# Date 2008-01-16 Time 02:32:12 PST -0800 (1200479532.30 s)
#phil __OFF__

Command line arguments: "../872.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29486
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 872

-------------------------------------------------------------------------------
  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: (70.9525, 46.2261, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.97157
Completeness in resolution range: 0.95954
Completeness with d_max=infinity: 0.956681

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9716

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: (70.9525, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.97157
Completeness in resolution range: 0.95954
Completeness with d_max=infinity: 0.956681

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0613 -  4.2194 [2136/2162]  1926   210   9.8%
  bin  2:  4.2194 -  3.3613 [2067/2087]  1857   210  10.2%
  bin  3:  3.3613 -  2.9400 [2032/2051]  1828   204  10.0%
  bin  4:  2.9400 -  2.6728 [2016/2046]  1815   201  10.0%
  bin  5:  2.6728 -  2.4822 [2015/2034]  1817   198   9.8%
  bin  6:  2.4822 -  2.3364 [1992/2017]  1785   207  10.4%
  bin  7:  2.3364 -  2.2198 [1976/2004]  1780   196   9.9%
  bin  8:  2.2198 -  2.1234 [1978/2014]  1781   197  10.0%
  bin  9:  2.1234 -  2.0419 [1960/2002]  1766   194   9.9%
  bin 10:  2.0419 -  1.9716 [1417/1998]  1275   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 33
        2.42 -     3.04: 2203
        3.04 -     3.66: 4752
        3.66 -     4.28: 9122
        4.28 -     4.90: 12378
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.918 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.075 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28483 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_872/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 = 70.9525 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4705   r_free= 0.4528   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.270556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.3976 0.3998      6.5762      6.5897|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.3851 0.3738      6.7703      6.7181|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.4194 0.3834      6.6401      6.6854|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.4496 0.4219      6.5285      6.4574|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.5035 0.4994      6.3612      6.3747|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.4898 0.4974      6.2678       6.212|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.5143 0.4613      6.2533      6.2266|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.5218 0.4148      6.1755      6.1377|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.5005 0.4949      6.1165      6.1411|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.5160 0.5348      6.1044      6.1014|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.5168 0.4869      6.0374      6.0346|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.5036 0.5670      5.9736      6.0184|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.5437 0.5343      5.8856      5.8162|
| 14:  2.0208 -  1.9716 0.59    759   88 0.5563 0.4788      5.8502      5.8099|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0613 -  4.7065  1392   156  0.67  36.49   0.80     0.73      78332.21|
|  2:  4.7065 -  3.7547  1338   146  0.73  33.10   0.88     0.80      98782.61|
|  3:  3.7547 -  3.2857  1323   144  0.63  40.99   0.86     0.77     101974.13|
|  4:  3.2857 -  2.9878  1306   153  0.57  46.47   0.81     0.67      90777.04|
|  5:  2.9878 -  2.7751  1294   142  0.45  55.87   0.74     0.54      77422.41|
|  6:  2.7751 -  2.6124  1295   142  0.44  56.80   0.74     0.50      68076.53|
|  7:  2.6124 -  2.4822  1295   140  0.43  57.68   0.75     0.49      60472.42|
|  8:  2.4822 -  2.3746  1254   144  0.43  57.59   0.73     0.51      53186.96|
|  9:  2.3746 -  2.2835  1290   148  0.44  56.64   0.73     0.49      47150.02|
| 10:  2.2835 -  2.2049  1278   138  0.41  59.12   0.77     0.48      44381.64|
| 11:  2.2049 -  2.1362  1272   136  0.37  62.01   0.78     0.45      44601.01|
| 12:  2.1362 -  2.0753  1250   145  0.34  64.98   0.78     0.42      43647.43|
