# Date 2008-01-16 Time 03:31:44 PST -0800 (1200483104.66 s)
#phil __OFF__

Command line arguments: "../1268.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5735
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1268

-------------------------------------------------------------------------------
  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: (72.0062, 46.93, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98112
Completeness in resolution range: 0.944094
Completeness with d_max=infinity: 0.941281

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9811

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: (72.0062, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98112
Completeness in resolution range: 0.944094
Completeness with d_max=infinity: 0.941281

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2403 [2168/2197]  1955   213   9.8%
  bin  2:  4.2403 -  3.3778 [2097/2113]  1884   213  10.2%
  bin  3:  3.3778 -  2.9543 [2053/2072]  1844   209  10.2%
  bin  4:  2.9543 -  2.6858 [2054/2084]  1858   196   9.5%
  bin  5:  2.6858 -  2.4942 [2042/2061]  1835   207  10.1%
  bin  6:  2.4942 -  2.3477 [2030/2055]  1820   210  10.3%
  bin  7:  2.3477 -  2.2305 [1999/2032]  1802   197   9.9%
  bin  8:  2.2305 -  2.1337 [2003/2034]  1801   202  10.1%
  bin  9:  2.1337 -  2.0518 [2009/2051]  1813   196   9.8%
  bin 10:  2.0518 -  1.9811 [1134/2050]  1018   116  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 15
        2.41 -     3.04: 2143
        3.04 -     3.66: 4603
        3.66 -     4.28: 9064
        4.28 -     4.90: 12331
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.793 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.802 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.937 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 202 "  2.192 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28151 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_1268/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/model_refine_001.geo

CPU time processing inputs: 9.38


============================ 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 = 72.00625 46.93 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 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4618   r_free= 0.4542   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.262036                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7300 0.99   1410  159 0.3841 0.3782      6.5671      6.5338|
|  2:  4.7300 -  3.7732 0.99   1361  145 0.3700 0.3868      6.7426      6.7909|
|  3:  3.7732 -  3.3018 0.99   1327  151 0.4179 0.3777      6.6199      6.6145|
|  4:  3.3018 -  3.0024 0.99   1336  151 0.4321 0.4368      6.4918      6.4501|
|  5:  3.0024 -  2.7886 0.99   1318  146 0.4801 0.5172      6.3471      6.3734|
|  6:  2.7886 -  2.6251 0.99   1310  148 0.4910 0.4868      6.2621      6.2511|
|  7:  2.6251 -  2.4942 0.99   1314  138 0.5244 0.4994       6.255      6.1988|
|  8:  2.4942 -  2.3861 0.98   1289  150 0.5089 0.4687      6.1536      6.1724|
|  9:  2.3861 -  2.2945 0.98   1300  146 0.5028 0.4906      6.1141      6.0776|
| 10:  2.2945 -  2.2156 0.99   1285  141 0.5113 0.5019      6.0775      6.0826|
| 11:  2.2156 -  2.1465 0.99   1298  138 0.5151 0.4930      6.0404      6.0234|
| 12:  2.1465 -  2.0853 0.97   1268  145 0.5126 0.5419      5.9476      6.0072|
| 13:  2.0853 -  2.0306 0.95   1244  143 0.5317 0.4915      5.8886      5.8029|
| 14:  2.0306 -  1.9811 0.43    570   58 0.5198 0.4667      5.8257      5.8274|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7300  1410   159  0.71  33.37   0.80     0.75      68016.85|
|  2:  4.7300 -  3.7732  1361   145  0.73  32.78   0.89     0.79      93142.65|
|  3:  3.7732 -  3.3018  1327   151  0.63  41.36   0.84     0.74     100740.60|
|  4:  3.3018 -  3.0024  1336   151  0.55  47.98   0.81     0.65      94336.72|
|  5:  3.0024 -  2.7886  1318   146  0.44  56.46   0.74     0.53      79784.26|
|  6:  2.7886 -  2.6251  1310   148  0.41  59.08   0.75     0.49      70484.81|
|  7:  2.6251 -  2.4942  1314   138  0.41  59.16   0.74     0.46      60964.23|
|  8:  2.4942 -  2.3861  1289   150  0.42  58.36   0.72     0.49      54489.99|
|  9:  2.3861 -  2.2945  1300   146  0.43  57.64   0.75     0.49      47699.21|
| 10:  2.2945 -  2.2156  1285   141  0.42  58.53   0.75     0.49      44818.96|
| 11:  2.2156 -  2.1465  1298   138  0.37  62.02   0.77     0.45      43768.69|
| 12:  2.1465 -  2.0853  1268   145  0.33  65.28   0.74     0.41      42240.23|
| 13:  2.0853 -  2.0306  1244   143  0.33  65.30   0.73     0.41      36386.85|
| 14:  2.0306 -  1.9811   570    58  0.43  58.14   0.70     0.47      26915.09|
|alpha:            min =        0.41 max =            0.79 mean =         0.55|
|beta:             min =    26915.09 max =       100740.60 mean =     63573.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.50|
|phase err.(test): min =        0.00 max =           89.95 mean =        53.55|
|-----------------------------------------------------------------------------|

