# Date 2008-01-16 Time 02:02:04 PST -0800 (1200477724.35 s)
#phil __OFF__

Command line arguments: "../658.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13286
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 658

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.99219
Completeness in resolution range: 0.959869
Completeness with d_max=infinity: 0.956915

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   1.9922

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.99219
Completeness in resolution range: 0.959869
Completeness with d_max=infinity: 0.956915

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0740 -  4.2627 [2148/2172]  1929   219  10.2%
  bin  2:  4.2627 -  3.3962 [2053/2073]  1849   204   9.9%
  bin  3:  3.3962 -  2.9706 [2031/2050]  1833   198   9.7%
  bin  4:  2.9706 -  2.7007 [2014/2044]  1811   203  10.1%
  bin  5:  2.7007 -  2.5081 [1996/2015]  1794   202  10.1%
  bin  6:  2.5081 -  2.3608 [2007/2032]  1803   204  10.2%
  bin  7:  2.3608 -  2.2430 [1972/2000]  1776   196   9.9%
  bin  8:  2.2430 -  2.1456 [1968/2004]  1772   196  10.0%
  bin  9:  2.1456 -  2.0632 [1958/2000]  1767   191   9.8%
  bin 10:  2.0632 -  1.9922 [1442/2018]  1296   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 10
        2.31 -     2.95: 1647
        2.95 -     3.60: 4485
        3.60 -     4.25: 9094
        4.25 -     4.90: 12844
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.656 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.768 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.802 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.903 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28075 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_658/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 88.1178 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: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4546   r_free= 0.4374   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.255459                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.3793 0.3434      6.5753      6.4819|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.3489 0.3740      6.6931      6.7782|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.4030 0.3698      6.6203      6.5788|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.4498 0.4089      6.5068      6.4245|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.4816 0.4390      6.3463       6.337|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.4732 0.5436      6.2539      6.2198|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.4938 0.4848      6.2175      6.1598|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.5092 0.4460      6.1798      6.1649|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.4884 0.5385         6.1      6.1605|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.5256 0.4325      6.1243      6.0255|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.4989 0.4927      6.0163      6.0314|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.5205 0.4730      5.9706      5.9919|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.5015 0.5000      5.8721      5.8351|
| 14:  2.0419 -  1.9922 0.60    779   91 0.5176 0.4680      5.8799      5.7439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7544  1393   154  0.74  31.04   0.80     0.77      59644.31|
|  2:  4.7544 -  3.7935  1339   152  0.76  30.00   0.89     0.82      82840.13|
|  3:  3.7935 -  3.3198  1303   142  0.68  36.95   0.85     0.78      87323.04|
|  4:  3.3198 -  3.0189  1310   145  0.60  43.89   0.80     0.67      79513.33|
|  5:  3.0189 -  2.8040  1297   147  0.51  51.29   0.77     0.58      69014.17|
|  6:  2.8040 -  2.6396  1300   143  0.46  55.48   0.73     0.51      64830.97|
|  7:  2.6396 -  2.5081  1274   143  0.43  57.67   0.75     0.49      60049.85|
|  8:  2.5081 -  2.3993  1279   137  0.44  57.09   0.73     0.50      53156.41|
|  9:  2.3993 -  2.3073  1275   147  0.46  55.09   0.75     0.53      46962.61|
| 10:  2.3073 -  2.2279  1297   139  0.46  55.62   0.74     0.53      41804.58|
| 11:  2.2279 -  2.1585  1258   140  0.44  56.83   0.76     0.53      40117.49|
| 12:  2.1585 -  2.0970  1250   144  0.43  58.01   0.76     0.52      36895.10|
| 13:  2.0970 -  2.0419  1276   135  0.42  58.36   0.72     0.51      32145.26|
| 14:  2.0419 -  1.9922   779    91  0.46  55.33   0.75     0.49      25816.67|
|alpha:            min =        0.49 max =            0.82 mean =         0.59|
|beta:             min =    25816.67 max =        87323.04 mean =     56837.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.97 mean =        49.81|
|phase err.(test): min =        0.00 max =           89.92 mean =        50.07|
|-----------------------------------------------------------------------------|

============================== 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 = 9.467348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.168   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.790054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.406   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1488 |
| 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:     3883 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5070 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6507 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7680 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.054 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.759 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    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 = 12.033)------------------------------------------|
|    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: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4632   r_free= 0.4429   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.260071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4462   r_free= 0.4266   ksol= 0.34   Bsol= 18.33   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,7.71,11.73,0.00,0.00,0.00); trace/3= 8.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.248521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.391084              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.537   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.959   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4462      final r-factor (work) = 0.3482          |
| start r-factor (free) = 0.4266      final r-factor (free) = 0.3678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.3112 = 8.39 * 0.50 * 6.2583 + 1.00 * 54.0542                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8224 = 8.39 * 0.50 * 6.1241 + 1.00 * 0.1285                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3482      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.3678      final r-factor (free) = 0.3354          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5293 = 0.74 * 1.00 * 6.1241 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4284 = 0.74 * 1.00 * 5.9887 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.67   11.79    None  None   None       |
|    all(noH): 2823   0      0.00    64.67   11.79    None  None   None       |
|    Sol.    : 438    0      0.00    64.67   27.29    None  None   None       |
|    Mac.    : 2385   0      0.00    53.39   8.94     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 -   6.467: 1139   |   5:    32.335 -  38.802:   93        |
|      1:     6.467 -  12.934:  755   |   6:    38.802 -  45.269:   52        |
|      2:    12.934 -  19.401:  407   |   7:    45.269 -  51.736:   37        |
|      3:    19.401 -  25.868:  188   |   8:    51.736 -  58.203:   12        |