| 13:  2.0753 -  2.0208  1284   137  0.29  68.66   0.73     0.37      38693.58|
| 14:  2.0208 -  1.9716   759    88  0.30  67.98   0.70     0.33      30571.11|
|alpha:            min =        0.33 max =            0.80 mean =         0.55|
|beta:             min =    30571.11 max =       101974.13 mean =     64081.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.95|
|phase err.(test): min =        0.00 max =           89.96 mean =        54.07|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.306145             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.986   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.091618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.865   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      697 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1534 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2640 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3979 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5101 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6578 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7775 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.455 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.829 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4758   r_free= 0.4587   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.273646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4607   r_free= 0.4414   ksol= 0.34   Bsol= 0.00   scale= 1.012    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,9.94,8.12,0.00,0.00,0.00); trace/3= 8.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.133439             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.020164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.773   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4607      final r-factor (work) = 0.3709          |
| start r-factor (free) = 0.4414      final r-factor (free) = 0.4004          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.3601 = 11.13 * 0.50 * 6.2703 + 1.00 * 53.4551                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.4545 = 11.13 * 0.50 * 6.1643 + 1.00 * 0.1396                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3709      final r-factor (work) = 0.3269          |
| start r-factor (free) = 0.4004      final r-factor (free) = 0.3769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3029 = 1.02 * 1.00 * 6.1643 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2057 = 1.02 * 1.00 * 6.0688 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.78   12.36    None  None   None       |
|    all(noH): 2823   0      0.00    82.78   12.36    None  None   None       |
|    Sol.    : 438    0      0.00    76.32   25.43    None  None   None       |
|    Mac.    : 2385   0      0.00    82.78   9.96     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 -   8.278: 1265   |   5:    41.389 -  49.667:   50        |
|      1:     8.278 -  16.556:  807   |   6:    49.667 -  57.945:   21        |
|      2:    16.556 -  24.833:  408   |   7:    57.945 -  66.222:    4        |
|      3:    24.833 -  33.111:  167   |   8:    66.222 -  74.500:    0        |
|      4:    33.111 -  41.389:   98   |   9:    74.500 -  82.778:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3269 r_free = 0.3769             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3265 r_free = 0.3772             target_work(ml) = 6.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3265   r_free= 0.3772   ksol= 0.34   Bsol= 0.00   scale= 1.110    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,9.94,8.12,0.00,0.00,0.00); trace/3= 8.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.044200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3221   r_free= 0.3705   ksol= 0.34   Bsol= 32.08   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.19,5.27,4.73,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.042560                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.521576              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.368   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.507705              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.803  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3221      final r-factor (work) = 0.2304          |
