# Date 2008-01-16 Time 02:02:40 PST -0800 (1200477760.28 s)
#phil __OFF__

Command line arguments: "../669.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25919
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 669

-------------------------------------------------------------------------------
  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, 46.93, 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: 3.25, 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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00033
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964215

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0003

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, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00033
Completeness in resolution range: 0.967215
Completeness with d_max=infinity: 0.964215

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2798 [2138/2162]  1920   218  10.2%
  bin  2:  4.2798 -  3.4099 [2036/2056]  1838   198   9.7%
  bin  3:  3.4099 -  2.9827 [2020/2039]  1817   203  10.0%
  bin  4:  2.9827 -  2.7117 [1980/2010]  1776   204  10.3%
  bin  5:  2.7117 -  2.5183 [2002/2021]  1806   196   9.8%
  bin  6:  2.5183 -  2.3704 [1975/2000]  1776   199  10.1%
  bin  7:  2.3704 -  2.2521 [1962/1990]  1768   194   9.9%
  bin  8:  2.2521 -  2.1544 [1962/1998]  1766   196  10.0%
  bin  9:  2.1544 -  2.0717 [1947/1989]  1755   192   9.9%
  bin 10:  2.0717 -  2.0003 [1567/1988]  1408   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/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:
        1.64 -     2.29: 10
        2.29 -     2.94: 1596
        2.94 -     3.59: 4414
        3.59 -     4.25: 9091
        4.25 -     4.90: 12900
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.636 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.824 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.830 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.889 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28006 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_669/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/model_refine_001.geo

CPU time processing inputs: 9.05


============================ 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 46.93 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: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4480   r_free= 0.4343   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.248489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.3718 0.3368      6.5623      6.4454|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.3420 0.3756      6.6816      6.8046|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.3993 0.3704      6.6145      6.5822|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.4389 0.4050      6.4935      6.3968|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.4700 0.4569      6.3377      6.3431|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.4647 0.5247      6.2487      6.1945|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.4870 0.4870      6.2176      6.1747|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.5061 0.4483      6.1729      6.1328|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.4837 0.5120      6.0965       6.126|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.5138 0.4334      6.1242      6.0314|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.4934 0.5010      6.0176      6.0671|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.5128 0.4675      5.9662      5.9936|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.4963 0.4980      5.8855      5.8424|
| 14:  2.0502 -  2.0003 0.71    903  106 0.5166 0.4544       5.881      5.7197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7732  1389   152  0.74  30.35   0.80     0.77      57005.90|
|  2:  4.7732 -  3.8088  1318   152  0.76  29.60   0.90     0.81      80510.88|
|  3:  3.8088 -  3.3333  1300   142  0.69  36.51   0.85     0.78      85356.20|
|  4:  3.3333 -  3.0312  1308   142  0.61  43.24   0.81     0.67      77660.37|
|  5:  3.0312 -  2.8154  1278   144  0.51  51.01   0.77     0.58      68158.53|
|  6:  2.8154 -  2.6504  1286   143  0.47  54.43   0.73     0.52      63276.66|
|  7:  2.6504 -  2.5183  1278   144  0.45  55.97   0.75     0.51      57923.91|
|  8:  2.5183 -  2.4091  1269   138  0.47  54.67   0.73     0.53      49997.93|
|  9:  2.4091 -  2.3167  1268   143  0.49  52.58   0.74     0.56      44566.93|
| 10:  2.3167 -  2.2371  1275   142  0.48  53.45   0.75     0.56      39832.28|
| 11:  2.2371 -  2.1673  1248   134  0.46  55.28   0.75     0.54      38994.64|
| 12:  2.1673 -  2.1055  1245   141  0.44  56.80   0.76     0.54      36173.10|
| 13:  2.1055 -  2.0502  1265   136  0.45  56.28   0.74     0.53      30827.58|
| 14:  2.0502 -  2.0003   903   106  0.51  51.70   0.73     0.52      22549.58|
|alpha:            min =        0.51 max =            0.81 mean =         0.60|
|beta:             min =    22549.58 max =        85356.20 mean =     54687.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.42|
|phase err.(test): min =        0.00 max =           89.92 mean =        48.69|
|-----------------------------------------------------------------------------|

