# Date 2008-01-16 Time 02:21:30 PST -0800 (1200478890.26 s)
#phil __OFF__

Command line arguments: "../795.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5745
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 795

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.1647, 85.5261, 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: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98116
Completeness in resolution range: 0.958272
Completeness with d_max=infinity: 0.955328

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98116
Completeness in resolution range: 0.958272
Completeness with d_max=infinity: 0.955328

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2392 [2141/2169]  1929   212   9.9%
  bin  2:  4.2392 -  3.3774 [2055/2071]  1847   208  10.1%
  bin  3:  3.3774 -  2.9542 [2035/2054]  1831   204  10.0%
  bin  4:  2.9542 -  2.6858 [2023/2053]  1826   197   9.7%
  bin  5:  2.6858 -  2.4942 [2009/2028]  1807   202  10.1%
  bin  6:  2.4942 -  2.3477 [1981/2017]  1783   198  10.0%
  bin  7:  2.3477 -  2.2305 [1970/2003]  1770   200  10.2%
  bin  8:  2.2305 -  2.1337 [1991/2025]  1792   199  10.0%
  bin  9:  2.1337 -  2.0518 [1974/2002]  1781   193   9.8%
  bin 10:  2.0518 -  1.9812 [1410/2020]  1264   146  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2197
        3.04 -     3.66: 4677
        3.66 -     4.28: 9008
        4.28 -     4.90: 12382
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.121 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.121 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.169 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28272 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_795/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/model_refine_001.geo

CPU time processing inputs: 8.68


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.16465 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4244   r_free= 0.4128   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.214711                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7282 0.99   1386  154 0.3604 0.3392      6.5121      6.4312|
|  2:  4.7282 -  3.7725 0.99   1353  147 0.3182 0.3325      6.6179       6.665|
|  3:  3.7725 -  3.3015 0.99   1307  150 0.3678 0.3437      6.5439      6.5458|
|  4:  3.3015 -  3.0022 0.99   1309  145 0.3942 0.3725      6.4275      6.3394|
|  5:  3.0022 -  2.7885 0.99   1305  143 0.4386 0.4510      6.2957      6.3402|
|  6:  2.7885 -  2.6250 0.99   1287  145 0.4464 0.4883      6.2088      6.2105|
|  7:  2.6250 -  2.4942 0.99   1293  139 0.4709 0.4245      6.2144      6.1288|
|  8:  2.4942 -  2.3861 0.98   1271  149 0.4712 0.4455      6.1354        6.11|
|  9:  2.3861 -  2.2945 0.98   1280  142 0.4766 0.4631      6.0848      6.0667|
| 10:  2.2945 -  2.2156 0.98   1267  134 0.4770 0.4991      6.0796      6.0776|
| 11:  2.2156 -  2.1465 1.00   1270  146 0.4850 0.4254      6.0151      6.0066|
| 12:  2.1465 -  2.0854 0.97   1263  135 0.4880 0.5041       5.952      6.0103|
| 13:  2.0854 -  2.0306 0.98   1266  144 0.5038 0.5026       5.872      5.8298|
| 14:  2.0306 -  1.9812 0.60    773   86 0.4995 0.4496      5.8175      5.7128|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7282  1386   154  0.74  30.41   0.82     0.76      56080.65|
|  2:  4.7282 -  3.7725  1353   147  0.78  27.73   0.92     0.83      69856.07|
|  3:  3.7725 -  3.3015  1307   150  0.71  34.43   0.87     0.81      73456.32|
|  4:  3.3015 -  3.0022  1309   145  0.66  39.05   0.84     0.72      66447.85|
|  5:  3.0022 -  2.7885  1305   143  0.56  47.20   0.78     0.64      60227.03|
|  6:  2.7885 -  2.6250  1287   145  0.55  48.36   0.77     0.61      52969.38|
|  7:  2.6250 -  2.4942  1293   139  0.55  48.02   0.76     0.61      47730.93|
|  8:  2.4942 -  2.3861  1271   149  0.54  48.83   0.76     0.61      42693.66|
|  9:  2.3861 -  2.2945  1280   142  0.54  49.32   0.76     0.60      38675.47|
| 10:  2.2945 -  2.2156  1267   134  0.52  50.52   0.79     0.59      36958.09|
| 11:  2.2156 -  2.1465  1270   146  0.49  53.11   0.78     0.56      35434.53|
| 12:  2.1465 -  2.0854  1263   135  0.45  56.53   0.78     0.53      36380.76|
| 13:  2.0854 -  2.0306  1266   144  0.41  59.11   0.75     0.49      32079.09|
| 14:  2.0306 -  1.9812   773    86  0.46  55.76   0.75     0.50      25199.51|
|alpha:            min =        0.49 max =            0.83 mean =         0.64|
|beta:             min =    25199.51 max =        73456.32 mean =     49084.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.94 mean =        45.81|
|phase err.(test): min =        0.00 max =           89.78 mean =        45.84|
|-----------------------------------------------------------------------------|