| start r-factor (free) = 0.3705      final r-factor (free) = 0.2815          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9204 = 6.52 * 0.50 * 6.0663 + 1.00 * 0.1396                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3309 = 6.52 * 0.50 * 5.9045 + 1.00 * 0.0776                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2304      final r-factor (work) = 0.2116          |
| start r-factor (free) = 0.2815      final r-factor (free) = 0.2707          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0125 = 0.51 * 1.00 * 5.9045 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9833 = 0.51 * 1.00 * 5.7163 + 1.00 * 0.0811                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.95   12.54    None  None   None       |
|    all(noH): 2823   0      0.00    82.95   12.54    None  None   None       |
|    Sol.    : 438    0      0.77    77.30   28.33    None  None   None       |
|    Mac.    : 2385   0      0.00    82.95   9.64     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 -   8.295: 1291   |   5:    41.477 -  49.772:   50        |
|      1:     8.295 -  16.591:  809   |   6:    49.772 -  58.067:   19        |
|      2:    16.591 -  24.886:  333   |   7:    58.067 -  66.362:    4        |
|      3:    24.886 -  33.181:  201   |   8:    66.362 -  74.658:    1        |
|      4:    33.181 -  41.477:  113   |   9:    74.658 -  82.953:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2116 r_free = 0.2707             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2114 r_free = 0.2705             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2114   r_free= 0.2705   ksol= 0.34   Bsol= 32.08   scale= 1.059   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.19,5.27,4.73,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.695185                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2098   r_free= 0.2666   ksol= 0.33   Bsol= 36.29   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.00,3.53,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.692402                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.141432              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.381  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.722116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.860   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2098      final r-factor (work) = 0.1605          |
| start r-factor (free) = 0.2666      final r-factor (free) = 0.2178          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9197 = 4.14 * 0.50 * 5.7188 + 1.00 * 0.0776                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6203 = 4.14 * 0.50 * 5.5789 + 1.00 * 0.0680                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1605      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2178      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.2649 = 2.72 * 1.00 * 5.5789 + 1.00 * 0.0786                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7152 = 2.72 * 1.00 * 5.4006 + 1.00 * 0.0141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.44   13.49    None  None   None       |
|    all(noH): 2823   0      0.00    94.44   13.49    None  None   None       |
|    Sol.    : 438    0      1.39    86.72   37.47    None  None   None       |
|    Mac.    : 2385   0      0.00    94.44   9.09     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.445: 1646   |   5:    47.222 -  56.667:  106        |
|      1:     9.445 -  18.889:  608   |   6:    56.667 -  66.111:   47        |
|      2:    18.889 -  28.333:  165   |   7:    66.111 -  75.556:   12        |
|      3:    28.333 -  37.778:  124   |   8:    75.556 -  85.000:    4        |