|      4:    25.868 -  32.335:  134   |   9:    58.203 -  64.670:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2932 r_free = 0.3354             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2924 r_free = 0.3359             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2924   r_free= 0.3359   ksol= 0.34   Bsol= 18.33   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,7.71,11.73,0.00,0.00,0.00); trace/3= 8.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.954831                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2879   r_free= 0.3324   ksol= 0.34   Bsol= 47.81   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.00,8.09,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.954081                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.901819              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.936   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392825              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.922  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2879      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.3324      final r-factor (free) = 0.2510          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8076 = 4.90 * 0.50 * 5.9892 + 1.00 * 0.1285                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2663 = 4.90 * 0.50 * 5.7913 + 1.00 * 0.0723                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2005      final r-factor (work) = 0.1799          |
| start r-factor (free) = 0.2510      final r-factor (free) = 0.2299          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2883 = 0.39 * 1.00 * 5.7913 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2033 = 0.39 * 1.00 * 5.5815 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.85   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    63.85   11.73    None  None   None       |
|    Sol.    : 438    0      0.00    63.85   31.88    None  None   None       |
|    Mac.    : 2385   0      0.00    54.60   8.03     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 -   6.385: 1301   |   5:    31.925 -  38.310:  119        |
|      1:     6.385 -  12.770:  734   |   6:    38.310 -  44.695:   85        |
|      2:    12.770 -  19.155:  271   |   7:    44.695 -  51.080:   45        |
|      3:    19.155 -  25.540:  127   |   8:    51.080 -  57.465:   24        |
|      4:    25.540 -  31.925:  107   |   9:    57.465 -  63.850:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1799 r_free = 0.2299             target_work(ml) = 5.540         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1799 r_free = 0.2299             target_work(ml) = 5.539         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1799   r_free= 0.2299   ksol= 0.34   Bsol= 47.81   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.00,8.09,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.539317                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1783   r_free= 0.2293   ksol= 0.32   Bsol= 47.81   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.99,5.37,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.538473                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.297200              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.629  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.265994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.874  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1783      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2293      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4935 = 2.30 * 0.50 * 5.5905 + 1.00 * 0.0723                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3095 = 2.30 * 0.50 * 5.4390 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3354 = 2.27 * 1.00 * 5.4390 + 1.00 * 0.0108                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0301 = 2.27 * 1.00 * 5.3021 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.89   12.73    None  None   None       |
|    all(noH): 2823   0      0.00    81.89   12.73    None  None   None       |
|    Sol.    : 438    0      0.79    81.89   37.69    None  None   None       |
|    Mac.    : 2385   0      0.00    75.25   8.15     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 -   8.189: 1600   |   5:    40.946 -  49.136:   83        |
|      1:     8.189 -  16.379:  606   |   6:    49.136 -  57.325:   76        |
|      2:    16.379 -  24.568:  176   |   7:    57.325 -  65.514:   55        |
|      3:    24.568 -  32.757:  107   |   8:    65.514 -  73.703:   16        |
|      4:    32.757 -  40.946:   96   |   9:    73.703 -  81.893:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1321 r_free = 0.1817             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1320 r_free = 0.1817             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1817   ksol= 0.32   Bsol= 47.81   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.99,5.37,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.287367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1823   ksol= 0.32   Bsol= 47.81   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.75,4.77,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.288262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.260883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.281  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279338              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.474  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1823      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7078 = 3.26 * 0.50 * 5.3026 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6196 = 3.26 * 0.50 * 5.2422 + 1.00 * 0.0725                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4797 = 0.28 * 1.00 * 5.2422 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4738 = 0.28 * 1.00 * 5.2029 + 1.00 * 0.0204                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.24   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    79.24   12.10    None  None   None       |
|    Sol.    : 438    0      1.01    79.24   35.30    None  None   None       |
|    Mac.    : 2385   0      0.00    76.48   7.84     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.924: 1624   |   5:    39.620 -  47.544:   75        |
|      1:     7.924 -  15.848:  608   |   6:    47.544 -  55.468:   77        |
|      2:    15.848 -  23.772:  168   |   7:    55.468 -  63.392:   42        |
|      3:    23.772 -  31.696:  100   |   8:    63.392 -  71.316:   14        |
|      4:    31.696 -  39.620:  107   |   9:    71.316 -  79.240:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1645             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1642             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1642   ksol= 0.32   Bsol= 47.81   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.75,4.77,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186092                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1642   ksol= 0.32   Bsol= 53.08   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.77,4.67,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.885876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.531  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.101   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5794 = 2.89 * 0.50 * 5.2025 + 1.00 * 0.0725                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5423 = 2.89 * 0.50 * 5.1753 + 1.00 * 0.0747                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8603 = 0.36 * 1.00 * 5.1753 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8546 = 0.36 * 1.00 * 5.1645 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.31   11.90    None  None   None       |
|    all(noH): 2823   0      0.00    79.31   11.90    None  None   None       |
|    Sol.    : 438    0      1.13    79.31   34.80    None  None   None       |
|    Mac.    : 2385   0      0.00    77.23   7.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.931: 1654   |   5:    39.653 -  47.583:   77        |
|      1:     7.931 -  15.861:  583   |   6:    47.583 -  55.514:   74        |
|      2:    15.861 -  23.792:  167   |   7:    55.514 -  63.444:   34        |
|      3:    23.792 -  31.722:  102   |   8:    63.444 -  71.375:   14        |