============================== 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 = 7.521945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.592351              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.556   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      686 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2630 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3896 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5082 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6583 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7700 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.788 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.673 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4332   r_free= 0.4216   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.220879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4162   r_free= 0.4035   ksol= 0.30   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,8.34,8.10,0.00,0.00,0.00); trace/3= 7.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.212811                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.046308              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.533   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4162      final r-factor (work) = 0.3053          |
| start r-factor (free) = 0.4035      final r-factor (free) = 0.3357          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.7261 = 7.05 * 0.50 * 6.2269 + 1.00 * 53.7877                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4141 = 7.05 * 0.50 * 6.0449 + 1.00 * 0.1170                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3053      final r-factor (work) = 0.2385          |
| start r-factor (free) = 0.3357      final r-factor (free) = 0.2779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6571 = 0.60 * 1.00 * 6.0449 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5368 = 0.60 * 1.00 * 5.8506 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.02   10.58    None  None   None       |
|    all(noH): 2823   0      0.00    67.02   10.58    None  None   None       |
|    Sol.    : 438    0      0.00    67.02   28.71    None  None   None       |
|    Mac.    : 2385   0      0.00    64.72   7.25     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 -   6.702: 1480   |   5:    33.509 -  40.210:   92        |
|      1:     6.702 -  13.404:  688   |   6:    40.210 -  46.912:   65        |
|      2:    13.404 -  20.105:  198   |   7:    46.912 -  53.614:   39        |
|      3:    20.105 -  26.807:  137   |   8:    53.614 -  60.316:    8        |
|      4:    26.807 -  33.509:  111   |   9:    60.316 -  67.017:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2385 r_free = 0.2779             target_work(ml) = 5.769         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2380 r_free = 0.2778             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2380   r_free= 0.2778   ksol= 0.30   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,8.34,8.10,0.00,0.00,0.00); trace/3= 7.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.767786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2337   r_free= 0.2709   ksol= 0.33   Bsol= 45.46   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.96,4.73,5.28,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.767591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.221655              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.567   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.310171              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.901  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2337      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2709      final r-factor (free) = 0.2030          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6258 = 2.22 * 0.50 * 5.8599 + 1.00 * 0.1165                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2788 = 2.22 * 0.50 * 5.6035 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1533          |
| start r-factor (free) = 0.2030      final r-factor (free) = 0.1926          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7494 = 0.31 * 1.00 * 5.6035 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6985 = 0.31 * 1.00 * 5.4175 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.92   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    66.92   11.01    None  None   None       |
|    Sol.    : 438    0      0.82    66.79   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    66.92   7.34     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 -   6.692: 1487   |   5:    33.458 -  40.150:  119        |
|      1:     6.692 -  13.383:  655   |   6:    40.150 -  46.842:   76        |
|      2:    13.383 -  20.075:  206   |   7:    46.842 -  53.533:   45        |
|      3:    20.075 -  26.767:  110   |   8:    53.533 -  60.225:    6        |
|      4:    26.767 -  33.458:  113   |   9:    60.225 -  66.917:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1533 r_free = 0.1926             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1532 r_free = 0.1927             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1532   r_free= 0.1927   ksol= 0.33   Bsol= 45.46   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.96,4.73,5.28,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.393952                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1527   r_free= 0.1922   ksol= 0.33   Bsol= 45.46   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.63,4.24,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.395072                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.651355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.594  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.579967              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.435   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1527      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1922      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2444 = 2.65 * 0.50 * 5.4238 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0912 = 2.65 * 0.50 * 5.3003 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1236      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0850 = 0.58 * 1.00 * 5.3003 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0234 = 0.58 * 1.00 * 5.1926 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.27   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    75.27   11.50    None  None   None       |
|    Sol.    : 438    0      0.66    67.81   33.79    None  None   None       |
|    Mac.    : 2385   0      0.00    75.27   7.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.527: 1637   |   5:    37.636 -  45.163:   96        |
|      1:     7.527 -  15.054:  580   |   6:    45.163 -  52.690:   83        |
|      2:    15.054 -  22.582:  168   |   7:    52.690 -  60.218:   29        |
|      3:    22.582 -  30.109:  104   |   8:    60.218 -  67.745:   13        |
|      4:    30.109 -  37.636:  106   |   9:    67.745 -  75.272:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1600             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1600             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1600   ksol= 0.33   Bsol= 45.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.63,4.24,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.180067                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1607   ksol= 0.33   Bsol= 45.46   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.63,4.24,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.181919                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.523974              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.158  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6185 = 2.52 * 0.50 * 5.1930 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5794 = 2.52 * 0.50 * 5.1611 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2228 = 0.23 * 1.00 * 5.1611 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2190 = 0.23 * 1.00 * 5.1511 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.98   11.25    None  None   None       |
|    all(noH): 2823   0      0.00    74.98   11.25    None  None   None       |
|    Sol.    : 438    0      0.93    66.17   32.77    None  None   None       |
|    Mac.    : 2385   0      0.00    74.98   7.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.498: 1658   |   5:    37.490 -  44.988:   88        |
|      1:     7.498 -  14.996:  579   |   6:    44.988 -  52.486:   75        |
|      2:    14.996 -  22.494:  157   |   7:    52.486 -  59.984:   26        |
|      3:    22.494 -  29.992:  106   |   8:    59.984 -  67.482:   11        |
|      4:    29.992 -  37.490:  117   |   9:    67.482 -  74.980:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1561             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1562             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1562   ksol= 0.33   Bsol= 45.46   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.63,4.24,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1562   ksol= 0.33   Bsol= 45.46   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.39,3.98,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.917508              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326835              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.282  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5797 = 2.92 * 0.50 * 5.1507 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5636 = 2.92 * 0.50 * 5.1351 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6887 = 0.33 * 1.00 * 5.1351 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6877 = 0.33 * 1.00 * 5.1288 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.05   11.17    None  None   None       |
|    all(noH): 2823   0      0.00    76.05   11.17    None  None   None       |
|    Sol.    : 438    0      0.92    64.35   32.50    None  None   None       |
|    Mac.    : 2385   0      0.00    76.05   7.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.605: 1676   |   5:    38.025 -  45.630:   94        |
|      1:     7.605 -  15.210:  563   |   6:    45.630 -  53.234:   67        |
|      2:    15.210 -  22.815:  160   |   7:    53.234 -  60.839:   25        |
|      3:    22.815 -  30.420:  114   |   8:    60.839 -  68.444:    8        |
|      4:    30.420 -  38.025:  111   |   9:    68.444 -  76.049:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1556             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1556             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1556   ksol= 0.33   Bsol= 45.46   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.39,3.98,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131628                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7282 0.99   1386  154 0.0992 0.1303      5.3805      5.5248|
|  2:  4.7282 -  3.7725 0.99   1353  147 0.0850 0.1111      5.4297      5.6373|
|  3:  3.7725 -  3.3015 0.99   1307  150 0.1036 0.1516      5.4586      5.8544|
|  4:  3.3015 -  3.0022 0.99   1309  145 0.1176 0.1491      5.4367      5.5633|
|  5:  3.0022 -  2.7885 0.99   1305  143 0.1282 0.1721      5.3111      5.5327|
|  6:  2.7885 -  2.6250 0.99   1287  145 0.1178 0.1806      5.1964      5.4567|
|  7:  2.6250 -  2.4942 0.99   1293  139 0.1208 0.1620      5.1502      5.3692|
|  8:  2.4942 -  2.3861 0.98   1271  149 0.1138 0.1714       5.051       5.323|
|  9:  2.3861 -  2.2945 0.98   1280  142 0.1152 0.1798      5.0253      5.3161|
| 10:  2.2945 -  2.2156 0.98   1267  134 0.1074 0.1705      4.9369      5.1992|
| 11:  2.2156 -  2.1465 1.00   1270  146 0.1100 0.1696      4.9216      5.2563|
| 12:  2.1465 -  2.0854 0.97   1263  135 0.1065 0.1614      4.8533      5.1057|
| 13:  2.0854 -  2.0306 0.98   1266  144 0.1135 0.1766      4.7837      5.0885|
| 14:  2.0306 -  1.9812 0.60    773   86 0.1033 0.1676      4.6496      4.8779|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7282  1386   154  0.94   8.85   0.98     0.96       7041.13|
|  2:  4.7282 -  3.7725  1353   147  0.95   7.78   1.01     1.00       8897.34|
|  3:  3.7725 -  3.3015  1307   150  0.93  11.25   1.02     1.02      10244.47|
|  4:  3.3015 -  3.0022  1309   145  0.92  13.63   1.00     0.98      10209.88|
|  5:  3.0022 -  2.7885  1305   143  0.90  15.93   0.99     0.95       8126.23|
|  6:  2.7885 -  2.6250  1287   145  0.90  15.78   0.98     0.96       7034.75|
|  7:  2.6250 -  2.4942  1293   139  0.91  15.12   0.99     0.95       6057.55|
|  8:  2.4942 -  2.3861  1271   149  0.91  15.16   0.99     0.96       5207.29|
|  9:  2.3861 -  2.2945  1280   142  0.91  15.17   1.01     0.98       4964.89|
| 10:  2.2945 -  2.2156  1267   134  0.90  15.28   1.00     0.96       4261.69|
| 11:  2.2156 -  2.1465  1270   146  0.90  16.18   1.00     0.97       4284.47|
| 12:  2.1465 -  2.0854  1263   135  0.92  14.47   1.00     0.98       3790.53|
| 13:  2.0854 -  2.0306  1266   144  0.90  16.33   1.01     1.00       3355.73|
| 14:  2.0306 -  1.9812   773    86  0.91  14.54   0.98     0.95       2465.92|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2465.92 max =        10244.47 mean =      6284.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1557   ksol= 0.33   Bsol= 48.98   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.08,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131604                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1557   ksol= 0.33   Bsol= 48.98   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,-0.08,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131604                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7282 0.99   1386  154 0.0992 0.1304      5.3808      5.5253|
|  2:  4.7282 -  3.7725 0.99   1353  147 0.0850 0.1111        5.43      5.6374|
|  3:  3.7725 -  3.3015 0.99   1307  150 0.1036 0.1516      5.4588      5.8548|
|  4:  3.3015 -  3.0022 0.99   1309  145 0.1176 0.1491      5.4367      5.5633|
|  5:  3.0022 -  2.7885 0.99   1305  143 0.1281 0.1721      5.3109      5.5323|
|  6:  2.7885 -  2.6250 0.99   1287  145 0.1178 0.1807      5.1962      5.4568|
|  7:  2.6250 -  2.4942 0.99   1293  139 0.1208 0.1620      5.1504      5.3697|
|  8:  2.4942 -  2.3861 0.98   1271  149 0.1138 0.1713       5.051      5.3228|
|  9:  2.3861 -  2.2945 0.98   1280  142 0.1152 0.1798      5.0253      5.3163|
| 10:  2.2945 -  2.2156 0.98   1267  134 0.1073 0.1705      4.9369       5.199|
| 11:  2.2156 -  2.1465 1.00   1270  146 0.1100 0.1694      4.9215      5.2556|
| 12:  2.1465 -  2.0854 0.97   1263  135 0.1065 0.1616       4.853      5.1059|
| 13:  2.0854 -  2.0306 0.98   1266  144 0.1135 0.1764      4.7833      5.0877|
| 14:  2.0306 -  1.9812 0.60    773   86 0.1033 0.1676      4.6493       4.878|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7282  1386   154  0.94   8.85   0.98     0.96       7047.64|
|  2:  4.7282 -  3.7725  1353   147  0.95   7.78   1.01     1.00       8904.03|
|  3:  3.7725 -  3.3015  1307   150  0.93  11.25   1.02     1.02      10251.75|
|  4:  3.3015 -  3.0022  1309   145  0.92  13.63   1.00     0.98      10208.45|
|  5:  3.0022 -  2.7885  1305   143  0.90  15.92   0.99     0.96       8124.52|
|  6:  2.7885 -  2.6250  1287   145  0.90  15.78   0.98     0.96       7033.05|
|  7:  2.6250 -  2.4942  1293   139  0.91  15.12   0.99     0.96       6059.39|
|  8:  2.4942 -  2.3861  1271   149  0.91  15.17   0.99     0.96       5207.27|
|  9:  2.3861 -  2.2945  1280   142  0.91  15.18   1.01     0.98       4966.56|
| 10:  2.2945 -  2.2156  1267   134  0.90  15.28   1.00     0.97       4260.57|
| 11:  2.2156 -  2.1465  1270   146  0.90  16.18   1.00     0.97       4282.76|
| 12:  2.1465 -  2.0854  1263   135  0.92  14.47   1.01     0.98       3788.03|
| 13:  2.0854 -  2.0306  1266   144  0.90  16.33   1.01     1.01       3352.62|
| 14:  2.0306 -  1.9812   773    86  0.91  14.52   0.98     0.95       2462.93|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2462.93 max =        10251.75 mean =      6285.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.51    79.56   14.68    None  None   None       |
|    all(noH): 2823   0      3.51    79.56   14.68    None  None   None       |
|    Sol.    : 438    0      4.43    67.86   36.01    None  None   None       |
|    Mac.    : 2385   0      3.51    79.56   10.77    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:     3.514 -  11.118: 1676   |   5:    41.538 -  49.143:   94        |
|      1:    11.118 -  18.723:  563   |   6:    49.143 -  56.748:   67        |
|      2:    18.723 -  26.328:  160   |   7:    56.748 -  64.353:   25        |
|      3:    26.328 -  33.933:  114   |   8:    64.353 -  71.958:    8        |
|      4:    33.933 -  41.538:  111   |   9:    71.958 -  79.563:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.387 - 5.979
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 329
   mapped sites are within: 0.702 - 5.979