|      4:    37.778 -  47.222:  108   |   9:    85.000 -  94.445:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1916             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1916             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1916   ksol= 0.33   Bsol= 36.29   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.00,3.53,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.328446                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1910   ksol= 0.32   Bsol= 42.86   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.00,2.94,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.326650                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.652262              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.672  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.080211              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5330 = 1.65 * 0.50 * 5.4047 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4270 = 1.65 * 0.50 * 5.2970 + 1.00 * 0.0510                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7359 = 1.08 * 1.00 * 5.2970 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6814 = 1.08 * 1.00 * 5.2470 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.33  13.37    None  None   None       |
|    all(noH): 2823   0      0.00    100.33  13.37    None  None   None       |
|    Sol.    : 438    0      1.53    86.68   37.91    None  None   None       |
|    Mac.    : 2385   0      0.00    100.33  8.87     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.033: 1763   |   5:    50.165 -  60.199:   71        |
|      1:    10.033 -  20.066:  540   |   6:    60.199 -  70.232:   39        |
|      2:    20.066 -  30.099:  147   |   7:    70.232 -  80.265:   13        |
|      3:    30.099 -  40.132:  123   |   8:    80.265 -  90.298:    5        |
|      4:    40.132 -  50.165:  120   |   9:    90.298 - 100.331:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1729             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1242 r_free = 0.1728             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1728   ksol= 0.32   Bsol= 42.86   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.26,2.00,2.94,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1728   ksol= 0.32   Bsol= 42.86   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,1.87,2.93,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.234570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.126349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.521  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.075274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.571  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1728      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6293 = 2.13 * 0.50 * 5.2468 + 1.00 * 0.0510                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5962 = 2.13 * 0.50 * 5.2068 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6122 = 1.08 * 1.00 * 5.2068 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5837 = 1.08 * 1.00 * 5.1806 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.77  13.12    None  None   None       |
|    all(noH): 2823   0      0.00    102.77  13.12    None  None   None       |
|    Sol.    : 438    0      1.51    90.00   37.31    None  None   None       |
|    Mac.    : 2385   0      0.00    102.77  8.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.277: 1816   |   5:    51.385 -  61.662:   61        |
|      1:    10.277 -  20.554:  513   |   6:    61.662 -  71.940:   33        |
|      2:    20.554 -  30.831:  143   |   7:    71.940 -  82.217:   11        |
|      3:    30.831 -  41.108:  120   |   8:    82.217 -  92.494:    6        |
|      4:    41.108 -  51.385:  118   |   9:    92.494 - 102.771:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1632             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1630             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1630   ksol= 0.32   Bsol= 42.86   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,1.87,2.93,0.00,0.00,0.00); trace/3= 2.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.173545                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.0967 0.1247      5.3694       5.524|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.0862 0.1178      5.4462      5.6574|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.1099 0.1524      5.5012      5.8657|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.1246 0.1655      5.4852      5.6199|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.1374 0.1869      5.3543      5.6067|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.1219 0.1816      5.2279      5.4855|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.1307 0.1710      5.2062      5.3997|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.1211 0.1853      5.0963      5.4092|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.1231 0.1795      5.0822      5.3425|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.1159 0.1833      4.9898        5.26|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.1181 0.1853      4.9904      5.3267|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.1112 0.1703      4.8989      5.1823|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.1189 0.1842      4.8257      5.1101|
