    1.638
peak=    3.748 closest distance to " CG  LEU A 167 " =    1.102
peak=    3.747 closest distance to " CG AARG A 275 " =    1.252
peak=    3.747 closest distance to " CA  ALA A 295 " =    1.107
peak=    3.741 closest distance to " CG1 ILE A  33 " =    1.279
peak=    3.732 closest distance to " OD1 ASN A  69 " =    2.466
peak=    3.730 closest distance to " CD  ARG A 159 " =    0.784
peak=    3.729 closest distance to " O   HOH Z  56 " =    1.750
peak=    3.726 closest distance to " O   HOH Z 298 " =    1.985
peak=    3.722 closest distance to " O   HOH Z  88 " =    3.345
peak=    3.713 closest distance to " O   HOH Z  68 " =    1.794
peak=    3.707 closest distance to " CA  ASP A 191 " =    0.769
peak=    3.704 closest distance to " O   HOH Z 402 " =    1.555
peak=    3.699 closest distance to " O   HOH Z 403 " =    1.790
peak=    3.694 closest distance to " CE3 TRP A  85 " =    1.182
peak=    3.692 closest distance to " CB  ALA A   9 " =    1.691
peak=    3.690 closest distance to " N   SER A 164 " =    0.959
peak=    3.689 closest distance to " O   HOH Z  19 " =    2.100
peak=    3.683 closest distance to " ND2 ASN A 249 " =    2.029
peak=    3.682 closest distance to " CD ALYS A 290 " =    1.109
peak=    3.680 closest distance to " CD1 LEU A   5 " =    1.350
peak=    3.671 closest distance to " O   HOH Z 214 " =    2.584
peak=    3.656 closest distance to " O   HOH Z 437 " =    1.975
peak=    3.650 closest distance to " CA  ALA A  51 " =    0.945
peak=    3.635 closest distance to " O   HOH Z  57 " =    1.657
peak=    3.631 closest distance to " O   HOH Z  43 " =    2.073
peak=    3.631 closest distance to " CB  PRO A 198 " =    1.008
peak=    3.625 closest distance to " CA  GLY A 267 " =    0.734
peak=    3.611 closest distance to " O   HOH Z 393 " =    3.826
peak=    3.609 closest distance to " CB  ALA A 291 " =    1.390
peak=    3.604 closest distance to " O   HOH Z 368 " =    3.479
peak=    3.602 closest distance to " O   HOH Z 346 " =    1.572
peak=    3.598 closest distance to " CB  MET A  40 " =    0.939
peak=    3.597 closest distance to " O   ALA A 165 " =    1.326
peak=    3.592 closest distance to " CB  GLU A  46 " =    0.947
peak=    3.590 closest distance to " O   HOH Z 141 " =    1.760
peak=    3.590 closest distance to " O   HOH Z 422 " =    2.704
peak=    3.588 closest distance to " CA  ALA A 160 " =    0.981
peak=    3.587 closest distance to " O   HOH Z  40 " =    1.730
peak=    3.581 closest distance to " CB  SER A 141 " =    1.084
peak=    3.578 closest distance to " CA  ASP A 162 " =    1.001
peak=    3.575 closest distance to " O   HOH Z 250 " =    1.366
peak=    3.575 closest distance to " O   HOH Z 383 " =    2.200
peak=    3.573 closest distance to " O   HOH Z  78 " =    2.427
peak=    3.571 closest distance to " CA  ALA A  21 " =    1.307
peak=    3.570 closest distance to " O   HOH Z  63 " =    1.247
peak=    3.565 closest distance to " CD2 TRP A 179 " =    1.345
peak=    3.562 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.561 closest distance to " O   HOH Z 148 " =    2.018
peak=    3.559 closest distance to " O   HOH Z 128 " =    1.517
peak=    3.555 closest distance to " CA  GLU A 152 " =    0.890
peak=    3.544 closest distance to " O   HOH Z 139 " =    4.913
peak=    3.541 closest distance to " O   MET A 105 " =    1.845
peak=    3.541 closest distance to " CB  ARG A  79 " =    1.484
peak=    3.537 closest distance to " CG1 ILE A  49 " =    1.694
peak=    3.537 closest distance to " O   HOH Z 227 " =    1.716
peak=    3.535 closest distance to " O   HOH Z  99 " =    2.574
peak=    3.534 closest distance to " CA  ASN A 127 " =    1.152
peak=    3.534 closest distance to " CA  ASP A 140 " =    1.300
peak=    3.526 closest distance to " O   HOH Z 104 " =    2.746
peak=    3.523 closest distance to " O   HOH Z 423 " =    1.688
peak=    3.522 closest distance to " O   HOH Z 280 " =    2.912
peak=    3.513 closest distance to " O   HOH Z 193 " =    1.748
peak=    3.511 closest distance to " CG  GLU A  37 " =    0.925
peak=    3.509 closest distance to " OG  SER A 276 " =    1.610
peak=    3.508 closest distance to " O   HOH Z 163 " =    1.738
peak=    3.507 closest distance to " CE1 TYR A 186 " =    1.420
peak=    3.503 closest distance to " O   HOH Z 158 " =    3.099
peak=    3.501 closest distance to " CD1 LEU A 300 " =    1.217
peak=    3.500 closest distance to " CZ3 TRP A  92 " =    1.309
peak=    3.499 closest distance to " CB  THR A  82 " =    1.392
peak=    3.498 closest distance to " N   VAL A 126 " =    1.528
peak=    3.495 closest distance to " O   HOH Z  44 " =    1.927
peak=    3.487 closest distance to " CA  THR A 264 " =    0.803
peak=    3.486 closest distance to " CE2 TYR A 186 " =    0.931
peak=    3.485 closest distance to " CB  GLU A 152 " =    1.195
peak=    3.484 closest distance to " O   HOH Z 201 " =    2.911
peak=    3.483 closest distance to " CD1 LEU A  96 " =    0.788
peak=    3.482 closest distance to " CA  MET A 105 " =    0.995