peak=   10.389 closest distance to " CG2 VAL A 230 " =    1.347
peak=    6.237 closest distance to " CG  LEU A   5 " =    1.232
peak=    6.074 closest distance to " CG2 VAL A 296 " =    1.055
peak=    5.746 closest distance to " NH2 ARG A  56 " =    2.219
peak=    5.677 closest distance to " CB  VAL A 296 " =    1.128
peak=    5.674 closest distance to " CG  LEU A 228 " =    1.177
peak=    5.317 closest distance to " CG  PRO A  54 " =    1.221
peak=    5.258 closest distance to " CB  GLN A 223 " =    1.460
peak=    5.193 closest distance to " CB  SER A  63 " =    1.242
peak=    5.184 closest distance to " O   HOH Z 126 " =    1.888
peak=    5.156 closest distance to " CB  VAL A 230 " =    1.214
peak=    4.921 closest distance to " CD2 LEU A   5 " =    1.176
peak=    4.866 closest distance to " O   HOH Z 272 " =    1.885
peak=    4.806 closest distance to " CB  GLN A 183 " =    1.283
peak=    4.710 closest distance to " NE2 GLN A  11 " =    1.112
peak=    4.659 closest distance to " CB  ARG A 275 " =    0.866
peak=    4.629 closest distance to " CB  PRO A  54 " =    0.886
peak=    4.585 closest distance to " CB  GLU A 152 " =    1.145
peak=    4.545 closest distance to " C   PRO A 198 " =    1.489
peak=    4.543 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.537 closest distance to " O   HOH Z 298 " =    1.807
peak=    4.532 closest distance to " OD1 ASN A  69 " =    2.617
peak=    4.530 closest distance to " O   HOH Z 193 " =    1.811
peak=    4.444 closest distance to " O   HOH Z 236 " =    1.876
peak=    4.409 closest distance to " O   HOH Z 142 " =    1.616
peak=    4.387 closest distance to " CB  TYR A 169 " =    0.702
peak=    4.367 closest distance to " O   SER A  87 " =    2.221
peak=    4.332 closest distance to " CG  PRO A 213 " =    1.177
peak=    4.324 closest distance to " O   HOH Z 368 " =    2.206
peak=    4.309 closest distance to " O   HOH Z 369 " =    2.088
peak=    4.293 closest distance to " O   HOH Z 316 " =    3.022
peak=    4.275 closest distance to " CB  SER A   3 " =    1.284
peak=    4.259 closest distance to " O   HOH Z 423 " =    1.804
peak=    4.238 closest distance to " O   HOH Z 403 " =    1.674
peak=    4.221 closest distance to " O   HOH Z 427 " =    3.001
peak=    4.205 closest distance to " CB  GLU A 128 " =    1.083
peak=    4.199 closest distance to " O   HOH Z 203 " =    1.722
peak=    4.184 closest distance to " O   HOH Z 158 " =    3.121
peak=    4.164 closest distance to " O   HOH Z 303 " =    2.035
peak=    4.135 closest distance to " CB  ASN A 148 " =    1.338
peak=    4.115 closest distance to " CG  PRO A 243 " =    1.150
peak=    4.075 closest distance to " ND2 ASN A 187 " =    1.457
peak=    4.053 closest distance to " CD2 LEU A 228 " =    1.179
peak=    4.039 closest distance to " OD2 ASP A 286 " =    2.829
peak=    4.031 closest distance to " O   HOH Z  43 " =    2.001
peak=    4.027 closest distance to " O   HOH Z 346 " =    1.581
peak=    4.024 closest distance to " O   HOH Z  61 " =    1.606
peak=    4.014 closest distance to " O   HOH Z 234 " =    3.597
peak=    4.005 closest distance to " CB  VAL A 265 " =    1.307
peak=    4.001 closest distance to " CB  ARG A  79 " =    1.444
peak=    3.992 closest distance to " CG1BVAL A  72 " =    1.644
peak=    3.990 closest distance to " CB  GLU A 277 " =    3.552
peak=    3.984 closest distance to " NH2 ARG A 156 " =    1.144
peak=    3.964 closest distance to " CB  TRP A 179 " =    1.358
peak=    3.951 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.950 closest distance to " CA  TYR A  30 " =    0.926
peak=    3.944 closest distance to " O   HOH Z 209 " =    2.351
peak=    3.943 closest distance to " O   HOH Z 265 " =    2.444
peak=    3.912 closest distance to " O   HOH Z 389 " =    1.931
peak=    3.899 closest distance to " CB  TRP A 266 " =    0.951
peak=    3.885 closest distance to " CA  ALA A  21 " =    1.176
peak=    3.884 closest distance to " CB  ASN A  39 " =    0.853
peak=    3.877 closest distance to " CB  ASP A 140 " =    0.909
peak=    3.871 closest distance to " O   HOH Z 263 " =    1.683
peak=    3.864 closest distance to " CB  ARG A 139 " =    0.967
peak=    3.853 closest distance to " O   HOH Z  78 " =    1.643
peak=    3.852 closest distance to " O   HOH Z 344 " =    2.882
peak=    3.828 closest distance to " O   HOH Z  97 " =    1.993
peak=    3.827 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.821 closest distance to " O   HOH Z  88 " =    3.155
peak=    3.818 closest distance to " O   HOH Z  63 " =    2.120
peak=    3.806 closest distance to " O   HOH Z 248 " =    1.727
peak=    3.803 closest distance to " O   HOH Z 145 " =    2.147
peak=    3.799 closest distance to " O   TRP A 274 " =    1.905
peak=    3.793 closest distance to " CB  ARG A 190 " =    1.629
peak=    3.781 closest distance to " CB  ASN A 187 " =    1.089
peak=    3.780 closest distance to " O   HOH Z 411 " =    3.780
peak=    3.779 closest distance to " O   HOH Z 402 " =    1.496
peak=    3.779 closest distance to " O   HOH Z 371 " =    3.208
peak=    3.776 closest distance to " O   HOH Z  54 " =    1.628
peak=    3.772 closest distance to " O   HOH Z 193 " =    1.989
peak=    3.768 closest distance to " CA  ALA A  51 " =    0.970
peak=    3.764 closest distance to " CA  THR A 221 " =    0.946
peak=    3.761 closest distance to " OG BSER A 164 " =    2.209
peak=    3.755 closest distance to " O   HOH Z 197 " =    2.987
peak=    3.738 closest distance to " CB  VAL A 202 " =    1.542
peak=    3.734 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.725 closest distance to " CA  ASN A 215 " =    1.266
peak=    3.711 closest distance to " O   HOH Z 245 " =    1.420
peak=    3.704 closest distance to " CG  ARG A  66 " =    2.761
peak=    3.703 closest distance to " O   HOH Z 250 " =    1.338
peak=    3.701 closest distance to " O   HOH Z  97 " =    2.573
peak=    3.680 closest distance to " CG2 THR A 221 " =    1.166
peak=    3.672 closest distance to " O   HOH Z  20 " =    2.210
peak=    3.659 closest distance to " O   HOH Z 133 " =    1.599
peak=    3.654 closest distance to " O   HOH Z 128 " =    2.104
peak=    3.644 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.643 closest distance to " CB  GLN A 278 " =    0.857
peak=    3.643 closest distance to " O   HOH Z 135 " =    1.720
peak=    3.641 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.639 closest distance to " O   HOH Z 189 " =    2.651
peak=    3.632 closest distance to " O   HOH Z  59 " =    2.296
peak=    3.628 closest distance to " CZ  PHE A 218 " =    1.086
peak=    3.614 closest distance to " O   HOH Z  68 " =    2.222
peak=    3.611 closest distance to " O   MET A 105 " =    1.787
peak=    3.609 closest distance to " O   HOH Z  48 " =    1.434
peak=    3.603 closest distance to " CB  LEU A 228 " =    1.241
peak=    3.602 closest distance to " CB  LEU A 143 " =    1.135