============================== 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 = 9.141441              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.269   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.711838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.204   (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:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 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:     2578 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3889 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5037 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6487 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7668 |
|-----------------------------------------------------------------------------|
|-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 |       54.182 |
| 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 |       1.737 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    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 = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4557   r_free= 0.4368   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.254331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4388   r_free= 0.4218   ksol= 0.34   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.80,7.44,11.84,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.240882                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.323437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.994   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4388      final r-factor (work) = 0.3384          |
| start r-factor (free) = 0.4218      final r-factor (free) = 0.3575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.2139 = 8.32 * 0.50 * 6.2550 + 1.00 * 54.1825                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5399 = 8.32 * 0.50 * 6.1063 + 1.00 * 0.1274                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3384      final r-factor (work) = 0.2811          |
| start r-factor (free) = 0.3575      final r-factor (free) = 0.3207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3326 = 0.71 * 1.00 * 6.1063 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2288 = 0.71 * 1.00 * 5.9626 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.49   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    63.49   11.36    None  None   None       |
|    Sol.    : 438    0      0.00    63.49   27.04    None  None   None       |
|    Mac.    : 2385   0      0.00    51.68   8.48     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 -   6.349: 1185   |   5:    31.745 -  38.094:  100        |
|      1:     6.349 -  12.698:  757   |   6:    38.094 -  44.443:   54        |
|      2:    12.698 -  19.047:  352   |   7:    44.443 -  50.792:   29        |
|      3:    19.047 -  25.396:  195   |   8:    50.792 -  57.141:   15        |
|      4:    25.396 -  31.745:  130   |   9:    57.141 -  63.490:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2811 r_free = 0.3207             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2805 r_free = 0.3216             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2805   r_free= 0.3216   ksol= 0.34   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.80,7.44,11.84,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.919967                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2763   r_free= 0.3169   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,4.00,8.16,0.00,0.00,0.00); trace/3= 5.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.919273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.045668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.063   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365354              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2763      final r-factor (work) = 0.2043          |
| start r-factor (free) = 0.3169      final r-factor (free) = 0.2507          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2103 = 3.05 * 0.50 * 5.9648 + 1.00 * 0.1269                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8523 = 3.05 * 0.50 * 5.7701 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2043      final r-factor (work) = 0.1866          |
| start r-factor (free) = 0.2507      final r-factor (free) = 0.2338          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1208 = 0.37 * 1.00 * 5.7701 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0581 = 0.37 * 1.00 * 5.6033 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.47   11.63    None  None   None       |
|    all(noH): 2823   0      0.00    64.47   11.63    None  None   None       |
|    Sol.    : 438    0      0.00    64.47   32.06    None  None   None       |
|    Mac.    : 2385   0      0.00    57.26   7.88     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 -   6.447: 1332   |   5:    32.235 -  38.683:   94        |
|      1:     6.447 -  12.894:  725   |   6:    38.683 -  45.130:   99        |
|      2:    12.894 -  19.341:  256   |   7:    45.130 -  51.577:   39        |
|      3:    19.341 -  25.788:  132   |   8:    51.577 -  58.024:   32        |
|      4:    25.788 -  32.235:  105   |   9:    58.024 -  64.471:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1866 r_free = 0.2338             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1865 r_free = 0.2341             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1865   r_free= 0.2341   ksol= 0.33   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,4.00,8.16,0.00,0.00,0.00); trace/3= 5.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.574552                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1850   r_free= 0.2343   ksol= 0.34   Bsol= 62.94   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,3.13,5.52,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.574256                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.439483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.509  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.541  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1850      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2343      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9071 = 2.44 * 0.50 * 5.6091 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7226 = 2.44 * 0.50 * 5.4592 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1349          |
| start r-factor (free) = 0.1876      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8815 = 0.34 * 1.00 * 5.4592 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8320 = 0.34 * 1.00 * 5.3135 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.80   11.80    None  None   None       |
|    all(noH): 2823   0      0.00    69.80   11.80    None  None   None       |
|    Sol.    : 438    0      0.79    69.80   34.13    None  None   None       |
|    Mac.    : 2385   0      0.00    63.64   7.70     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 -   6.980: 1466   |   5:    34.900 -  41.880:   88        |
|      1:     6.980 -  13.960:  686   |   6:    41.880 -  48.859:   96        |
|      2:    13.960 -  20.940:  197   |   7:    48.859 -  55.839:   51        |
|      3:    20.940 -  27.920:   98   |   8:    55.839 -  62.819:   25        |
|      4:    27.920 -  34.900:  110   |   9:    62.819 -  69.799:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1349 r_free = 0.1778             target_work(ml) = 5.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1348 r_free = 0.1777             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1348   r_free= 0.1777   ksol= 0.34   Bsol= 62.94   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,3.13,5.52,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.290120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1780   ksol= 0.34   Bsol= 62.94   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.87,4.74,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.290455                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.565562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.886  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.337387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.827  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1346      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2232 = 1.57 * 0.50 * 5.3138 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1755 = 1.57 * 0.50 * 5.2612 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7864 = 0.34 * 1.00 * 5.2612 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8107 = 0.34 * 1.00 * 5.2322 + 1.00 * 0.0454                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.29   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    72.29   11.73    None  None   None       |
|    Sol.    : 438    0      0.82    72.29   34.15    None  None   None       |
|    Mac.    : 2385   0      0.00    67.40   7.61     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 -   7.229: 1542   |   5:    36.147 -  43.376:   85        |