| 14:  2.0208 -  1.9716 0.59    759   88 0.1088 0.1645      4.7094      4.9318|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0613 -  4.7065  1392   156  0.94   9.00   0.98     0.96       7155.00|
|  2:  4.7065 -  3.7547  1338   146  0.95   8.21   1.02     1.01       9367.65|
|  3:  3.7547 -  3.2857  1323   144  0.93  11.70   1.04     1.03      10867.98|
|  4:  3.2857 -  2.9878  1306   153  0.91  14.35   1.02     0.99      11001.78|
|  5:  2.9878 -  2.7751  1294   142  0.89  16.72   1.00     0.97       8800.07|
|  6:  2.7751 -  2.6124  1295   142  0.90  16.41   0.99     0.96       7542.74|
|  7:  2.6124 -  2.4822  1295   140  0.90  16.50   1.00     0.97       6848.21|
|  8:  2.4822 -  2.3746  1254   144  0.90  16.40   0.98     0.95       5642.09|
|  9:  2.3746 -  2.2835  1290   148  0.90  16.46   1.00     0.98       5664.57|
| 10:  2.2835 -  2.2049  1278   138  0.90  16.29   1.00     0.97       4744.46|
| 11:  2.2049 -  2.1362  1272   136  0.89  17.05   0.99     0.94       4745.42|
| 12:  2.1362 -  2.0753  1250   145  0.91  15.63   1.02     1.02       4208.92|
| 13:  2.0753 -  2.0208  1284   137  0.90  16.84   1.01     0.99       3620.89|
| 14:  2.0208 -  1.9716   759    88  0.91  15.68   0.99     0.96       2865.19|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2865.19 max =        11001.78 mean =      6797.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.71|
|phase err.(test): min =        0.00 max =           88.25 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1630   ksol= 0.32   Bsol= 46.36   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,-0.48,0.59,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.173583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1630   ksol= 0.32   Bsol= 46.36   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,-0.48,0.59,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.173583                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0613 -  4.7065 0.99   1392  156 0.0967 0.1249      5.3702      5.5251|
|  2:  4.7065 -  3.7547 0.99   1338  146 0.0863 0.1179      5.4471      5.6582|
|  3:  3.7547 -  3.2857 0.99   1323  144 0.1099 0.1525      5.5016      5.8662|
|  4:  3.2857 -  2.9878 0.99   1306  153 0.1246 0.1654      5.4851      5.6197|
|  5:  2.9878 -  2.7751 0.99   1294  142 0.1373 0.1868      5.3541      5.6062|
|  6:  2.7751 -  2.6124 0.99   1295  142 0.1218 0.1815      5.2276      5.4852|
|  7:  2.6124 -  2.4822 0.99   1295  140 0.1307 0.1710      5.2059      5.3995|
|  8:  2.4822 -  2.3746 0.98   1254  144 0.1211 0.1851      5.0962      5.4088|
|  9:  2.3746 -  2.2835 0.98   1290  148 0.1231 0.1795      5.0821      5.3427|
| 10:  2.2835 -  2.2049 1.00   1278  138 0.1158 0.1833      4.9897      5.2597|
| 11:  2.2049 -  2.1362 0.98   1272  136 0.1181 0.1853      4.9904      5.3268|
| 12:  2.1362 -  2.0753 0.98   1250  145 0.1112 0.1702      4.8987      5.1822|
| 13:  2.0753 -  2.0208 0.99   1284  137 0.1189 0.1841      4.8256      5.1097|
| 14:  2.0208 -  1.9716 0.59    759   88 0.1088 0.1645      4.7093      4.9317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0613 -  4.7065  1392   156  0.94   9.02   0.98     0.96       7169.46|
|  2:  4.7065 -  3.7547  1338   146  0.95   8.21   1.02     1.01       9385.09|
|  3:  3.7547 -  3.2857  1323   144  0.93  11.71   1.04     1.03      10879.80|
|  4:  3.2857 -  2.9878  1306   153  0.91  14.35   1.02     1.00      11002.03|
|  5:  2.9878 -  2.7751  1294   142  0.89  16.71   1.00     0.97       8794.29|
|  6:  2.7751 -  2.6124  1295   142  0.90  16.40   0.99     0.96       7538.62|
|  7:  2.6124 -  2.4822  1295   140  0.90  16.50   1.00     0.97       6843.39|
|  8:  2.4822 -  2.3746  1254   144  0.90  16.39   0.99     0.96       5639.65|
|  9:  2.3746 -  2.2835  1290   148  0.90  16.46   1.01     0.99       5662.62|