============================== 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 = 12.493666             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.647   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.804   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2601 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3916 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5032 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6535 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7695 |
|-----------------------------------------------------------------------------|
|-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 |       53.960 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.668 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    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 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4678   r_free= 0.4622   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.264142                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4534   r_free= 0.4436   ksol= 0.32   Bsol= 15.02   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.61,7.44,7.69,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.257009                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.066659             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.928111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.955   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4534      final r-factor (work) = 0.3616          |
| start r-factor (free) = 0.4436      final r-factor (free) = 0.3900          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.6151 = 11.07 * 0.50 * 6.2630 + 1.00 * 53.9598                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.1690 = 11.07 * 0.50 * 6.1505 + 1.00 * 0.1364                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3616      final r-factor (work) = 0.3114          |
| start r-factor (free) = 0.3900      final r-factor (free) = 0.3574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7227 = 0.93 * 1.00 * 6.1505 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6233 = 0.93 * 1.00 * 6.0437 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    57.91   11.26    None  None   None       |
|    all(noH): 2823   0      0.00    57.91   11.26    None  None   None       |
|    Sol.    : 438    0      0.00    57.91   25.12    None  None   None       |
|    Mac.    : 2385   0      0.00    57.62   8.72     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 -   5.791: 1066   |   5:    28.955 -  34.745:  105        |
|      1:     5.791 -  11.582:  745   |   6:    34.745 -  40.536:   63        |
|      2:    11.582 -  17.373:  397   |   7:    40.536 -  46.327:   36        |
|      3:    17.373 -  23.164:  241   |   8:    46.327 -  52.118:   19        |
|      4:    23.164 -  28.955:  145   |   9:    52.118 -  57.909:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3114 r_free = 0.3574             target_work(ml) = 6.010         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3105 r_free = 0.3575             target_work(ml) = 6.010         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3105   r_free= 0.3575   ksol= 0.32   Bsol= 15.02   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.61,7.44,7.69,0.00,0.00,0.00); trace/3= 8.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.009568                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3076   r_free= 0.3538   ksol= 0.34   Bsol= 42.24   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.95,4.21,5.21,0.00,0.00,0.00); trace/3= 5.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.009873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.118744              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.736   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.526  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3076      final r-factor (work) = 0.2252          |
| start r-factor (free) = 0.3538      final r-factor (free) = 0.2829          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5983 = 5.12 * 0.50 * 6.0413 + 1.00 * 0.1364                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1245 = 5.12 * 0.50 * 5.8817 + 1.00 * 0.0710                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2252      final r-factor (work) = 0.2061          |
| start r-factor (free) = 0.2829      final r-factor (free) = 0.2622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8857 = 0.49 * 1.00 * 5.8817 + 1.00 * 0.0274                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7863 = 0.49 * 1.00 * 5.7113 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.86   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    62.86   11.67    None  None   None       |
|    Sol.    : 438    0      0.45    61.66   30.35    None  None   None       |
|    Mac.    : 2385   0      0.00    62.86   8.24     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 -   6.286: 1230   |   5:    31.429 -  37.715:  120        |
|      1:     6.286 -  12.572:  750   |   6:    37.715 -  44.001:   83        |
|      2:    12.572 -  18.858:  310   |   7:    44.001 -  50.287:   44        |
|      3:    18.858 -  25.144:  133   |   8:    50.287 -  56.573:   19        |
|      4:    25.144 -  31.429:  129   |   9:    56.573 -  62.859:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2061 r_free = 0.2622             target_work(ml) = 5.676         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2060 r_free = 0.2623             target_work(ml) = 5.676         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2060   r_free= 0.2623   ksol= 0.34   Bsol= 42.24   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.95,4.21,5.21,0.00,0.00,0.00); trace/3= 5.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.676116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2046   r_free= 0.2597   ksol= 0.33   Bsol= 42.24   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.14,2.88,3.77,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.675685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.832654              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.605  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.271865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2046      final r-factor (work) = 0.1568          |
| start r-factor (free) = 0.2597      final r-factor (free) = 0.2061          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1699 = 2.83 * 0.50 * 5.7181 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9519 = 2.83 * 0.50 * 5.5681 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1568      final r-factor (work) = 0.1432          |
| start r-factor (free) = 0.2061      final r-factor (free) = 0.1951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0926 = 1.27 * 1.00 * 5.5681 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8738 = 1.27 * 1.00 * 5.3928 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.11   12.97    None  None   None       |
|    all(noH): 2823   0      0.00    88.11   12.97    None  None   None       |
|    Sol.    : 438    0      1.03    88.11   37.81    None  None   None       |
|    Mac.    : 2385   0      0.00    83.20   8.41     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 -   8.811: 1651   |   5:    44.056 -  52.867:   92        |
|      1:     8.811 -  17.622:  591   |   6:    52.867 -  61.678:   65        |
|      2:    17.622 -  26.434:  169   |   7:    61.678 -  70.490:   28        |
|      3:    26.434 -  35.245:  103   |   8:    70.490 -  79.301:   12        |
|      4:    35.245 -  44.056:  108   |   9:    79.301 -  88.112:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1432 r_free = 0.1951             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1431 r_free = 0.1946             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1946   ksol= 0.33   Bsol= 42.24   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.14,2.88,3.77,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364770                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1948   ksol= 0.33   Bsol= 56.80   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,2.51,3.26,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.363435                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.275997              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599887              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.773  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1431      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2043 = 2.28 * 0.50 * 5.3943 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1124 = 2.28 * 0.50 * 5.3160 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1801      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2039 = 0.60 * 1.00 * 5.3160 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1696 = 0.60 * 1.00 * 5.2614 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.24   12.84    None  None   None       |
|    all(noH): 2823   0      0.00    90.24   12.84    None  None   None       |
|    Sol.    : 438    0      1.37    90.24   37.38    None  None   None       |