|      4:    31.722 -  39.653:  110   |   9:    71.375 -  79.305:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1605   ksol= 0.32   Bsol= 53.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,2.77,4.67,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162762                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.1016 0.1366      5.4156      5.5737|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.0861 0.1151      5.4535       5.663|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.1073 0.1498      5.4965      5.8354|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.1225 0.1763      5.4633      5.6538|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.1333 0.1635      5.3427      5.5472|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.1230 0.2117      5.2243      5.5433|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.1309 0.1644      5.2033      5.3442|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.1196 0.1664      5.0995      5.3675|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.1192 0.1890      5.0622      5.3413|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.1156 0.1642      4.9764      5.1806|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.1174 0.1765      4.9679      5.2527|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.1149 0.1774      4.8941      5.2616|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.1112 0.1603      4.7779      4.9985|
| 14:  2.0419 -  1.9922 0.60    779   91 0.0957 0.1595      4.6335      4.8661|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7544  1393   154  0.94   9.69   0.98     0.95       7815.40|
|  2:  4.7544 -  3.7935  1339   152  0.95   8.33   1.01     1.00       9588.74|
|  3:  3.7935 -  3.3198  1303   142  0.93  11.53   1.02     1.02      10856.89|
|  4:  3.3198 -  3.0189  1310   145  0.92  13.73   1.00     0.99      10563.26|
|  5:  3.0189 -  2.8040  1297   147  0.90  15.92   1.00     0.97       8605.12|
|  6:  2.8040 -  2.6396  1300   143  0.90  16.51   0.98     0.95       7332.58|
|  7:  2.6396 -  2.5081  1274   143  0.90  16.12   0.99     0.95       6539.71|
|  8:  2.5081 -  2.3993  1279   137  0.90  15.64   0.99     0.96       5633.30|
|  9:  2.3993 -  2.3073  1275   147  0.91  15.55   1.01     0.97       5325.51|
| 10:  2.3073 -  2.2279  1297   139  0.89  16.48   1.00     0.96       4598.91|
| 11:  2.2279 -  2.1585  1258   140  0.90  16.65   0.99     0.95       4656.97|
| 12:  2.1585 -  2.0970  1250   144  0.90  16.13   1.01     1.00       4096.55|
| 13:  2.0970 -  2.0419  1276   135  0.90  15.96   0.99     0.97       3293.85|
| 14:  2.0419 -  1.9922   779    91  0.93  13.24   0.98     0.95       2419.02|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2419.02 max =        10856.89 mean =      6679.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.55 mean =        13.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1605   ksol= 0.32   Bsol= 56.42   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.55,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1605   ksol= 0.32   Bsol= 56.42   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.55,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162769                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.1016 0.1366      5.4157      5.5738|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.0861 0.1151      5.4536      5.6632|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.1073 0.1498      5.4966      5.8357|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.1225 0.1763      5.4634      5.6539|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.1332 0.1634      5.3426       5.547|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.1230 0.2118      5.2243      5.5435|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.1309 0.1644      5.2034      5.3443|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.1196 0.1664      5.0997      5.3677|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.1192 0.1890      5.0622      5.3414|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.1156 0.1642      4.9763      5.1804|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.1174 0.1764      4.9676      5.2522|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.1149 0.1772      4.8939      5.2611|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.1112 0.1604      4.7779      4.9991|
| 14:  2.0419 -  1.9922 0.60    779   91 0.0957 0.1595      4.6338       4.866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7544  1393   154  0.94   9.69   0.98     0.95       7817.18|
|  2:  4.7544 -  3.7935  1339   152  0.95   8.33   1.01     1.00       9591.55|
|  3:  3.7935 -  3.3198  1303   142  0.93  11.53   1.02     1.02      10860.90|
|  4:  3.3198 -  3.0189  1310   145  0.92  13.73   1.00     0.99      10564.34|
|  5:  3.0189 -  2.8040  1297   147  0.90  15.92   1.00     0.97       8606.46|
|  6:  2.8040 -  2.6396  1300   143  0.90  16.51   0.98     0.95       7331.80|
|  7:  2.6396 -  2.5081  1274   143  0.90  16.12   0.99     0.95       6541.14|
|  8:  2.5081 -  2.3993  1279   137  0.90  15.64   0.99     0.96       5635.36|
|  9:  2.3993 -  2.3073  1275   147  0.91  15.55   1.01     0.97       5327.64|
| 10:  2.3073 -  2.2279  1297   139  0.89  16.48   1.00     0.96       4596.60|
| 11:  2.2279 -  2.1585  1258   140  0.90  16.64   0.99     0.95       4653.37|
| 12:  2.1585 -  2.0970  1250   144  0.90  16.12   1.01     1.00       4093.78|
| 13:  2.0970 -  2.0419  1276   135  0.90  15.96   0.99     0.97       3293.74|
| 14:  2.0419 -  1.9922   779    91  0.93  13.26   0.98     0.95       2420.10|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2420.10 max =        10860.90 mean =      6680.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.55 mean =        13.80|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.34    82.65   15.24    None  None   None       |
|    all(noH): 2823   0      3.34    82.65   15.24    None  None   None       |
|    Sol.    : 438    0      4.47    82.65   38.14    None  None   None       |
|    Mac.    : 2385   0      3.34    80.58   11.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.345 -  11.275: 1654   |   5:    42.997 -  50.928:   77        |
|      1:    11.275 -  19.206:  583   |   6:    50.928 -  58.858:   74        |
|      2:    19.206 -  27.136:  167   |   7:    58.858 -  66.789:   34        |
|      3:    27.136 -  35.067:  102   |   8:    66.789 -  74.719:   14        |
|      4:    35.067 -  42.997:  110   |   9:    74.719 -  82.650:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.222 - 4.567
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 304
   mapped sites are within: 0.731 - 4.567

peak=   11.144 closest distance to " CB  VAL A 230 " =    1.480
peak=    7.642 closest distance to " CG2 VAL A 296 " =    1.212
peak=    6.134 closest distance to " CG  LEU A   5 " =    1.225
peak=    6.000 closest distance to " NH2 ARG A  56 " =    2.129
peak=    5.795 closest distance to " NE2 GLN A  11 " =    1.157
peak=    5.585 closest distance to " O   HOH Z 142 " =    2.027
peak=    5.440 closest distance to " CG  PRO A  54 " =    1.349
peak=    5.352 closest distance to " CG  LEU A 228 " =    1.167
peak=    5.302 closest distance to " CD2 LEU A   5 " =    1.153
peak=    5.181 closest distance to " CB  GLN A 223 " =    1.513
peak=    5.057 closest distance to " O   HOH Z 232 " =    2.278
peak=    5.044 closest distance to " O   HOH Z   9 " =    1.749
peak=    4.866 closest distance to " CB  PRO A  54 " =    0.995
peak=    4.834 closest distance to " O   HOH Z 248 " =    1.510
peak=    4.728 closest distance to " CB  GLN A 183 " =    1.230
peak=    4.608 closest distance to " O   HOH Z 265 " =    2.121
peak=    4.543 closest distance to " CB  ASN A 142 " =    1.082
peak=    4.506 closest distance to " O   SER A  87 " =    2.384
peak=    4.489 closest distance to " O   HOH Z 346 " =    1.584
peak=    4.481 closest distance to " CB  ARG A  79 " =    1.472
peak=    4.470 closest distance to " ND2 ASN A 187 " =    1.609
peak=    4.419 closest distance to " CZ  PHE A 218 " =    1.120
peak=    4.364 closest distance to " O   HOH Z 313 " =    1.959
peak=    4.331 closest distance to " CB  SER A  63 " =    1.220
peak=    4.326 closest distance to " O   HOH Z 427 " =    3.002
peak=    4.301 closest distance to " CB  ARG A 190 " =    1.449
peak=    4.296 closest distance to " O   HOH Z 126 " =    1.931