peak=    3.476 closest distance to " CA  ILE A  33 " =    1.715
peak=    3.471 closest distance to " O   HOH Z 180 " =    2.142
peak=    3.470 closest distance to " CB  ALA A 100 " =    1.386
peak=    3.469 closest distance to " O   HOH Z 427 " =    3.312
peak=    3.467 closest distance to " O   HOH Z 344 " =    3.008
peak=    3.466 closest distance to " O   HOH Z 193 " =    2.313
peak=    3.463 closest distance to " CA  ARG A 139 " =    1.329
peak=    3.460 closest distance to " O   HOH Z  78 " =    1.877
peak=    3.454 closest distance to " O   HOH Z 332 " =    1.584
peak=    3.454 closest distance to " O   HOH Z 109 " =    2.411
peak=    3.453 closest distance to " O   HOH Z 285 " =    2.947
peak=    3.451 closest distance to " N   TYR A  15 " =    0.778
peak=    3.448 closest distance to " CB  ALA A 248 " =    1.189
peak=    3.448 closest distance to " O   HOH Z 128 " =    2.397
peak=    3.446 closest distance to " CB  GLN A  89 " =    1.121
peak=    3.442 closest distance to " CB  PRO A 243 " =    1.230
peak=    3.429 closest distance to " O   ASP A 200 " =    1.627
peak=    3.428 closest distance to " NZ  LYS A  48 " =    1.404
peak=    3.427 closest distance to " CH2 TRP A 266 " =    1.076
peak=    3.427 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.426 closest distance to " CZ3 TRP A  85 " =    0.904
peak=    3.424 closest distance to " CB  ASN A 187 " =    1.082
peak=    3.423 closest distance to " O   HOH Z 327 " =    2.287
peak=    3.419 closest distance to " O   HOH Z  47 " =    1.461
peak=    3.418 closest distance to " CA  ASP A 124 " =    0.774
peak=    3.418 closest distance to " OE1 GLN A  11 " =    1.946
peak=    3.416 closest distance to " CA  ALA A 100 " =    1.096
peak=    3.416 closest distance to " OG BSER A 164 " =    2.091
peak=    3.405 closest distance to " N   ARG A 190 " =    1.129
peak=    3.405 closest distance to " CA  LEU A 282 " =    1.087
peak=    3.403 closest distance to " CG2 THR A  42 " =    0.828
peak=    3.399 closest distance to " O   HOH Z 134 " =    2.263
peak=    3.397 closest distance to " CB  SER A   3 " =    1.462
peak=    3.397 closest distance to " N   SER A 135 " =    1.486
peak=    3.396 closest distance to " O   HOH Z 256 " =    2.071
peak=    3.396 closest distance to " CA  SER A  87 " =    0.925
peak=    3.395 closest distance to " CA  GLN A  88 " =    1.244
peak=    3.394 closest distance to " O   HOH Z 133 " =    2.278
peak=    3.392 closest distance to " O   HOH Z 368 " =    4.131
peak=    3.388 closest distance to " CB  TRP A 150 " =    1.491
peak=    3.388 closest distance to " CA  MET A  40 " =    1.215
peak=    3.387 closest distance to " CB  VAL A 296 " =    1.331
peak=    3.384 closest distance to " O   HOH Z 301 " =    1.901
peak=    3.381 closest distance to " O   HOH Z 188 " =    3.142
peak=    3.377 closest distance to " OD2 ASP A 298 " =    3.899
peak=    3.375 closest distance to " NH2 ARG A 156 " =    1.144
peak=    3.370 closest distance to " O   HOH Z 326 " =    2.177
peak=    3.369 closest distance to " ND1 HIS A  81 " =    1.739
peak=    3.364 closest distance to " CB  SER A 273 " =    0.909
peak=    3.363 closest distance to " O   HOH Z 433 " =    2.092
peak=    3.362 closest distance to " O   HOH Z 183 " =    1.206
peak=    3.357 closest distance to " O   HOH Z 132 " =    2.614
peak=    3.355 closest distance to " CD2 LEU A 297 " =    0.930
peak=    3.354 closest distance to " CB  ALA A 104 " =    0.830
peak=    3.354 closest distance to " N   ALA A 256 " =    1.028
peak=    3.351 closest distance to " CA  VAL A  41 " =    0.835
peak=    3.349 closest distance to " OE1 GLU A   2 " =    1.833
peak=    3.347 closest distance to " CG2 ILE A 106 " =    0.921
peak=    3.347 closest distance to " O   THR A 294 " =    1.396
peak=    3.345 closest distance to " CB  LEU A  83 " =    0.796
peak=    3.343 closest distance to " O   ASN A 209 " =    1.323
peak=    3.329 closest distance to " O   HOH Z 431 " =    1.097
peak=    3.325 closest distance to " O   HOH Z 258 " =    2.288
peak=    3.323 closest distance to " CA  GLU A  46 " =    0.809
peak=    3.321 closest distance to " O   HOH Z 214 " =    1.428
peak=    3.319 closest distance to " O   HOH Z 125 " =    3.869
peak=    3.319 closest distance to " CE1 PHE A 208 " =    1.091
peak=    3.316 closest distance to " CB  PHE A 204 " =    1.051
peak=    3.312 closest distance to " O   HOH Z 116 " =    1.956
peak=    3.312 closest distance to " O   PRO A  90 " =    1.380
peak=    3.307 closest distance to " N   PHE A 130 " =    1.185
peak=    3.305 closest distance to " OE1 GLN A  55 " =    1.353
peak=    3.305 closest distance to " O   HOH Z 185 " =    1.963
peak=    3.304 closest distance to " OG BSER A 134 " =    2.806
peak=    3.303 closest distance to " CA  ARG A 156 " =    1.070
peak=    3.301 closest distance to " CB  VAL A 265 " =    1.298
peak=    3.295 closest distance to " OH  TYR A 186 " =    1.046
peak=    3.292 closest distance to " O   HOH Z 261 " =    1.737