peak=    3.601 closest distance to " CD  ARG A 159 " =    0.756
peak=    3.599 closest distance to " O   HOH Z  15 " =    2.069
peak=    3.592 closest distance to " O   HOH Z 180 " =    2.086
peak=    3.591 closest distance to " CB  TRP A 150 " =    1.436
peak=    3.589 closest distance to " N   VAL A 126 " =    1.357
peak=    3.585 closest distance to " CA  THR A 264 " =    0.777
peak=    3.584 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.577 closest distance to " CE1 TYR A 186 " =    1.283
peak=    3.574 closest distance to " O   HOH Z 147 " =    1.735
peak=    3.573 closest distance to " CD BLYS A 290 " =    1.119
peak=    3.570 closest distance to " CB  ASN A 142 " =    1.030
peak=    3.568 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.563 closest distance to " CG1 ILE A  33 " =    1.263
peak=    3.556 closest distance to " O   HOH Z 426 " =    1.524
peak=    3.554 closest distance to " CD1 LEU A 300 " =    1.176
peak=    3.554 closest distance to " CB  SER A 212 " =    1.186
peak=    3.547 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.544 closest distance to " CG1 ILE A  49 " =    1.415
peak=    3.544 closest distance to " CG  MET A 185 " =    1.137
peak=    3.538 closest distance to " O   HOH Z 214 " =    2.144
peak=    3.536 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.532 closest distance to " CD1 ILE A 106 " =    1.080
peak=    3.526 closest distance to " CD2 TRP A 179 " =    1.387
peak=    3.521 closest distance to " CB  SER A  26 " =    1.641
peak=    3.518 closest distance to " CB  ALA A 248 " =    1.554
peak=    3.515 closest distance to " O   HOH Z 329 " =    3.846
peak=    3.508 closest distance to " OG  SER A  22 " =    2.803
peak=    3.508 closest distance to " O   HOH Z  61 " =    1.633
peak=    3.503 closest distance to " O   HOH Z 134 " =    1.422
peak=    3.502 closest distance to " CB  ILE A 120 " =    1.426
peak=    3.501 closest distance to " O   HOH Z 291 " =    1.617
peak=    3.500 closest distance to " O   HOH Z 132 " =    2.665
peak=    3.500 closest distance to " O   HOH Z 273 " =    2.663
peak=    3.499 closest distance to " O   HOH Z 407 " =    2.473
peak=    3.491 closest distance to " ND2 ASN A 110 " =    1.693
peak=    3.489 closest distance to " CB  ALA A 291 " =    1.369
peak=    3.486 closest distance to " O   HOH Z 411 " =    1.830
peak=    3.484 closest distance to " ND1 HIS A  81 " =    1.690
peak=    3.481 closest distance to " O   HOH Z 112 " =    1.623
peak=    3.473 closest distance to " O   HOH Z 130 " =    2.278
peak=    3.470 closest distance to " OE1 GLU A   2 " =    2.151
peak=    3.467 closest distance to " O   HOH Z 271 " =    2.580
peak=    3.467 closest distance to " O   HOH Z  10 " =    1.822
peak=    3.465 closest distance to " NZ  LYS A 117 " =    3.193
peak=    3.458 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.447 closest distance to " O   HOH Z 187 " =    2.286
peak=    3.447 closest distance to " O   HOH Z  80 " =    1.641
peak=    3.441 closest distance to " O   HOH Z 313 " =    1.781
peak=    3.437 closest distance to " O   HOH Z 425 " =    1.283
peak=    3.436 closest distance to " N   SER A 135 " =    1.437
peak=    3.431 closest distance to " CG BARG A 102 " =    1.788
peak=    3.427 closest distance to " CD1 LEU A   5 " =    1.380
peak=    3.425 closest distance to " O   HOH Z 193 " =    1.623
peak=    3.422 closest distance to " O   HOH Z 345 " =    3.274
peak=    3.419 closest distance to " CE  LYS A  76 " =    0.899
peak=    3.419 closest distance to " CA  VAL A  41 " =    0.835
peak=    3.414 closest distance to " CG  GLN A  77 " =    2.191
peak=    3.412 closest distance to " CB  THR A  31 " =    1.633
peak=    3.412 closest distance to " CA  ALA A 158 " =    1.164
peak=    3.410 closest distance to " NH1BARG A 190 " =    1.838
peak=    3.410 closest distance to " CA  ASP A 140 " =    1.210
peak=    3.407 closest distance to " CG1 VAL A 153 " =    0.909
peak=    3.406 closest distance to " CA  ALA A 233 " =    1.326
peak=    3.400 closest distance to " CG  PRO A 198 " =    1.208
peak=    3.399 closest distance to " O   HOH Z 126 " =    1.699
peak=    3.397 closest distance to " NH1AARG A 145 " =    1.053
peak=    3.394 closest distance to " CG2 ILE A 120 " =    1.240
peak=    3.390 closest distance to " CB  THR A 157 " =    1.177
peak=    3.390 closest distance to " O   HOH Z 285 " =    3.090
peak=    3.388 closest distance to " O   HOH Z 171 " =    2.391
peak=    3.385 closest distance to " O   HOH Z  20 " =    1.567
peak=    3.383 closest distance to " O   HOH Z 420 " =    1.947
peak=    3.382 closest distance to " NZ  LYS A  48 " =    1.395
peak=    3.377 closest distance to " CG1 VAL A 296 " =    1.187
peak=    3.377 closest distance to " O   HOH Z  48 " =    1.710
peak=    3.376 closest distance to " O   HOH Z 417 " =    3.261
peak=    3.374 closest distance to " O   HOH Z 133 " =    2.368
peak=    3.372 closest distance to " O   ALA A 158 " =    1.383
peak=    3.371 closest distance to " O   HOH Z 227 " =    1.632
peak=    3.370 closest distance to " CB  HIS A 108 " =    0.792
peak=    3.369 closest distance to " CB  MET A  40 " =    0.841
peak=    3.367 closest distance to " CG2 THR A 294 " =    1.682
peak=    3.365 closest distance to " CB BVAL A  41 " =    1.149
peak=    3.356 closest distance to " O   HOH Z  40 " =    2.593
peak=    3.355 closest distance to " CA  MET A  40 " =    1.117
peak=    3.350 closest distance to " CB  ALA A 248 " =    0.997
peak=    3.350 closest distance to " CB  SER A 216 " =    0.731
peak=    3.348 closest distance to " N   ASN A  39 " =    1.186
peak=    3.346 closest distance to " CA  ASP A 162 " =    1.058
peak=    3.345 closest distance to " CG2 ILE A  20 " =    1.457
peak=    3.342 closest distance to " O   HOH Z 368 " =    3.594
peak=    3.338 closest distance to " O   HOH Z  40 " =    1.656
peak=    3.336 closest distance to " O   HOH Z 250 " =    1.381
peak=    3.330 closest distance to " CA  SER A  87 " =    0.990
peak=    3.327 closest distance to " OG1 THR A 294 " =    2.377
peak=    3.325 closest distance to " O   HOH Z 286 " =    2.270
peak=    3.323 closest distance to " CA  ALA A 295 " =    1.028
peak=    3.319 closest distance to " CG  GLN A  88 " =    1.050
peak=    3.318 closest distance to " CB  GLU A  46 " =    1.064
peak=    3.316 closest distance to " CB  GLN A 205 " =    1.180
peak=    3.314 closest distance to " O   HOH Z 281 " =    4.672
peak=    3.313 closest distance to " O   HOH Z 299 " =    4.337
peak=    3.310 closest distance to " O   HOH Z 123 " =    2.274
peak=    3.309 closest distance to " CB  ARG A  79 " =    0.888
peak=    3.308 closest distance to " O   ASP A 124 " =    1.167
peak=    3.307 closest distance to " CD2 LEU A 255 " =    1.498
peak=    3.305 closest distance to " CG  MET A 185 " =    1.108
peak=    3.304 closest distance to " CD  ARG A 269 " =    0.959