| 10:  2.2835 -  2.2049  1278   138  0.90  16.29   1.01     0.97       4743.85|
| 11:  2.2049 -  2.1362  1272   136  0.89  17.05   1.00     0.94       4744.47|
| 12:  2.1362 -  2.0753  1250   145  0.91  15.63   1.03     1.02       4207.13|
| 13:  2.0753 -  2.0208  1284   137  0.90  16.84   1.01     1.00       3619.11|
| 14:  2.0208 -  1.9716   759    88  0.91  15.68   1.00     0.97       2863.84|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2863.84 max =        11002.03 mean =      6798.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.71|
|phase err.(test): min =        0.00 max =           88.31 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.738)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.45    105.22  15.56    None  None   None       |
|    all(noH): 2823   0      2.45    105.22  15.56    None  None   None       |
|    Sol.    : 438    0      3.96    92.45   39.76    None  None   None       |
|    Mac.    : 2385   0      2.45    105.22  11.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.446 -  12.723: 1816   |   5:    53.831 -  64.109:   61        |
|      1:    12.723 -  23.000:  513   |   6:    64.109 -  74.386:   33        |
|      2:    23.000 -  33.277:  143   |   7:    74.386 -  84.663:   11        |
|      3:    33.277 -  43.554:  120   |   8:    84.663 -  94.940:    6        |
|      4:    43.554 -  53.831:  118   |   9:    94.940 - 105.217:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.277 - 4.449
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 311
   mapped sites are within: 0.725 - 4.449

peak=   10.953 closest distance to " CB  VAL A 230 " =    1.447
peak=    8.027 closest distance to " CG2 VAL A 296 " =    1.218
peak=    7.249 closest distance to " CG  ARG A 138 " =    1.129
peak=    6.341 closest distance to " CD2 LEU A   5 " =    1.229
peak=    5.833 closest distance to " NE2 GLN A  11 " =    1.183
peak=    5.784 closest distance to " O   HOH Z 130 " =    1.128
peak=    5.622 closest distance to " NH2 ARG A  56 " =    2.123
peak=    5.585 closest distance to " CG  PRO A  54 " =    1.301
peak=    5.426 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.147 closest distance to " CG  LEU A 228 " =    1.146
peak=    5.115 closest distance to " O   HOH Z   7 " =    1.429
peak=    5.108 closest distance to " O   HOH Z 144 " =    2.002
peak=    5.049 closest distance to " O   HOH Z 232 " =    2.301
peak=    4.930 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.863 closest distance to " CG  PRO A 198 " =    1.200
peak=    4.804 closest distance to " O   HOH Z 427 " =    2.496
peak=    4.774 closest distance to " CB  VAL A 296 " =    1.103
peak=    4.754 closest distance to " O   HOH Z 425 " =    1.608
peak=    4.752 closest distance to " CD1AILE A 234 " =    0.985
peak=    4.711 closest distance to " CB  PRO A  54 " =    0.991
peak=    4.657 closest distance to " CB  GLN A 223 " =    1.408
peak=    4.612 closest distance to " O   HOH Z 316 " =    2.935
peak=    4.611 closest distance to " O   HOH Z 126 " =    2.002
peak=    4.601 closest distance to " CB  ASN A 148 " =    1.384
peak=    4.588 closest distance to " CB  SER A   3 " =    1.456
peak=    4.575 closest distance to " CG  PRO A 213 " =    1.252
peak=    4.559 closest distance to " CD2 LEU A 228 " =    1.168
peak=    4.526 closest distance to " O   HOH Z 298 " =    1.811
peak=    4.507 closest distance to " NH1 ARG A 138 " =    0.983
peak=    4.462 closest distance to " CB  SER A  63 " =    1.311
peak=    4.450 closest distance to " O   HOH Z  63 " =    1.396
peak=    4.428 closest distance to " O   HOH Z 369 " =    1.962
peak=    4.401 closest distance to " CB  VAL A 230 " =    1.133
peak=    4.361 closest distance to " O   HOH Z 427 " =    1.217
peak=    4.337 closest distance to " O   HOH Z   9 " =    1.227
peak=    4.321 closest distance to " CG  LEU A 167 " =    1.178
peak=    4.306 closest distance to " O   HOH Z 287 " =    1.853
peak=    4.239 closest distance to " O   HOH Z 193 " =    1.798
peak=    4.232 closest distance to " O   HOH Z 124 " =    1.420
peak=    4.207 closest distance to " O   HOH Z 217 " =    3.103
peak=    4.186 closest distance to " O   PRO A 198 " =    1.538
peak=    4.174 closest distance to " O   HOH Z 392 " =    1.329
peak=    4.163 closest distance to " O   HOH Z   9 " =    1.798