peak=    3.291 closest distance to " NH1 ARG A  14 " =    1.058
peak=    3.291 closest distance to " CB  MET A  47 " =    1.115
peak=    3.290 closest distance to " O   HOH Z  20 " =    1.827
peak=    3.288 closest distance to " C   TYR A 214 " =    1.647
peak=    3.288 closest distance to " N   ASN A 252 " =    1.279
peak=    3.287 closest distance to " O   HOH Z 213 " =    1.755
peak=    3.286 closest distance to " O   ALA A 158 " =    1.328
peak=    3.285 closest distance to " N   ASN A  39 " =    1.209
peak=    3.284 closest distance to " CB  LEU A 228 " =    1.212
peak=    3.283 closest distance to " CB  MET A 105 " =    1.225
peak=    3.282 closest distance to " CA  ASN A 217 " =    1.371
peak=    3.277 closest distance to " O   HOH Z 298 " =    2.347
peak=    3.276 closest distance to " CD  ARG A  66 " =    2.466
peak=    3.275 closest distance to " O   HOH Z 244 " =    1.658
peak=    3.274 closest distance to " OG  SER A  22 " =    2.914
peak=    3.274 closest distance to " CD  ARG A 195 " =    0.992
peak=    3.269 closest distance to " O   HOH Z 271 " =    1.951
peak=    3.265 closest distance to " O   HOH Z 368 " =    4.520
peak=    3.262 closest distance to " OG  SER A 245 " =    1.635
peak=    3.258 closest distance to " C   VAL A 265 " =    1.185
peak=    3.256 closest distance to " CB  SER A 288 " =    1.512
peak=    3.254 closest distance to " NE2 HIS A 115 " =    1.020
peak=    3.254 closest distance to " N   ILE A  33 " =    1.064
peak=    3.250 closest distance to " O   HOH Z 313 " =    1.843
peak=    3.250 closest distance to " CZ3 TRP A 274 " =    4.716
peak=    3.246 closest distance to " CG BARG A 275 " =    1.392
peak=    3.245 closest distance to " CB  SER A 216 " =    0.898
peak=    3.244 closest distance to " O  BHOH Z 338 " =    1.154
peak=    3.243 closest distance to " CA  ALA A 291 " =    0.917
peak=    3.240 closest distance to " O   HOH Z 435 " =    1.961
peak=    3.238 closest distance to " O   HOH Z  89 " =    1.719
peak=    3.237 closest distance to " O   HOH Z 377 " =    1.478
peak=    3.236 closest distance to " CG1 VAL A 174 " =    1.279
peak=    3.235 closest distance to " O   HOH Z 188 " =    2.032
peak=    3.235 closest distance to " CE  LYS A  76 " =    0.843
peak=    3.230 closest distance to " CE2 PHE A 204 " =    0.924
peak=    3.224 closest distance to " CA  GLY A 241 " =    0.960
peak=    3.224 closest distance to " CB  ALA A  43 " =    0.988
peak=    3.224 closest distance to " O   HOH Z 126 " =    2.011
peak=    3.224 closest distance to " CB  SER A  62 " =    0.835
peak=    3.223 closest distance to " O   HOH Z 295 " =    1.535
peak=    3.223 closest distance to " O   HOH Z 281 " =    4.641
peak=    3.222 closest distance to " CB  THR A  31 " =    1.441
peak=    3.217 closest distance to " CA  TYR A 116 " =    1.463
peak=    3.215 closest distance to " CA  VAL A 125 " =    1.414
peak=    3.213 closest distance to " O   TRP A 274 " =    1.884
peak=    3.212 closest distance to " CB  ALA A 242 " =    0.830
peak=    3.208 closest distance to " CB  ALA A 248 " =    1.391
peak=    3.206 closest distance to " O   HOH Z 166 " =    1.621
peak=    3.204 closest distance to " N   CYS A 260 " =    0.765
peak=    3.202 closest distance to " CB  THR A 235 " =    1.176
peak=    3.202 closest distance to " O   HOH Z 357 " =    2.633
peak=    3.199 closest distance to " O   HOH Z  59 " =    2.164
peak=    3.198 closest distance to " O   HOH Z  21 " =    1.762
peak=    3.186 closest distance to " N   ASN A 127 " =    1.226
peak=    3.186 closest distance to " O   HOH Z 146 " =    2.200
peak=    3.186 closest distance to " CB  ILE A 199 " =    0.900
peak=    3.185 closest distance to " CB  GLN A 103 " =    0.956
peak=    3.182 closest distance to " O   HOH Z 272 " =    2.011
peak=    3.182 closest distance to " ND2 ASN A 187 " =    1.474
peak=    3.180 closest distance to " O   HOH Z 423 " =    3.092
peak=    3.179 closest distance to " OG  SER A  28 " =    1.521
peak=    3.179 closest distance to " O   HOH Z 392 " =    1.385
peak=    3.177 closest distance to " O   HOH Z 290 " =    1.311
peak=    3.172 closest distance to " CB  ASN A 285 " =    0.855
peak=    3.171 closest distance to " O   HOH Z 199 " =    1.739
peak=    3.169 closest distance to " CB  GLN A  88 " =    1.280
peak=    3.168 closest distance to " O   HOH Z 371 " =    3.038
peak=    3.160 closest distance to " N   TYR A 247 " =    1.152
peak=    3.160 closest distance to " CB  ALA A 256 " =    1.544
peak=    3.155 closest distance to " O   GLN A 278 " =    1.204
peak=    3.154 closest distance to " CB  ASN A 215 " =    1.236
peak=    3.154 closest distance to " CA  VAL A 112 " =    1.160
peak=    3.153 closest distance to " CB  SER A  26 " =    1.794
peak=    3.152 closest distance to " CB  ASP A 140 " =    0.738
peak=    3.151 closest distance to " CE1 HIS A 108 " =    1.087
peak=    3.148 closest distance to " NH2 ARG A  79 " =    1.489
peak=    3.144 closest distance to " CB  TYR A  30 " =    1.073
peak=    3.139 closest distance to " CA  ASN A  74 " =    1.334