|      1:     7.229 -  14.459:  646   |   6:    43.376 -  50.606:   87        |
|      2:    14.459 -  21.688:  184   |   7:    50.606 -  57.835:   50        |
|      3:    21.688 -  28.918:   96   |   8:    57.835 -  65.065:   17        |
|      4:    28.918 -  36.147:  109   |   9:    65.065 -  72.294:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1678             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1677             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1677   ksol= 0.34   Bsol= 62.94   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.87,4.74,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1678   ksol= 0.33   Bsol= 57.08   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.93,4.67,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228482                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.731548              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.269  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.396756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.633   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1678      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5870 = 1.73 * 0.50 * 5.2320 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5768 = 1.73 * 0.50 * 5.2116 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.7176 = 3.40 * 1.00 * 5.2116 + 1.00 * 0.0149                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6621 = 3.40 * 1.00 * 5.1944 + 1.00 * 0.0179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.63   12.29    None  None   None       |
|    all(noH): 2823   0      0.00    87.63   12.29    None  None   None       |
|    Sol.    : 438    0      0.45    87.63   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    83.14   7.79     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 -   8.763: 1738   |   5:    43.816 -  52.580:   89        |
|      1:     8.763 -  17.527:  526   |   6:    52.580 -  61.343:   64        |
|      2:    17.527 -  26.290:  153   |   7:    61.343 -  70.106:   34        |
|      3:    26.290 -  35.053:  118   |   8:    70.106 -  78.870:   13        |
|      4:    35.053 -  43.816:   85   |   9:    78.870 -  87.633:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1185 r_free = 0.1659             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1659             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1659   ksol= 0.33   Bsol= 57.08   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,2.93,4.67,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.199082                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.1037 0.1344      5.4249        5.55|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.0865 0.1148      5.4557       5.661|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.1102 0.1503      5.5145       5.855|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.1266 0.1767      5.4922      5.6767|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.1404 0.1701      5.3893      5.5655|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.1295 0.2299      5.2745      5.6094|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.1365 0.1658      5.2455      5.3828|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.1276 0.1761      5.1637      5.4056|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.1286 0.2016       5.115      5.3887|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.1203 0.1663      5.0203      5.2262|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.1215 0.1780      4.9961      5.2686|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.1204 0.1897      4.9246      5.3455|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.1179 0.1752      4.8517      5.0555|
| 14:  2.0502 -  2.0003 0.71    903  106 0.1088 0.1764       4.722        4.99|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7732  1389   152  0.94   9.79   0.97     0.94       7923.26|
|  2:  4.7732 -  3.8088  1318   152  0.95   8.20   1.01     0.99       9483.73|
|  3:  3.8088 -  3.3333  1300   142  0.93  11.40   1.02     1.02      10917.20|
|  4:  3.3333 -  3.0312  1308   142  0.92  14.08   1.00     0.99      11051.56|
|  5:  3.0312 -  2.8154  1278   144  0.90  16.55   0.99     0.96       9225.23|
|  6:  2.8154 -  2.6504  1286   143  0.89  17.26   0.98     0.95       8124.54|
|  7:  2.6504 -  2.5183  1278   144  0.90  16.81   0.98     0.94       7131.38|
|  8:  2.5183 -  2.4091  1269   138  0.89  16.90   0.98     0.95       6441.25|
|  9:  2.4091 -  2.3167  1268   143  0.90  16.84   1.00     0.96       6019.87|
| 10:  2.3167 -  2.2371  1275   142  0.89  16.93   0.99     0.94       4892.57|
| 11:  2.2371 -  2.1673  1248   134  0.89  16.98   0.99     0.94       4919.59|
| 12:  2.1673 -  2.1055  1245   141  0.90  16.66   0.99     0.97       4309.09|
| 13:  2.1055 -  2.0502  1265   136  0.90  16.92   0.98     0.95       3797.94|
| 14:  2.0502 -  2.0003   903   106  0.91  15.16   0.96     0.92       2792.95|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2792.95 max =        11051.56 mean =      7055.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.97|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1657   ksol= 0.33   Bsol= 60.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.45,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.199230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1657   ksol= 0.33   Bsol= 60.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.45,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.199230                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7732 0.99   1389  152 0.1038 0.1345      5.4257      5.5512|
|  2:  4.7732 -  3.8088 0.99   1318  152 0.0866 0.1149      5.4562      5.6611|
|  3:  3.8088 -  3.3333 0.99   1300  142 0.1102 0.1504      5.5147      5.8558|
|  4:  3.3333 -  3.0312 0.99   1308  142 0.1266 0.1767      5.4923      5.6769|
|  5:  3.0312 -  2.8154 0.99   1278  144 0.1404 0.1700      5.3893      5.5651|
|  6:  2.8154 -  2.6504 0.99   1286  143 0.1295 0.2301      5.2745      5.6098|
|  7:  2.6504 -  2.5183 0.99   1278  144 0.1365 0.1659      5.2456      5.3829|
|  8:  2.5183 -  2.4091 0.98   1269  138 0.1276 0.1761      5.1641      5.4057|
|  9:  2.4091 -  2.3167 0.98   1268  143 0.1286 0.2018       5.115       5.389|
| 10:  2.3167 -  2.2371 1.00   1275  142 0.1203 0.1664      5.0202      5.2262|
| 11:  2.2371 -  2.1673 0.97   1248  134 0.1215 0.1779      4.9959      5.2679|
| 12:  2.1673 -  2.1055 0.98   1245  141 0.1205 0.1895      4.9244      5.3447|
| 13:  2.1055 -  2.0502 1.00   1265  136 0.1179 0.1755      4.8517      5.0564|
| 14:  2.0502 -  2.0003 0.71    903  106 0.1089 0.1763      4.7224      4.9897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7732  1389   152  0.94   9.80   0.97     0.95       7940.69|
|  2:  4.7732 -  3.8088  1318   152  0.95   8.20   1.01     0.99       9497.08|
|  3:  3.8088 -  3.3333  1300   142  0.93  11.41   1.03     1.02      10925.93|
|  4:  3.3333 -  3.0312  1308   142  0.92  14.09   1.01     0.99      11054.25|
|  5:  3.0312 -  2.8154  1278   144  0.90  16.55   1.00     0.97       9227.96|
|  6:  2.8154 -  2.6504  1286   143  0.89  17.27   0.98     0.95       8124.17|
|  7:  2.6504 -  2.5183  1278   144  0.90  16.82   0.98     0.95       7135.43|
|  8:  2.5183 -  2.4091  1269   138  0.89  16.91   0.99     0.96       6445.84|
|  9:  2.4091 -  2.3167  1268   143  0.90  16.85   1.01     0.97       6024.25|
| 10:  2.3167 -  2.2371  1275   142  0.89  16.92   1.00     0.95       4889.18|
| 11:  2.2371 -  2.1673  1248   134  0.89  16.97   1.00     0.95       4915.15|
| 12:  2.1673 -  2.1055  1245   141  0.90  16.65   1.00     0.98       4305.35|
| 13:  2.1055 -  2.0502  1265   136  0.90  16.91   0.99     0.96       3797.55|
| 14:  2.0502 -  2.0003   903   106  0.91  15.17   0.97     0.93       2794.71|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2794.71 max =        11054.25 mean =      7058.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.97|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.097)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.60    91.24   15.90    None  None   None       |
|    all(noH): 2823   0      3.60    91.24   15.90    None  None   None       |
|    Sol.    : 438    0      4.05    91.24   40.43    None  None   None       |
|    Mac.    : 2385   0      3.60    86.75   11.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.605 -  12.368: 1738   |   5:    47.421 -  56.184:   89        |
|      1:    12.368 -  21.131:  526   |   6:    56.184 -  64.948:   64        |
|      2:    21.131 -  29.895:  153   |   7:    64.948 -  73.711:   34        |
|      3:    29.895 -  38.658:  118   |   8:    73.711 -  82.474:   13        |
|      4:    38.658 -  47.421:   85   |   9:    82.474 -  91.238:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.204 - 4.531
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 298 from: 307
   mapped sites are within: 0.716 - 4.531