peak=    3.302 closest distance to " O   GLN A 278 " =    1.173
peak=    3.302 closest distance to " O   HOH Z 295 " =    1.510
peak=    3.300 closest distance to " CA  ASP A 191 " =    0.813
peak=    3.295 closest distance to " O   HOH Z 423 " =    3.042
peak=    3.293 closest distance to " CD1 ILE A  33 " =    1.572
peak=    3.291 closest distance to " CZ  PHE A 192 " =    0.997
peak=    3.289 closest distance to " O   HOH Z  19 " =    2.195
peak=    3.288 closest distance to " ND1 HIS A  86 " =    1.604
peak=    3.286 closest distance to " O   HOH Z 258 " =    1.679
peak=    3.286 closest distance to " CB  ASN A 224 " =    1.059
peak=    3.285 closest distance to " CB  ALA A   1 " =    1.255
peak=    3.285 closest distance to " NH2AARG A 275 " =    3.658
peak=    3.281 closest distance to " O   HOH Z 279 " =    2.178
peak=    3.280 closest distance to " O   HOH Z 251 " =    1.659
peak=    3.279 closest distance to " O   HOH Z 359 " =    3.789
peak=    3.279 closest distance to " CB  MET A  47 " =    1.132
peak=    3.278 closest distance to " CD  LYS A 119 " =    1.804
peak=    3.278 closest distance to " O   HOH Z 189 " =    2.792
peak=    3.277 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.274 closest distance to " CG  LEU A 167 " =    1.189
peak=    3.273 closest distance to " CA  ALA A 291 " =    0.958
peak=    3.273 closest distance to " CA  VAL A 126 " =    0.867
peak=    3.273 closest distance to " O   HOH Z 435 " =    1.933
peak=    3.272 closest distance to " CD2 HIS A  81 " =    1.079
peak=    3.270 closest distance to " O   HOH Z 419 " =    1.623
peak=    3.270 closest distance to " O   HOH Z 128 " =    1.711
peak=    3.268 closest distance to " O   HOH Z 172 " =    3.846
peak=    3.267 closest distance to " NH2 ARG A  79 " =    1.328
peak=    3.264 closest distance to " O   HOH Z 227 " =    2.082
peak=    3.262 closest distance to " CG2 VAL A 197 " =    1.023
peak=    3.259 closest distance to " CE1 HIS A 108 " =    1.144
peak=    3.258 closest distance to " O   HOH Z 175 " =    2.163
peak=    3.258 closest distance to " O   HOH Z 392 " =    1.497
peak=    3.258 closest distance to " CB  LEU A 255 " =    0.805
peak=    3.254 closest distance to " O   HOH Z 366 " =    3.016
peak=    3.253 closest distance to " O   HOH Z  49 " =    2.543
peak=    3.245 closest distance to " N   PHE A 130 " =    1.313
peak=    3.244 closest distance to " O   HOH Z 302 " =    1.923
peak=    3.238 closest distance to " CG  GLN A  58 " =    2.797
peak=    3.232 closest distance to " CA  ASN A 176 " =    1.035
peak=    3.225 closest distance to " CB  ALA A 100 " =    1.192
peak=    3.223 closest distance to " CA  GLY A 267 " =    0.784
peak=    3.220 closest distance to " CA  ILE A 106 " =    0.771
peak=    3.215 closest distance to " O   HOH Z 199 " =    1.550
peak=    3.210 closest distance to " CZ2 TRP A 179 " =    1.680
peak=    3.208 closest distance to " CA  ALA A  84 " =    1.486
peak=    3.206 closest distance to " OD1 ASN A 217 " =    1.688
peak=    3.202 closest distance to " CB  ASN A 110 " =    1.145
peak=    3.199 closest distance to " O   HOH Z 388 " =    1.918
peak=    3.199 closest distance to " NE2 GLN A  58 " =    5.979
peak=    3.198 closest distance to " O   HOH Z 353 " =    2.715
peak=    3.197 closest distance to " NH2BARG A 190 " =    1.848
peak=    3.197 closest distance to " O   ALA A   1 " =    1.555
peak=    3.197 closest distance to " O   HOH Z 406 " =    1.633
peak=    3.197 closest distance to " O   HOH Z 374 " =    2.668
peak=    3.196 closest distance to " CA  LEU A 282 " =    1.039
peak=    3.195 closest distance to " CB  ALA A 114 " =    1.367
peak=    3.186 closest distance to " CG2 THR A 220 " =    0.849
peak=    3.186 closest distance to " O   HOH Z 305 " =    3.611
peak=    3.184 closest distance to " O   HOH Z  90 " =    2.242
peak=    3.182 closest distance to " O   HOH Z  62 " =    2.070
peak=    3.179 closest distance to " O   HOH Z 290 " =    1.044
peak=    3.179 closest distance to " N   SER A  12 " =    1.595
peak=    3.177 closest distance to " NH2BARG A 145 " =    2.049
peak=    3.173 closest distance to " CB  TYR A 169 " =    1.197
peak=    3.172 closest distance to " OD1 ASP A 231 " =    1.898
peak=    3.171 closest distance to " O   HOH Z 383 " =    1.974
peak=    3.171 closest distance to " O   HOH Z 209 " =    2.357
peak=    3.168 closest distance to " CA  TYR A 116 " =    1.395
peak=    3.165 closest distance to " O   HOH Z 124 " =    1.301
peak=    3.165 closest distance to " C   ALA A 299 " =    0.968
peak=    3.162 closest distance to " CB  LYS A 117 " =    1.141
peak=    3.161 closest distance to " O   HOH Z 409 " =    3.389
peak=    3.157 closest distance to " CB  ALA A 295 " =    1.273
peak=    3.149 closest distance to " O   HOH Z 256 " =    2.324
peak=    3.148 closest distance to " O   GLU A   2 " =    1.790
peak=    3.147 closest distance to " OE1 GLU A 236 " =    1.710
peak=    3.147 closest distance to " NZ  LYS A  76 " =    1.287
peak=    3.146 closest distance to " O   HOH Z   4 " =    1.897
peak=    3.144 closest distance to " O   HOH Z 116 " =    1.771
peak=    3.144 closest distance to " O   HOH Z  85 " =    2.138
peak=    3.140 closest distance to " O   HOH Z   9 " =    2.112
peak=    3.132 closest distance to " O   HOH Z 173 " =    2.249
peak=    3.125 closest distance to " CB  ASN A 215 " =    1.159
peak=    3.125 closest distance to " O   HOH Z 417 " =    2.601
peak=    3.125 closest distance to " O   HOH Z 213 " =    1.584
peak=    3.124 closest distance to " CG  LYS A  76 " =    0.983
peak=    3.113 closest distance to " OD2 ASP A 200 " =    1.389
peak=    3.113 closest distance to " CA  GLN A 194 " =    1.321
peak=    3.112 closest distance to " O   HOH Z 250 " =    1.726
peak=    3.111 closest distance to " N   ARG A 156 " =    1.338
peak=    3.104 closest distance to " O   HOH Z 329 " =    2.717
peak=    3.103 closest distance to " O   HOH Z 336 " =    1.741
peak=    3.102 closest distance to " CZ2 TRP A 274 " =    1.568
peak=    3.088 closest distance to " N   ASP A 162 " =    1.335
peak=    3.088 closest distance to " O   HOH Z 301 " =    1.894
peak=    3.086 closest distance to " CA  SER A 146 " =    1.749
peak=    3.083 closest distance to " O   HOH Z 420 " =    5.891
peak=    3.061 closest distance to " O   SER A 164 " =    1.179
peak=    3.057 closest distance to " CD  ARG A  79 " =    1.998
peak=    3.052 closest distance to " O   HOH Z 357 " =    1.851
peak=    3.044 closest distance to " CA  LYS A 290 " =    1.305
peak=    3.042 closest distance to " CB  ILE A  20 " =    1.463
peak=    3.041 closest distance to " O   HOH Z 256 " =    1.548
peak=    3.041 closest distance to " OG1 THR A 246 " =    3.156
peak=    3.036 closest distance to " CB  LYS A 290 " =    1.022
peak=    3.019 closest distance to " CZ3 TRP A  85 " =    0.954
peak=    3.007 closest distance to " O   HOH Z 371 " =    3.361