peak=    3.138 closest distance to " CD  ARG A 219 " =    1.117
peak=    3.134 closest distance to " CA  ASN A 215 " =    1.193
peak=    3.118 closest distance to " O   HOH Z 391 " =    3.082
peak=    3.118 closest distance to " OD1 ASN A 301 " =    1.575
peak=    3.116 closest distance to " CA  LYS A 117 " =    1.196
peak=    3.115 closest distance to " CD1 LEU A 101 " =    1.037
peak=    3.114 closest distance to " CD2 LEU A 255 " =    1.531
peak=    3.105 closest distance to " O   ASN A  74 " =    1.503
peak=    3.099 closest distance to " O   HOH Z 329 " =    3.925
peak=    3.099 closest distance to " O  BHOH Z 338 " =    2.420
peak=    3.093 closest distance to " O   HOH Z 293 " =    1.959
peak=    3.083 closest distance to " O   THR A  31 " =    1.540
peak=    3.079 closest distance to " CA  ARG A  36 " =    1.098
peak=    3.072 closest distance to " CG2 THR A 220 " =    0.788
peak=    3.068 closest distance to " CG  ARG A 269 " =    1.817
peak=    3.047 closest distance to " O   GLY A 203 " =    1.484
peak=    3.043 closest distance to " CB  VAL A 257 " =    0.780
peak=    3.035 closest distance to " O  BHOH Z 338 " =    1.605
peak=    3.017 closest distance to " CD1 ILE A 199 " =    0.843

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.795 - 5.341
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.795 - 5.341

peak=   -5.026 closest distance to " CG2 VAL A 230 " =    0.839
peak=   -4.482 closest distance to " O   HOH Z 166 " =    1.561
peak=   -4.375 closest distance to " CD2 LEU A 237 " =    2.705
peak=   -4.278 closest distance to " CD  ARG A 138 " =    1.302
peak=   -4.266 closest distance to " O   HOH Z   5 " =    1.612
peak=   -4.191 closest distance to " CD1 PHE A  59 " =    1.989
peak=   -4.157 closest distance to " NH2 ARG A  66 " =    1.651
peak=   -4.025 closest distance to " O   HOH Z 211 " =    1.151
peak=   -3.987 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.975 closest distance to " CB  ALA A 291 " =    2.541
peak=   -3.971 closest distance to " CG2BVAL A  41 " =    2.545
peak=   -3.955 closest distance to " O   HOH Z 351 " =    1.555
peak=   -3.953 closest distance to " C   ASN A 285 " =    2.500
peak=   -3.940 closest distance to " CB  ALA A 161 " =    2.713
peak=   -3.936 closest distance to " O   HOH Z 411 " =    5.170
peak=   -3.930 closest distance to " CG1 VAL A 296 " =    1.352
peak=   -3.927 closest distance to " O   HOH Z  52 " =    1.850
peak=   -3.924 closest distance to " CZ2 TRP A  92 " =    2.841
peak=   -3.912 closest distance to " O   SER A 271 " =    2.244
peak=   -3.898 closest distance to " CD  ARG A 156 " =    2.069
peak=   -3.897 closest distance to " O   HOH Z  19 " =    2.102
peak=   -3.889 closest distance to " CG  ARG A 269 " =    2.441
peak=   -3.874 closest distance to " OG  SER A  97 " =    2.281
peak=   -3.873 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -3.865 closest distance to " O   HOH Z  13 " =    1.687
peak=   -3.846 closest distance to " CD2 LEU A 167 " =    1.774
peak=   -3.846 closest distance to " O   HOH Z 231 " =    2.039
peak=   -3.845 closest distance to " CD  GLN A  58 " =    1.026
peak=   -3.831 closest distance to " CD  GLN A  88 " =    0.952
peak=   -3.822 closest distance to " CG  ASP A 231 " =    0.795
peak=   -3.819 closest distance to " O   GLY A 203 " =    2.480
peak=   -3.812 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.806 closest distance to " CG  ARG A 138 " =    0.918
peak=   -3.796 closest distance to " CA  GLU A 277 " =    1.376
peak=   -3.774 closest distance to " OD1 ASN A 148 " =    1.474
peak=   -3.759 closest distance to " O   HOH Z 103 " =    2.167
peak=   -3.726 closest distance to " CB  PRO A 243 " =    2.751
peak=   -3.720 closest distance to " CD  GLN A 223 " =    1.296
peak=   -3.708 closest distance to " CZ3 TRP A 179 " =    1.131
peak=   -3.706 closest distance to " O   HOH Z 394 " =    1.594
peak=   -3.706 closest distance to " CG  MET A 105 " =    0.908
peak=   -3.697 closest distance to " O   HOH Z  73 " =    2.195
peak=   -3.696 closest distance to " CA  ALA A 158 " =    1.281
peak=   -3.688 closest distance to " CD1 LEU A  25 " =    2.478
peak=   -3.686 closest distance to " O   GLY A 262 " =    2.474
peak=   -3.680 closest distance to " O   HOH Z 183 " =    1.340
peak=   -3.674 closest distance to " O   HOH Z 184 " =    1.227
peak=   -3.664 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.658 closest distance to " O   HOH Z 368 " =    1.818
peak=   -3.653 closest distance to " CG1 VAL A 112 " =    2.814
peak=   -3.648 closest distance to " CD1 LEU A   5 " =    2.597
peak=   -3.648 closest distance to " CE3 TRP A  70 " =    1.817
peak=   -3.618 closest distance to " CA  GLY A 133 " =    2.358
peak=   -3.613 closest distance to " O   HOH Z 231 " =    1.437
peak=   -3.608 closest distance to " O   HOH Z 407 " =    3.506
peak=   -3.591 closest distance to " O   HOH Z  49 " =    0.810
peak=   -3.589 closest distance to " O   LEU A 101 " =    2.874