peak=   10.608 closest distance to " CB  VAL A 230 " =    1.441
peak=    6.378 closest distance to " CG  ARG A 138 " =    1.082
peak=    5.781 closest distance to " NH1 ARG A 138 " =    0.999
peak=    5.724 closest distance to " CD2 LEU A   5 " =    1.147
peak=    5.709 closest distance to " CG  LEU A   5 " =    1.176
peak=    5.596 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.589 closest distance to " CG2 VAL A 296 " =    1.082
peak=    5.435 closest distance to " CG  PRO A  54 " =    1.362
peak=    5.352 closest distance to " CG  LEU A 228 " =    1.162
peak=    5.248 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.166 closest distance to " O   HOH Z 142 " =    1.962
peak=    5.126 closest distance to " NE2 GLN A  11 " =    1.083
peak=    5.040 closest distance to " CB  VAL A 296 " =    1.074
peak=    4.818 closest distance to " CD1AILE A 234 " =    1.011
peak=    4.804 closest distance to " CG  PRO A 198 " =    1.237
peak=    4.735 closest distance to " O   HOH Z 248 " =    1.310
peak=    4.669 closest distance to " CB  GLN A 183 " =    1.258
peak=    4.645 closest distance to " CB  PRO A  54 " =    0.982
peak=    4.641 closest distance to " CG1 VAL A 296 " =    1.215
peak=    4.594 closest distance to " CG  PRO A 243 " =    1.125
peak=    4.540 closest distance to " CZ  PHE A 218 " =    1.146
peak=    4.529 closest distance to " O   HOH Z 232 " =    2.316
peak=    4.519 closest distance to " O   HOH Z 265 " =    2.248
peak=    4.493 closest distance to " CB  ARG A 275 " =    0.962
peak=    4.328 closest distance to " CB  ASN A 148 " =    1.446
peak=    4.325 closest distance to " O   SER A  87 " =    2.418
peak=    4.325 closest distance to " CB  VAL A 230 " =    1.177
peak=    4.298 closest distance to " O   HOH Z 369 " =    2.119
peak=    4.290 closest distance to " O   HOH Z 427 " =    3.002
peak=    4.276 closest distance to " O   HOH Z 425 " =    1.455
peak=    4.258 closest distance to " O   HOH Z 313 " =    1.913
peak=    4.255 closest distance to " CB  SER A  63 " =    1.151
peak=    4.233 closest distance to " O   HOH Z   9 " =    1.400
peak=    4.232 closest distance to " CZ3 TRP A 266 " =    1.175
peak=    4.217 closest distance to " CB  ASN A 142 " =    1.126
peak=    4.207 closest distance to " O   HOH Z  78 " =    1.704
peak=    4.190 closest distance to " O   HOH Z 298 " =    1.843
peak=    4.189 closest distance to " O   HOH Z 126 " =    2.033
peak=    4.184 closest distance to " CB  ARG A 190 " =    1.618
peak=    4.152 closest distance to " O   HOH Z 303 " =    2.067
peak=    4.146 closest distance to " CD2 LEU A 228 " =    1.311
peak=    4.126 closest distance to " NH2AARG A 145 " =    1.127
peak=    4.120 closest distance to " O   HOH Z 402 " =    1.408
peak=    4.100 closest distance to " O   HOH Z 346 " =    1.592
peak=    4.093 closest distance to " O   HOH Z 411 " =    3.815
peak=    4.085 closest distance to " O   PRO A 198 " =    1.549
peak=    4.083 closest distance to " CA  ALA A  51 " =    0.964
peak=    4.061 closest distance to " CD  ARG A 159 " =    0.716
peak=    4.058 closest distance to " O   HOH Z  92 " =    2.274
peak=    4.044 closest distance to " CB  ARG A  79 " =    1.438
peak=    4.043 closest distance to " CB  GLU A 277 " =    3.691
peak=    4.032 closest distance to " CA  ARG A 195 " =    1.226
peak=    4.032 closest distance to " CB  ASN A  39 " =    0.958
peak=    4.022 closest distance to " O   HOH Z 368 " =    2.270
peak=    4.010 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.007 closest distance to " O   HOH Z 287 " =    2.022
peak=    4.003 closest distance to " O   HOH Z   4 " =    1.481
peak=    3.984 closest distance to " CG  PRO A 213 " =    1.178
peak=    3.977 closest distance to " CG  MET A 185 " =    1.258
peak=    3.975 closest distance to " CB  ASP A 124 " =    0.810
peak=    3.969 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.953 closest distance to " CB AVAL A  41 " =    1.237
peak=    3.953 closest distance to " CD2 TRP A 179 " =    1.288
peak=    3.951 closest distance to " O   HOH Z 290 " =    1.096
peak=    3.925 closest distance to " O   HOH Z 251 " =    1.577
peak=    3.902 closest distance to " NH1AARG A 145 " =    1.160
peak=    3.897 closest distance to " O   HOH Z 261 " =    1.957
peak=    3.896 closest distance to " O   HOH Z  43 " =    2.070
peak=    3.887 closest distance to " ND2 ASN A 187 " =    1.578
peak=    3.880 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.871 closest distance to " CB  VAL A 265 " =    1.260
peak=    3.862 closest distance to " CG2 VAL A 257 " =    0.865
peak=    3.854 closest distance to " O   HOH Z 359 " =    1.535
peak=    3.843 closest distance to " CB  TRP A 266 " =    1.050
peak=    3.828 closest distance to " ND2 ASN A 249 " =    0.882
peak=    3.815 closest distance to " O   HOH Z 316 " =    3.119
peak=    3.793 closest distance to " CB  GLN A  89 " =    1.228
peak=    3.792 closest distance to " O   HOH Z 214 " =    2.485
peak=    3.786 closest distance to " O   HOH Z 188 " =    2.897
peak=    3.781 closest distance to " O  BHOH Z 338 " =    2.347
peak=    3.780 closest distance to " CA  VAL A 125 " =    1.213
peak=    3.778 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.776 closest distance to " CG2 ILE A 234 " =    0.911
peak=    3.763 closest distance to " O   HOH Z 126 " =    1.593
peak=    3.759 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.756 closest distance to " O   HOH Z 406 " =    1.553
peak=    3.755 closest distance to " CD  LYS A 166 " =    1.349
peak=    3.739 closest distance to " O   HOH Z 273 " =    3.023
peak=    3.732 closest distance to " CB  SER A   3 " =    1.333
peak=    3.712 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.711 closest distance to " O   HOH Z 365 " =    2.937
peak=    3.701 closest distance to " CG  LEU A   5 " =    0.731
peak=    3.700 closest distance to " O   HOH Z  80 " =    1.736
peak=    3.700 closest distance to " O   HOH Z 353 " =    2.643
peak=    3.696 closest distance to " CB  TRP A 179 " =    1.457
peak=    3.689 closest distance to " CB  ASN A 110 " =    1.191
peak=    3.681 closest distance to " CG AARG A 275 " =    1.181
peak=    3.680 closest distance to " O   HOH Z   3 " =    1.935
peak=    3.677 closest distance to " OG BSER A 164 " =    2.268
peak=    3.675 closest distance to " CB  VAL A 202 " =    1.582
peak=    3.671 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.668 closest distance to " CD  ARG A 138 " =    1.265
peak=    3.665 closest distance to " CG BARG A 102 " =    1.828
peak=    3.663 closest distance to " CB  GLU A 128 " =    1.018
peak=    3.660 closest distance to " O   HOH Z  40 " =    1.793
peak=    3.655 closest distance to " O   HOH Z 261 " =    1.562
peak=    3.646 closest distance to " CG  ARG A  66 " =    2.667
peak=    3.644 closest distance to " O   HOH Z 272 " =    1.825
peak=    3.637 closest distance to " CB  LYS A 117 " =    1.228
peak=    3.631 closest distance to " O   HOH Z 234 " =    3.597
peak=    3.625 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.619 closest distance to " CA  PHE A 283 " =    1.085
peak=    3.618 closest distance to " CB  THR A  31 " =    1.520
peak=    3.616 closest distance to " N   ASN A  39 " =    1.199
peak=    3.608 closest distance to " O   HOH Z 130 " =    0.983
peak=    3.606 closest distance to " O   HOH Z 209 " =    2.321
peak=    3.596 closest distance to " CG1 ILE A  49 " =    1.667
peak=    3.594 closest distance to " O   HOH Z 158 " =    3.145
peak=    3.591 closest distance to " CA  ALA A 291 " =    0.872
peak=    3.588 closest distance to " O   HOH Z  88 " =    3.689
peak=    3.576 closest distance to " O   HOH Z  61 " =    1.760
peak=    3.572 closest distance to " O   HOH Z 172 " =    3.683
peak=    3.569 closest distance to " O   HOH Z  59 " =    2.324
peak=    3.565 closest distance to " CG2AVAL A 121 " =    2.443
peak=    3.560 closest distance to " OE1 GLN A  55 " =    1.463
peak=    3.560 closest distance to " CB  THR A  82 " =    1.342
peak=    3.554 closest distance to " CG  GLN A  58 " =    0.935
peak=    3.553 closest distance to " CB  ASN A 173 " =    1.072
peak=    3.553 closest distance to " O   HOH Z  63 " =    1.762
peak=    3.552 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.538 closest distance to " O   HOH Z 385 " =    3.884
peak=    3.530 closest distance to " O   HOH Z 371 " =    2.837
peak=    3.528 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.524 closest distance to " CB  GLU A 152 " =    1.164
peak=    3.524 closest distance to " CA  ASP A 162 " =    0.989
peak=    3.522 closest distance to " CA  ALA A 295 " =    1.091
peak=    3.521 closest distance to " CB  SER A 273 " =    0.907
peak=    3.520 closest distance to " CD1 ILE A 199 " =    0.849
peak=    3.515 closest distance to " CB  PRO A 243 " =    1.430
peak=    3.510 closest distance to " CB  ASN A 187 " =    1.197
peak=    3.506 closest distance to " N   PHE A 130 " =    1.293
peak=    3.506 closest distance to " N   ALA A 256 " =    1.115
peak=    3.503 closest distance to " OD1 ASN A  69 " =    2.548
peak=    3.500 closest distance to " O   HOH Z 280 " =    3.018
peak=    3.498 closest distance to " CA  ARG A 139 " =    1.083
peak=    3.497 closest distance to " O   HOH Z 337 " =    1.733
peak=    3.490 closest distance to " CA  SER A  87 " =    1.011
peak=    3.489 closest distance to " CD BLYS A 290 " =    1.020
peak=    3.486 closest distance to " O   HOH Z 368 " =    3.429