|    Mac.    : 2385   0      0.00    87.57   8.34     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 -   9.024: 1708   |   5:    45.118 -  54.141:   90        |
|      1:     9.024 -  18.047:  555   |   6:    54.141 -  63.165:   53        |
|      2:    18.047 -  27.071:  167   |   7:    63.165 -  72.188:   22        |
|      3:    27.071 -  36.094:  104   |   8:    72.188 -  81.212:   12        |
|      4:    36.094 -  45.118:  108   |   9:    81.212 -  90.235:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1250 r_free = 0.1760             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1758             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1758   ksol= 0.33   Bsol= 56.80   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,2.51,3.26,0.00,0.00,0.00); trace/3= 3.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1249   r_free= 0.1757   ksol= 0.33   Bsol= 55.21   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,2.40,3.14,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248463                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.524725              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.601  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.731  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7043 = 2.52 * 0.50 * 5.2612 + 1.00 * 0.0627                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6673 = 2.52 * 0.50 * 5.2256 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2696 = 0.24 * 1.00 * 5.2256 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2619 = 0.24 * 1.00 * 5.2032 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.26   12.43    None  None   None       |
|    all(noH): 2823   0      0.00    87.26   12.43    None  None   None       |
|    Sol.    : 438    0      1.77    85.42   35.40    None  None   None       |
|    Mac.    : 2385   0      0.00    87.26   8.21     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.726: 1690   |   5:    43.630 -  52.355:   88        |
|      1:     8.726 -  17.452:  585   |   6:    52.355 -  61.081:   49        |
|      2:    17.452 -  26.178:  157   |   7:    61.081 -  69.807:   20        |
|      3:    26.178 -  34.904:  120   |   8:    69.807 -  78.533:    8        |
|      4:    34.904 -  43.630:  100   |   9:    78.533 -  87.259:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1658             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1656             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1656   ksol= 0.33   Bsol= 55.21   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,2.40,3.14,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193750                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7300 0.99   1410  159 0.1010 0.1416      5.4063       5.601|
|  2:  4.7300 -  3.7732 0.99   1361  145 0.0895 0.1123      5.4719      5.6522|
|  3:  3.7732 -  3.3018 0.99   1327  151 0.1106 0.1666      5.5078      5.8979|
|  4:  3.3018 -  3.0024 0.99   1336  151 0.1290 0.1607      5.5051      5.6145|
|  5:  3.0024 -  2.7886 0.99   1318  146 0.1423 0.1856       5.381      5.5896|
|  6:  2.7886 -  2.6251 0.99   1310  148 0.1309 0.1923      5.2586       5.507|
|  7:  2.6251 -  2.4942 0.99   1314  138 0.1330 0.1696      5.2269      5.3849|
|  8:  2.4942 -  2.3861 0.98   1289  150 0.1237 0.1865      5.0996      5.4008|
|  9:  2.3861 -  2.2945 0.98   1300  146 0.1268 0.1898      5.0891      5.3569|
| 10:  2.2945 -  2.2156 0.99   1285  141 0.1192 0.1790      4.9888      5.2346|
| 11:  2.2156 -  2.1465 0.99   1298  138 0.1232 0.1940      4.9898      5.3466|
| 12:  2.1465 -  2.0853 0.97   1268  145 0.1163 0.1666      4.9143      5.1262|
| 13:  2.0853 -  2.0306 0.95   1244  143 0.1268 0.1864      4.8459      5.0944|
| 14:  2.0306 -  1.9811 0.43    570   58 0.1079 0.1629      4.6434      4.9546|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7300  1410   159  0.94   9.47   0.98     0.95       7891.50|
|  2:  4.7300 -  3.7732  1361   145  0.95   8.49   1.01     0.99       9701.93|
|  3:  3.7732 -  3.3018  1327   151  0.93  12.13   1.02     1.02      11197.74|
|  4:  3.3018 -  3.0024  1336   151  0.91  14.43   1.00     0.98      11291.47|
|  5:  3.0024 -  2.7886  1318   146  0.89  17.07   0.99     0.98       9263.68|
|  6:  2.7886 -  2.6251  1310   148  0.89  16.88   0.98     0.95       7766.14|
|  7:  2.6251 -  2.4942  1314   138  0.90  16.29   0.99     0.97       6887.60|
|  8:  2.4942 -  2.3861  1289   150  0.90  16.10   0.98     0.95       5580.74|
|  9:  2.3861 -  2.2945  1300   146  0.90  16.66   1.00     0.97       5555.63|
| 10:  2.2945 -  2.2156  1285   141  0.90  15.69   1.00     0.97       4547.42|
| 11:  2.2156 -  2.1465  1298   138  0.89  17.29   0.99     0.95       4727.32|
| 12:  2.1465 -  2.0853  1268   145  0.90  16.17   1.01     1.01       4316.70|
| 13:  2.0853 -  2.0306  1244   143  0.90  16.86   1.00     0.99       3620.74|
| 14:  2.0306 -  1.9811   570    58  0.91  15.02   0.98     0.96       2446.44|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2446.44 max =        11291.47 mean =      7003.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.68 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.53 mean =        14.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1654   ksol= 0.33   Bsol= 57.89   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,-0.37,0.34,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.194120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1654   ksol= 0.33   Bsol= 57.89   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,-0.37,0.34,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.194120                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7300 0.99   1410  159 0.1014 0.1368      5.4032      5.5899|
|  2:  4.7300 -  3.7732 0.99   1361  145 0.0904 0.1133      5.4761      5.6608|
|  3:  3.7732 -  3.3018 0.99   1327  151 0.1106 0.1668       5.511      5.8967|
|  4:  3.3018 -  3.0024 0.99   1336  151 0.1293 0.1604      5.5053      5.6144|
|  5:  3.0024 -  2.7886 0.99   1318  146 0.1424 0.1853      5.3812      5.5873|
|  6:  2.7886 -  2.6251 0.99   1310  148 0.1310 0.1913      5.2578      5.5068|
|  7:  2.6251 -  2.4942 0.99   1314  138 0.1331 0.1693      5.2269      5.3856|
|  8:  2.4942 -  2.3861 0.98   1289  150 0.1236 0.1863      5.0995       5.401|
|  9:  2.3861 -  2.2945 0.98   1300  146 0.1267 0.1895      5.0891      5.3566|
| 10:  2.2945 -  2.2156 0.99   1285  141 0.1192 0.1786      4.9889      5.2333|
| 11:  2.2156 -  2.1465 0.99   1298  138 0.1231 0.1942      4.9899      5.3484|
| 12:  2.1465 -  2.0853 0.97   1268  145 0.1164 0.1664      4.9148      5.1262|
| 13:  2.0853 -  2.0306 0.95   1244  143 0.1268 0.1865      4.8463      5.0947|
| 14:  2.0306 -  1.9811 0.43    570   58 0.1079 0.1634      4.6437      4.9568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7300  1410   159  0.94   9.31   0.97     0.95       7613.72|
|  2:  4.7300 -  3.7732  1361   145  0.95   8.46   1.00     0.99       9660.43|
|  3:  3.7732 -  3.3018  1327   151  0.93  12.14   1.02     1.02      11304.46|
|  4:  3.3018 -  3.0024  1336   151  0.91  14.41   1.00     0.98      11259.56|
|  5:  3.0024 -  2.7886  1318   146  0.89  17.01   0.99     0.97       9227.83|
|  6:  2.7886 -  2.6251  1310   148  0.89  16.84   0.98     0.95       7736.61|
|  7:  2.6251 -  2.4942  1314   138  0.90  16.27   0.99     0.97       6886.13|
|  8:  2.4942 -  2.3861  1289   150  0.90  16.10   0.98     0.95       5586.27|
|  9:  2.3861 -  2.2945  1300   146  0.90  16.66   1.00     0.97       5556.94|
| 10:  2.2945 -  2.2156  1285   141  0.90  15.71   0.99     0.96       4555.24|
| 11:  2.2156 -  2.1465  1298   138  0.89  17.30   0.99     0.94       4732.58|
| 12:  2.1465 -  2.0853  1268   145  0.90  16.20   1.00     1.00       4325.97|
| 13:  2.0853 -  2.0306  1244   143  0.90  16.87   0.99     0.98       3625.93|
| 14:  2.0306 -  1.9811   570    58  0.91  15.03   0.97     0.95       2449.84|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2449.84 max =        11304.46 mean =      6981.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.80|
|phase err.(test): min =        0.00 max =           88.68 mean =        14.21|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.080)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.69    89.95   15.12    None  None   None       |
|    all(noH): 2823   0      2.69    89.95   15.12    None  None   None       |
|    Sol.    : 438    0      4.45    88.10   38.09    None  None   None       |
|    Mac.    : 2385   0      2.69    89.95   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.686 -  11.412: 1690   |   5:    46.316 -  55.042:   88        |
|      1:    11.412 -  20.138:  585   |   6:    55.042 -  63.768:   49        |
|      2:    20.138 -  28.864:  157   |   7:    63.768 -  72.493:   20        |
|      3:    28.864 -  37.590:  120   |   8:    72.493 -  81.219:    8        |
|      4:    37.590 -  46.316:  100   |   9:    81.219 -  89.945:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.381 - 5.721
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 343
   mapped sites are within: 0.704 - 5.721