peak=   -3.589 closest distance to " CA  SER A 164 " =    2.218
peak=   -3.580 closest distance to " O   HOH Z 177 " =    1.593
peak=   -3.569 closest distance to " O   SER A 276 " =    1.642
peak=   -3.565 closest distance to " CD  ARG A  14 " =    3.298
peak=   -3.558 closest distance to " O   HOH Z 290 " =    1.222
peak=   -3.551 closest distance to " O   HOH Z 210 " =    0.989
peak=   -3.542 closest distance to " OE1 GLN A 223 " =    2.374
peak=   -3.541 closest distance to " C   HIS A 108 " =    1.149
peak=   -3.541 closest distance to " O   HOH Z 185 " =    2.539
peak=   -3.541 closest distance to " O   HOH Z 113 " =    2.218
peak=   -3.541 closest distance to " CG  ASP A  50 " =    2.358
peak=   -3.536 closest distance to " O   HOH Z 111 " =    2.144
peak=   -3.535 closest distance to " N   THR A 235 " =    1.218
peak=   -3.530 closest distance to " N   THR A  18 " =    1.264
peak=   -3.521 closest distance to " OG  SER A  87 " =    1.710
peak=   -3.519 closest distance to " O   HOH Z 396 " =    1.749
peak=   -3.518 closest distance to " OXT GLY A 302 " =    3.144
peak=   -3.513 closest distance to " CA  GLY A 203 " =    2.311
peak=   -3.508 closest distance to " OG  SER A  26 " =    1.351
peak=   -3.503 closest distance to " CD2 PHE A  61 " =    2.045
peak=   -3.503 closest distance to " N   ALA A 226 " =    2.326
peak=   -3.496 closest distance to " CA  TYR A  68 " =    2.879
peak=   -3.490 closest distance to " CA  GLY A 241 " =    3.152
peak=   -3.485 closest distance to " O   HOH Z 216 " =    1.502
peak=   -3.485 closest distance to " N   SER A 134 " =    1.206
peak=   -3.484 closest distance to " O   HOH Z 350 " =    1.668
peak=   -3.475 closest distance to " O   HOH Z 200 " =    1.632
peak=   -3.471 closest distance to " O   HOH Z 105 " =    2.065
peak=   -3.463 closest distance to " N   ALA A  43 " =    2.697
peak=   -3.457 closest distance to " O   HOH Z 150 " =    1.610
peak=   -3.451 closest distance to " CG1 VAL A  78 " =    2.638
peak=   -3.430 closest distance to " CD2 TYR A 293 " =    1.954
peak=   -3.429 closest distance to " CD1 TYR A 247 " =    2.320
peak=   -3.425 closest distance to " CG  TRP A 266 " =    1.823
peak=   -3.418 closest distance to " CB  PRO A 163 " =    2.611
peak=   -3.416 closest distance to " O   HOH Z 234 " =    4.530
peak=   -3.409 closest distance to " O   HOH Z 308 " =    1.636
peak=   -3.400 closest distance to " O   HOH Z 165 " =    1.881
peak=   -3.400 closest distance to " CB  ALA A  10 " =    2.241
peak=   -3.399 closest distance to " O   HOH Z 241 " =    1.092
peak=   -3.398 closest distance to " O   HOH Z  38 " =    1.005
peak=   -3.398 closest distance to " NH1AARG A 102 " =    1.406
peak=   -3.396 closest distance to " CG2 VAL A 112 " =    2.616
peak=   -3.395 closest distance to " NH2 ARG A 159 " =    2.438
peak=   -3.387 closest distance to " N   SER A 212 " =    2.020
peak=   -3.387 closest distance to " CA  GLY A 241 " =    2.232
peak=   -3.373 closest distance to " NE2 GLN A 103 " =    1.847
peak=   -3.362 closest distance to " SG ACYS A 201 " =    1.080
peak=   -3.358 closest distance to " CB  TRP A  85 " =    2.584
peak=   -3.354 closest distance to " O   HOH Z 174 " =    2.330
peak=   -3.346 closest distance to " O   HOH Z 292 " =    4.546
peak=   -3.340 closest distance to " CD1 LEU A 101 " =    2.554
peak=   -3.339 closest distance to " NH2AARG A 275 " =    5.341
peak=   -3.328 closest distance to " O   VAL A  67 " =    2.543
peak=   -3.326 closest distance to " O   HOH Z  11 " =    1.928
peak=   -3.325 closest distance to " O   HOH Z 166 " =    1.600
peak=   -3.317 closest distance to " O   HOH Z 198 " =    1.473
peak=   -3.316 closest distance to " O   HOH Z 149 " =    2.110
peak=   -3.315 closest distance to " OG  SER A  62 " =    4.402
peak=   -3.312 closest distance to " O   HOH Z 275 " =    1.587
peak=   -3.311 closest distance to " CB  TYR A  15 " =    2.242
peak=   -3.306 closest distance to " OG ASER A 134 " =    1.276
peak=   -3.298 closest distance to " O   HOH Z 109 " =    0.931
peak=   -3.297 closest distance to " CA  ARG A  36 " =    1.325
peak=   -3.295 closest distance to " OE1 GLN A  88 " =    0.994
peak=   -3.293 closest distance to " CZ2 TRP A 274 " =    1.073
peak=   -3.292 closest distance to " O   HOH Z 377 " =    1.900
peak=   -3.291 closest distance to " CD1 ILE A 151 " =    2.455
peak=   -3.291 closest distance to " O   HOH Z  60 " =    2.088
peak=   -3.290 closest distance to " O   HOH Z 426 " =    1.930
peak=   -3.290 closest distance to " O   HOH Z 251 " =    4.992
peak=   -3.286 closest distance to " CB  ARG A  79 " =    2.522
peak=   -3.286 closest distance to " NE2 HIS A  86 " =    1.060
peak=   -3.281 closest distance to " CZ  ARG A  79 " =    1.837
peak=   -3.280 closest distance to " OG BSER A 134 " =    1.490
peak=   -3.278 closest distance to " CA  HIS A  86 " =    2.169
peak=   -3.277 closest distance to " CD1 LEU A   5 " =    1.780
peak=   -3.275 closest distance to " OG1 THR A  82 " =    1.516