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.553 - 5.484
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.797 - 5.484

peak=   -5.728 closest distance to " CG2 VAL A 230 " =    0.844
peak=   -4.637 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.574 closest distance to " SG  CYS A 254 " =    3.173
peak=   -4.389 closest distance to " O   HOH Z 266 " =    4.753
peak=   -4.342 closest distance to " O   HOH Z 290 " =    1.162
peak=   -4.320 closest distance to " CB  PRO A 243 " =    2.647
peak=   -4.316 closest distance to " CB  ALA A 161 " =    2.531
peak=   -4.205 closest distance to " CD2 LEU A 300 " =    2.827
peak=   -4.109 closest distance to " C   HIS A 108 " =    1.212
peak=   -4.061 closest distance to " CG2BVAL A  41 " =    2.608
peak=   -4.035 closest distance to " CG  GLN A 223 " =    2.044
peak=   -4.006 closest distance to " O   HOH Z 196 " =    2.125
peak=   -3.986 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.983 closest distance to " OG  SER A  97 " =    2.253
peak=   -3.969 closest distance to " O   PRO A 163 " =    2.103
peak=   -3.932 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.858 closest distance to " O   HOH Z 231 " =    1.945
peak=   -3.826 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.817 closest distance to " CD1 LEU A 101 " =    2.466
peak=   -3.805 closest distance to " N   GLN A  58 " =    1.709
peak=   -3.803 closest distance to " CG  LEU A 101 " =    2.456
peak=   -3.800 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.798 closest distance to " OG BSER A 134 " =    1.192
peak=   -3.796 closest distance to " CZ3 TRP A 179 " =    1.224
peak=   -3.793 closest distance to " OXT GLY A 302 " =    2.837
peak=   -3.787 closest distance to " O   HOH Z  11 " =    1.883
peak=   -3.784 closest distance to " O   VAL A  67 " =    2.713
peak=   -3.774 closest distance to " NH2AARG A 275 " =    5.168
peak=   -3.765 closest distance to " O   HOH Z 103 " =    1.836
peak=   -3.753 closest distance to " O   HOH Z 166 " =    1.903
peak=   -3.727 closest distance to " O   HOH Z 389 " =    1.846
peak=   -3.715 closest distance to " C   ALA A 158 " =    1.299
peak=   -3.715 closest distance to " CD  LYS A 289 " =    2.531
peak=   -3.702 closest distance to " CB  ALA A 291 " =    2.272
peak=   -3.697 closest distance to " O   HOH Z 394 " =    1.523
peak=   -3.695 closest distance to " CB  ALA A  43 " =    2.416
peak=   -3.692 closest distance to " CG2 VAL A 296 " =    1.311
peak=   -3.686 closest distance to " O   HOH Z 114 " =    3.199
peak=   -3.662 closest distance to " CD  ARG A 139 " =    1.596
peak=   -3.655 closest distance to " O   HOH Z  52 " =    1.513
peak=   -3.645 closest distance to " NE2 GLN A  88 " =    2.029
peak=   -3.641 closest distance to " CG1 VAL A 250 " =    2.766
peak=   -3.639 closest distance to " C   ILE A 239 " =    2.112
peak=   -3.639 closest distance to " O   HOH Z 311 " =    3.685
peak=   -3.633 closest distance to " OG  SER A  62 " =    1.633
peak=   -3.626 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.620 closest distance to " O   HOH Z 407 " =    3.092
peak=   -3.619 closest distance to " O   HOH Z 185 " =    2.390
peak=   -3.609 closest distance to " CG  TRP A 266 " =    1.851
peak=   -3.595 closest distance to " CD  GLN A  58 " =    1.133
peak=   -3.591 closest distance to " ND2 ASN A  45 " =    1.486
peak=   -3.590 closest distance to " CB  ALA A 248 " =    2.070
peak=   -3.588 closest distance to " O   HOH Z 436 " =    1.591
peak=   -3.582 closest distance to " O   HOH Z  43 " =    1.693
peak=   -3.571 closest distance to " OG BSER A 134 " =    1.740
peak=   -3.564 closest distance to " CG  PHE A 283 " =    2.831
peak=   -3.559 closest distance to " CG1 VAL A 112 " =    2.828
peak=   -3.554 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.551 closest distance to " CD1 PHE A  59 " =    1.855
peak=   -3.542 closest distance to " N   ALA A  43 " =    2.425
peak=   -3.528 closest distance to " N   ALA A 226 " =    2.055
peak=   -3.525 closest distance to " CD1 LEU A 228 " =    2.268
peak=   -3.525 closest distance to " O   HOH Z 166 " =    1.490
peak=   -3.522 closest distance to " O   HOH Z  13 " =    1.413
peak=   -3.510 closest distance to " CB  PHE A 192 " =    1.830
peak=   -3.508 closest distance to " OG  SER A  26 " =    1.210
peak=   -3.507 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.501 closest distance to " O   HOH Z 283 " =    1.927
peak=   -3.501 closest distance to " N   THR A 235 " =    1.376
peak=   -3.495 closest distance to " CD1 LEU A 101 " =    2.623
peak=   -3.495 closest distance to " CG  ARG A 269 " =    2.332
peak=   -3.495 closest distance to " CE  MET A 105 " =    2.080
peak=   -3.483 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.480 closest distance to " CE2 PHE A 218 " =    2.605
peak=   -3.472 closest distance to " C   MET A 188 " =    1.402
peak=   -3.463 closest distance to " O   HOH Z 211 " =    1.677
peak=   -3.457 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.456 closest distance to " CG1 VAL A 230 " =    1.855
peak=   -3.441 closest distance to " NZ  LYS A 119 " =    3.481
peak=   -3.440 closest distance to " O   HOH Z  60 " =    2.172
peak=   -3.439 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.437 closest distance to " N   THR A 157 " =    1.469
peak=   -3.436 closest distance to " CZ  TYR A 169 " =    1.690
peak=   -3.432 closest distance to " CG  ASP A  50 " =    2.340
peak=   -3.428 closest distance to " NH2 ARG A  66 " =    1.777
peak=   -3.428 closest distance to " O   VAL A 125 " =    2.305
peak=   -3.428 closest distance to " CG2 ILE A 263 " =    2.370
peak=   -3.426 closest distance to " CE BMET A  47 " =    1.961
peak=   -3.425 closest distance to " ND2 ASN A 187 " =    1.634
peak=   -3.424 closest distance to " C   ASP A 231 " =    2.605
peak=   -3.423 closest distance to " O   VAL A 189 " =    2.585
peak=   -3.419 closest distance to " CB  TYR A  15 " =    2.222
peak=   -3.415 closest distance to " CG1 VAL A 296 " =    1.343
peak=   -3.414 closest distance to " O   GLY A 196 " =    1.130
peak=   -3.413 closest distance to " CG  LEU A 228 " =    0.964
peak=   -3.413 closest distance to " O   HOH Z  10 " =    1.548
peak=   -3.409 closest distance to " O   HOH Z 353 " =    2.085
peak=   -3.409 closest distance to " OG ASER A 134 " =    1.285
peak=   -3.408 closest distance to " CA  GLY A 241 " =    3.034
peak=   -3.407 closest distance to " N   MET A 105 " =    2.654
peak=   -3.401 closest distance to " OD1 ASN A 148 " =    1.534