peak=   10.583 closest distance to " CB  VAL A 230 " =    1.461
peak=    8.952 closest distance to " CG2 VAL A 296 " =    1.306
peak=    7.829 closest distance to " CG  ARG A 138 " =    1.221
peak=    6.017 closest distance to " O   HOH Z 111 " =    2.106
peak=    5.912 closest distance to " CG  LEU A   5 " =    1.232
peak=    5.823 closest distance to " CD2 LEU A   5 " =    1.226
peak=    5.648 closest distance to " O   HOH Z 102 " =    1.032
peak=    5.495 closest distance to " CB  GLN A 223 " =    1.414
peak=    4.954 closest distance to " CD1AILE A 234 " =    1.086
peak=    4.951 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.950 closest distance to " CG  LEU A 228 " =    1.225
peak=    4.885 closest distance to " O   HOH Z 368 " =    2.107
peak=    4.826 closest distance to " CB  SER A  63 " =    1.309
peak=    4.817 closest distance to " CG  PRO A 213 " =    1.268
peak=    4.816 closest distance to " NH1 ARG A 138 " =    1.052
peak=    4.806 closest distance to " O   HOH Z 232 " =    2.245
peak=    4.765 closest distance to " CG  PRO A 198 " =    1.297
peak=    4.691 closest distance to " O   HOH Z 369 " =    1.920
peak=    4.673 closest distance to " NE2 GLN A  11 " =    1.108
peak=    4.644 closest distance to " O   HOH Z 112 " =    1.472
peak=    4.596 closest distance to " O   HOH Z 183 " =    1.468
peak=    4.590 closest distance to " CB  ASN A 148 " =    1.327
peak=    4.552 closest distance to " CG  PRO A 243 " =    1.143
peak=    4.548 closest distance to " CD2 LEU A 228 " =    1.220
peak=    4.531 closest distance to " CB  GLU A 152 " =    1.270
peak=    4.499 closest distance to " NH1 ARG A  56 " =    1.015
peak=    4.475 closest distance to " CB  VAL A 230 " =    1.268
peak=    4.441 closest distance to " O   PRO A 198 " =    1.557
peak=    4.416 closest distance to " O   HOH Z 272 " =    1.927
peak=    4.413 closest distance to " O   HOH Z 303 " =    2.148
peak=    4.411 closest distance to " O   HOH Z 425 " =    1.514
peak=    4.392 closest distance to " O   HOH Z 193 " =    1.769
peak=    4.389 closest distance to " CD  ARG A 138 " =    1.093
peak=    4.383 closest distance to " CG  PRO A 280 " =    0.791
peak=    4.369 closest distance to " O   HOH Z 298 " =    1.746
peak=    4.348 closest distance to " O   HOH Z 236 " =    1.941
peak=    4.344 closest distance to " O   HOH Z 126 " =    1.933
peak=    4.289 closest distance to " CB  TRP A 266 " =    0.925
peak=    4.229 closest distance to " O   HOH Z 247 " =    1.442
peak=    4.219 closest distance to " NH1AARG A 145 " =    1.198
peak=    4.218 closest distance to " CB  GLU A 128 " =    1.080
peak=    4.216 closest distance to " O   HOH Z  15 " =    2.061
peak=    4.203 closest distance to " O   HOH Z 316 " =    3.035
peak=    4.195 closest distance to " O   HOH Z 263 " =    1.640
peak=    4.188 closest distance to " CB  ASP A 124 " =    0.764
peak=    4.149 closest distance to " O   HOH Z  80 " =    1.776
peak=    4.127 closest distance to " OD2 ASP A 286 " =    2.935
peak=    4.105 closest distance to " O   HOH Z 410 " =    1.476
peak=    4.104 closest distance to " O   HOH Z 132 " =    2.539
peak=    4.085 closest distance to " O   HOH Z  37 " =    1.211
peak=    4.083 closest distance to " CD  ARG A 159 " =    0.813
peak=    4.079 closest distance to " CG2 THR A 221 " =    1.003
peak=    4.071 closest distance to " CB  VAL A 265 " =    1.295
peak=    4.068 closest distance to " CB  LEU A 228 " =    1.237
peak=    4.050 closest distance to " O   HOH Z 427 " =    3.337
peak=    4.046 closest distance to " O   HOH Z  88 " =    3.344
peak=    4.046 closest distance to " CB  SER A   3 " =    1.510
peak=    4.012 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.997 closest distance to " O   HOH Z 186 " =    1.214
peak=    3.984 closest distance to " O   ASP A 132 " =    3.804
peak=    3.966 closest distance to " CB  VAL A 202 " =    1.538
peak=    3.940 closest distance to " O   HOH Z 411 " =    3.463
peak=    3.933 closest distance to " OD1 ASN A 217 " =    1.655
peak=    3.924 closest distance to " CA  LEU A 282 " =    0.972
peak=    3.918 closest distance to " CB  LEU A 143 " =    1.146
peak=    3.917 closest distance to " O   HOH Z 346 " =    1.535
peak=    3.916 closest distance to " CB  TYR A 169 " =    0.777
peak=    3.905 closest distance to " O   HOH Z 184 " =    1.552
peak=    3.897 closest distance to " O   HOH Z  78 " =    2.182
peak=    3.884 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.880 closest distance to " O   HOH Z 126 " =    1.625
peak=    3.867 closest distance to " O   HOH Z 437 " =    1.926
peak=    3.865 closest distance to " CZ  PHE A 192 " =    1.016
peak=    3.863 closest distance to " CD  ARG A  66 " =    2.487
peak=    3.860 closest distance to " O   HOH Z 193 " =    2.088
peak=    3.854 closest distance to " O   HOH Z  63 " =    1.921
peak=    3.853 closest distance to " O   HOH Z 295 " =    1.554
peak=    3.850 closest distance to " CB  ASN A 187 " =    1.013
peak=    3.850 closest distance to " O   HOH Z  68 " =    1.556
peak=    3.843 closest distance to " CA  MET A  40 " =    1.157
peak=    3.839 closest distance to " O   HOH Z  58 " =    1.636
peak=    3.835 closest distance to " O   HOH Z 144 " =    1.511
peak=    3.828 closest distance to " CA  GLY A 267 " =    0.897
peak=    3.817 closest distance to " OD1 ASN A  69 " =    2.747
peak=    3.811 closest distance to " CA  ALA A  21 " =    1.197
peak=    3.786 closest distance to " CB  ASP A 140 " =    0.807
peak=    3.781 closest distance to " O   HOH Z 280 " =    3.025
peak=    3.780 closest distance to " O   HOH Z  54 " =    2.441
peak=    3.761 closest distance to " CD  ARG A 269 " =    0.941
peak=    3.759 closest distance to " CG1 ILE A  33 " =    1.317
peak=    3.748 closest distance to " O   HOH Z 403 " =    1.708
peak=    3.747 closest distance to " O   HOH Z  97 " =    1.959
peak=    3.731 closest distance to " O   HOH Z 158 " =    2.869
peak=    3.721 closest distance to " CG BARG A 275 " =    1.549
peak=    3.716 closest distance to " O   HOH Z  48 " =    1.497
peak=    3.710 closest distance to " O   HOH Z  44 " =    2.148
peak=    3.703 closest distance to " O   HOH Z 392 " =    1.926
peak=    3.702 closest distance to " O   HOH Z 281 " =    4.426
peak=    3.702 closest distance to " O   SER A  87 " =    2.264
peak=    3.695 closest distance to " CB  GLU A 277 " =    3.620
peak=    3.694 closest distance to " CB  SER A 216 " =    0.829
peak=    3.690 closest distance to " O   HOH Z  78 " =    1.770
peak=    3.687 closest distance to " CB  ALA A 291 " =    1.304
peak=    3.686 closest distance to " O   HOH Z 116 " =    1.777
peak=    3.684 closest distance to " CA  ASP A 124 " =    0.704
peak=    3.684 closest distance to " CZ  PHE A 218 " =    1.052
peak=    3.683 closest distance to " NZ  LYS A 117 " =    3.320
peak=    3.683 closest distance to " O   HOH Z 135 " =    2.051
peak=    3.681 closest distance to " CA  ALA A  51 " =    1.049
peak=    3.679 closest distance to " CD2 LEU A 255 " =    1.562
peak=    3.678 closest distance to " CG1BVAL A  72 " =    1.595
peak=    3.678 closest distance to " O   HOH Z 371 " =    3.251