peak=   -3.273 closest distance to " CB  ALA A 256 " =    2.792
peak=   -3.272 closest distance to " N   ILE A 120 " =    1.080
peak=   -3.270 closest distance to " N   SER A   3 " =    2.226
peak=   -3.266 closest distance to " O   HOH Z 114 " =    1.459
peak=   -3.265 closest distance to " O   HOH Z 259 " =    4.343
peak=   -3.263 closest distance to " NE2 GLN A  88 " =    1.021
peak=   -3.262 closest distance to " O   HOH Z 118 " =    3.713
peak=   -3.261 closest distance to " O   HOH Z 222 " =    1.525
peak=   -3.258 closest distance to " CB  ALA A 248 " =    2.104
peak=   -3.257 closest distance to " C   LEU A 143 " =    1.175
peak=   -3.254 closest distance to " CE3 TRP A 150 " =    2.375
peak=   -3.254 closest distance to " OD1 ASN A 173 " =    1.337
peak=   -3.251 closest distance to " CA  ASN A 127 " =    0.962
peak=   -3.251 closest distance to " C   THR A 279 " =    1.226
peak=   -3.250 closest distance to " ND2 ASN A  45 " =    2.347
peak=   -3.249 closest distance to " O   HOH Z 227 " =    1.210
peak=   -3.249 closest distance to " OD1 ASP A 171 " =    1.584
peak=   -3.245 closest distance to " O   HOH Z 411 " =    1.791
peak=   -3.237 closest distance to " O   HOH Z  70 " =    2.257
peak=   -3.236 closest distance to " O   GLU A  44 " =    1.648
peak=   -3.235 closest distance to " CH2 TRP A 177 " =    2.252
peak=   -3.228 closest distance to " O   HOH Z 371 " =    1.253
peak=   -3.227 closest distance to " CD2 LEU A 300 " =    2.624
peak=   -3.225 closest distance to " CA  VAL A 197 " =    1.058
peak=   -3.225 closest distance to " O   HOH Z 236 " =    1.626
peak=   -3.221 closest distance to " ND2 ASN A  60 " =    1.959
peak=   -3.219 closest distance to " O   ASP A  27 " =    2.081
peak=   -3.215 closest distance to " CB  SER A 146 " =    2.236
peak=   -3.213 closest distance to " C   ASP A 270 " =    1.237
peak=   -3.204 closest distance to " OG1 THR A  82 " =    1.845
peak=   -3.198 closest distance to " O   HOH Z 150 " =    2.016
peak=   -3.191 closest distance to " CG  PRO A 243 " =    1.661
peak=   -3.189 closest distance to " O   HOH Z 177 " =    1.222
peak=   -3.186 closest distance to " CB  ALA A   9 " =    2.624
peak=   -3.185 closest distance to " C   ALA A 165 " =    1.981
peak=   -3.176 closest distance to " O   HOH Z  60 " =    2.120
peak=   -3.174 closest distance to " O   HOH Z 252 " =    3.923
peak=   -3.170 closest distance to " CD  GLN A 223 " =    0.886
peak=   -3.170 closest distance to " O   HOH Z 189 " =    2.438
peak=   -3.169 closest distance to " O   HOH Z 387 " =    3.775
peak=   -3.168 closest distance to " CH2 TRP A 150 " =    1.013
peak=   -3.159 closest distance to " CD  PRO A 243 " =    1.918
peak=   -3.154 closest distance to " O   HOH Z   6 " =    1.686
peak=   -3.153 closest distance to " CD2 PHE A 225 " =    1.336
peak=   -3.143 closest distance to " N   THR A  52 " =    1.694
peak=   -3.142 closest distance to " O   HOH Z 388 " =    1.946
peak=   -3.140 closest distance to " O   HOH Z 377 " =    1.106
peak=   -3.134 closest distance to " O   HOH Z 111 " =    1.346
peak=   -3.131 closest distance to " O   HOH Z  40 " =    2.484
peak=   -3.131 closest distance to " CD2 PHE A  61 " =    2.536
peak=   -3.130 closest distance to " O   HOH Z 136 " =    0.939
peak=   -3.129 closest distance to " CB  ALA A 291 " =    2.335
peak=   -3.119 closest distance to " C   GLY A  13 " =    0.972
peak=   -3.116 closest distance to " CG2 VAL A 189 " =    2.026
peak=   -3.109 closest distance to " O   PHE A 218 " =    1.405
peak=   -3.101 closest distance to " O   HOH Z 171 " =    2.304
peak=   -3.092 closest distance to " C   THR A  18 " =    1.305
peak=   -3.088 closest distance to " O   HOH Z 196 " =    2.057
peak=   -3.088 closest distance to " O   HOH Z 410 " =    1.563
peak=   -3.087 closest distance to " O   HOH Z 120 " =    4.293
peak=   -3.078 closest distance to " O   SER A 258 " =    2.237
peak=   -3.073 closest distance to " O   HOH Z  58 " =    1.210
peak=   -3.070 closest distance to " OE2 GLU A  53 " =    1.308
peak=   -3.051 closest distance to " CZ  TYR A 169 " =    1.812
peak=   -3.050 closest distance to " CD1 LEU A 228 " =    2.524
peak=   -3.044 closest distance to " O   HOH Z 423 " =    2.207
peak=   -3.037 closest distance to " CD2 HIS A 207 " =    2.555
peak=   -3.031 closest distance to " O   GLN A 240 " =    2.551
peak=   -3.029 closest distance to " OG  SER A  63 " =    1.149
peak=   -3.013 closest distance to " O   HOH Z 109 " =    1.559

================= 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    :  0.4872 0.4702   6.286138e+00   6.267881e+00
   1_bss:  0.4803 0.4632   6.282287e+00   6.261164e+00
   1_xyz:  0.3933 0.4137   6.167588e+00   6.196817e+00
   1_adp:  0.3503 0.3921   6.093765e+00   6.169215e+00
   1_occ:  0.3496 0.3927   6.092853e+00   6.170459e+00
   2_bss:  0.3486 0.3898   6.093982e+00   6.169132e+00
   2_xyz:  0.2696 0.3221   5.889459e+00   6.026654e+00
   2_adp:  0.2507 0.3021   5.834530e+00   5.979650e+00
   2_occ:  0.2505 0.3024   5.834250e+00   5.979680e+00