peak=    4.286 closest distance to " O   HOH Z  61 " =    1.749
peak=    4.271 closest distance to " CB  VAL A 265 " =    1.376
peak=    4.270 closest distance to " O   HOH Z 369 " =    2.271
peak=    4.260 closest distance to " CG  PRO A 213 " =    1.199
peak=    4.246 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.241 closest distance to " CB  ASN A 148 " =    1.375
peak=    4.224 closest distance to " O   PRO A 198 " =    1.561
peak=    4.203 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.196 closest distance to " O   HOH Z 303 " =    2.111
peak=    4.170 closest distance to " CB  VAL A 296 " =    1.034
peak=    4.159 closest distance to " CB  TRP A 266 " =    1.058
peak=    4.127 closest distance to " O   HOH Z 425 " =    1.427
peak=    4.097 closest distance to " O   HOH Z 287 " =    2.072
peak=    4.079 closest distance to " CG  PRO A 243 " =    1.102
peak=    4.048 closest distance to " CZ3 TRP A 266 " =    1.147
peak=    4.044 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.041 closest distance to " OG  SER A  97 " =    2.959
peak=    3.991 closest distance to " CG2 VAL A 257 " =    0.898
peak=    3.958 closest distance to " N   PHE A 130 " =    1.269
peak=    3.951 closest distance to " O   HOH Z 251 " =    1.580
peak=    3.944 closest distance to " O   HOH Z 298 " =    1.737
peak=    3.943 closest distance to " CB  GLU A 277 " =    3.646
peak=    3.931 closest distance to " O   HOH Z  43 " =    1.985
peak=    3.927 closest distance to " N   ASN A  39 " =    1.191
peak=    3.924 closest distance to " CA  ALA A  51 " =    0.955
peak=    3.924 closest distance to " O   HOH Z 411 " =    3.814
peak=    3.923 closest distance to " CB  VAL A 230 " =    1.172
peak=    3.916 closest distance to " O   HOH Z 214 " =    2.244
peak=    3.885 closest distance to " CA  TYR A  30 " =    1.005
peak=    3.879 closest distance to " CD2 LEU A 228 " =    1.159
peak=    3.865 closest distance to " O  BHOH Z 338 " =    2.411
peak=    3.863 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.861 closest distance to " CB  ALA A   9 " =    1.607
peak=    3.853 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.849 closest distance to " O   HOH Z  78 " =    1.594
peak=    3.848 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.846 closest distance to " O   HOH Z 353 " =    2.556
peak=    3.845 closest distance to " O   HOH Z 422 " =    2.640
peak=    3.834 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.821 closest distance to " O   HOH Z 406 " =    1.583
peak=    3.807 closest distance to " O   HOH Z  21 " =    1.784
peak=    3.803 closest distance to " O   HOH Z 368 " =    2.129
peak=    3.800 closest distance to " OG BSER A 164 " =    2.214
peak=    3.798 closest distance to " CG  LEU A 167 " =    1.246
peak=    3.797 closest distance to " O   HOH Z 126 " =    1.559
peak=    3.796 closest distance to " O   HOH Z 234 " =    3.694
peak=    3.779 closest distance to " CB  ARG A  79 " =    0.929
peak=    3.776 closest distance to " CB  ASP A 140 " =    0.989
peak=    3.776 closest distance to " CA  SER A  87 " =    0.993
peak=    3.771 closest distance to " CG  MET A 185 " =    1.148
peak=    3.762 closest distance to " CG1 ILE A  49 " =    1.575
peak=    3.756 closest distance to " CD2 TRP A 179 " =    1.265
peak=    3.739 closest distance to " NH1AARG A 145 " =    1.216
peak=    3.735 closest distance to " CB  SER A   3 " =    1.307
peak=    3.733 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.732 closest distance to " ND2 ASN A 249 " =    0.901
peak=    3.725 closest distance to " O   HOH Z  40 " =    1.660
peak=    3.713 closest distance to " O   HOH Z 158 " =    3.264
peak=    3.713 closest distance to " CB  LEU A  83 " =    0.731
peak=    3.702 closest distance to " CB  LYS A 117 " =    1.207
peak=    3.696 closest distance to " O   HOH Z  10 " =    1.753
peak=    3.686 closest distance to " O   HOH Z 180 " =    2.136
peak=    3.685 closest distance to " O   HOH Z  92 " =    2.399
peak=    3.681 closest distance to " OD1 ASN A  69 " =    2.554
peak=    3.672 closest distance to " O   HOH Z 359 " =    1.483
peak=    3.668 closest distance to " CD  LYS A 166 " =    1.292
peak=    3.665 closest distance to " CB  SER A 212 " =    1.300
peak=    3.663 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.655 closest distance to " O   HOH Z   3 " =    2.020
peak=    3.648 closest distance to " CA  TYR A 116 " =    1.396
peak=    3.635 closest distance to " CA  THR A 264 " =    0.855
peak=    3.628 closest distance to " O   HOH Z 261 " =    1.776
peak=    3.622 closest distance to " OG ASER A 258 " =    3.073
peak=    3.621 closest distance to " CB  GLU A  46 " =    0.931
peak=    3.620 closest distance to " O   HOH Z 371 " =    2.796
peak=    3.619 closest distance to " O   HOH Z  30 " =    1.430
peak=    3.613 closest distance to " O   HOH Z 273 " =    2.938
peak=    3.610 closest distance to " CB BVAL A  41 " =    1.197
peak=    3.603 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.579 closest distance to " O   HOH Z 423 " =    1.791
peak=    3.575 closest distance to " CD1 LEU A  96 " =    0.784
peak=    3.574 closest distance to " CA  ASN A 215 " =    1.059
peak=    3.572 closest distance to " CG1 VAL A 153 " =    0.961
peak=    3.569 closest distance to " O   HOH Z 290 " =    1.077
peak=    3.568 closest distance to " CD  ARG A  66 " =    2.672
peak=    3.568 closest distance to " O   HOH Z  90 " =    2.283
peak=    3.565 closest distance to " CG  MET A 185 " =    0.997
peak=    3.564 closest distance to " CB  PRO A  90 " =    1.171
peak=    3.554 closest distance to " O   HOH Z 365 " =    2.977
peak=    3.551 closest distance to " CG  GLN A  88 " =    1.089
peak=    3.549 closest distance to " CG2AVAL A  72 " =    1.669
peak=    3.544 closest distance to " O   HOH Z 126 " =    1.688
peak=    3.541 closest distance to " CD1 ILE A  33 " =    1.767
peak=    3.539 closest distance to " O   HOH Z   1 " =    1.691
peak=    3.537 closest distance to " O   HOH Z 261 " =    1.765
peak=    3.537 closest distance to " O   HOH Z  88 " =    2.956
peak=    3.527 closest distance to " CG AARG A 275 " =    1.190
peak=    3.523 closest distance to " NH2AARG A 145 " =    1.224
peak=    3.512 closest distance to " O   HOH Z 197 " =    3.160
peak=    3.508 closest distance to " CG2 ILE A  20 " =    1.510
peak=    3.505 closest distance to " CZ  PHE A  38 " =    1.123
peak=    3.503 closest distance to " O   HOH Z  59 " =    1.904
peak=    3.502 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.498 closest distance to " CB  GLN A  89 " =    1.224
peak=    3.495 closest distance to " CB  ASN A 148 " =    1.966
peak=    3.494 closest distance to " NZ  LYS A 117 " =    3.202
peak=    3.487 closest distance to " O   HOH Z 286 " =    2.489
peak=    3.475 closest distance to " O   PHE A 192 " =    1.387
peak=    3.473 closest distance to " O   HOH Z 389 " =    1.790
peak=    3.469 closest distance to " CG AARG A 102 " =    1.130
peak=    3.468 closest distance to " CB  LEU A 143 " =    1.223
peak=    3.467 closest distance to " CB  ASN A 187 " =    1.081
peak=    3.464 closest distance to " OE2 GLU A   2 " =    1.926
peak=    3.458 closest distance to " O   HOH Z 299 " =    4.195
peak=    3.458 closest distance to " O   HOH Z 402 " =    1.387
peak=    3.457 closest distance to " O   HOH Z 280 " =    3.063
peak=    3.457 closest distance to " CB  LEU A 228 " =    1.224
peak=    3.448 closest distance to " CB  THR A  31 " =    1.565
peak=    3.447 closest distance to " NE2 HIS A 207 " =    1.186
peak=    3.442 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.437 closest distance to " CA  ARG A  36 " =    1.095
peak=    3.428 closest distance to " CG BARG A 102 " =    1.830
peak=    3.427 closest distance to " CB  THR A  82 " =    1.348
peak=    3.426 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.421 closest distance to " O   HOH Z 368 " =    3.475
peak=    3.419 closest distance to " O   HOH Z  88 " =    3.256
peak=    3.418 closest distance to " CB  TRP A 179 " =    1.415
peak=    3.418 closest distance to " O   ASP A 124 " =    1.138
peak=    3.416 closest distance to " N   ASP A 162 " =    1.191