peak=   -3.398 closest distance to " O   HOH Z 435 " =    2.759
peak=   -3.397 closest distance to " C   ASN A 187 " =    1.927
peak=   -3.394 closest distance to " N   PHE A  59 " =    2.201
peak=   -3.391 closest distance to " O   HOH Z 165 " =    1.902
peak=   -3.385 closest distance to " O   HOH Z  38 " =    1.598
peak=   -3.379 closest distance to " O   HOH Z 292 " =    4.495
peak=   -3.378 closest distance to " O   HOH Z  47 " =    1.569
peak=   -3.378 closest distance to " CZ  PHE A  59 " =    1.629
peak=   -3.376 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.369 closest distance to " O   HOH Z 174 " =    2.346
peak=   -3.366 closest distance to " O   HOH Z 198 " =    1.372
peak=   -3.363 closest distance to " CE3 TRP A 150 " =    2.023
peak=   -3.360 closest distance to " O   HOH Z 102 " =    1.598
peak=   -3.357 closest distance to " O   HOH Z 372 " =    2.380
peak=   -3.354 closest distance to " OG  SER A  87 " =    1.431
peak=   -3.346 closest distance to " NH1 ARG A 195 " =    2.547
peak=   -3.343 closest distance to " O   LYS A 117 " =    1.702
peak=   -3.340 closest distance to " C   LEU A 143 " =    1.003
peak=   -3.324 closest distance to " C   GLN A 205 " =    1.999
peak=   -3.323 closest distance to " CB  ASP A 132 " =    2.249
peak=   -3.322 closest distance to " CG1 VAL A 197 " =    2.242
peak=   -3.321 closest distance to " CZ3 TRP A 274 " =    1.093
peak=   -3.320 closest distance to " O   HOH Z 262 " =    2.781
peak=   -3.319 closest distance to " N   HIS A 115 " =    2.056
peak=   -3.315 closest distance to " CG2 ILE A  20 " =    2.803
peak=   -3.313 closest distance to " O   ALA A 161 " =    1.697
peak=   -3.313 closest distance to " O   HOH Z  19 " =    2.225
peak=   -3.312 closest distance to " OD2 ASP A 171 " =    2.290
peak=   -3.311 closest distance to " NE2 GLN A 103 " =    1.728
peak=   -3.307 closest distance to " CG  GLU A 277 " =    1.112
peak=   -3.298 closest distance to " O   HOH Z 222 " =    1.476
peak=   -3.296 closest distance to " ND2 ASN A  60 " =    1.439
peak=   -3.295 closest distance to " N   SER A 212 " =    2.043
peak=   -3.292 closest distance to " O   HOH Z 426 " =    1.615
peak=   -3.290 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.284 closest distance to " OG  SER A 206 " =    1.703
peak=   -3.283 closest distance to " N   ASP A 171 " =    2.354
peak=   -3.283 closest distance to " O   HOH Z 417 " =    2.776
peak=   -3.276 closest distance to " C   ASN A 285 " =    2.448
peak=   -3.275 closest distance to " OD1 ASN A 187 " =    1.632
peak=   -3.269 closest distance to " N   SER A 276 " =    1.345
peak=   -3.268 closest distance to " CA  GLY A  98 " =    1.912
peak=   -3.259 closest distance to " C   LEU A 222 " =    0.896
peak=   -3.255 closest distance to " SG ACYS A 201 " =    2.187
peak=   -3.254 closest distance to " CG  ARG A  66 " =    2.463
peak=   -3.252 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.252 closest distance to " O   HOH Z 234 " =    4.126
peak=   -3.244 closest distance to " O   SER A 271 " =    2.084
peak=   -3.243 closest distance to " O   HOH Z 134 " =    2.676
peak=   -3.240 closest distance to " O   HOH Z 241 " =    1.310
peak=   -3.238 closest distance to " CB  ASN A  39 " =    2.104
peak=   -3.236 closest distance to " CD1 TYR A 247 " =    2.343
peak=   -3.226 closest distance to " CG  GLU A  53 " =    1.549
peak=   -3.226 closest distance to " O   HOH Z 389 " =    4.512
peak=   -3.219 closest distance to " O   HOH Z 348 " =    1.897
peak=   -3.217 closest distance to " O   HOH Z 252 " =    4.021
peak=   -3.216 closest distance to " CD  ARG A 195 " =    5.149
peak=   -3.214 closest distance to " O   HOH Z 193 " =    1.894
peak=   -3.212 closest distance to " O   HOH Z 313 " =    1.909
peak=   -3.204 closest distance to " O   HOH Z 369 " =    2.202
peak=   -3.202 closest distance to " O   PHE A 218 " =    1.748
peak=   -3.200 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.198 closest distance to " CD2 LEU A 167 " =    1.738
peak=   -3.196 closest distance to " O   HOH Z 191 " =    5.484
peak=   -3.194 closest distance to " CA  GLY A 203 " =    2.329
peak=   -3.192 closest distance to " O   HOH Z 359 " =    3.130
peak=   -3.190 closest distance to " O   MET A  40 " =    2.722
peak=   -3.190 closest distance to " CG2 THR A 221 " =    2.030
peak=   -3.190 closest distance to " O   HOH Z 275 " =    1.469
peak=   -3.178 closest distance to " O   HOH Z 385 " =    2.206
peak=   -3.176 closest distance to " CG2 VAL A 112 " =    2.527
peak=   -3.176 closest distance to " NE2 GLN A 194 " =    1.779
peak=   -3.174 closest distance to " O   LEU A 167 " =    1.474
peak=   -3.174 closest distance to " CB  VAL A 296 " =    1.069
peak=   -3.172 closest distance to " CB  ASN A  69 " =    1.163
peak=   -3.166 closest distance to " O   HOH Z 431 " =    1.731
peak=   -3.164 closest distance to " O   SER A  95 " =    1.579
peak=   -3.163 closest distance to " OG1 THR A 178 " =    1.271
peak=   -3.157 closest distance to " N   ALA A 248 " =    1.737
peak=   -3.151 closest distance to " CD1 LEU A 297 " =    2.423
peak=   -3.145 closest distance to " CA  GLY A 133 " =    2.244
peak=   -3.138 closest distance to " O   HOH Z 207 " =    2.142
peak=   -3.132 closest distance to " NH2 ARG A  79 " =    1.627
peak=   -3.130 closest distance to " O   HOH Z 244 " =    2.007
peak=   -3.127 closest distance to " OD1 ASN A 301 " =    2.017
peak=   -3.126 closest distance to " O   HOH Z  22 " =    2.477
peak=   -3.124 closest distance to " CG  PRO A 163 " =    2.661
peak=   -3.118 closest distance to " N   GLN A  77 " =    1.556
peak=   -3.115 closest distance to " CB  ASP A 286 " =    2.268
peak=   -3.104 closest distance to " O   HOH Z 292 " =    2.827
peak=   -3.093 closest distance to " O   HOH Z 317 " =    2.305
peak=   -3.092 closest distance to " O   HOH Z 175 " =    4.340
peak=   -3.090 closest distance to " CD2 TYR A 293 " =    2.111
peak=   -3.088 closest distance to " CZ  PHE A  38 " =    2.260
peak=   -3.088 closest distance to " O   HOH Z 150 " =    1.891
peak=   -3.074 closest distance to " O   HOH Z  51 " =    1.414
peak=   -3.072 closest distance to " OXT GLY A 302 " =    3.432
peak=   -3.067 closest distance to " CG  GLU A   2 " =    1.772
peak=   -3.066 closest distance to " O   HOH Z 120 " =    4.230
peak=   -3.063 closest distance to " O   HOH Z 298 " =    2.691
peak=   -3.053 closest distance to " CE1 HIS A  81 " =    1.380
peak=   -3.013 closest distance to " CD2 TYR A 247 " =    2.337