peak=    3.481 closest distance to " CB  PRO A  90 " =    1.105
peak=    3.480 closest distance to " CD1 LEU A 101 " =    1.393
peak=    3.478 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.470 closest distance to " CD1 ILE A  33 " =    1.769
peak=    3.469 closest distance to " O   HOH Z 258 " =    1.907
peak=    3.449 closest distance to " CB  ALA A  43 " =    0.844
peak=    3.447 closest distance to " CA  GLY A 211 " =    1.397
peak=    3.446 closest distance to " CB  GLU A  46 " =    0.932
peak=    3.441 closest distance to " OG  SER A 276 " =    1.278
peak=    3.440 closest distance to " CB  ALA A   9 " =    1.647
peak=    3.438 closest distance to " CB  MET A  40 " =    0.860
peak=    3.438 closest distance to " O   ASP A 124 " =    1.034
peak=    3.438 closest distance to " O   ASP A 200 " =    1.647
peak=    3.424 closest distance to " CA  GLY A 267 " =    0.750
peak=    3.424 closest distance to " CA  ALA A 154 " =    1.095
peak=    3.423 closest distance to " CB  LEU A 143 " =    1.263
peak=    3.415 closest distance to " CA  ALA A 160 " =    1.005
peak=    3.415 closest distance to " CB  ASN A 215 " =    1.170
peak=    3.413 closest distance to " O  BHOH Z  74 " =    1.218
peak=    3.412 closest distance to " CB  ASP A 140 " =    1.192
peak=    3.411 closest distance to " CA  ASN A 217 " =    1.242
peak=    3.410 closest distance to " O   THR A 251 " =    1.130
peak=    3.404 closest distance to " CA  LYS A 117 " =    1.280
peak=    3.398 closest distance to " N   GLY A 133 " =    3.844
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.384 closest distance to " CB  SER A 212 " =    1.311
peak=    3.381 closest distance to " CA  ILE A 234 " =    0.926
peak=    3.381 closest distance to " CD  LYS A  76 " =    2.041
peak=    3.380 closest distance to " CA  LEU A 282 " =    1.158
peak=    3.378 closest distance to " O   HOH Z  68 " =    2.214
peak=    3.378 closest distance to " O   HOH Z 250 " =    1.343
peak=    3.372 closest distance to " O   PHE A 192 " =    1.424
peak=    3.370 closest distance to " CA  MET A 105 " =    0.958
peak=    3.368 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.365 closest distance to " O   ASN A  74 " =    1.456
peak=    3.365 closest distance to " CA  ASN A 215 " =    1.145
peak=    3.362 closest distance to " O   HOH Z 147 " =    1.694
peak=    3.362 closest distance to " CB  SER A 216 " =    0.874
peak=    3.357 closest distance to " O   HOH Z 285 " =    2.392
peak=    3.356 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.355 closest distance to " CB  ALA A 248 " =    1.435
peak=    3.354 closest distance to " CB  TRP A 150 " =    1.369
peak=    3.354 closest distance to " CG1 ILE A 151 " =    1.130
peak=    3.352 closest distance to " CB  SER A  26 " =    1.783
peak=    3.350 closest distance to " NZ  LYS A 117 " =    3.165
peak=    3.349 closest distance to " O   HOH Z 180 " =    2.171
peak=    3.347 closest distance to " O   HOH Z 187 " =    2.301
peak=    3.346 closest distance to " O   HOH Z 423 " =    1.692
peak=    3.343 closest distance to " O   HOH Z 247 " =    1.324
peak=    3.341 closest distance to " CA  ASN A  74 " =    1.255
peak=    3.341 closest distance to " CG AARG A 102 " =    1.138
peak=    3.336 closest distance to " CA  TYR A 116 " =    1.468
peak=    3.334 closest distance to " CA  ALA A  21 " =    1.082
peak=    3.333 closest distance to " CE3 TRP A 150 " =    1.064
peak=    3.326 closest distance to " O   HOH Z 329 " =    4.246
peak=    3.326 closest distance to " O   HOH Z 392 " =    3.051
peak=    3.324 closest distance to " CA  ASP A 191 " =    1.249
peak=    3.324 closest distance to " CD  ARG A  66 " =    2.554
peak=    3.323 closest distance to " CA  THR A 264 " =    0.754
peak=    3.317 closest distance to " CB  THR A  52 " =    0.873
peak=    3.308 closest distance to " O   HOH Z  76 " =    1.033
peak=    3.306 closest distance to " O   HOH Z 193 " =    1.764
peak=    3.304 closest distance to " CB  ALA A 227 " =    1.009
peak=    3.303 closest distance to " N   ASP A 162 " =    1.243
peak=    3.303 closest distance to " CE  LYS A  48 " =    1.104
peak=    3.302 closest distance to " O   HOH Z 403 " =    1.638
peak=    3.301 closest distance to " O   HOH Z 263 " =    1.641
peak=    3.300 closest distance to " O   HOH Z   1 " =    1.689
peak=    3.293 closest distance to " CG  MET A 185 " =    0.965
peak=    3.292 closest distance to " CG2AVAL A  72 " =    1.756
peak=    3.289 closest distance to " O   ASN A 284 " =    1.666
peak=    3.288 closest distance to " CG2 THR A 221 " =    1.187
peak=    3.288 closest distance to " O   GLN A  88 " =    1.596
peak=    3.285 closest distance to " O   THR A 182 " =    1.396
peak=    3.285 closest distance to " O   HOH Z  97 " =    2.463
peak=    3.284 closest distance to " O   HOH Z 102 " =    1.302
peak=    3.284 closest distance to " CB  VAL A 268 " =    0.841
peak=    3.282 closest distance to " O   HOH Z 389 " =    1.826
peak=    3.280 closest distance to " CZ3 TRP A 274 " =    4.531
peak=    3.265 closest distance to " CG  GLU A  37 " =    0.954
peak=    3.259 closest distance to " CB  SER A 288 " =    1.424
peak=    3.255 closest distance to " CB  ARG A 145 " =    0.880
peak=    3.253 closest distance to " CB  PHE A 204 " =    0.967
peak=    3.252 closest distance to " O   HOH Z 238 " =    2.306
peak=    3.247 closest distance to " NE2 GLN A  73 " =    1.379
peak=    3.245 closest distance to " CB  ALA A 104 " =    0.746
peak=    3.244 closest distance to " O   HOH Z 203 " =    1.694
peak=    3.242 closest distance to " C   ALA A 299 " =    0.868
peak=    3.241 closest distance to " CG2 ILE A  20 " =    1.474
peak=    3.240 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.238 closest distance to " OE2 GLU A   2 " =    1.961
peak=    3.237 closest distance to " O   PHE A  61 " =    1.433
peak=    3.234 closest distance to " O   MET A 105 " =    1.776
peak=    3.233 closest distance to " CG1 ILE A 120 " =    0.996
peak=    3.231 closest distance to " O   HOH Z  88 " =    3.018
peak=    3.229 closest distance to " OE2 GLU A  53 " =    2.018
peak=    3.227 closest distance to " O   HOH Z 133 " =    2.748
peak=    3.224 closest distance to " O   HOH Z 350 " =    1.520
peak=    3.223 closest distance to " O   HOH Z 294 " =    1.478
peak=    3.215 closest distance to " CB  GLN A 205 " =    1.101
peak=    3.214 closest distance to " NZ  LYS A  48 " =    1.176
peak=    3.206 closest distance to " O   ILE A  49 " =    1.174
peak=    3.206 closest distance to " CB  SER A  62 " =    0.873
peak=    3.204 closest distance to " O   THR A 220 " =    1.275
peak=    3.204 closest distance to " CD1 LEU A 300 " =    1.083
peak=    3.203 closest distance to " O   PRO A 213 " =    1.475
peak=    3.201 closest distance to " CB  ALA A 295 " =    1.562
peak=    3.198 closest distance to " O   HOH Z 171 " =    4.046
peak=    3.197 closest distance to " O   HOH Z 148 " =    3.495
peak=    3.195 closest distance to " O   HOH Z 344 " =    2.942
peak=    3.195 closest distance to " CG  LEU A 281 " =    1.039
peak=    3.192 closest distance to " CB  THR A 235 " =    1.281
peak=    3.186 closest distance to " O   HOH Z 145 " =    2.171
peak=    3.186 closest distance to " CB  GLN A 103 " =    1.093
peak=    3.184 closest distance to " O   HOH Z   9 " =    1.640
peak=    3.177 closest distance to " CG2 ILE A 120 " =    1.263
peak=    3.173 closest distance to " O   HOH Z  97 " =    2.073
peak=    3.169 closest distance to " O   HOH Z 299 " =    4.317
peak=    3.166 closest distance to " CB  ARG A 138 " =    1.259
peak=    3.163 closest distance to " CZ3 TRP A  92 " =    1.304
peak=    3.163 closest distance to " CB  SER A 210 " =    0.803
peak=    3.158 closest distance to " O   HOH Z 213 " =    1.839
peak=    3.154 closest distance to " O   HOH Z 357 " =    2.761
peak=    3.151 closest distance to " O   HOH Z 389 " =    1.232
peak=    3.146 closest distance to " O   HOH Z 222 " =    2.404
peak=    3.146 closest distance to " CA  ASN A 127 " =    1.153
peak=    3.138 closest distance to " CB  VAL A 257 " =    0.771
peak=    3.135 closest distance to " CA  ALA A 129 " =    1.412
peak=    3.129 closest distance to " CB  SER A  62 " =    1.102
peak=    3.117 closest distance to " CE3 TRP A 274 " =    1.255
peak=    3.114 closest distance to " O   HOH Z 425 " =    2.124
peak=    3.100 closest distance to " O   SER A 164 " =    1.276
peak=    3.099 closest distance to " OH  TYR A 214 " =    1.310
peak=    3.098 closest distance to " O   HOH Z 371 " =    3.381
peak=    3.094 closest distance to " O   HOH Z 258 " =    1.462
peak=    3.093 closest distance to " CB  ALA A 114 " =    0.746
peak=    3.093 closest distance to " O   HOH Z 116 " =    1.776
peak=    3.082 closest distance to " O   ALA A 158 " =    1.349
peak=    3.082 closest distance to " CE  LYS A 119 " =    1.017
peak=    3.077 closest distance to " O   HOH Z  21 " =    1.730
peak=    3.077 closest distance to " O   HOH Z 148 " =    2.239
peak=    3.070 closest distance to " CG2 VAL A 197 " =    1.046
peak=    3.069 closest distance to " CD1 LEU A  96 " =    1.294
peak=    3.068 closest distance to " CD  LYS A 119 " =    2.115
peak=    3.062 closest distance to " CB  ALA A 291 " =    1.312
peak=    3.051 closest distance to " OG BSER A  99 " =    2.226
peak=    3.050 closest distance to " O   HOH Z 345 " =    3.487
peak=    3.048 closest distance to " O   HOH Z 128 " =    2.417
peak=    3.035 closest distance to " CA  LYS A 290 " =    1.226