peak=    3.414 closest distance to " CB  SER A 216 " =    0.781
peak=    3.409 closest distance to " N   SER A 135 " =    1.395
peak=    3.409 closest distance to " CG2 ILE A 120 " =    1.258
peak=    3.407 closest distance to " O   HOH Z  68 " =    2.246
peak=    3.405 closest distance to " O   HOH Z 385 " =    3.974
peak=    3.404 closest distance to " O   GLN A  88 " =    1.701
peak=    3.402 closest distance to " NH2AARG A 275 " =    3.490
peak=    3.400 closest distance to " O   HOH Z 409 " =    3.158
peak=    3.399 closest distance to " CA  LYS A 117 " =    1.236
peak=    3.399 closest distance to " O   HOH Z  97 " =    2.440
peak=    3.396 closest distance to " CB  SER A 210 " =    0.770
peak=    3.396 closest distance to " O   HOH Z 171 " =    3.991
peak=    3.390 closest distance to " O   HOH Z  97 " =    2.011
peak=    3.389 closest distance to " CB  MET A  40 " =    0.823
peak=    3.387 closest distance to " O   HOH Z 403 " =    1.606
peak=    3.384 closest distance to " CB  ASN A 173 " =    1.000
peak=    3.379 closest distance to " O   HOH Z 213 " =    1.882
peak=    3.375 closest distance to " OE2 GLU A  53 " =    1.986
peak=    3.375 closest distance to " O   HOH Z 435 " =    2.026
peak=    3.369 closest distance to " CA  ARG A 159 " =    1.191
peak=    3.369 closest distance to " O   HOH Z 130 " =    2.129
peak=    3.368 closest distance to " CB  GLU A 128 " =    0.928
peak=    3.361 closest distance to " O   HOH Z 172 " =    3.554
peak=    3.359 closest distance to " CA  ASP A 162 " =    0.999
peak=    3.356 closest distance to " O   HOH Z 145 " =    2.079
peak=    3.354 closest distance to " CB  ALA A 248 " =    1.100
peak=    3.353 closest distance to " CB  ARG A 138 " =    0.967
peak=    3.352 closest distance to " CA  LEU A 282 " =    1.196
peak=    3.346 closest distance to " O   ASN A  74 " =    1.460
peak=    3.340 closest distance to " CA  VAL A 125 " =    1.188
peak=    3.339 closest distance to " O   HOH Z 187 " =    2.315
peak=    3.338 closest distance to " CB  ASP A 298 " =    1.173
peak=    3.336 closest distance to " O   HOH Z 285 " =    2.241
peak=    3.335 closest distance to " CG1 ILE A 151 " =    1.143
peak=    3.334 closest distance to " CD BLYS A 290 " =    1.123
peak=    3.325 closest distance to " C   ALA A 299 " =    0.914
peak=    3.318 closest distance to " CG  ARG A 138 " =    1.305
peak=    3.316 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.316 closest distance to " CA  ALA A 233 " =    1.189
peak=    3.313 closest distance to " CB  SER A 273 " =    0.891
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.304
peak=    3.310 closest distance to " O   HOH Z 421 " =    2.127
peak=    3.304 closest distance to " CE3 TRP A 150 " =    1.014
peak=    3.299 closest distance to " O   HOH Z 329 " =    4.197
peak=    3.295 closest distance to " CD1 ILE A 199 " =    1.035
peak=    3.294 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.294 closest distance to " CA  PHE A 283 " =    1.173
peak=    3.293 closest distance to " O   HOH Z 419 " =    1.934
peak=    3.291 closest distance to " O   ASN A 284 " =    1.770
peak=    3.291 closest distance to " CD2 LEU A 255 " =    1.731
peak=    3.290 closest distance to " CG1 VAL A 296 " =    1.237
peak=    3.289 closest distance to " CG  GLU A  37 " =    0.896
peak=    3.289 closest distance to " O   HOH Z 148 " =    3.439
peak=    3.284 closest distance to " CG  GLN A  58 " =    1.008
peak=    3.283 closest distance to " CA  ILE A 234 " =    0.925
peak=    3.282 closest distance to " O   HOH Z 128 " =    2.182
peak=    3.279 closest distance to " O   HOH Z 322 " =    1.949
peak=    3.278 closest distance to " CA  TYR A  30 " =    1.068
peak=    3.277 closest distance to " O   HOH Z 294 " =    1.528
peak=    3.277 closest distance to " CA  ALA A 154 " =    1.056
peak=    3.274 closest distance to " CG2 THR A 221 " =    1.072
peak=    3.271 closest distance to " CB  ALA A 242 " =    0.839
peak=    3.268 closest distance to " NZ  LYS A  48 " =    1.219
peak=    3.267 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.264 closest distance to " CA  ASN A 217 " =    1.265
peak=    3.260 closest distance to " CB  HIS A 108 " =    0.801
peak=    3.253 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.252 closest distance to " O   PHE A  61 " =    1.405
peak=    3.252 closest distance to " CA  ALA A 291 " =    0.853
peak=    3.249 closest distance to " CE1 TYR A 186 " =    1.260
peak=    3.248 closest distance to " CB  VAL A 268 " =    0.832
peak=    3.248 closest distance to " CA  ALA A 295 " =    1.126
peak=    3.247 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.245 closest distance to " O   LEU A 228 " =    1.930
peak=    3.242 closest distance to " O   HOH Z  88 " =    2.736
peak=    3.241 closest distance to " CA  VAL A  41 " =    0.792
peak=    3.239 closest distance to " O   HOH Z 193 " =    1.843
peak=    3.235 closest distance to " O   HOH Z   4 " =    1.563
peak=    3.234 closest distance to " O   HOH Z  48 " =    1.648
peak=    3.232 closest distance to " O   HOH Z 263 " =    1.702
peak=    3.229 closest distance to " OG BSER A  99 " =    2.227
peak=    3.229 closest distance to " CB  GLN A 205 " =    1.124
peak=    3.226 closest distance to " CA  ASP A 191 " =    1.167
peak=    3.225 closest distance to " CB  THR A  52 " =    0.882
peak=    3.224 closest distance to " CG2 ILE A 234 " =    0.979
peak=    3.222 closest distance to " CA  MET A 105 " =    0.959
peak=    3.221 closest distance to " CB  PHE A 204 " =    0.877
peak=    3.220 closest distance to " CB  SER A  62 " =    1.080
peak=    3.219 closest distance to " O   HOH Z 303 " =    2.436
peak=    3.218 closest distance to " N   ASN A 127 " =    1.284
peak=    3.216 closest distance to " CA  ASP A 149 " =    1.136
peak=    3.214 closest distance to " CB  GLN A 278 " =    0.886
peak=    3.213 closest distance to " CD  LYS A  76 " =    1.792
peak=    3.208 closest distance to " O   HOH Z 133 " =    2.729
peak=    3.206 closest distance to " O   HOH Z  80 " =    1.586
peak=    3.206 closest distance to " CB  THR A 157 " =    1.172
peak=    3.198 closest distance to " CB  ALA A 291 " =    1.281
peak=    3.195 closest distance to " N   ARG A 156 " =    1.367
peak=    3.184 closest distance to " O   HOH Z   1 " =    1.770
peak=    3.183 closest distance to " CB  ALA A  43 " =    0.838
peak=    3.178 closest distance to " O   PRO A  90 " =    1.540
peak=    3.177 closest distance to " O   HOH Z 350 " =    1.655
peak=    3.177 closest distance to " CD1 LEU A 261 " =    1.178
peak=    3.169 closest distance to " CB  TRP A 150 " =    1.354
peak=    3.168 closest distance to " O   HOH Z 162 " =    3.847
peak=    3.160 closest distance to " O   HOH Z 238 " =    3.609
peak=    3.159 closest distance to " CB  LEU A 300 " =    0.882
peak=    3.159 closest distance to " OG  SER A 245 " =    1.615
peak=    3.158 closest distance to " O   HOH Z 193 " =    1.730
peak=    3.156 closest distance to " CZ3 TRP A 274 " =    4.567
peak=    3.152 closest distance to " O   HOH Z 215 " =    3.010
peak=    3.149 closest distance to " O   MET A 105 " =    1.768
peak=    3.148 closest distance to " CB  ALA A 114 " =    1.179
peak=    3.146 closest distance to " CB  PRO A 243 " =    1.548
peak=    3.146 closest distance to " CB  ARG A 139 " =    0.947
peak=    3.145 closest distance to " O   LYS A 290 " =    2.424
peak=    3.141 closest distance to " O   HOH Z 116 " =    3.164
peak=    3.137 closest distance to " CA  ALA A 158 " =    1.284
peak=    3.136 closest distance to " CD1 ILE A 263 " =    1.201
peak=    3.130 closest distance to " CA  ARG A 102 " =    1.173
peak=    3.130 closest distance to " O   HOH Z 329 " =    3.021
peak=    3.123 closest distance to " CD  LYS A 119 " =    1.976
peak=    3.113 closest distance to " CD1 LEU A 300 " =    1.103
peak=    3.109 closest distance to " CA  ALA A 129 " =    1.463
peak=    3.105 closest distance to " O   HOH Z 424 " =    2.505
peak=    3.105 closest distance to " CB  SER A  26 " =    1.767
peak=    3.103 closest distance to " CA  ILE A 106 " =    0.745
peak=    3.102 closest distance to " CD1 ILE A 106 " =    1.005