   3_bss:  0.2495 0.3009   5.834901e+00   5.978200e+00
   3_xyz:  0.1815 0.2287   5.545164e+00   5.736281e+00
   3_adp:  0.1644 0.2116   5.464807e+00   5.666236e+00
   3_occ:  0.1641 0.2118   5.464444e+00   5.666544e+00
   4_bss:  0.1639 0.2115   5.464450e+00   5.666388e+00
   4_xyz:  0.1423 0.1902   5.346513e+00   5.560825e+00
   4_adp:  0.1373 0.1867   5.321155e+00   5.542397e+00
   4_occ:  0.1373 0.1865   5.320694e+00   5.541794e+00
   5_bss:  0.1375 0.1867   5.321326e+00   5.541739e+00
   5_xyz:  0.1270 0.1755   5.254555e+00   5.488218e+00
   5_adp:  0.1255 0.1744   5.246515e+00   5.482688e+00
   5_occ:  0.1255 0.1741   5.245786e+00   5.481781e+00
   5_bss:  0.1255 0.1741   5.245615e+00   5.481664e+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:  0.286  20.000   7.648   9.046   7.908   0.000   0.000   0.000
   1_xyz:  0.286  20.000   7.648   9.046   7.908   0.000   0.000   0.000
   1_adp:  0.286  20.000   7.648   9.046   7.908   0.000   0.000   0.000
   1_occ:  0.286  20.000   7.648   9.046   7.908   0.000   0.000   0.000
   2_bss:  0.308  50.000   5.199   6.345   5.463   0.000   0.000   0.000
   2_xyz:  0.308  50.000   5.199   6.345   5.463   0.000   0.000   0.000
   2_adp:  0.308  50.000   5.199   6.345   5.463   0.000   0.000   0.000
   2_occ:  0.308  50.000   5.199   6.345   5.463   0.000   0.000   0.000
   3_bss:  0.304  50.000   3.441   4.317   4.009   0.000   0.000   0.000
   3_xyz:  0.304  50.000   3.441   4.317   4.009   0.000   0.000   0.000
   3_adp:  0.304  50.000   3.441   4.317   4.009   0.000   0.000   0.000
   3_occ:  0.304  50.000   3.441   4.317   4.009   0.000   0.000   0.000
   4_bss:  0.330  69.248   2.499   3.021   3.451   0.000   0.000   0.000
   4_xyz:  0.330  69.248   2.499   3.021   3.451   0.000   0.000   0.000
   4_adp:  0.330  69.248   2.499   3.021   3.451   0.000   0.000   0.000
   4_occ:  0.330  69.248   2.499   3.021   3.451   0.000   0.000   0.000
   5_bss:  0.330  69.248   2.385   2.786   3.479   0.000   0.000   0.000
   5_xyz:  0.330  69.248   2.385   2.786   3.479   0.000   0.000   0.000
   5_adp:  0.330  69.248   2.385   2.786   3.479   0.000   0.000   0.000
   5_occ:  0.330  69.248   2.385   2.786   3.479   0.000   0.000   0.000
   5_bss:  0.321  68.344  -0.450  -0.189   0.639   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.120 0.4175  0.4673    68242.067
   1_bss:  57.104 0.4297  0.6098    66371.586
   1_xyz:  48.633 0.5357  0.7399    49972.717
   1_adp:  44.986 0.5814  0.8313    44942.398
   1_occ:  45.039 0.5807  0.8291    45072.073
   2_bss:  44.920 0.5822  0.7640    44894.260
   2_xyz:  34.771 0.7030  0.9115    28713.337
   2_adp:  31.791 0.7379  0.9448    25221.814
   2_occ:  31.811 0.7377  0.9440    25232.242
   3_bss:  31.722 0.7386  0.8883    25100.873
   3_xyz:  22.649 0.8349  0.9693    13495.669
   3_adp:  20.413 0.8576  0.9751    11430.787
   3_occ:  20.419 0.8576  0.9747    11448.556
   4_bss:  20.381 0.8580  0.9431    11416.063
   4_xyz:  17.713 0.8833  0.9586     9032.762
   4_adp:  17.192 0.8883  0.9551     8739.649
   4_occ:  17.179 0.8884  0.9550     8728.315
   5_bss:  17.181 0.8884  0.9513     8729.529
   5_xyz:  15.962 0.8990  0.9576     7773.112
   5_adp:  15.791 0.9006  0.9524     7670.582
   5_occ:  15.769 0.9008  0.9524     7656.329
   5_bss:  15.768 0.9008  0.9558     7655.151
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4615e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4615e+01
   1_xyz:   1.777  0.014  0.113 18.081  0.007  4.111   1.5486e-01
   1_adp:   1.777  0.014  0.113 18.081  0.007  4.111   1.5486e-01
   1_occ:   1.777  0.014  0.113 18.081  0.007  4.111   1.5486e-01
   2_bss:   1.777  0.014  0.113 18.081  0.007  4.111   1.5486e-01
   2_xyz:   1.190  0.009  0.079 16.136  0.005  4.134   7.9387e-02
   2_adp:   1.190  0.009  0.079 16.136  0.005  4.134   7.9387e-02
   2_occ:   1.190  0.009  0.079 16.136  0.005  4.134   7.9387e-02
   3_bss:   1.190  0.009  0.079 16.136  0.005  4.134   7.9387e-02
   3_xyz:   1.152  0.009  0.087 15.863  0.004  4.120   7.8674e-02
   3_adp:   1.152  0.009  0.087 15.863  0.004  4.120   7.8674e-02
   3_occ:   1.152  0.009  0.087 15.863  0.004  4.120   7.8674e-02
   4_bss:   1.152  0.009  0.087 15.863  0.004  4.120   7.8674e-02
   4_xyz:   1.016  0.008  0.078 15.350  0.003  4.132   6.3541e-02
   4_adp:   1.016  0.008  0.078 15.350  0.003  4.132   6.3541e-02
   4_occ:   1.016  0.008  0.078 15.350  0.003  4.132   6.3541e-02
   5_bss:   1.016  0.008  0.078 15.350  0.003  4.132   6.3541e-02
   5_xyz:   1.113  0.010  0.086 15.502  0.004  4.139   7.2973e-02
   5_adp:   1.113  0.010  0.086 15.502  0.004  4.139   7.2973e-02
   5_occ:   1.113  0.010  0.086 15.502  0.004  4.139   7.2973e-02
   5_bss:   1.113  0.010  0.086 15.502  0.004  4.139   7.2973e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0815e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0815e+00
   1_xyz:  15.259  0.176  0.478 86.559  0.041  2.195   1.1313e-01
   1_adp:  15.259  0.176  0.478 86.559  0.041  2.195   1.1313e-01