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.822 - 5.621
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 215
   mapped sites are within: 0.822 - 5.621

peak=   -4.609 closest distance to " CD  ARG A  14 " =    3.302
peak=   -4.563 closest distance to " CD  GLN A  58 " =    1.053
peak=   -4.472 closest distance to " CG1 VAL A 296 " =    1.085
peak=   -4.397 closest distance to " CB  PRO A 243 " =    2.690
peak=   -4.282 closest distance to " CD  ARG A 138 " =    1.245
peak=   -4.276 closest distance to " CB  PHE A 192 " =    1.993
peak=   -4.248 closest distance to " O   HOH Z 231 " =    2.093
peak=   -4.238 closest distance to " O   HOH Z 211 " =    1.127
peak=   -4.218 closest distance to " CG2 VAL A 230 " =    0.822
peak=   -4.206 closest distance to " CD  ARG A 156 " =    2.092
peak=   -4.174 closest distance to " CG1 VAL A 112 " =    2.768
peak=   -4.157 closest distance to " OG BSER A 134 " =    1.298
peak=   -4.154 closest distance to " CG1 VAL A 112 " =    2.689
peak=   -4.107 closest distance to " O   VAL A  67 " =    2.706
peak=   -4.100 closest distance to " C   HIS A 108 " =    1.131
peak=   -4.093 closest distance to " O   HOH Z 411 " =    5.621
peak=   -4.068 closest distance to " CZ2 TRP A  92 " =    2.850
peak=   -4.039 closest distance to " O   PRO A 163 " =    2.122
peak=   -4.039 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.024 closest distance to " O   HOH Z 166 " =    2.318
peak=   -4.012 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.962 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.961 closest distance to " CG  GLN A 223 " =    2.314
peak=   -3.923 closest distance to " O   HOH Z 100 " =    0.925
peak=   -3.909 closest distance to " O   SER A 271 " =    2.076
peak=   -3.890 closest distance to " CE3 TRP A 150 " =    2.273
peak=   -3.890 closest distance to " O   HOH Z 133 " =    1.108
peak=   -3.876 closest distance to " O   HOH Z 193 " =    1.186
peak=   -3.876 closest distance to " CD2 TYR A 293 " =    2.021
peak=   -3.859 closest distance to " O   HOH Z 394 " =    1.569
peak=   -3.788 closest distance to " O   HOH Z 359 " =    2.963
peak=   -3.787 closest distance to " OE1 GLN A  88 " =    0.949
peak=   -3.787 closest distance to " CE2 TYR A  30 " =    2.638
peak=   -3.784 closest distance to " CB  PRO A 280 " =    2.090
peak=   -3.774 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.774 closest distance to " O   HOH Z  44 " =    2.457
peak=   -3.773 closest distance to " CA  VAL A  67 " =    2.881
peak=   -3.772 closest distance to " O   HOH Z  73 " =    2.296
peak=   -3.771 closest distance to " CB  VAL A 230 " =    1.152
peak=   -3.748 closest distance to " C   ALA A 158 " =    1.349
peak=   -3.746 closest distance to " O   HOH Z 103 " =    1.788
peak=   -3.739 closest distance to " N   THR A  52 " =    1.723
peak=   -3.738 closest distance to " CB  HIS A  86 " =    1.081
peak=   -3.714 closest distance to " NE2 GLN A  11 " =    1.682
peak=   -3.691 closest distance to " CD1 LEU A 101 " =    2.385
peak=   -3.678 closest distance to " CG2 VAL A 202 " =    2.769
peak=   -3.676 closest distance to " CB  ALA A  43 " =    2.632
peak=   -3.669 closest distance to " O   HOH Z 216 " =    1.166
peak=   -3.657 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.652 closest distance to " C   GLY A  17 " =    1.231
peak=   -3.644 closest distance to " CG1 VAL A 250 " =    2.739
peak=   -3.641 closest distance to " CG2 VAL A 296 " =    1.200
peak=   -3.632 closest distance to " O   HOH Z 106 " =    1.705
peak=   -3.591 closest distance to " O   HOH Z 102 " =    1.701
peak=   -3.585 closest distance to " CE2 TRP A  70 " =    2.185
peak=   -3.576 closest distance to " CA  GLY A 241 " =    2.340
peak=   -3.575 closest distance to " O   HOH Z 351 " =    1.558
peak=   -3.561 closest distance to " CD1 LEU A 255 " =    2.835
peak=   -3.558 closest distance to " O   HOH Z   9 " =    1.606
peak=   -3.525 closest distance to " N   ALA A 248 " =    1.746
peak=   -3.521 closest distance to " CG  TRP A 266 " =    1.763
peak=   -3.520 closest distance to " CD2 PHE A 225 " =    1.135
peak=   -3.515 closest distance to " CG  GLU A 277 " =    1.222
peak=   -3.511 closest distance to " CE  MET A 105 " =    2.378
peak=   -3.505 closest distance to " N   ALA A  43 " =    2.590
peak=   -3.497 closest distance to " CE BMET A  47 " =    1.356
peak=   -3.492 closest distance to " O   HOH Z 431 " =    1.858
peak=   -3.491 closest distance to " CE3 TRP A  70 " =    1.722
peak=   -3.481 closest distance to " O   HOH Z 185 " =    2.379
peak=   -3.478 closest distance to " CG2 THR A  29 " =    2.678
peak=   -3.477 closest distance to " O   HOH Z  52 " =    1.628
peak=   -3.475 closest distance to " O   HOH Z 191 " =    5.585
peak=   -3.466 closest distance to " O   HOH Z 201 " =    2.105
peak=   -3.465 closest distance to " CG  ARG A 138 " =    0.913
peak=   -3.465 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.461 closest distance to " CB  PRO A 163 " =    2.420
peak=   -3.455 closest distance to " O   ASN A 252 " =    1.308
peak=   -3.454 closest distance to " OH  TYR A 172 " =    1.781
peak=   -3.454 closest distance to " OG  SER A  87 " =    1.516
peak=   -3.453 closest distance to " C   MET A 188 " =    1.424
peak=   -3.452 closest distance to " O   HOH Z 131 " =    3.995
peak=   -3.451 closest distance to " O   HOH Z 252 " =    3.882
peak=   -3.447 closest distance to " O   HOH Z 286 " =    1.873
peak=   -3.443 closest distance to " O   HOH Z  11 " =    1.755
peak=   -3.440 closest distance to " OD1 ASN A 249 " =    2.500
peak=   -3.437 closest distance to " CA  ASP A  27 " =    2.466
peak=   -3.437 closest distance to " O   HOH Z  44 " =    1.016
peak=   -3.436 closest distance to " N   ALA A 226 " =    2.062
peak=   -3.430 closest distance to " O   HOH Z 429 " =    1.930
peak=   -3.425 closest distance to " O   HOH Z 128 " =    2.495
peak=   -3.421 closest distance to " ND2 ASN A  45 " =    1.190
peak=   -3.419 closest distance to " O   MET A  40 " =    2.853
peak=   -3.418 closest distance to " O   ASP A  27 " =    2.081
peak=   -3.412 closest distance to " O   HOH Z  43 " =    1.697
peak=   -3.400 closest distance to " O   ILE A 106 " =    1.962
peak=   -3.400 closest distance to " CG1 VAL A  67 " =    2.949
peak=   -3.399 closest distance to " O   SER A 276 " =    1.730
peak=   -3.392 closest distance to " CD2 LEU A 167 " =    1.831
peak=   -3.390 closest distance to " OXT GLY A 302 " =    3.017
peak=   -3.389 closest distance to " O   HOH Z  11 " =    2.186
peak=   -3.382 closest distance to " C   LEU A 143 " =    1.063
peak=   -3.373 closest distance to " OD1 ASN A 148 " =    1.343
peak=   -3.371 closest distance to " O   HOH Z 149 " =    2.106
peak=   -3.366 closest distance to " O   HOH Z 285 " =    2.026
peak=   -3.365 closest distance to " O   HOH Z 411 " =    1.466
peak=   -3.362 closest distance to " O   HOH Z 371 " =    2.398