peak=    3.100 closest distance to " O   SER A 164 " =    1.292
peak=    3.089 closest distance to " O   HOH Z 390 " =    2.601
peak=    3.089 closest distance to " O   HOH Z 371 " =    3.338
peak=    3.085 closest distance to " CB  ALA A 227 " =    1.020
peak=    3.076 closest distance to " CA  ASN A 127 " =    1.046
peak=    3.067 closest distance to " O   HOH Z 345 " =    3.442
peak=    3.064 closest distance to " O   GLY A  75 " =    1.508
peak=    3.059 closest distance to " OG BSER A 164 " =    2.456
peak=    3.057 closest distance to " CG  LEU A 281 " =    0.990
peak=    3.055 closest distance to " O   HOH Z 425 " =    2.037
peak=    3.039 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.033 closest distance to " OE1 GLU A  37 " =    1.221
peak=    3.033 closest distance to " CA  LYS A 290 " =    1.200
peak=    3.017 closest distance to " O   HOH Z 222 " =    2.287

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.710 - 5.596
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 206
   mapped sites are within: 0.710 - 5.596

peak=   -5.150 closest distance to " CG2 VAL A 230 " =    0.710
peak=   -4.511 closest distance to " CD  ARG A  14 " =    3.154
peak=   -4.482 closest distance to " O   HOH Z 211 " =    1.032
peak=   -4.416 closest distance to " CD  ARG A 156 " =    2.069
peak=   -4.410 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.367 closest distance to " CD  GLN A  58 " =    0.983
peak=   -4.313 closest distance to " CB  PHE A 192 " =    1.949
peak=   -4.225 closest distance to " OG BSER A 134 " =    1.277
peak=   -4.183 closest distance to " CG1 VAL A 112 " =    2.683
peak=   -4.173 closest distance to " O   VAL A  67 " =    2.613
peak=   -4.153 closest distance to " OE1 GLN A 223 " =    2.236
peak=   -4.132 closest distance to " CZ2 TRP A  92 " =    2.856
peak=   -4.103 closest distance to " O   HOH Z 231 " =    2.042
peak=   -3.950 closest distance to " C   HIS A 108 " =    1.182
peak=   -3.950 closest distance to " O   HOH Z 290 " =    1.291
peak=   -3.946 closest distance to " CG2 VAL A 202 " =    2.762
peak=   -3.938 closest distance to " O   HOH Z 411 " =    5.596
peak=   -3.915 closest distance to " O   HOH Z 394 " =    1.524
peak=   -3.867 closest distance to " CB  ALA A 248 " =    2.373
peak=   -3.866 closest distance to " CG2 VAL A 296 " =    0.910
peak=   -3.864 closest distance to " O   HOH Z 166 " =    1.964
peak=   -3.849 closest distance to " CG1 VAL A 112 " =    2.792
peak=   -3.836 closest distance to " O   PRO A 198 " =    1.214
peak=   -3.836 closest distance to " CB  ALA A  43 " =    2.549
peak=   -3.827 closest distance to " CB  ALA A 248 " =    2.118
peak=   -3.822 closest distance to " CA  GLY A 241 " =    2.385
peak=   -3.814 closest distance to " CA  VAL A  67 " =    2.835
peak=   -3.802 closest distance to " CB  ALA A 161 " =    2.533
peak=   -3.792 closest distance to " CD1 LEU A 101 " =    2.363
peak=   -3.779 closest distance to " CE2 TYR A  30 " =    2.676
peak=   -3.766 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.760 closest distance to " O   HOH Z 166 " =    2.296
peak=   -3.745 closest distance to " CE BMET A  47 " =    1.533
peak=   -3.736 closest distance to " O   PRO A 163 " =    2.027
peak=   -3.725 closest distance to " O   HOH Z 185 " =    2.412
peak=   -3.709 closest distance to " N   ALA A  43 " =    2.586
peak=   -3.699 closest distance to " ND2 ASN A  45 " =    1.720
peak=   -3.687 closest distance to " O   HOH Z 359 " =    3.028
peak=   -3.670 closest distance to " N   THR A 157 " =    1.491
peak=   -3.670 closest distance to " CG2 THR A 178 " =    2.407
peak=   -3.669 closest distance to " OG  SER A  97 " =    2.364
peak=   -3.664 closest distance to " CZ3 TRP A 179 " =    1.204
peak=   -3.643 closest distance to " ND2 ASN A  45 " =    1.338
peak=   -3.640 closest distance to " CG  TRP A 266 " =    1.906
peak=   -3.637 closest distance to " CD1 LEU A 255 " =    2.890
peak=   -3.629 closest distance to " CD2 TYR A 293 " =    2.040
peak=   -3.625 closest distance to " O   HOH Z  73 " =    2.275
peak=   -3.611 closest distance to " OG  SER A  87 " =    1.415
peak=   -3.601 closest distance to " CE3 TRP A 150 " =    2.200
peak=   -3.598 closest distance to " CG1 VAL A 250 " =    2.799
peak=   -3.585 closest distance to " CB  VAL A 230 " =    1.133
peak=   -3.583 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -3.578 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.571 closest distance to " O   HOH Z  11 " =    1.878
peak=   -3.568 closest distance to " O   HOH Z 193 " =    1.337
peak=   -3.563 closest distance to " NE2 GLN A 194 " =    1.849
peak=   -3.562 closest distance to " O   HOH Z 216 " =    1.122
peak=   -3.557 closest distance to " O   HOH Z 198 " =    1.972
peak=   -3.554 closest distance to " OH  TYR A 172 " =    1.748
peak=   -3.546 closest distance to " CE  MET A 105 " =    2.382
peak=   -3.545 closest distance to " O   HOH Z 103 " =    1.811
peak=   -3.535 closest distance to " O   HOH Z 357 " =    2.038
peak=   -3.516 closest distance to " CA  GLY A 241 " =    3.175
peak=   -3.513 closest distance to " N   ALA A 248 " =    1.624
peak=   -3.506 closest distance to " CB  PRO A 280 " =    2.172
peak=   -3.501 closest distance to " ND2 ASN A 249 " =    2.406
peak=   -3.490 closest distance to " O   HOH Z 407 " =    3.004
peak=   -3.477 closest distance to " NE2 GLN A 278 " =    1.768
peak=   -3.475 closest distance to " N   THR A  52 " =    1.691
peak=   -3.474 closest distance to " CD  PRO A 213 " =    2.065
peak=   -3.470 closest distance to " O   HOH Z 138 " =    1.325
peak=   -3.470 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.470 closest distance to " N   HIS A 115 " =    2.162
peak=   -3.467 closest distance to " C   MET A 188 " =    1.467
peak=   -3.462 closest distance to " O   SER A 271 " =    2.194
peak=   -3.461 closest distance to " O   HOH Z 285 " =    2.089
peak=   -3.461 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.454 closest distance to " OE1 GLN A  88 " =    1.000
peak=   -3.451 closest distance to " O   HOH Z 114 " =    3.058
peak=   -3.450 closest distance to " OXT GLY A 302 " =    3.029
peak=   -3.447 closest distance to " O   HOH Z 140 " =    1.812
peak=   -3.445 closest distance to " CG  GLU A 277 " =    1.259
peak=   -3.440 closest distance to " C   LEU A 143 " =    1.069
peak=   -3.436 closest distance to " O   HOH Z  51 " =    1.058
peak=   -3.431 closest distance to " O   HOH Z 389 " =    2.185
peak=   -3.424 closest distance to " O   HOH Z 100 " =    1.014
peak=   -3.423 closest distance to " O   HOH Z 131 " =    4.070
peak=   -3.422 closest distance to " CD1 LEU A 228 " =    2.278
peak=   -3.421 closest distance to " O   HOH Z 243 " =    1.868
peak=   -3.415 closest distance to " CB  PRO A 163 " =    2.490
peak=   -3.414 closest distance to " C   LEU A 222 " =    0.848
peak=   -3.413 closest distance to " N   ALA A 226 " =    2.089
peak=   -3.412 closest distance to " NH2AARG A 275 " =    5.164
peak=   -3.407 closest distance to " O   HOH Z 334 " =    2.553
peak=   -3.394 closest distance to " O   HOH Z  52 " =    1.503
peak=   -3.391 closest distance to " CG2 ILE A 263 " =    2.397
peak=   -3.380 closest distance to " O   HOH Z 262 " =    2.866
peak=   -3.368 closest distance to " O   HOH Z  38 " =    1.844
peak=   -3.362 closest distance to " OG  SER A  62 " =    4.397
peak=   -3.357 closest distance to " O   GLY A  80 " =    2.545
peak=   -3.355 closest distance to " O   HOH Z 286 " =    1.832
peak=   -3.351 closest distance to " CB  HIS A  86 " =    1.124
peak=   -3.350 closest distance to " C   ALA A 158 " =    1.424
peak=   -3.348 closest distance to " O   HOH Z 345 " =    2.089
peak=   -3.346 closest distance to " CD2 PHE A  61 " =    2.016
peak=   -3.346 closest distance to " CG1 VAL A 125 " =    1.849
peak=   -3.343 closest distance to " CD1 PHE A  59 " =    2.071
peak=   -3.318 closest distance to " O   HOH Z 176 " =    0.728
peak=   -3.315 closest distance to " O   HOH Z 313 " =    1.559
peak=   -3.313 closest distance to " CA  PRO A 243 " =    2.261
peak=   -3.311 closest distance to " O   GLY A  80 " =    2.579
peak=   -3.310 closest distance to " O   HOH Z 102 " =    1.664