   1_occ:  15.259  0.176  0.478 86.559  0.041  2.195   1.1313e-01
   2_bss:  15.259  0.176  0.478 86.559  0.041  2.195   1.1313e-01
   2_xyz:   8.258  0.078  0.286 82.979  0.035  2.129   6.3476e-02
   2_adp:   8.258  0.078  0.286 82.979  0.035  2.129   6.3476e-02
   2_occ:   8.258  0.078  0.286 82.979  0.035  2.129   6.3476e-02
   3_bss:   8.258  0.078  0.286 82.979  0.035  2.129   6.3476e-02
   3_xyz:   8.016  0.070  0.386 85.229  0.047  2.282   6.2267e-02
   3_adp:   8.016  0.070  0.386 85.229  0.047  2.282   6.2267e-02
   3_occ:   8.016  0.070  0.386 85.229  0.047  2.282   6.2267e-02
   4_bss:   8.016  0.070  0.386 85.229  0.047  2.282   6.2267e-02
   4_xyz:   7.802  0.048  0.377 79.470  0.041  2.363   3.7490e-02
   4_adp:   7.802  0.048  0.377 79.470  0.041  2.363   3.7490e-02
   4_occ:   7.802  0.048  0.377 79.470  0.041  2.363   3.7490e-02
   5_bss:   7.802  0.048  0.377 79.470  0.041  2.363   3.7490e-02
   5_xyz:   8.855  0.064  0.524 82.478  0.037  2.272   4.5710e-02
   5_adp:   8.855  0.064  0.524 82.478  0.037  2.272   4.5710e-02
   5_occ:   8.855  0.064  0.524 82.478  0.037  2.272   4.5710e-02
   5_bss:   8.855  0.064  0.524 82.478  0.037  2.272   4.5710e-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: 110.78   0.00  13.19  75.75   0.00  10.60 110.78   0.00  27.34
   1_occ: 110.78   0.00  13.19  75.75   0.00  10.60 110.78   0.00  27.34
   2_bss: 110.78   0.00  13.19  75.75   0.00  10.60 110.78   0.00  27.34
   2_xyz: 110.78   0.00  13.19  75.75   0.00  10.60 110.78   0.00  27.34
   2_adp: 113.43   0.00  12.92  77.97   0.00   9.33 113.43   0.00  32.47
   2_occ: 113.43   0.00  12.92  77.97   0.00   9.33 113.43   0.00  32.47
   3_bss: 113.43   0.00  12.92  77.97   0.00   9.33 113.43   0.00  32.47
   3_xyz: 113.43   0.00  12.92  77.97   0.00   9.33 113.43   0.00  32.47
   3_adp: 108.26   0.00  13.15  83.51   0.00   8.77 108.26   0.29  36.98
   3_occ: 108.26   0.00  13.15  83.51   0.00   8.77 108.26   0.29  36.98
   4_bss: 108.26   0.00  13.15  83.51   0.00   8.77 108.26   0.29  36.98
   4_xyz: 108.26   0.00  13.15  83.51   0.00   8.77 108.26   0.29  36.98
   4_adp: 104.59   0.00  13.13  85.05   0.00   8.57 104.59   0.94  37.91
   4_occ: 104.59   0.00  13.13  85.05   0.00   8.57 104.59   0.94  37.91
   5_bss: 104.59   0.00  13.13  85.05   0.00   8.57 104.59   0.94  37.91
   5_xyz: 104.59   0.00  13.13  85.05   0.00   8.57 104.59   0.94  37.91
   5_adp:  99.66   0.00  12.98  86.52   0.00   8.40  99.66   1.32  37.93
   5_occ:  99.66   0.00  12.98  86.52   0.00   8.40  99.66   1.32  37.93
   5_bss: 102.65   2.98  15.97  89.51   2.98  11.39 102.65   4.30  40.91
------------------------------------------------------------------------
 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:    1.235    0.028    0.418
   1_adp:    1.235    0.028    0.418
   1_occ:    1.235    0.028    0.418
   2_bss:    1.235    0.028    0.418
   2_xyz:    1.763    0.052    0.578
   2_adp:    1.763    0.052    0.578
   2_occ:    1.763    0.052    0.578
   3_bss:    1.763    0.052    0.578
   3_xyz:    1.606    0.030    0.683
   3_adp:    1.606    0.030    0.683
   3_occ:    1.606    0.030    0.683
   4_bss:    1.606    0.030    0.683
   4_xyz:    1.804    0.024    0.733
   4_adp:    1.804    0.024    0.733
   4_occ:    1.804    0.024    0.733
   5_bss:    1.804    0.024    0.733
   5_xyz:    1.864    0.044    0.754
   5_adp:    1.864    0.044    0.754
   5_occ:    1.864    0.044    0.754
   5_bss:    1.864    0.044    0.754
------------------------------------------------------------------------

CPU time actual refinement: 335.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/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_1184/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1184/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.96 
  Macro-tasks:
    bulk solvent and scale       = 41.25  
    individual site refinement   = 136.55 
    weights calculation          = 32.02  
    collect and process          = 6.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.48 
  Micro-tasks:
    mask                            = 2.31   
    f_calc                          = 102.93 
    alpha_beta                      = 8.54   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.79 
    fmodel                         = 7.52   
    r_factors                      = 0.28   
    phase_errors                   = 10.51  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 247.26 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.715 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    655 calls, 102.63 s
gradients_fft:          600 calls, 100.49 s

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

# Date 2008-01-16 Time 03:24:04 PST -0800 (1200482644.16 s)
Start R-work = 0.4872, R-free = 0.4702 (no bulk solvent and anisotropic scale)
Final R-work = 0.1412, R-free = 0.1884 (no bulk solvent and anisotropic scale)

Start R-work = 0.4803, R-free = 0.4632
Final R-work = 0.1255, R-free = 0.1741