peak=   -3.361 closest distance to " N   THR A 157 " =    1.457
peak=   -3.360 closest distance to " O   HOH Z 136 " =    2.572
peak=   -3.356 closest distance to " CD1 LEU A 228 " =    2.285
peak=   -3.350 closest distance to " CG  ASP A 231 " =    0.838
peak=   -3.349 closest distance to " O   HOH Z 295 " =    1.505
peak=   -3.348 closest distance to " NE2 GLN A 194 " =    1.910
peak=   -3.347 closest distance to " O   HOH Z 357 " =    2.192
peak=   -3.344 closest distance to " OD2 ASP A 191 " =    1.433
peak=   -3.343 closest distance to " CZ3 TRP A 179 " =    1.234
peak=   -3.342 closest distance to " O   GLY A  80 " =    2.575
peak=   -3.334 closest distance to " OH  TYR A 247 " =    1.801
peak=   -3.327 closest distance to " CA  GLY A 203 " =    2.508
peak=   -3.325 closest distance to " NE  ARG A  66 " =    4.158
peak=   -3.323 closest distance to " O   GLY A  80 " =    2.620
peak=   -3.322 closest distance to " O   HOH Z 345 " =    2.101
peak=   -3.321 closest distance to " C   LEU A 222 " =    1.102
peak=   -3.314 closest distance to " CA  GLY A 241 " =    3.161
peak=   -3.311 closest distance to " O   HOH Z 191 " =    3.454
peak=   -3.309 closest distance to " CG1 VAL A 197 " =    2.348
peak=   -3.306 closest distance to " O   HOH Z 114 " =    3.061
peak=   -3.305 closest distance to " CD2 PHE A  61 " =    2.139
peak=   -3.303 closest distance to " NH2 ARG A 159 " =    2.357
peak=   -3.299 closest distance to " ND2 ASN A 249 " =    2.493
peak=   -3.298 closest distance to " O   HOH Z 198 " =    1.991
peak=   -3.296 closest distance to " CE2 PHE A  61 " =    2.658
peak=   -3.295 closest distance to " CG1 VAL A 125 " =    1.885
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.232
peak=   -3.287 closest distance to " O   ALA A 227 " =    1.417
peak=   -3.287 closest distance to " O   HOH Z 128 " =    1.180
peak=   -3.285 closest distance to " O   SER A 210 " =    1.765
peak=   -3.284 closest distance to " ND2 ASN A  45 " =    1.568
peak=   -3.279 closest distance to " CD1 ILE A 199 " =    2.488
peak=   -3.278 closest distance to " CD2 LEU A   5 " =    1.143
peak=   -3.273 closest distance to " O   HOH Z  68 " =    1.386
peak=   -3.269 closest distance to " O   HOH Z 350 " =    1.880
peak=   -3.267 closest distance to " SG BCYS A 201 " =    2.389
peak=   -3.264 closest distance to " CB  ALA A  10 " =    2.256
peak=   -3.264 closest distance to " NE2 GLN A  88 " =    2.143
peak=   -3.261 closest distance to " CD  GLN A 223 " =    1.669
peak=   -3.256 closest distance to " NH2AARG A 275 " =    5.180
peak=   -3.254 closest distance to " O   HOH Z 389 " =    1.411
peak=   -3.250 closest distance to " CD  LYS A 289 " =    2.427
peak=   -3.248 closest distance to " NE2 GLN A 278 " =    1.755
peak=   -3.248 closest distance to " CG1 VAL A  78 " =    2.647
peak=   -3.244 closest distance to " O   TRP A  70 " =    1.470
peak=   -3.243 closest distance to " O   HOH Z 407 " =    2.969
peak=   -3.239 closest distance to " CB  HIS A  81 " =    0.948
peak=   -3.237 closest distance to " O   HOH Z 251 " =    4.892
peak=   -3.232 closest distance to " CG2 VAL A 189 " =    1.971
peak=   -3.228 closest distance to " O   HOH Z 238 " =    0.915
peak=   -3.225 closest distance to " N   TRP A 274 " =    1.153
peak=   -3.223 closest distance to " O   HOH Z 177 " =    1.897
peak=   -3.222 closest distance to " O   HOH Z 256 " =    1.395
peak=   -3.218 closest distance to " CG  PRO A 163 " =    2.373
peak=   -3.218 closest distance to " O   HOH Z 275 " =    1.502
peak=   -3.216 closest distance to " NH2 ARG A  79 " =    1.580
peak=   -3.216 closest distance to " CD1 PHE A  59 " =    2.061
peak=   -3.213 closest distance to " O   HOH Z 123 " =    2.549
peak=   -3.210 closest distance to " O   HOH Z 236 " =    1.452
peak=   -3.204 closest distance to " O   HOH Z  10 " =    1.498
peak=   -3.202 closest distance to " O   HOH Z 259 " =    4.009
peak=   -3.201 closest distance to " O   VAL A 189 " =    2.632
peak=   -3.201 closest distance to " O   HOH Z 290 " =    1.249
peak=   -3.200 closest distance to " O   HOH Z 111 " =    1.721
peak=   -3.197 closest distance to " CA  ASN A 110 " =    2.410
peak=   -3.197 closest distance to " O   HOH Z 127 " =    1.079
peak=   -3.191 closest distance to " O   HOH Z 165 " =    1.884
peak=   -3.183 closest distance to " CD  PRO A 243 " =    2.052
peak=   -3.183 closest distance to " N   TYR A  68 " =    3.045
peak=   -3.182 closest distance to " O   HOH Z 189 " =    2.248
peak=   -3.178 closest distance to " N   SER A 276 " =    1.349
peak=   -3.171 closest distance to " CD2 HIS A 207 " =    2.283
peak=   -3.163 closest distance to " OG  SER A  28 " =    2.094
peak=   -3.160 closest distance to " OD1 ASN A 173 " =    1.371
peak=   -3.158 closest distance to " O   HOH Z 138 " =    1.294
peak=   -3.155 closest distance to " CG  ARG A 269 " =    2.043
peak=   -3.154 closest distance to " CB  ALA A 248 " =    2.358
peak=   -3.151 closest distance to " CZ  PHE A 192 " =    2.784
peak=   -3.150 closest distance to " CD1 ILE A 239 " =    2.317
peak=   -3.149 closest distance to " N   VAL A 125 " =    1.497
peak=   -3.146 closest distance to " CG1BVAL A  72 " =    2.449
peak=   -3.145 closest distance to " CD  PRO A 213 " =    2.048
peak=   -3.145 closest distance to " O   HOH Z 341 " =    1.064
peak=   -3.142 closest distance to " CA  VAL A 296 " =    1.016
peak=   -3.141 closest distance to " N   ASP A 191 " =    1.237
peak=   -3.138 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.133 closest distance to " CB  ASP A 171 " =    2.203
peak=   -3.131 closest distance to " CG  PRO A 163 " =    2.148
peak=   -3.126 closest distance to " O   HOH Z 368 " =    1.858
peak=   -3.115 closest distance to " O   HOH Z 352 " =    1.533
peak=   -3.115 closest distance to " CA  SER A 135 " =    1.338
peak=   -3.113 closest distance to " O   ARG A 145 " =    1.592
peak=   -3.106 closest distance to " O   HOH Z 313 " =    1.503
peak=   -3.106 closest distance to " CG  ARG A 259 " =    2.410
peak=   -3.106 closest distance to " CB  ALA A 291 " =    2.175
peak=   -3.105 closest distance to " OD1 ASP A 171 " =    1.547
peak=   -3.102 closest distance to " O   HOH Z 244 " =    2.040
peak=   -3.101 closest distance to " O   HOH Z 421 " =    3.102
peak=   -3.101 closest distance to " O   HOH Z  38 " =    1.765
peak=   -3.093 closest distance to " O   LYS A  76 " =    1.636
peak=   -3.088 closest distance to " O   ALA A 180 " =    1.438
peak=   -3.088 closest distance to " OD1 ASN A 187 " =    1.627
peak=   -3.080 closest distance to " CG2 ILE A 151 " =    2.491
peak=   -3.076 closest distance to " CD2 LEU A 237 " =    2.897
peak=   -3.070 closest distance to " O   HOH Z 392 " =    1.940
peak=   -3.056 closest distance to " C   ASP A 270 " =    1.330
peak=   -3.056 closest distance to " OD1 ASP A 200 " =    1.596
peak=   -3.041 closest distance to " O   HOH Z  51 " =    1.145