peak=   -3.306 closest distance to " O   HOH Z 191 " =    5.563
peak=   -3.299 closest distance to " O   ALA A  51 " =    1.308
peak=   -3.298 closest distance to " O   HOH Z 437 " =    1.640
peak=   -3.297 closest distance to " O   SER A 210 " =    1.835
peak=   -3.291 closest distance to " O   HOH Z 252 " =    3.770
peak=   -3.287 closest distance to " O   GLY A  17 " =    1.212
peak=   -3.285 closest distance to " N   ALA A 248 " =    2.393
peak=   -3.280 closest distance to " CB  ALA A 129 " =    2.496
peak=   -3.279 closest distance to " CD1 ILE A 199 " =    2.529
peak=   -3.277 closest distance to " O   HOH Z 106 " =    1.768
peak=   -3.274 closest distance to " O   HOH Z 389 " =    1.402
peak=   -3.273 closest distance to " O   HOH Z 371 " =    2.279
peak=   -3.271 closest distance to " CE2 TRP A  70 " =    2.141
peak=   -3.267 closest distance to " N   SER A   3 " =    2.065
peak=   -3.264 closest distance to " CG1 VAL A  67 " =    2.868
peak=   -3.260 closest distance to " CB  ALA A 291 " =    2.229
peak=   -3.259 closest distance to " OD1 ASP A 171 " =    1.656
peak=   -3.258 closest distance to " OH  TYR A 247 " =    2.078
peak=   -3.257 closest distance to " O   ARG A 145 " =    1.598
peak=   -3.257 closest distance to " OD1 ASN A 148 " =    1.409
peak=   -3.256 closest distance to " CG2 THR A 178 " =    2.237
peak=   -3.253 closest distance to " ND2 ASN A 252 " =    1.968
peak=   -3.250 closest distance to " CD2 LEU A 237 " =    2.862
peak=   -3.249 closest distance to " O   SER A  22 " =    2.360
peak=   -3.245 closest distance to " CG  PHE A 283 " =    2.597
peak=   -3.244 closest distance to " O   HOH Z 295 " =    1.540
peak=   -3.243 closest distance to " CB  ALA A 291 " =    2.358
peak=   -3.242 closest distance to " CD  LYS A 289 " =    2.457
peak=   -3.238 closest distance to " CG2 VAL A 189 " =    1.899
peak=   -3.236 closest distance to " NE2 GLN A  88 " =    1.136
peak=   -3.235 closest distance to " O   MET A  40 " =    2.863
peak=   -3.232 closest distance to " CG  PRO A 163 " =    2.640
peak=   -3.231 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.231 closest distance to " CD1 ILE A  33 " =    2.516
peak=   -3.230 closest distance to " SG BCYS A 201 " =    2.070
peak=   -3.229 closest distance to " NE2 GLN A  88 " =    1.990
peak=   -3.228 closest distance to " CA  GLY A 203 " =    2.508
peak=   -3.227 closest distance to " CA  SER A 135 " =    1.340
peak=   -3.224 closest distance to " CG  LEU A   5 " =    1.279
peak=   -3.220 closest distance to " O   SER A 276 " =    1.621
peak=   -3.219 closest distance to " O   HOH Z 189 " =    2.181
peak=   -3.212 closest distance to " ND2 ASN A 187 " =    1.548
peak=   -3.212 closest distance to " O   HOH Z  60 " =    1.856
peak=   -3.210 closest distance to " O   HOH Z 187 " =    1.791
peak=   -3.209 closest distance to " CE2 PHE A  61 " =    2.679
peak=   -3.206 closest distance to " N   SER A 276 " =    1.435
peak=   -3.206 closest distance to " CA  GLY A  98 " =    1.859
peak=   -3.201 closest distance to " O   HOH Z 123 " =    2.549
peak=   -3.192 closest distance to " O   ALA A 227 " =    1.580
peak=   -3.187 closest distance to " OD1 ASN A 187 " =    1.639
peak=   -3.183 closest distance to " O   HOH Z  43 " =    1.765
peak=   -3.177 closest distance to " OH  TYR A 214 " =    1.241
peak=   -3.176 closest distance to " CD  PRO A 243 " =    2.080
peak=   -3.176 closest distance to " O   ASN A 301 " =    1.683
peak=   -3.174 closest distance to " NE2 GLN A  11 " =    1.835
peak=   -3.174 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.172 closest distance to " CG1BVAL A  72 " =    2.420
peak=   -3.166 closest distance to " O   GLY A 196 " =    1.307
peak=   -3.158 closest distance to " O   HOH Z 426 " =    1.584
peak=   -3.155 closest distance to " O   HOH Z 318 " =    2.105
peak=   -3.154 closest distance to " O   ILE A 106 " =    2.121
peak=   -3.153 closest distance to " CB  TRP A  85 " =    2.610
peak=   -3.149 closest distance to " O   ALA A 161 " =    1.769
peak=   -3.148 closest distance to " O   ALA A   1 " =    1.751
peak=   -3.146 closest distance to " CB  ASP A 132 " =    2.425
peak=   -3.136 closest distance to " N   GLN A  58 " =    1.852
peak=   -3.132 closest distance to " CB  ASP A 132 " =    2.310
peak=   -3.132 closest distance to " O   HOH Z  10 " =    1.459
peak=   -3.130 closest distance to " C   ASP A 231 " =    2.420
peak=   -3.126 closest distance to " N   ASP A 171 " =    2.401
peak=   -3.126 closest distance to " O   PRO A 198 " =    1.353
peak=   -3.125 closest distance to " CE3 TRP A  70 " =    1.756
peak=   -3.125 closest distance to " O   HOH Z 350 " =    2.006
peak=   -3.119 closest distance to " CE1 PHE A 218 " =    2.659
peak=   -3.117 closest distance to " CG2 VAL A 296 " =    1.831
peak=   -3.115 closest distance to " O   ASP A  27 " =    1.950
peak=   -3.110 closest distance to " CB  ASN A 252 " =    1.824
peak=   -3.107 closest distance to " CG1 VAL A 197 " =    2.311
peak=   -3.107 closest distance to " CZ  TYR A 169 " =    1.733
peak=   -3.106 closest distance to " O   HOH Z 128 " =    2.574
peak=   -3.105 closest distance to " CB  ALA A  10 " =    2.312
peak=   -3.103 closest distance to " O   SER A 135 " =    1.374
peak=   -3.096 closest distance to " CD2 PHE A 225 " =    1.157
peak=   -3.094 closest distance to " O   HOH Z   9 " =    3.021
peak=   -3.094 closest distance to " O   HOH Z 256 " =    1.411
peak=   -3.094 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.084 closest distance to " O   HOH Z 431 " =    1.925
peak=   -3.079 closest distance to " CG  ARG A 269 " =    2.355
peak=   -3.059 closest distance to " O   HOH Z 166 " =    1.673
peak=   -3.058 closest distance to " O   HOH Z 251 " =    5.181
peak=   -3.050 closest distance to " O   HOH Z 390 " =    2.266
peak=   -3.045 closest distance to " CE  LYS A  76 " =    2.711
peak=   -3.029 closest distance to " OD1 ASN A 301 " =    1.962
peak=   -3.011 closest distance to " O   HOH Z 377 " =    0.807

================= 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    :  0.4546 0.4374   6.255459e+00   6.228402e+00
   1_bss:  0.4462 0.4266   6.248521e+00   6.215075e+00
   1_xyz:  0.3482 0.3678   6.085891e+00   6.113051e+00
   1_adp:  0.2932 0.3354   5.955463e+00   6.051470e+00
   1_occ:  0.2924 0.3359   5.954831e+00   6.053953e+00
   2_bss:  0.2879 0.3324   5.954081e+00   6.052935e+00
   2_xyz:  0.2005 0.2510   5.635107e+00   5.809247e+00
   2_adp:  0.1799 0.2299   5.539684e+00   5.727235e+00
   2_occ:  0.1799 0.2299   5.539317e+00   5.727347e+00
   3_bss:  0.1783 0.2293   5.538473e+00   5.726576e+00
   3_xyz:  0.1419 0.1875   5.335525e+00   5.544872e+00
   3_adp:  0.1321 0.1817   5.287313e+00   5.513979e+00
   3_occ:  0.1320 0.1817   5.287367e+00   5.514375e+00
   4_bss:  0.1320 0.1823   5.288262e+00   5.515477e+00
   4_xyz:  0.1178 0.1691   5.203238e+00   5.451180e+00
   4_adp:  0.1172 0.1645   5.187097e+00   5.424970e+00
   4_occ:  0.1170 0.1642   5.186092e+00   5.424158e+00
   5_bss:  0.1170 0.1642   5.185830e+00   5.423999e+00
   5_xyz:  0.1139 0.1613   5.166862e+00   5.410193e+00
   5_adp:  0.1134 0.1605   5.162829e+00   5.406459e+00
   5_occ:  0.1133 0.1605   5.162762e+00   5.406437e+00
   5_bss:  0.1133 0.1605   5.162769e+00   5.406468e+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:  0.342  18.334   6.828   7.708  11.727   0.000   0.000   0.000
   1_xyz:  0.342  18.334   6.828   7.708  11.727   0.000   0.000   0.000
   1_adp:  0.342  18.334   6.828   7.708  11.727   0.000   0.000   0.000
   1_occ:  0.342  18.334   6.828   7.708  11.727   0.000   0.000   0.000
   2_bss:  0.344  47.812   3.633   3.995   8.086   0.000   0.000   0.000
   2_xyz:  0.344  47.812   3.633   3.995   8.086   0.000   0.000   0.000
   2_adp:  0.344  47.812   3.633   3.995   8.086   0.000   0.000   0.000
   2_occ:  0.344  47.812   3.633   3.995   8.086   0.000   0.000   0.000
   3_bss:  0.322  47.812   2.574   2.990   5.372   0.000   0.000   0.000
   3_xyz:  0.322  47.812   2.574   2.990   5.372   0.000   0.000   0.000
   3_adp:  0.322  47.812   2.574   2.990   5.372   0.000   0.000   0.000
   3_occ:  0.322  47.812   2.574   2.990   5.372   0.000   0.000   0.000