peak=    3.673 closest distance to " O   HOH Z 134 " =    1.450
peak=    3.671 closest distance to " CG  GLN A  88 " =    1.072
peak=    3.668 closest distance to " ND2 ASN A 187 " =    1.528
peak=    3.663 closest distance to " CB  ALA A   9 " =    1.576
peak=    3.661 closest distance to " CB  MET A  47 " =    1.081
peak=    3.659 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.657 closest distance to " CD1 ILE A  33 " =    1.637
peak=    3.648 closest distance to " CE  LYS A  76 " =    0.890
peak=    3.646 closest distance to " O   HOH Z 180 " =    2.085
peak=    3.646 closest distance to " O   TRP A 274 " =    1.807
peak=    3.641 closest distance to " O   HOH Z  68 " =    2.046
peak=    3.634 closest distance to " CD ALYS A 290 " =    1.065
peak=    3.614 closest distance to " O   HOH Z   9 " =    2.040
peak=    3.613 closest distance to " CB  ARG A 275 " =    0.846
peak=    3.612 closest distance to " O   HOH Z 313 " =    1.870
peak=    3.608 closest distance to " O   HOH Z 344 " =    3.007
peak=    3.604 closest distance to " CA  THR A 221 " =    0.895
peak=    3.596 closest distance to " O   MET A 105 " =    1.767
peak=    3.589 closest distance to " CA  ASP A 140 " =    1.296
peak=    3.579 closest distance to " CB  ILE A 234 " =    0.938
peak=    3.575 closest distance to " NH2BARG A 102 " =    0.960
peak=    3.573 closest distance to " CA  TYR A  30 " =    0.977
peak=    3.570 closest distance to " CB  SER A 212 " =    1.197
peak=    3.563 closest distance to " O   HOH Z 128 " =    2.063
peak=    3.561 closest distance to " O   HOH Z 189 " =    2.871
peak=    3.554 closest distance to " CB  TRP A 150 " =    1.490
peak=    3.549 closest distance to " O   HOH Z  57 " =    1.371
peak=    3.548 closest distance to " ND1 HIS A  86 " =    1.609
peak=    3.543 closest distance to " C   ALA A 299 " =    0.940
peak=    3.541 closest distance to " O   HOH Z 163 " =    1.611
peak=    3.538 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.530 closest distance to " OE1 GLN A  11 " =    2.035
peak=    3.526 closest distance to " CB  LEU A 237 " =    0.867
peak=    3.526 closest distance to " O   ALA A 291 " =    1.526
peak=    3.524 closest distance to " CG1 VAL A 174 " =    1.065
peak=    3.511 closest distance to " OD1 ASP A 231 " =    1.892
peak=    3.496 closest distance to " CB  ARG A  79 " =    1.543
peak=    3.491 closest distance to " O   HOH Z 171 " =    3.855
peak=    3.490 closest distance to " CA  ALA A 158 " =    1.138
peak=    3.486 closest distance to " O   HOH Z 290 " =    1.194
peak=    3.485 closest distance to " CB  ALA A 104 " =    0.801
peak=    3.484 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.483 closest distance to " NE AARG A 275 " =    1.440
peak=    3.482 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.480 closest distance to " CA  TYR A 116 " =    1.442
peak=    3.478 closest distance to " CG BARG A 102 " =    1.813
peak=    3.477 closest distance to " O   HOH Z 271 " =    2.104
peak=    3.475 closest distance to " CD1 LEU A   5 " =    1.307
peak=    3.475 closest distance to " CA  LYS A 117 " =    1.195
peak=    3.474 closest distance to " CA  SER A  87 " =    0.870
peak=    3.466 closest distance to " O   HOH Z 286 " =    2.372
peak=    3.465 closest distance to " CB  PHE A  16 " =    1.136
peak=    3.462 closest distance to " CG1 VAL A 153 " =    0.922
peak=    3.457 closest distance to " O   HOH Z 214 " =    1.899
peak=    3.447 closest distance to " O   HOH Z  20 " =    2.276
peak=    3.442 closest distance to " ND2 ASN A 249 " =    1.794
peak=    3.439 closest distance to " ND1 HIS A  81 " =    1.625
peak=    3.438 closest distance to " CA  ILE A 234 " =    0.925
peak=    3.436 closest distance to " O   HOH Z 197 " =    2.949
peak=    3.430 closest distance to " CA  GLY A 211 " =    1.207
peak=    3.430 closest distance to " O   HOH Z 133 " =    1.774
peak=    3.425 closest distance to " CB  ALA A 248 " =    1.302
peak=    3.424 closest distance to " O   HOH Z 345 " =    3.479
peak=    3.419 closest distance to " O   HOH Z 153 " =    1.843
peak=    3.417 closest distance to " CD  ARG A  14 " =    1.272
peak=    3.412 closest distance to " N   PHE A 130 " =    1.301
peak=    3.410 closest distance to " O   HOH Z 271 " =    2.637
peak=    3.409 closest distance to " O   HOH Z 227 " =    1.744
peak=    3.408 closest distance to " O   HOH Z 175 " =    2.210
peak=    3.406 closest distance to " CG  LEU A  25 " =    1.836
peak=    3.400 closest distance to " O   HOH Z  92 " =    0.805
peak=    3.399 closest distance to " CB  ASN A 142 " =    0.940
peak=    3.399 closest distance to " CA  THR A 264 " =    0.740
peak=    3.393 closest distance to " CA  ASN A 127 " =    1.022
peak=    3.393 closest distance to " N   ASN A  39 " =    1.219
peak=    3.392 closest distance to " O   HOH Z 244 " =    1.617
peak=    3.391 closest distance to " CA  ASP A 162 " =    1.017
peak=    3.391 closest distance to " O   HOH Z 109 " =    2.702
peak=    3.388 closest distance to " N   ARG A 156 " =    1.415
peak=    3.384 closest distance to " OG1 THR A 246 " =    3.278
peak=    3.383 closest distance to " CB  MET A  40 " =    0.779
peak=    3.383 closest distance to " CB  GLU A 236 " =    1.216
peak=    3.381 closest distance to " CB  GLU A  46 " =    1.033
peak=    3.379 closest distance to " O   HOH Z 302 " =    1.880
peak=    3.378 closest distance to " CB  ILE A 120 " =    1.318
peak=    3.376 closest distance to " CA  ASN A 215 " =    1.209
peak=    3.370 closest distance to " N   TYR A  15 " =    0.848
peak=    3.370 closest distance to " O   HOH Z  21 " =    1.710
peak=    3.367 closest distance to " CD  LYS A 166 " =    1.313
peak=    3.365 closest distance to " O   HOH Z 133 " =    2.413
peak=    3.358 closest distance to " NE2 GLN A  58 " =    5.721
peak=    3.358 closest distance to " CB  SER A 210 " =    0.845
peak=    3.356 closest distance to " O   HOH Z 156 " =    2.889
peak=    3.351 closest distance to " CA  ASP A 191 " =    0.744
peak=    3.350 closest distance to " O   GLN A 278 " =    1.176
peak=    3.346 closest distance to " CB  ALA A 161 " =    0.937
peak=    3.342 closest distance to " O   HOH Z   4 " =    1.826
peak=    3.337 closest distance to " CB  SER A 141 " =    0.908
peak=    3.334 closest distance to " O   HOH Z 175 " =    3.588
peak=    3.333 closest distance to " O   HOH Z  53 " =    2.684
peak=    3.332 closest distance to " CB  THR A  82 " =    1.348
peak=    3.332 closest distance to " CA  ALA A 154 " =    1.112
peak=    3.332 closest distance to " CD1 TRP A 266 " =    1.118
peak=    3.325 closest distance to " O   HOH Z  88 " =    2.757
peak=    3.322 closest distance to " CE3 TRP A 274 " =    1.076
peak=    3.319 closest distance to " NH1 ARG A  14 " =    0.993
peak=    3.319 closest distance to " CA  ILE A  33 " =    1.613
peak=    3.318 closest distance to " CB  ALA A  34 " =    0.890
peak=    3.314 closest distance to " CA  VAL A  41 " =    0.949
peak=    3.312 closest distance to " CA  ALA A 291 " =    0.986
peak=    3.311 closest distance to " CB  THR A 157 " =    1.136
peak=    3.309 closest distance to " O   HOH Z  61 " =    1.592