peak=    4.146 closest distance to " O   HOH Z   2 " =    1.780
peak=    4.144 closest distance to " CB  ARG A 275 " =    0.879
peak=    4.131 closest distance to " O   HOH Z 236 " =    1.544
peak=    4.128 closest distance to " O   SER A  87 " =    2.309
peak=    4.096 closest distance to " CB  GLU A 277 " =    3.524
peak=    4.091 closest distance to " O   HOH Z 411 " =    3.631
peak=    4.081 closest distance to " CB  TRP A 266 " =    1.063
peak=    4.079 closest distance to " CB  TRP A 179 " =    1.374
peak=    4.063 closest distance to " O   HOH Z 371 " =    2.593
peak=    4.057 closest distance to " CB  GLU A 152 " =    1.362
peak=    4.053 closest distance to " O   HOH Z 263 " =    1.615
peak=    4.043 closest distance to " CB  GLU A 128 " =    1.106
peak=    4.042 closest distance to " O   PRO A 198 " =    1.248
peak=    4.039 closest distance to " CB  VAL A 265 " =    1.279
peak=    3.997 closest distance to " OD2 ASP A 286 " =    2.771
peak=    3.982 closest distance to " CB  MET A  40 " =    0.859
peak=    3.981 closest distance to " OD1 ASN A  69 " =    2.733
peak=    3.977 closest distance to " O   HOH Z   3 " =    1.973
peak=    3.972 closest distance to " CG2 THR A 221 " =    1.124
peak=    3.945 closest distance to " O   HOH Z 303 " =    2.356
peak=    3.944 closest distance to " O   HOH Z 368 " =    1.870
peak=    3.928 closest distance to " O   HOH Z  61 " =    1.609
peak=    3.924 closest distance to " O   HOH Z 193 " =    1.852
peak=    3.919 closest distance to " O   HOH Z 272 " =    1.804
peak=    3.914 closest distance to " O   HOH Z 222 " =    2.294
peak=    3.895 closest distance to " NH1AARG A 145 " =    1.056
peak=    3.895 closest distance to " ND2 ASN A 187 " =    1.585
peak=    3.883 closest distance to " OG  SER A  62 " =    3.081
peak=    3.860 closest distance to " N   PHE A 130 " =    1.312
peak=    3.856 closest distance to " CG  GLN A  88 " =    1.147
peak=    3.841 closest distance to " O   HOH Z  78 " =    1.587
peak=    3.839 closest distance to " CB  ASN A  39 " =    0.970
peak=    3.837 closest distance to " CG  PRO A 243 " =    1.168
peak=    3.820 closest distance to " CB  SER A 216 " =    0.911
peak=    3.818 closest distance to " CB  TYR A 169 " =    0.883
peak=    3.816 closest distance to " CB  THR A 157 " =    1.065
peak=    3.811 closest distance to " CA  TYR A  30 " =    0.957
peak=    3.800 closest distance to " OG  SER A  62 " =    2.890
peak=    3.796 closest distance to " O   HOH Z  30 " =    1.693
peak=    3.787 closest distance to " O   HOH Z   1 " =    1.836
peak=    3.783 closest distance to " O   HOH Z  97 " =    1.991
peak=    3.779 closest distance to " CA  GLY A 267 " =    0.960
peak=    3.771 closest distance to " O   HOH Z 234 " =    3.368
peak=    3.770 closest distance to " O   HOH Z 134 " =    1.458
peak=    3.762 closest distance to " CB BVAL A  41 " =    1.283
peak=    3.761 closest distance to " CG  ARG A  66 " =    2.638
peak=    3.756 closest distance to " O   HOH Z 419 " =    2.004
peak=    3.752 closest distance to " O   HOH Z 193 " =    1.623
peak=    3.748 closest distance to " O   HOH Z  55 " =    2.078
peak=    3.731 closest distance to " CB  ASN A 187 " =    1.083
peak=    3.729 closest distance to " O   HOH Z 423 " =    1.505
peak=    3.715 closest distance to " O   HOH Z 389 " =    1.911
peak=    3.715 closest distance to " O   HOH Z 126 " =    1.527
peak=    3.705 closest distance to " O   HOH Z 371 " =    1.821
peak=    3.703 closest distance to " O   HOH Z  58 " =    1.714
peak=    3.678 closest distance to " CG1 ILE A  33 " =    1.323
peak=    3.676 closest distance to " CA  ALA A 299 " =    0.956
peak=    3.660 closest distance to " CB  ARG A  79 " =    1.393
peak=    3.660 closest distance to " CB  LEU A 143 " =    1.115
peak=    3.657 closest distance to " CD  ARG A 138 " =    1.077
peak=    3.657 closest distance to " O   HOH Z 144 " =    2.419
peak=    3.652 closest distance to " CB  GLN A  88 " =    1.345
peak=    3.648 closest distance to " CG1BVAL A  72 " =    1.509
peak=    3.634 closest distance to " O   HOH Z 405 " =    1.380
peak=    3.632 closest distance to " O   HOH Z 145 " =    3.478
peak=    3.630 closest distance to " O   HOH Z 203 " =    1.817
peak=    3.629 closest distance to " O   HOH Z 422 " =    2.600
peak=    3.620 closest distance to " ND1 HIS A  86 " =    1.860