================= 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    :  0.4244 0.4128   6.214711e+00   6.194851e+00
   1_bss:  0.4162 0.4035   6.212811e+00   6.180910e+00
   1_xyz:  0.3053 0.3357   5.985034e+00   6.044865e+00
   1_adp:  0.2385 0.2779   5.768938e+00   5.892589e+00
   1_occ:  0.2380 0.2778   5.767786e+00   5.892696e+00
   2_bss:  0.2337 0.2709   5.767591e+00   5.888582e+00
   2_xyz:  0.1647 0.2030   5.455555e+00   5.633262e+00
   2_adp:  0.1533 0.1926   5.394156e+00   5.583805e+00
   2_occ:  0.1532 0.1927   5.393952e+00   5.583980e+00
   3_bss:  0.1527 0.1922   5.395072e+00   5.584625e+00
   3_xyz:  0.1236 0.1644   5.215522e+00   5.437860e+00
   3_adp:  0.1175 0.1600   5.180074e+00   5.412923e+00
   3_occ:  0.1175 0.1600   5.180067e+00   5.413161e+00
   4_bss:  0.1179 0.1607   5.181919e+00   5.414040e+00
   4_xyz:  0.1119 0.1571   5.149521e+00   5.395355e+00
   4_adp:  0.1121 0.1561   5.145928e+00   5.387055e+00
   4_occ:  0.1121 0.1562   5.146062e+00   5.387423e+00
   5_bss:  0.1121 0.1562   5.145829e+00   5.387285e+00
   5_xyz:  0.1094 0.1550   5.130845e+00   5.380208e+00
   5_adp:  0.1090 0.1556   5.131514e+00   5.383494e+00
   5_occ:  0.1090 0.1556   5.131628e+00   5.383709e+00
   5_bss:  0.1090 0.1557   5.131604e+00   5.383707e+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:  0.300  20.000   7.177   8.336   8.101   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.177   8.336   8.101   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.177   8.336   8.101   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.177   8.336   8.101   0.000   0.000   0.000
   2_bss:  0.332  45.463   3.963   4.734   5.276   0.000   0.000   0.000
   2_xyz:  0.332  45.463   3.963   4.734   5.276   0.000   0.000   0.000
   2_adp:  0.332  45.463   3.963   4.734   5.276   0.000   0.000   0.000
   2_occ:  0.332  45.463   3.963   4.734   5.276   0.000   0.000   0.000
   3_bss:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   3_xyz:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   3_adp:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   3_occ:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   4_bss:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   4_xyz:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   4_adp:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   4_occ:  0.335  45.463   3.070   3.635   4.239   0.000   0.000   0.000
   5_bss:  0.335  45.463   2.953   3.386   3.984   0.000   0.000   0.000
   5_xyz:  0.335  45.463   2.953   3.386   3.984   0.000   0.000   0.000
   5_adp:  0.335  45.463   2.953   3.386   3.984   0.000   0.000   0.000
   5_occ:  0.335  45.463   2.953   3.386   3.984   0.000   0.000   0.000
   5_bss:  0.335  48.977  -0.448  -0.078   0.525   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.815 0.5740  0.6401    49084.394
   1_bss:  45.711 0.5727  0.8050    46697.712
   1_xyz:  35.598 0.6933  0.9514    30038.737
   1_adp:  27.396 0.7866  1.0469    19370.241
   1_occ:  27.403 0.7865  1.0465    19361.111
   2_bss:  27.203 0.7885  0.9351    19143.084
   2_xyz:  19.454 0.8667  0.9941    10440.916
   2_adp:  18.125 0.8797  1.0051     9426.084
   2_occ:  18.133 0.8796  1.0049     9428.205
   3_bss:  18.138 0.8796  0.9684     9465.116
   3_xyz:  14.987 0.9069  0.9823     6987.173
   3_adp:  14.486 0.9111  0.9840     6679.925
   3_occ:  14.489 0.9111  0.9838     6683.257
   4_bss:  14.522 0.9109  0.9830     6722.434
   4_xyz:  14.086 0.9145  0.9835     6419.017
   4_adp:  13.869 0.9164  0.9828     6328.070
   4_occ:  13.874 0.9164  0.9826     6335.270
   5_bss:  13.869 0.9164  0.9754     6334.016
   5_xyz:  13.750 0.9172  0.9755     6242.278
   5_adp:  13.832 0.9166  0.9734     6280.790
   5_occ:  13.835 0.9165  0.9733     6284.982
   5_bss:  13.835 0.9166  0.9759     6285.706
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3788e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3788e+01
   1_xyz:   1.523  0.011  0.101 17.747  0.006  4.123   1.1700e-01
   1_adp:   1.523  0.011  0.101 17.747  0.006  4.123   1.1700e-01
   1_occ:   1.523  0.011  0.101 17.747  0.006  4.123   1.1700e-01
   2_bss:   1.523  0.011  0.101 17.747  0.006  4.123   1.1700e-01
   2_xyz:   0.903  0.006  0.067 15.793  0.003  4.123   5.4189e-02
   2_adp:   0.903  0.006  0.067 15.793  0.003  4.123   5.4189e-02
   2_occ:   0.903  0.006  0.067 15.793  0.003  4.123   5.4189e-02
   3_bss:   0.903  0.006  0.067 15.793  0.003  4.123   5.4189e-02
   3_xyz:   1.053  0.007  0.084 15.682  0.004  4.131   6.4785e-02
   3_adp:   1.053  0.007  0.084 15.682  0.004  4.131   6.4785e-02
   3_occ:   1.053  0.007  0.084 15.682  0.004  4.131   6.4785e-02
   4_bss:   1.053  0.007  0.084 15.682  0.004  4.131   6.4785e-02
   4_xyz:   1.041  0.008  0.085 15.650  0.004  4.118   6.6106e-02
   4_adp:   1.041  0.008  0.085 15.650  0.004  4.118   6.6106e-02
   4_occ:   1.041  0.008  0.085 15.650  0.004  4.118   6.6106e-02
   5_bss:   1.041  0.008  0.085 15.650  0.004  4.118   6.6106e-02
   5_xyz:   1.104  0.009  0.090 15.637  0.004  4.122   7.2691e-02
   5_adp:   1.104  0.009  0.090 15.637  0.004  4.122   7.2691e-02
   5_occ:   1.104  0.009  0.090 15.637  0.004  4.122   7.2691e-02
   5_bss:   1.104  0.009  0.090 15.637  0.004  4.122   7.2691e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9741e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9741e+00
   1_xyz:  13.023  0.140  0.442 88.671  0.044  2.249   8.8636e-02
   1_adp:  13.023  0.140  0.442 88.671  0.044  2.249   8.8636e-02
   1_occ:  13.023  0.140  0.442 88.671  0.044  2.249   8.8636e-02
   2_bss:  13.023  0.140  0.442 88.671  0.044  2.249   8.8636e-02
   2_xyz:   6.149  0.044  0.253 80.515  0.032  2.366   4.6373e-02
   2_adp:   6.149  0.044  0.253 80.515  0.032  2.366   4.6373e-02
   2_occ:   6.149  0.044  0.253 80.515  0.032  2.366   4.6373e-02
   3_bss:   6.149  0.044  0.253 80.515  0.032  2.366   4.6373e-02
   3_xyz:   6.760  0.047  0.572 83.559  0.040  2.334   4.3482e-02
   3_adp:   6.760  0.047  0.572 83.559  0.040  2.334   4.3482e-02
   3_occ:   6.760  0.047  0.572 83.559  0.040  2.334   4.3482e-02
   4_bss:   6.760  0.047  0.572 83.559  0.040  2.334   4.3482e-02
   4_xyz:   6.981  0.041  0.620 82.716  0.040  2.335   4.6985e-02
   4_adp:   6.981  0.041  0.620 82.716  0.040  2.335   4.6985e-02
   4_occ:   6.981  0.041  0.620 82.716  0.040  2.335   4.6985e-02
   5_bss:   6.981  0.041  0.620 82.716  0.040  2.335   4.6985e-02
   5_xyz:   7.320  0.048  0.681 82.909  0.042  2.270   5.3393e-02
   5_adp:   7.320  0.048  0.681 82.909  0.042  2.270   5.3393e-02
   5_occ:   7.320  0.048  0.681 82.909  0.042  2.270   5.3393e-02
   5_bss:   7.320  0.048  0.681 82.909  0.042  2.270   5.3393e-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:  67.02   0.00  10.58  64.72   0.00   7.25  67.02   0.00  28.71
   1_occ:  67.02   0.00  10.58  64.72   0.00   7.25  67.02   0.00  28.71
   2_bss:  67.02   0.00  10.58  64.72   0.00   7.25  67.02   0.00  28.71
   2_xyz:  67.02   0.00  10.58  64.72   0.00   7.25  67.02   0.00  28.71
   2_adp:  66.92   0.00  11.01  66.92   0.00   7.34  66.79   0.82  30.98
   2_occ:  66.92   0.00  11.01  66.92   0.00   7.34  66.79   0.82  30.98
   3_bss:  66.92   0.00  11.01  66.92   0.00   7.34  66.79   0.82  30.98
   3_xyz:  66.92   0.00  11.01  66.92   0.00   7.34  66.79   0.82  30.98
   3_adp:  75.27   0.00  11.50  75.27   0.00   7.41  67.81   0.66  33.79
   3_occ:  75.27   0.00  11.50  75.27   0.00   7.41  67.81   0.66  33.79
   4_bss:  75.27   0.00  11.50  75.27   0.00   7.41  67.81   0.66  33.79
   4_xyz:  75.27   0.00  11.50  75.27   0.00   7.41  67.81   0.66  33.79
   4_adp:  74.98   0.00  11.25  74.98   0.00   7.30  66.17   0.93  32.77
   4_occ:  74.98   0.00  11.25  74.98   0.00   7.30  66.17   0.93  32.77
   5_bss:  74.98   0.00  11.25  74.98   0.00   7.30  66.17   0.93  32.77
   5_xyz:  74.98   0.00  11.25  74.98   0.00   7.30  66.17   0.93  32.77
   5_adp:  76.05   0.00  11.17  76.05   0.00   7.25  64.35   0.92  32.50
   5_occ:  76.05   0.00  11.17  76.05   0.00   7.25  64.35   0.92  32.50
   5_bss:  79.56   3.51  14.68  79.56   3.51  10.77  67.86   4.43  36.01
------------------------------------------------------------------------
 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:    1.179    0.015    0.405
   1_adp:    1.179    0.015    0.405
   1_occ:    1.179    0.015    0.405
   2_bss:    1.179    0.015    0.405
   2_xyz:    1.501    0.038    0.486
   2_adp:    1.501    0.038    0.486
   2_occ:    1.501    0.038    0.486
   3_bss:    1.501    0.038    0.486
   3_xyz:    1.494    0.040    0.527
   3_adp:    1.494    0.040    0.527
   3_occ:    1.494    0.040    0.527
   4_bss:    1.494    0.040    0.527
   4_xyz:    1.511    0.045    0.541
   4_adp:    1.511    0.045    0.541
   4_occ:    1.511    0.045    0.541
   5_bss:    1.511    0.045    0.541
   5_xyz:    1.490    0.032    0.550
   5_adp:    1.490    0.032    0.550
   5_occ:    1.490    0.032    0.550
   5_bss:    1.490    0.032    0.550
------------------------------------------------------------------------

CPU time actual refinement: 337.46


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/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_795/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_795/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.32 
  Macro-tasks:
    bulk solvent and scale       = 44.60  
    individual site refinement   = 140.83 
    weights calculation          = 32.49  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 224.66 
  Micro-tasks:
    mask                            = 1.63   
    f_calc                          = 102.82 
    alpha_beta                      = 8.03   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.74 
    fmodel                         = 7.75   
    r_factors                      = 0.23   
    phase_errors                   = 11.84  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 244.50 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.617 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    674 calls, 102.42 s
gradients_fft:          619 calls,  98.35 s

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

# Date 2008-01-16 Time 02:27:20 PST -0800 (1200479240.94 s)
Start R-work = 0.4244, R-free = 0.4128 (no bulk solvent and anisotropic scale)
Final R-work = 0.1265, R-free = 0.1710 (no bulk solvent and anisotropic scale)

Start R-work = 0.4162, R-free = 0.4035
Final R-work = 0.1090, R-free = 0.1557