peak=    3.308 closest distance to " CG2 VAL A 189 " =    1.339
peak=    3.306 closest distance to " O   HOH Z 216 " =    2.642
peak=    3.303 closest distance to " O   HOH Z 148 " =    2.043
peak=    3.300 closest distance to " NH2BARG A 145 " =    2.028
peak=    3.299 closest distance to " O   HOH Z 174 " =    1.156
peak=    3.294 closest distance to " CA  ALA A 160 " =    0.958
peak=    3.292 closest distance to " CB  ALA A 248 " =    1.068
peak=    3.289 closest distance to " CA  TYR A 186 " =    1.445
peak=    3.286 closest distance to " CG1 ILE A  49 " =    1.572
peak=    3.283 closest distance to " O   HOH Z 128 " =    2.350
peak=    3.282 closest distance to " OE1 GLN A  58 " =    1.209
peak=    3.282 closest distance to " O   HOH Z 209 " =    2.558
peak=    3.279 closest distance to " CB  ALA A 100 " =    1.434
peak=    3.274 closest distance to " CE2 TYR A 186 " =    0.952
peak=    3.273 closest distance to " O   HOH Z 145 " =    1.602
peak=    3.271 closest distance to " O   HOH Z 409 " =    3.027
peak=    3.270 closest distance to " CD  ARG A 219 " =    1.046
peak=    3.269 closest distance to " CB  LYS A 117 " =    1.142
peak=    3.267 closest distance to " NH2 ARG A 219 " =    1.799
peak=    3.266 closest distance to " O   HOH Z 407 " =    2.200
peak=    3.256 closest distance to " O   HOH Z 298 " =    2.502
peak=    3.256 closest distance to " CB  TRP A 179 " =    1.404
peak=    3.251 closest distance to " CG AARG A 275 " =    1.234
peak=    3.250 closest distance to " O   HOH Z 203 " =    1.829
peak=    3.245 closest distance to " CA  VAL A 126 " =    1.089
peak=    3.245 closest distance to " O   HOH Z 426 " =    1.483
peak=    3.243 closest distance to " O   HOH Z 151 " =    1.692
peak=    3.241 closest distance to " O   HOH Z  66 " =    2.236
peak=    3.240 closest distance to " O   HOH Z 128 " =    1.772
peak=    3.234 closest distance to " O   HOH Z 173 " =    2.113
peak=    3.229 closest distance to " NH2BARG A 190 " =    1.662
peak=    3.228 closest distance to " CB  GLN A  88 " =    1.238
peak=    3.226 closest distance to " O   HOH Z 383 " =    2.143
peak=    3.224 closest distance to " O   HOH Z 185 " =    1.854
peak=    3.223 closest distance to " O   HOH Z 332 " =    1.593
peak=    3.219 closest distance to " O   HOH Z 189 " =    3.395
peak=    3.219 closest distance to " CB  LEU A 255 " =    0.961
peak=    3.218 closest distance to " O   HOH Z 334 " =    1.530
peak=    3.217 closest distance to " NH2 ARG A  79 " =    1.499
peak=    3.217 closest distance to " CG2 THR A 220 " =    1.044
peak=    3.216 closest distance to " CA  ARG A 102 " =    1.203
peak=    3.212 closest distance to " O   HOH Z 181 " =    2.224
peak=    3.210 closest distance to " O   HOH Z 353 " =    2.824
peak=    3.209 closest distance to " O   HOH Z 215 " =    1.564
peak=    3.209 closest distance to " CG2 VAL A 174 " =    1.285
peak=    3.207 closest distance to " CB  ARG A 190 " =    1.699
peak=    3.204 closest distance to " O   HOH Z 423 " =    2.806
peak=    3.202 closest distance to " O   HOH Z 261 " =    1.937
peak=    3.200 closest distance to " O   HOH Z 118 " =    1.706
peak=    3.200 closest distance to " O   HOH Z  43 " =    2.048
peak=    3.200 closest distance to " O   HOH Z 172 " =    3.852
peak=    3.193 closest distance to " O   HOH Z 374 " =    2.684
peak=    3.191 closest distance to " CB  GLN A 103 " =    1.030
peak=    3.187 closest distance to " CA  LEU A 101 " =    1.536
peak=    3.187 closest distance to " OH  TYR A 214 " =    1.239
peak=    3.187 closest distance to " O   HOH Z 248 " =    1.963
peak=    3.184 closest distance to " O   HOH Z 193 " =    1.891
peak=    3.184 closest distance to " O   HOH Z 301 " =    1.835
peak=    3.182 closest distance to " O   HOH Z 163 " =    1.817
peak=    3.180 closest distance to " C   GLN A  88 " =    1.526
peak=    3.179 closest distance to " O   HOH Z 185 " =    2.190
peak=    3.176 closest distance to " O   HOH Z 294 " =    1.600
peak=    3.176 closest distance to " O   HOH Z 166 " =    3.342
peak=    3.174 closest distance to " CB  ALA A 242 " =    0.803
peak=    3.174 closest distance to " O   HOH Z 227 " =    2.046
peak=    3.172 closest distance to " N   GLU A   2 " =    1.660
peak=    3.168 closest distance to " O   ALA A 165 " =    1.363
peak=    3.167 closest distance to " CD  LYS A 119 " =    1.447
peak=    3.165 closest distance to " O   HOH Z 327 " =    2.178
peak=    3.164 closest distance to " O   HOH Z   2 " =    1.645
peak=    3.162 closest distance to " OG BSER A 212 " =    2.432
peak=    3.161 closest distance to " O   HOH Z 355 " =    1.741
peak=    3.160 closest distance to " CB  TYR A  30 " =    1.377
peak=    3.160 closest distance to " O   HOH Z 124 " =    1.716
peak=    3.159 closest distance to " CA  ASN A  74 " =    1.174
peak=    3.155 closest distance to " O   HOH Z 374 " =    3.169
peak=    3.153 closest distance to " O   HOH Z 162 " =    2.101
peak=    3.153 closest distance to " CG2 VAL A 257 " =    0.940
peak=    3.151 closest distance to " O   HOH Z 339 " =    2.291
peak=    3.148 closest distance to " N   SER A 135 " =    1.372
peak=    3.147 closest distance to " O   HOH Z 286 " =    2.395
peak=    3.142 closest distance to " CA  GLN A 223 " =    0.918
peak=    3.141 closest distance to " O   HOH Z 130 " =    2.230
peak=    3.141 closest distance to " CB  TYR A 116 " =    0.954
peak=    3.141 closest distance to " CA  LYS A  48 " =    1.365
peak=    3.140 closest distance to " O   HOH Z 328 " =    1.655
peak=    3.139 closest distance to " OG  SER A  22 " =    2.913
peak=    3.137 closest distance to " O   ALA A   1 " =    1.562
peak=    3.134 closest distance to " OG BSER A 164 " =    2.205
peak=    3.132 closest distance to " CD1 LEU A 101 " =    1.111
peak=    3.130 closest distance to " CB  ASN A 110 " =    1.261
peak=    3.130 closest distance to " CG1 ILE A 151 " =    1.190
peak=    3.122 closest distance to " O   HOH Z 255 " =    1.697
peak=    3.122 closest distance to " O   HOH Z  10 " =    1.861
peak=    3.122 closest distance to " OG  SER A 206 " =    1.219
peak=    3.120 closest distance to " O   HOH Z   1 " =    1.804
peak=    3.120 closest distance to " CG  MET A 188 " =    1.234
peak=    3.117 closest distance to " CD  LYS A 119 " =    2.118
peak=    3.117 closest distance to " O   HOH Z 368 " =    3.545
peak=    3.115 closest distance to " O   ALA A 158 " =    1.404
peak=    3.108 closest distance to " CD1 ILE A 106 " =    0.822
peak=    3.105 closest distance to " O   HOH Z  59 " =    2.061
peak=    3.096 closest distance to " CZ  PHE A 192 " =    0.742
peak=    3.096 closest distance to " CA  ILE A 106 " =    0.848
peak=    3.085 closest distance to " O   HOH Z 213 " =    2.181
peak=    3.084 closest distance to " CB  ARG A 139 " =    0.886
peak=    3.080 closest distance to " O   HOH Z 359 " =    2.061
peak=    3.073 closest distance to " CE1 PHE A 208 " =    1.106
peak=    3.072 closest distance to " O   HOH Z 250 " =    1.233
peak=    3.064 closest distance to " CB  ALA A 227 " =    0.892
peak=    3.063 closest distance to " O   HOH Z 173 " =    1.683
peak=    3.057 closest distance to " CA  ARG A  36 " =    1.207