   4_bss:  0.316  47.812   2.414   2.748   4.768   0.000   0.000   0.000
   4_xyz:  0.316  47.812   2.414   2.748   4.768   0.000   0.000   0.000
   4_adp:  0.316  47.812   2.414   2.748   4.768   0.000   0.000   0.000
   4_occ:  0.316  47.812   2.414   2.748   4.768   0.000   0.000   0.000
   5_bss:  0.325  53.076   2.547   2.770   4.672   0.000   0.000   0.000
   5_xyz:  0.325  53.076   2.547   2.770   4.672   0.000   0.000   0.000
   5_adp:  0.325  53.076   2.547   2.770   4.672   0.000   0.000   0.000
   5_occ:  0.325  53.076   2.547   2.770   4.672   0.000   0.000   0.000
   5_bss:  0.325  56.421  -0.763  -0.547   1.310  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.835 0.5238  0.5922    56836.564
   1_bss:  49.540 0.5261  0.7728    54616.219
   1_xyz:  39.918 0.6433  0.9121    37012.956
   1_adp:  35.120 0.7003  0.9995    30485.943
   1_occ:  35.260 0.6986  0.9960    30649.057
   2_bss:  35.002 0.7015  0.8832    30301.373
   2_xyz:  24.833 0.8130  0.9938    15915.015
   2_adp:  21.994 0.8426  1.0131    13232.558
   2_occ:  22.001 0.8425  1.0131    13228.534
   3_bss:  21.908 0.8436  0.9580    13217.960
   3_xyz:  17.515 0.8849  0.9809     8905.622
   3_adp:  16.739 0.8920  0.9773     8360.133
   3_occ:  16.745 0.8920  0.9772     8361.783
   4_bss:  16.757 0.8920  0.9652     8396.519
   4_xyz:  15.374 0.9036  0.9729     7290.464
   4_adp:  14.771 0.9089  0.9727     6941.867
   4_occ:  14.756 0.9090  0.9728     6931.724
   5_bss:  14.745 0.9091  0.9739     6932.554
   5_xyz:  14.413 0.9120  0.9740     6736.327
   5_adp:  14.309 0.9130  0.9704     6684.313
   5_occ:  14.309 0.9129  0.9703     6679.530
   5_bss:  14.310 0.9129  0.9709     6680.126
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4054e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4054e+01
   1_xyz:   1.607  0.012  0.104 18.183  0.006  4.111   1.2852e-01
   1_adp:   1.607  0.012  0.104 18.183  0.006  4.111   1.2852e-01
   1_occ:   1.607  0.012  0.104 18.183  0.006  4.111   1.2852e-01
   2_bss:   1.607  0.012  0.104 18.183  0.006  4.111   1.2852e-01
   2_xyz:   1.085  0.008  0.079 16.398  0.004  4.113   7.2318e-02
   2_adp:   1.085  0.008  0.079 16.398  0.004  4.113   7.2318e-02
   2_occ:   1.085  0.008  0.079 16.398  0.004  4.113   7.2318e-02
   3_bss:   1.085  0.008  0.079 16.398  0.004  4.113   7.2318e-02
   3_xyz:   0.996  0.007  0.077 15.914  0.003  4.125   6.2280e-02
   3_adp:   0.996  0.007  0.077 15.914  0.003  4.125   6.2280e-02
   3_occ:   0.996  0.007  0.077 15.914  0.003  4.125   6.2280e-02
   4_bss:   0.996  0.007  0.077 15.914  0.003  4.125   6.2280e-02
   4_xyz:   1.090  0.009  0.086 15.666  0.004  4.133   7.2512e-02
   4_adp:   1.090  0.009  0.086 15.666  0.004  4.133   7.2512e-02
   4_occ:   1.090  0.009  0.086 15.666  0.004  4.133   7.2512e-02
   5_bss:   1.090  0.009  0.086 15.666  0.004  4.133   7.2512e-02
   5_xyz:   1.098  0.010  0.088 15.569  0.004  4.113   7.4661e-02
   5_adp:   1.098  0.010  0.088 15.569  0.004  4.113   7.4661e-02
   5_occ:   1.098  0.010  0.088 15.569  0.004  4.113   7.4661e-02
   5_bss:   1.098  0.010  0.088 15.569  0.004  4.113   7.4661e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0079e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0079e+00
   1_xyz:  13.092  0.159  0.396 86.509  0.032  2.139   9.5400e-02
   1_adp:  13.092  0.159  0.396 86.509  0.032  2.139   9.5400e-02
   1_occ:  13.092  0.159  0.396 86.509  0.032  2.139   9.5400e-02
   2_bss:  13.092  0.159  0.396 86.509  0.032  2.139   9.5400e-02
   2_xyz:   6.053  0.073  0.284 88.429  0.034  2.325   6.1233e-02
   2_adp:   6.053  0.073  0.284 88.429  0.034  2.325   6.1233e-02
   2_occ:   6.053  0.073  0.284 88.429  0.034  2.325   6.1233e-02
   3_bss:   6.053  0.073  0.284 88.429  0.034  2.325   6.1233e-02
   3_xyz:   7.653  0.046  0.397 84.054  0.036  2.326   6.3186e-02
   3_adp:   7.653  0.046  0.397 84.054  0.036  2.326   6.3186e-02
   3_occ:   7.653  0.046  0.397 84.054  0.036  2.326   6.3186e-02
   4_bss:   7.653  0.046  0.397 84.054  0.036  2.326   6.3186e-02
   4_xyz:   6.899  0.060  0.499 82.098  0.040  2.316   5.5591e-02
   4_adp:   6.899  0.060  0.499 82.098  0.040  2.316   5.5591e-02
   4_occ:   6.899  0.060  0.499 82.098  0.040  2.316   5.5591e-02
   5_bss:   6.899  0.060  0.499 82.098  0.040  2.316   5.5591e-02
   5_xyz:   6.717  0.057  0.545 83.022  0.039  2.290   5.4866e-02
   5_adp:   6.717  0.057  0.545 83.022  0.039  2.290   5.4866e-02
   5_occ:   6.717  0.057  0.545 83.022  0.039  2.290   5.4866e-02
   5_bss:   6.717  0.057  0.545 83.022  0.039  2.290   5.4866e-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:  64.67   0.00  11.79  53.39   0.00   8.94  64.67   0.00  27.29
   1_occ:  64.67   0.00  11.79  53.39   0.00   8.94  64.67   0.00  27.29
   2_bss:  64.67   0.00  11.79  53.39   0.00   8.94  64.67   0.00  27.29
   2_xyz:  64.67   0.00  11.79  53.39   0.00   8.94  64.67   0.00  27.29
   2_adp:  63.85   0.00  11.73  54.60   0.00   8.03  63.85   0.00  31.88
   2_occ:  63.85   0.00  11.73  54.60   0.00   8.03  63.85   0.00  31.88
   3_bss:  63.85   0.00  11.73  54.60   0.00   8.03  63.85   0.00  31.88
   3_xyz:  63.85   0.00  11.73  54.60   0.00   8.03  63.85   0.00  31.88
   3_adp:  81.89   0.00  12.73  75.25   0.00   8.15  81.89   0.79  37.69
   3_occ:  81.89   0.00  12.73  75.25   0.00   8.15  81.89   0.79  37.69
   4_bss:  81.89   0.00  12.73  75.25   0.00   8.15  81.89   0.79  37.69
   4_xyz:  81.89   0.00  12.73  75.25   0.00   8.15  81.89   0.79  37.69
   4_adp:  79.24   0.00  12.10  76.48   0.00   7.84  79.24   1.01  35.30
   4_occ:  79.24   0.00  12.10  76.48   0.00   7.84  79.24   1.01  35.30
   5_bss:  79.24   0.00  12.10  76.48   0.00   7.84  79.24   1.01  35.30
   5_xyz:  79.24   0.00  12.10  76.48   0.00   7.84  79.24   1.01  35.30
   5_adp:  79.31   0.00  11.90  77.23   0.00   7.69  79.31   1.13  34.80
   5_occ:  79.31   0.00  11.90  77.23   0.00   7.69  79.31   1.13  34.80
   5_bss:  82.65   3.34  15.24  80.58   3.34  11.03  82.65   4.47  38.14
------------------------------------------------------------------------
 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:    1.247    0.015    0.406
   1_adp:    1.247    0.015    0.406
   1_occ:    1.247    0.015    0.406
   2_bss:    1.247    0.015    0.406
   2_xyz:    1.662    0.036    0.541
   2_adp:    1.662    0.036    0.541
   2_occ:    1.662    0.036    0.541
   3_bss:    1.662    0.036    0.541
   3_xyz:    1.717    0.029    0.589
   3_adp:    1.717    0.029    0.589
   3_occ:    1.717    0.029    0.589
   4_bss:    1.717    0.029    0.589
   4_xyz:    1.813    0.043    0.614
   4_adp:    1.813    0.043    0.614
   4_occ:    1.813    0.043    0.614
   5_bss:    1.813    0.043    0.614
   5_xyz:    1.781    0.035    0.622
   5_adp:    1.781    0.035    0.622
   5_occ:    1.781    0.035    0.622
   5_bss:    1.781    0.035    0.622
------------------------------------------------------------------------

CPU time actual refinement: 324.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/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_658/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_658/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.97 
  Macro-tasks:
    bulk solvent and scale       = 40.77  
    individual site refinement   = 129.88 
    weights calculation          = 31.28  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.57 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 98.42  
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 108.72 
    fmodel                         = 7.35   
    r_factors                      = 0.25   
    phase_errors                   = 10.90  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 237.17 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.594 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    647 calls, 98.11 s
gradients_fft:          592 calls, 95.65 s

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

# Date 2008-01-16 Time 02:07:41 PST -0800 (1200478061.48 s)
Start R-work = 0.4546, R-free = 0.4374 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.4462, R-free = 0.4266
Final R-work = 0.1133, R-free = 0.1605