================= 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    :  0.4480 0.4343   6.248489e+00   6.219061e+00
   1_bss:  0.4388 0.4218   6.240882e+00   6.206076e+00
   1_xyz:  0.3384 0.3575   6.065833e+00   6.097497e+00
   1_adp:  0.2811 0.3207   5.921104e+00   6.018686e+00
   1_occ:  0.2805 0.3216   5.919967e+00   6.020500e+00
   2_bss:  0.2763 0.3169   5.919273e+00   6.016846e+00
   2_xyz:  0.2043 0.2507   5.648854e+00   5.805346e+00
   2_adp:  0.1866 0.2338   5.574113e+00   5.745866e+00
   2_occ:  0.1865 0.2341   5.574552e+00   5.747500e+00
   3_bss:  0.1850 0.2343   5.574256e+00   5.747469e+00
   3_xyz:  0.1429 0.1876   5.341031e+00   5.546943e+00
   3_adp:  0.1349 0.1778   5.290773e+00   5.502866e+00
   3_occ:  0.1348 0.1777   5.290120e+00   5.502389e+00
   4_bss:  0.1346 0.1780   5.290455e+00   5.502902e+00
   4_xyz:  0.1257 0.1692   5.238005e+00   5.457643e+00
   4_adp:  0.1242 0.1678   5.228961e+00   5.450425e+00
   4_occ:  0.1242 0.1677   5.228667e+00   5.450274e+00
   5_bss:  0.1241 0.1678   5.228482e+00   5.450287e+00
   5_xyz:  0.1197 0.1642   5.201630e+00   5.433678e+00
   5_adp:  0.1185 0.1659   5.199142e+00   5.439120e+00
   5_occ:  0.1185 0.1659   5.199082e+00   5.439078e+00
   5_bss:  0.1184 0.1657   5.199230e+00   5.439216e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.336  20.001   6.804   7.442  11.839   0.000   0.000   0.000
   1_xyz:  0.336  20.001   6.804   7.442  11.839   0.000   0.000   0.000
   1_adp:  0.336  20.001   6.804   7.442  11.839   0.000   0.000   0.000
   1_occ:  0.336  20.001   6.804   7.442  11.839   0.000   0.000   0.000
   2_bss:  0.328  50.001   3.638   4.001   8.160   0.000   0.000   0.000
   2_xyz:  0.328  50.001   3.638   4.001   8.160   0.000   0.000   0.000
   2_adp:  0.328  50.001   3.638   4.001   8.160   0.000   0.000   0.000
   2_occ:  0.328  50.001   3.638   4.001   8.160   0.000   0.000   0.000
   3_bss:  0.336  62.938   2.590   3.134   5.518   0.000   0.000   0.000
   3_xyz:  0.336  62.938   2.590   3.134   5.518   0.000   0.000   0.000
   3_adp:  0.336  62.938   2.590   3.134   5.518   0.000   0.000   0.000
   3_occ:  0.336  62.938   2.590   3.134   5.518   0.000   0.000   0.000
   4_bss:  0.337  62.938   2.416   2.868   4.737   0.000   0.000   0.000
   4_xyz:  0.337  62.938   2.416   2.868   4.737   0.000   0.000   0.000
   4_adp:  0.337  62.938   2.416   2.868   4.737   0.000   0.000   0.000
   4_occ:  0.337  62.938   2.416   2.868   4.737   0.000   0.000   0.000
   5_bss:  0.329  57.084   2.569   2.930   4.667   0.000   0.000   0.000
   5_xyz:  0.329  57.084   2.569   2.930   4.667   0.000   0.000   0.000
   5_adp:  0.329  57.084   2.569   2.930   4.667   0.000   0.000   0.000
   5_occ:  0.329  57.084   2.569   2.930   4.667   0.000   0.000   0.000
   5_bss:  0.329  60.689  -0.779  -0.453   1.231   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.450 0.5414  0.6046    54685.879
   1_bss:  47.835 0.5479  0.7966    52522.953
   1_xyz:  38.905 0.6553  0.9199    35255.330
   1_adp:  33.339 0.7210  1.0059    27760.845
   1_occ:  33.399 0.7203  1.0042    27848.659
   2_bss:  33.089 0.7237  0.8929    27410.823
   2_xyz:  24.815 0.8133  0.9807    15960.004
   2_adp:  22.604 0.8367  0.9995    13898.471
   2_occ:  22.662 0.8360  0.9988    13939.564
   3_bss:  22.593 0.8369  0.9470    13961.634
   3_xyz:  17.559 0.8846  0.9754     8931.983
   3_adp:  16.404 0.8952  0.9758     8164.474
   3_occ:  16.390 0.8953  0.9759     8150.009
   4_bss:  16.394 0.8954  0.9618     8169.304
   4_xyz:  15.365 0.9041  0.9661     7364.571
   4_adp:  15.169 0.9060  0.9624     7263.298
   4_occ:  15.167 0.9060  0.9625     7261.470
   5_bss:  15.167 0.9060  0.9641     7259.712
   5_xyz:  14.817 0.9089  0.9659     7012.012
   5_adp:  14.918 0.9081  0.9596     7058.227
   5_occ:  14.917 0.9081  0.9595     7054.326
   5_bss:  14.920 0.9081  0.9670     7057.890
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4182e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4182e+01
   1_xyz:   1.597  0.012  0.104 17.961  0.006  4.124   1.2735e-01
   1_adp:   1.597  0.012  0.104 17.961  0.006  4.124   1.2735e-01
   1_occ:   1.597  0.012  0.104 17.961  0.006  4.124   1.2735e-01
   2_bss:   1.597  0.012  0.104 17.961  0.006  4.124   1.2735e-01
   2_xyz:   1.043  0.007  0.073 16.062  0.004  4.126   6.5400e-02
   2_adp:   1.043  0.007  0.073 16.062  0.004  4.126   6.5400e-02
   2_occ:   1.043  0.007  0.073 16.062  0.004  4.126   6.5400e-02
   3_bss:   1.043  0.007  0.073 16.062  0.004  4.126   6.5400e-02
   3_xyz:   1.036  0.007  0.079 15.976  0.003  4.131   6.3713e-02
   3_adp:   1.036  0.007  0.079 15.976  0.003  4.131   6.3713e-02
   3_occ:   1.036  0.007  0.079 15.976  0.003  4.131   6.3713e-02
   4_bss:   1.036  0.007  0.079 15.976  0.003  4.131   6.3713e-02
   4_xyz:   0.951  0.007  0.075 15.621  0.003  4.135   5.7205e-02
   4_adp:   0.951  0.007  0.075 15.621  0.003  4.135   5.7205e-02
   4_occ:   0.951  0.007  0.075 15.621  0.003  4.135   5.7205e-02
   5_bss:   0.951  0.007  0.075 15.621  0.003  4.135   5.7205e-02
   5_xyz:   1.038  0.008  0.081 15.683  0.003  4.113   6.4682e-02
   5_adp:   1.038  0.008  0.081 15.683  0.003  4.113   6.4682e-02
   5_occ:   1.038  0.008  0.081 15.683  0.003  4.113   6.4682e-02
   5_bss:   1.038  0.008  0.081 15.683  0.003  4.113   6.4682e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0247e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0247e+00
   1_xyz:  13.026  0.151  0.402 87.878  0.037  2.158   9.6515e-02
   1_adp:  13.026  0.151  0.402 87.878  0.037  2.158   9.6515e-02
   1_occ:  13.026  0.151  0.402 87.878  0.037  2.158   9.6515e-02
   2_bss:  13.026  0.151  0.402 87.878  0.037  2.158   9.6515e-02
   2_xyz:   6.284  0.056  0.253 87.062  0.031  2.402   4.7246e-02
   2_adp:   6.284  0.056  0.253 87.062  0.031  2.402   4.7246e-02
   2_occ:   6.284  0.056  0.253 87.062  0.031  2.402   4.7246e-02
   3_bss:   6.284  0.056  0.253 87.062  0.031  2.402   4.7246e-02
   3_xyz:   7.442  0.050  0.354 85.080  0.038  2.331   3.7077e-02
   3_adp:   7.442  0.050  0.354 85.080  0.038  2.331   3.7077e-02
   3_occ:   7.442  0.050  0.354 85.080  0.038  2.331   3.7077e-02
   4_bss:   7.442  0.050  0.354 85.080  0.038  2.331   3.7077e-02
   4_xyz:   7.559  0.047  0.319 81.242  0.034  2.409   3.8728e-02
   4_adp:   7.559  0.047  0.319 81.242  0.034  2.409   3.8728e-02
   4_occ:   7.559  0.047  0.319 81.242  0.034  2.409   3.8728e-02
   5_bss:   7.559  0.047  0.319 81.242  0.034  2.409   3.8728e-02
   5_xyz:   8.709  0.055  0.372 82.530  0.036  2.376   3.6323e-02
   5_adp:   8.709  0.055  0.372 82.530  0.036  2.376   3.6323e-02
   5_occ:   8.709  0.055  0.372 82.530  0.036  2.376   3.6323e-02
   5_bss:   8.709  0.055  0.372 82.530  0.036  2.376   3.6323e-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:  63.49   0.00  11.36  51.68   0.00   8.48  63.49   0.00  27.04
   1_occ:  63.49   0.00  11.36  51.68   0.00   8.48  63.49   0.00  27.04
   2_bss:  63.49   0.00  11.36  51.68   0.00   8.48  63.49   0.00  27.04
   2_xyz:  63.49   0.00  11.36  51.68   0.00   8.48  63.49   0.00  27.04
   2_adp:  64.47   0.00  11.63  57.26   0.00   7.88  64.47   0.00  32.06
   2_occ:  64.47   0.00  11.63  57.26   0.00   7.88  64.47   0.00  32.06
   3_bss:  64.47   0.00  11.63  57.26   0.00   7.88  64.47   0.00  32.06
   3_xyz:  64.47   0.00  11.63  57.26   0.00   7.88  64.47   0.00  32.06
   3_adp:  69.80   0.00  11.80  63.64   0.00   7.70  69.80   0.79  34.13
   3_occ:  69.80   0.00  11.80  63.64   0.00   7.70  69.80   0.79  34.13
   4_bss:  69.80   0.00  11.80  63.64   0.00   7.70  69.80   0.79  34.13
   4_xyz:  69.80   0.00  11.80  63.64   0.00   7.70  69.80   0.79  34.13
   4_adp:  72.29   0.00  11.73  67.40   0.00   7.61  72.29   0.82  34.15
   4_occ:  72.29   0.00  11.73  67.40   0.00   7.61  72.29   0.82  34.15
   5_bss:  72.29   0.00  11.73  67.40   0.00   7.61  72.29   0.82  34.15
   5_xyz:  72.29   0.00  11.73  67.40   0.00   7.61  72.29   0.82  34.15
   5_adp:  87.63   0.00  12.29  83.14   0.00   7.79  87.63   0.45  36.83
   5_occ:  87.63   0.00  12.29  83.14   0.00   7.79  87.63   0.45  36.83
   5_bss:  91.24   3.60  15.90  86.75   3.60  11.39  91.24   4.05  40.43
------------------------------------------------------------------------
 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:    1.242    0.016    0.407
   1_adp:    1.242    0.016    0.407
   1_occ:    1.242    0.016    0.407
   2_bss:    1.242    0.016    0.407
   2_xyz:    1.785    0.024    0.521
   2_adp:    1.785    0.024    0.521
   2_occ:    1.785    0.024    0.521
   3_bss:    1.785    0.024    0.521
   3_xyz:    1.742    0.031    0.570
   3_adp:    1.742    0.031    0.570
   3_occ:    1.742    0.031    0.570
   4_bss:    1.742    0.031    0.570
   4_xyz:    1.878    0.050    0.593
   4_adp:    1.878    0.050    0.593
   4_occ:    1.878    0.050    0.593
   5_bss:    1.878    0.050    0.593
   5_xyz:    1.875    0.058    0.598
   5_adp:    1.875    0.058    0.598
   5_occ:    1.875    0.058    0.598
   5_bss:    1.875    0.058    0.598
------------------------------------------------------------------------

CPU time actual refinement: 314.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/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_669/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_669/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.12 
  Macro-tasks:
    bulk solvent and scale       = 41.20  
    individual site refinement   = 121.90 
    weights calculation          = 31.54  
    collect and process          = 6.39   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 201.14 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 94.49  
    alpha_beta                      = 7.83   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 103.94 
    fmodel                         = 7.15   
    r_factors                      = 0.28   
    phase_errors                   = 10.89  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 227.71 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.493 micro seconds
Total CPU time: 5.46 minutes
from_scatterers_fft:    638 calls, 94.26 s
gradients_fft:          583 calls, 91.10 s

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

# Date 2008-01-16 Time 02:08:06 PST -0800 (1200478086.38 s)
Start R-work = 0.4480, R-free = 0.4343 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1820 (no bulk solvent and anisotropic scale)

Start R-work = 0.4388, R-free = 0.4218
Final R-work = 0.1184, R-free = 0.1657