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.489
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 183 from: 185
   mapped sites are within: 0.793 - 5.489

peak=   -5.463 closest distance to " CG2 VAL A 230 " =    0.837
peak=   -4.583 closest distance to " O   HOH Z 231 " =    1.425
peak=   -4.439 closest distance to " CD  ARG A 138 " =    1.115
peak=   -4.418 closest distance to " O   HOH Z 102 " =    1.382
peak=   -4.403 closest distance to " CG  ARG A 138 " =    0.862
peak=   -4.336 closest distance to " CA  ASP A  27 " =    2.478
peak=   -4.336 closest distance to " O   HOH Z 377 " =    1.500
peak=   -4.224 closest distance to " O   HOH Z 290 " =    1.249
peak=   -4.081 closest distance to " OE1 GLN A  88 " =    1.031
peak=   -4.072 closest distance to " O   HOH Z  13 " =    1.325
peak=   -4.064 closest distance to " O   ILE A 109 " =    2.701
peak=   -4.054 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.025 closest distance to " CG  LEU A 101 " =    2.615
peak=   -4.000 closest distance to " CD1 LEU A 228 " =    2.475
peak=   -3.986 closest distance to " O   HOH Z 231 " =    0.968
peak=   -3.921 closest distance to " O   PRO A 163 " =    1.946
peak=   -3.909 closest distance to " CD2 LEU A 237 " =    2.707
peak=   -3.894 closest distance to " OG  SER A  87 " =    1.450
peak=   -3.877 closest distance to " O   HOH Z  43 " =    1.572
peak=   -3.857 closest distance to " C   ALA A 158 " =    1.282
peak=   -3.828 closest distance to " CD  ARG A  14 " =    3.244
peak=   -3.826 closest distance to " CG  ASP A 231 " =    0.794
peak=   -3.823 closest distance to " O   HOH Z 274 " =    2.986
peak=   -3.815 closest distance to " CG1 VAL A 296 " =    1.428
peak=   -3.812 closest distance to " CD  LYS A 289 " =    2.528
peak=   -3.811 closest distance to " O   HOH Z 266 " =    4.853
peak=   -3.810 closest distance to " CG  GLN A 223 " =    2.209
peak=   -3.810 closest distance to " CG2 VAL A 296 " =    0.884
peak=   -3.796 closest distance to " CG2BVAL A  41 " =    2.532
peak=   -3.765 closest distance to " O   HOH Z  38 " =    1.434
peak=   -3.762 closest distance to " C   ASN A 285 " =    2.543
peak=   -3.742 closest distance to " CD  GLN A  88 " =    0.793
peak=   -3.742 closest distance to " CD1 PHE A  59 " =    1.789
peak=   -3.727 closest distance to " O   HOH Z  71 " =    1.181
peak=   -3.717 closest distance to " O   HOH Z 166 " =    1.916
peak=   -3.713 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.713 closest distance to " CZ3 TRP A 179 " =    1.132
peak=   -3.692 closest distance to " N   ALA A 226 " =    2.114
peak=   -3.686 closest distance to " CG  MET A 105 " =    0.975
peak=   -3.683 closest distance to " O   GLY A  80 " =    2.585
peak=   -3.667 closest distance to " O   HOH Z 389 " =    1.898
peak=   -3.645 closest distance to " OG BSER A 134 " =    1.255
peak=   -3.643 closest distance to " CB  PRO A 243 " =    2.626
peak=   -3.621 closest distance to " CG  TRP A 266 " =    1.765
peak=   -3.614 closest distance to " O   HOH Z 275 " =    1.576
peak=   -3.611 closest distance to " CE2 TYR A  30 " =    2.897
peak=   -3.598 closest distance to " OG  SER A  26 " =    1.265
peak=   -3.593 closest distance to " CD1 LEU A 101 " =    2.752
peak=   -3.591 closest distance to " O   GLY A 211 " =    1.494
peak=   -3.590 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.580 closest distance to " O   HOH Z 394 " =    1.489
peak=   -3.577 closest distance to " N   ALA A  43 " =    2.548
peak=   -3.577 closest distance to " NH2AARG A 275 " =    5.489
peak=   -3.576 closest distance to " OG ASER A 134 " =    1.304
peak=   -3.576 closest distance to " O   HOH Z 388 " =    2.041
peak=   -3.575 closest distance to " O   HOH Z 211 " =    1.512
peak=   -3.561 closest distance to " CB  TRP A  85 " =    2.473
peak=   -3.555 closest distance to " SG  CYS A 254 " =    3.169
peak=   -3.548 closest distance to " O   HOH Z 350 " =    1.668
peak=   -3.545 closest distance to " NH2 ARG A  79 " =    1.922
peak=   -3.541 closest distance to " O   HOH Z 436 " =    1.534
peak=   -3.538 closest distance to " CD2 LEU A 300 " =    3.001
peak=   -3.535 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.533 closest distance to " ND2 ASN A  45 " =    1.112
peak=   -3.530 closest distance to " CD  GLN A  88 " =    2.340
peak=   -3.529 closest distance to " NH2 ARG A  66 " =    1.980
peak=   -3.528 closest distance to " O   HOH Z 184 " =    1.530
peak=   -3.523 closest distance to " CA  SER A 271 " =    2.348
peak=   -3.520 closest distance to " CE1 TYR A 169 " =    2.510
peak=   -3.520 closest distance to " N   THR A 157 " =    1.567
peak=   -3.505 closest distance to " CG2 ILE A  49 " =    2.852
peak=   -3.503 closest distance to " OG1 THR A 178 " =    1.299
peak=   -3.497 closest distance to " CD  ARG A 139 " =    1.645
peak=   -3.492 closest distance to " O   HOH Z 241 " =    1.184
peak=   -3.484 closest distance to " CD2 LEU A 167 " =    1.751
peak=   -3.478 closest distance to " O   HOH Z 426 " =    1.700
peak=   -3.460 closest distance to " SD BMET A  47 " =    0.828
peak=   -3.446 closest distance to " CG  PRO A 163 " =    2.403
peak=   -3.443 closest distance to " CG2 VAL A 112 " =    2.581
peak=   -3.441 closest distance to " CB  CYS A 254 " =    2.090
peak=   -3.428 closest distance to " O   HOH Z 407 " =    3.374
peak=   -3.421 closest distance to " CE BMET A  47 " =    1.664
peak=   -3.412 closest distance to " O   HOH Z  52 " =    1.665
peak=   -3.408 closest distance to " CG  LEU A 228 " =    0.915
peak=   -3.407 closest distance to " O   HOH Z 351 " =    1.443
peak=   -3.404 closest distance to " C   ASN A 187 " =    1.616
peak=   -3.397 closest distance to " CG1 VAL A 112 " =    3.054
peak=   -3.396 closest distance to " O   HOH Z 283 " =    1.984
peak=   -3.396 closest distance to " CA  GLY A 241 " =    2.960
peak=   -3.394 closest distance to " OD2 ASP A  50 " =    2.205
peak=   -3.381 closest distance to " O   HOH Z 435 " =    2.755
peak=   -3.380 closest distance to " CD1 LEU A   5 " =    2.521
peak=   -3.376 closest distance to " CD1 TRP A 179 " =    0.961
peak=   -3.371 closest distance to " O   HOH Z 243 " =    1.530
peak=   -3.365 closest distance to " O   HOH Z 353 " =    2.266
peak=   -3.365 closest distance to " O   HOH Z 218 " =    5.172
peak=   -3.364 closest distance to " O   HOH Z 222 " =    1.421
peak=   -3.354 closest distance to " OG BSER A 134 " =    1.841
peak=   -3.351 closest distance to " CA  GLY A 241 " =    2.263
peak=   -3.345 closest distance to " O   HOH Z 177 " =    1.562
peak=   -3.338 closest distance to " CD1 ILE A 199 " =    2.582
peak=   -3.336 closest distance to " CA  GLY A  98 " =    2.075
peak=   -3.333 closest distance to " O   HOH Z  10 " =    1.600
peak=   -3.332 closest distance to " ND2 ASN A  60 " =    1.471
peak=   -3.330 closest distance to " CG2 THR A 178 " =    2.215
peak=   -3.325 closest distance to " OH  TYR A 172 " =    1.614
peak=   -3.320 closest distance to " CG2 THR A   4 " =    2.020
peak=   -3.319 closest distance to " C   HIS A 108 " =    1.232
peak=   -3.319 closest distance to " CD2 LEU A 237 " =    2.832
peak=   -3.314 closest distance to " CH2 TRP A 177 " =    2.255
peak=   -3.309 closest distance to " CG  ARG A  66 " =    2.156
peak=   -3.305 closest distance to " CG  PHE A 283 " =    2.640
peak=   -3.303 closest distance to " O   HOH Z  63 " =    1.167
peak=   -3.301 closest distance to " C   GLN A 240 " =    2.370
peak=   -3.295 closest distance to " OG1 THR A  82 " =    2.083
peak=   -3.292 closest distance to " OG1 THR A 246 " =    1.507
peak=   -3.286 closest distance to " CB  ALA A  43 " =    2.479
peak=   -3.284 closest distance to " CG  ASN A  45 " =    1.756
peak=   -3.281 closest distance to " N   SER A 212 " =    1.853
peak=   -3.276 closest distance to " CB  ASN A  39 " =    2.098
peak=   -3.272 closest distance to " OH  TYR A 214 " =    1.161
peak=   -3.272 closest distance to " CB  ILE A 239 " =    2.051
peak=   -3.271 closest distance to " O   HOH Z 165 " =    1.937
peak=   -3.268 closest distance to " OD1 ASN A 148 " =    1.546
peak=   -3.268 closest distance to " NH1 ARG A  56 " =    2.432
peak=   -3.266 closest distance to " CB  ALA A 291 " =    2.158
peak=   -3.265 closest distance to " CD1 LEU A 297 " =    2.426
peak=   -3.264 closest distance to " O   HOH Z  98 " =    1.587
peak=   -3.256 closest distance to " O   HOH Z  44 " =    2.022
peak=   -3.256 closest distance to " CB  SER A  63 " =    3.394
peak=   -3.249 closest distance to " CG1 VAL A 197 " =    2.432
peak=   -3.246 closest distance to " O   HOH Z 396 " =    1.769
peak=   -3.242 closest distance to " CB  ALA A 291 " =    2.253
peak=   -3.233 closest distance to " O   GLY A 203 " =    2.486
peak=   -3.229 closest distance to " SG  CYS A 168 " =    1.020
peak=   -3.226 closest distance to " CE2 PHE A 283 " =    2.543
peak=   -3.224 closest distance to " CD2 LEU A   5 " =    1.168
peak=   -3.215 closest distance to " O   HOH Z 166 " =    1.445
peak=   -3.213 closest distance to " N   GLN A  58 " =    1.732
peak=   -3.213 closest distance to " N   ALA A 248 " =    2.468
peak=   -3.208 closest distance to " O   HOH Z 196 " =    2.323
peak=   -3.205 closest distance to " O   HOH Z 185 " =    2.388
peak=   -3.204 closest distance to " O   HOH Z 128 " =    2.571
peak=   -3.202 closest distance to " O   HOH Z 317 " =    2.282
peak=   -3.202 closest distance to " O   HOH Z 207 " =    2.150
peak=   -3.199 closest distance to " O   HOH Z  92 " =    1.242
peak=   -3.196 closest distance to " ND2 ASN A  60 " =    1.823
peak=   -3.193 closest distance to " O   HOH Z 295 " =    1.286
peak=   -3.190 closest distance to " O   HOH Z 128 " =    4.095
peak=   -3.190 closest distance to " OD1 ASN A 249 " =    1.341
peak=   -3.189 closest distance to " NE2 GLN A 278 " =    1.118
peak=   -3.188 closest distance to " CD2 PHE A  61 " =    1.851
peak=   -3.186 closest distance to " O   HOH Z 119 " =    2.566
peak=   -3.185 closest distance to " O   VAL A  67 " =    2.503
peak=   -3.181 closest distance to " CE3 TRP A  70 " =    1.844
peak=   -3.169 closest distance to " CA  GLY A  35 " =    2.034
peak=   -3.163 closest distance to " OG  SER A 206 " =    1.819
peak=   -3.161 closest distance to " N   SER A   3 " =    2.213
peak=   -3.160 closest distance to " O   THR A  18 " =    1.599
peak=   -3.157 closest distance to " O   HOH Z 437 " =    1.891
peak=   -3.157 closest distance to " O   VAL A 189 " =    2.546
peak=   -3.152 closest distance to " CA  ASP A 298 " =    1.121
peak=   -3.144 closest distance to " CD2 TYR A 293 " =    2.105
peak=   -3.142 closest distance to " C   GLU A 236 " =    0.973
peak=   -3.136 closest distance to " CE2 PHE A 218 " =    2.549
peak=   -3.135 closest distance to " O   HOH Z 377 " =    1.303
peak=   -3.129 closest distance to " N   ALA A 248 " =    1.913
peak=   -3.128 closest distance to " N   GLY A  23 " =    2.229
peak=   -3.124 closest distance to " O   HOH Z 219 " =    1.093
peak=   -3.120 closest distance to " O   HOH Z 313 " =    1.674
peak=   -3.114 closest distance to " CE  MET A 105 " =    2.158
peak=   -3.108 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.100 closest distance to " CB  ALA A 248 " =    1.956
peak=   -3.096 closest distance to " O   SER A 164 " =    1.979
peak=   -3.092 closest distance to " O   HOH Z 109 " =    1.605
peak=   -3.086 closest distance to " CA  GLY A 133 " =    2.177
peak=   -3.084 closest distance to " OD1 ASN A  39 " =    2.166
peak=   -3.074 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.073 closest distance to " CB  ALA A 227 " =    2.392
peak=   -3.072 closest distance to " NH2BARG A 275 " =    1.878
peak=   -3.046 closest distance to " N   PHE A  59 " =    2.179
peak=   -3.043 closest distance to " O   HOH Z 252 " =    4.112
peak=   -3.035 closest distance to " CA  TYR A  68 " =    2.782

================= 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    :  0.4618 0.4542   6.262036e+00   6.252358e+00
   1_bss:  0.4534 0.4436   6.257009e+00   6.245269e+00
   1_xyz:  0.3616 0.3900   6.114625e+00   6.168910e+00
   1_adp:  0.3114 0.3574   6.010134e+00   6.117983e+00
   1_occ:  0.3105 0.3575   6.009568e+00   6.118975e+00
   2_bss:  0.3076 0.3538   6.009873e+00   6.116884e+00
   2_xyz:  0.2252 0.2829   5.750032e+00   5.925487e+00
   2_adp:  0.2061 0.2622   5.676367e+00   5.858293e+00
   2_occ:  0.2060 0.2623   5.676116e+00   5.858497e+00
   3_bss:  0.2046 0.2597   5.675685e+00   5.856722e+00
   3_xyz:  0.1568 0.2061   5.432715e+00   5.645871e+00
   3_adp:  0.1432 0.1951   5.366312e+00   5.593634e+00
   3_occ:  0.1431 0.1946   5.364770e+00   5.591690e+00
   4_bss:  0.1431 0.1948   5.363435e+00   5.589463e+00
   4_xyz:  0.1280 0.1801   5.269245e+00   5.510600e+00
   4_adp:  0.1250 0.1760   5.249002e+00   5.491098e+00
   4_occ:  0.1250 0.1758   5.248575e+00   5.490597e+00
   5_bss:  0.1249 0.1757   5.248463e+00   5.490277e+00
   5_xyz:  0.1180 0.1686   5.201540e+00   5.450102e+00
   5_adp:  0.1182 0.1658   5.194117e+00   5.436956e+00
   5_occ:  0.1181 0.1656   5.193750e+00   5.436469e+00
   5_bss:  0.1184 0.1654   5.194120e+00   5.436067e+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:  0.323  15.016  10.605   7.441   7.688   0.000   0.000   0.000
   1_xyz:  0.323  15.016  10.605   7.441   7.688   0.000   0.000   0.000
   1_adp:  0.323  15.016  10.605   7.441   7.688   0.000   0.000   0.000
   1_occ:  0.323  15.016  10.605   7.441   7.688   0.000   0.000   0.000
   2_bss:  0.336  42.239   6.953   4.207   5.206   0.000   0.000   0.000
   2_xyz:  0.336  42.239   6.953   4.207   5.206   0.000   0.000   0.000
   2_adp:  0.336  42.239   6.953   4.207   5.206   0.000   0.000   0.000
   2_occ:  0.336  42.239   6.953   4.207   5.206   0.000   0.000   0.000
   3_bss:  0.327  42.240   4.142   2.879   3.774   0.000   0.000   0.000
   3_xyz:  0.327  42.240   4.142   2.879   3.774   0.000   0.000   0.000
   3_adp:  0.327  42.240   4.142   2.879   3.774   0.000   0.000   0.000
   3_occ:  0.327  42.240   4.142   2.879   3.774   0.000   0.000   0.000
   4_bss:  0.326  56.800   3.227   2.510   3.264   0.000   0.000   0.000
   4_xyz:  0.326  56.800   3.227   2.510   3.264   0.000   0.000   0.000
   4_adp:  0.326  56.800   3.227   2.510   3.264   0.000   0.000   0.000
   4_occ:  0.326  56.800   3.227   2.510   3.264   0.000   0.000   0.000
   5_bss:  0.330  55.208   2.887   2.400   3.136   0.000   0.000   0.000
   5_xyz:  0.330  55.208   2.887   2.400   3.136   0.000   0.000   0.000
   5_adp:  0.330  55.208   2.887   2.400   3.136   0.000   0.000   0.000
   5_occ:  0.330  55.208   2.887   2.400   3.136   0.000   0.000   0.000
   5_bss:  0.330  57.894   0.032  -0.368   0.336  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.506 0.4773  0.5503    63579.568
   1_bss:  53.937 0.4696  0.6913    61071.728
   1_xyz:  45.052 0.5799  0.8365    44942.416
   1_adp:  39.690 0.6458  0.9422    37272.729
   1_occ:  39.786 0.6445  0.9390    37402.398
   2_bss:  39.625 0.6464  0.8462    37213.442
   2_xyz:  29.351 0.7640  0.9708    21616.380
   2_adp:  26.480 0.7958  1.0008    18470.918
   2_occ:  26.493 0.7956  1.0009    18479.698
   3_bss:  26.385 0.7967  0.9373    18375.310
   3_xyz:  19.853 0.8628  0.9817    10991.114
   3_adp:  18.526 0.8757  0.9870     9813.246
   3_occ:  18.477 0.8762  0.9872     9769.180
   4_bss:  18.414 0.8767  0.9664     9704.726
   4_xyz:  16.551 0.8936  0.9757     8207.219
   4_adp:  15.999 0.8988  0.9770     7885.242
   4_occ:  15.986 0.8989  0.9769     7873.130
   5_bss:  15.983 0.8989  0.9703     7865.263
   5_xyz:  15.133 0.9060  0.9735     7205.441
   5_adp:  14.777 0.9091  0.9746     7012.872
   5_occ:  14.767 0.9092  0.9745     7004.668
   5_bss:  14.745 0.9094  0.9702     6982.473
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3960e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3960e+01
   1_xyz:   1.654  0.013  0.107 18.186  0.006  4.112   1.3645e-01
   1_adp:   1.654  0.013  0.107 18.186  0.006  4.112   1.3645e-01
   1_occ:   1.654  0.013  0.107 18.186  0.006  4.112   1.3645e-01
   2_bss:   1.654  0.013  0.107 18.186  0.006  4.112   1.3645e-01
   2_xyz:   1.045  0.007  0.074 16.489  0.004  4.128   7.0969e-02
   2_adp:   1.045  0.007  0.074 16.489  0.004  4.128   7.0969e-02
   2_occ:   1.045  0.007  0.074 16.489  0.004  4.128   7.0969e-02
   3_bss:   1.045  0.007  0.074 16.489  0.004  4.128   7.0969e-02
   3_xyz:   1.023  0.007  0.075 15.648  0.004  4.128   6.5669e-02
   3_adp:   1.023  0.007  0.075 15.648  0.004  4.128   6.5669e-02
   3_occ:   1.023  0.007  0.075 15.648  0.004  4.128   6.5669e-02
   4_bss:   1.023  0.007  0.075 15.648  0.004  4.128   6.5669e-02
   4_xyz:   1.008  0.007  0.077 15.678  0.003  4.135   6.2715e-02
   4_adp:   1.008  0.007  0.077 15.678  0.003  4.135   6.2715e-02
   4_occ:   1.008  0.007  0.077 15.678  0.003  4.135   6.2715e-02
   5_bss:   1.008  0.007  0.077 15.678  0.003  4.135   6.2715e-02
   5_xyz:   1.093  0.009  0.083 15.788  0.004  4.116   7.0653e-02
   5_adp:   1.093  0.009  0.083 15.788  0.004  4.116   7.0653e-02
   5_occ:   1.093  0.009  0.083 15.788  0.004  4.116   7.0653e-02
   5_bss:   1.093  0.009  0.083 15.788  0.004  4.116   7.0653e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9965e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9965e+00
   1_xyz:  13.817  0.163  0.459 84.911  0.038  2.215   1.0064e-01
   1_adp:  13.817  0.163  0.459 84.911  0.038  2.215   1.0064e-01
   1_occ:  13.817  0.163  0.459 84.911  0.038  2.215   1.0064e-01
   2_bss:  13.817  0.163  0.459 84.911  0.038  2.215   1.0064e-01
   2_xyz:   7.289  0.057  0.292 82.886  0.045  2.303   5.8268e-02
   2_adp:   7.289  0.057  0.292 82.886  0.045  2.303   5.8268e-02
   2_occ:   7.289  0.057  0.292 82.886  0.045  2.303   5.8268e-02
   3_bss:   7.289  0.057  0.292 82.886  0.045  2.303   5.8268e-02
   3_xyz:   8.405  0.058  0.335 87.974  0.043  2.365   1.1959e-01
   3_adp:   8.405  0.058  0.335 87.974  0.043  2.365   1.1959e-01
   3_occ:   8.405  0.058  0.335 87.974  0.043  2.365   1.1959e-01
   4_bss:   8.405  0.058  0.335 87.974  0.043  2.365   1.1959e-01
   4_xyz:   8.392  0.059  0.358 82.742  0.033  2.355   4.2048e-02
   4_adp:   8.392  0.059  0.358 82.742  0.033  2.355   4.2048e-02
   4_occ:   8.392  0.059  0.358 82.742  0.033  2.355   4.2048e-02
   5_bss:   8.392  0.059  0.358 82.742  0.033  2.355   4.2048e-02
   5_xyz:   8.546  0.066  0.475 85.381  0.031  2.337   4.3226e-02
   5_adp:   8.546  0.066  0.475 85.381  0.031  2.337   4.3226e-02
   5_occ:   8.546  0.066  0.475 85.381  0.031  2.337   4.3226e-02
   5_bss:   8.546  0.066  0.475 85.381  0.031  2.337   4.3226e-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:  57.91   0.00  11.26  57.62   0.00   8.72  57.91   0.00  25.12
   1_occ:  57.91   0.00  11.26  57.62   0.00   8.72  57.91   0.00  25.12
   2_bss:  57.91   0.00  11.26  57.62   0.00   8.72  57.91   0.00  25.12
   2_xyz:  57.91   0.00  11.26  57.62   0.00   8.72  57.91   0.00  25.12
   2_adp:  62.86   0.00  11.67  62.86   0.00   8.24  61.66   0.45  30.35
   2_occ:  62.86   0.00  11.67  62.86   0.00   8.24  61.66   0.45  30.35
   3_bss:  62.86   0.00  11.67  62.86   0.00   8.24  61.66   0.45  30.35
   3_xyz:  62.86   0.00  11.67  62.86   0.00   8.24  61.66   0.45  30.35
   3_adp:  88.11   0.00  12.97  83.20   0.00   8.41  88.11   1.03  37.81
   3_occ:  88.11   0.00  12.97  83.20   0.00   8.41  88.11   1.03  37.81
   4_bss:  88.11   0.00  12.97  83.20   0.00   8.41  88.11   1.03  37.81
   4_xyz:  88.11   0.00  12.97  83.20   0.00   8.41  88.11   1.03  37.81
   4_adp:  90.24   0.00  12.84  87.57   0.00   8.34  90.24   1.37  37.38
   4_occ:  90.24   0.00  12.84  87.57   0.00   8.34  90.24   1.37  37.38
   5_bss:  90.24   0.00  12.84  87.57   0.00   8.34  90.24   1.37  37.38
   5_xyz:  90.24   0.00  12.84  87.57   0.00   8.34  90.24   1.37  37.38
   5_adp:  87.26   0.00  12.43  87.26   0.00   8.21  85.42   1.77  35.40
   5_occ:  87.26   0.00  12.43  87.26   0.00   8.21  85.42   1.77  35.40
   5_bss:  89.95   2.69  15.12  89.95   2.69  10.90  88.10   4.45  38.09
------------------------------------------------------------------------
 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:    1.199    0.027    0.411
   1_adp:    1.199    0.027    0.411
   1_occ:    1.199    0.027    0.411
   2_bss:    1.199    0.027    0.411
   2_xyz:    1.485    0.047    0.548
   2_adp:    1.485    0.047    0.548
   2_occ:    1.485    0.047    0.548
   3_bss:    1.485    0.047    0.548
   3_xyz:    1.488    0.032    0.615
   3_adp:    1.488    0.032    0.615
   3_occ:    1.488    0.032    0.615
   4_bss:    1.488    0.032    0.615
   4_xyz:    1.709    0.052    0.652
   4_adp:    1.709    0.052    0.652
   4_occ:    1.709    0.052    0.652
   5_bss:    1.709    0.052    0.652
   5_xyz:    1.870    0.040    0.669
   5_adp:    1.870    0.040    0.669
   5_occ:    1.870    0.040    0.669
   5_bss:    1.870    0.040    0.669
------------------------------------------------------------------------

CPU time actual refinement: 369.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/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_1268/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1268/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 369.04 
  Macro-tasks:
    bulk solvent and scale       = 42.67  
    individual site refinement   = 161.44 
    weights calculation          = 34.05  
    collect and process          = 6.72   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 245.02 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 116.84 
    alpha_beta                      = 8.87   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 128.03 
    fmodel                         = 8.01   
    r_factors                      = 0.21   
    phase_errors                   = 10.73  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 276.65 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.058 micro seconds
Total CPU time: 6.38 minutes
from_scatterers_fft:    667 calls, 116.32 s
gradients_fft:          612 calls, 113.49 s

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

# Date 2008-01-16 Time 03:38:07 PST -0800 (1200483487.09 s)
Start R-work = 0.4618, R-free = 0.4542 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1815 (no bulk solvent and anisotropic scale)

Start R-work = 0.4534, R-free = 0.4436
Final R-work = 0.1184, R-free = 0.1654