peak=    3.618 closest distance to " O   HOH Z 133 " =    1.708
peak=    3.611 closest distance to " CD1 LEU A 300 " =    1.198
peak=    3.607 closest distance to " O   HOH Z 227 " =    1.593
peak=    3.606 closest distance to " CD1 ILE A  33 " =    1.706
peak=    3.605 closest distance to " O   HOH Z  40 " =    2.066
peak=    3.600 closest distance to " O   HOH Z 108 " =    2.150
peak=    3.599 closest distance to " CA  ALA A 158 " =    1.128
peak=    3.596 closest distance to " CB  VAL A 250 " =    1.045
peak=    3.595 closest distance to " O   HOH Z 158 " =    2.878
peak=    3.593 closest distance to " O   HOH Z 346 " =    1.537
peak=    3.591 closest distance to " O   HOH Z 145 " =    1.561
peak=    3.590 closest distance to " CA  LYS A 117 " =    1.161
peak=    3.590 closest distance to " CB  ILE A 234 " =    0.962
peak=    3.560 closest distance to " O   HOH Z 214 " =    1.969
peak=    3.560 closest distance to " O   HOH Z 403 " =    1.670
peak=    3.560 closest distance to " CG  PRO A 280 " =    0.851
peak=    3.559 closest distance to " O   HOH Z 119 " =    1.549
peak=    3.558 closest distance to " CA  ALA A  51 " =    1.028
peak=    3.557 closest distance to " CG2 VAL A 257 " =    0.912
peak=    3.556 closest distance to " O   HOH Z 368 " =    3.658
peak=    3.554 closest distance to " O   HOH Z 290 " =    0.948
peak=    3.551 closest distance to " O   HOH Z 146 " =    1.623
peak=    3.546 closest distance to " CA  SER A  87 " =    0.935
peak=    3.546 closest distance to " O   HOH Z 410 " =    1.498
peak=    3.544 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.540 closest distance to " O   HOH Z 344 " =    1.063
peak=    3.540 closest distance to " O   HOH Z 423 " =    2.377
peak=    3.537 closest distance to " O   HOH Z 180 " =    2.036
peak=    3.534 closest distance to " CB  LEU A 228 " =    1.270
peak=    3.532 closest distance to " CB  SER A 212 " =    1.318
peak=    3.522 closest distance to " CD BLYS A 290 " =    1.122
peak=    3.516 closest distance to " CG1 ILE A 151 " =    1.159
peak=    3.515 closest distance to " CB  THR A  82 " =    1.234
peak=    3.514 closest distance to " O   HOH Z 132 " =    2.463
peak=    3.504 closest distance to " CE3 TRP A 274 " =    2.370
peak=    3.504 closest distance to " O   HOH Z  59 " =    1.661
peak=    3.502 closest distance to " CB  VAL A 202 " =    1.610
peak=    3.502 closest distance to " O   HOH Z 195 " =    1.335
peak=    3.501 closest distance to " NH2BARG A 145 " =    2.117
peak=    3.498 closest distance to " CB  LEU A 255 " =    0.778
peak=    3.487 closest distance to " CG  GLN A  89 " =    1.386
peak=    3.484 closest distance to " CB  ASN A 142 " =    0.856
peak=    3.483 closest distance to " CE1 TYR A 186 " =    1.335
peak=    3.471 closest distance to " CD  ARG A 159 " =    0.730
peak=    3.465 closest distance to " CG BARG A 102 " =    1.854
peak=    3.460 closest distance to " O   HOH Z 380 " =    1.652
peak=    3.458 closest distance to " O   HOH Z 334 " =    1.666
peak=    3.455 closest distance to " O   HOH Z  68 " =    1.946
peak=    3.450 closest distance to " NH2AARG A 190 " =    1.803
peak=    3.448 closest distance to " O   HOH Z 135 " =    1.971
peak=    3.443 closest distance to " O   HOH Z  10 " =    1.720
peak=    3.442 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.440 closest distance to " CA  ASN A 127 " =    1.077
peak=    3.433 closest distance to " O   HOH Z 280 " =    3.017
peak=    3.432 closest distance to " NH1 ARG A  14 " =    0.943
peak=    3.431 closest distance to " O   HOH Z 175 " =    2.137
peak=    3.428 closest distance to " CB  GLN A  89 " =    1.180
peak=    3.425 closest distance to " O   HOH Z 437 " =    2.336
peak=    3.422 closest distance to " CA  ALA A 160 " =    0.902
peak=    3.414 closest distance to " O   HOH Z 207 " =    1.844
peak=    3.414 closest distance to " CA  LYS A 290 " =    1.304
peak=    3.412 closest distance to " O   HOH Z 280 " =    1.588
peak=    3.400 closest distance to " O   HOH Z 273 " =    2.727
peak=    3.400 closest distance to " O   HOH Z  78 " =    1.930
peak=    3.398 closest distance to " O   HOH Z 344 " =    2.817
peak=    3.397 closest distance to " CA  ALA A  21 " =    1.178
peak=    3.390 closest distance to " CD  PRO A 243 " =    1.579
peak=    3.389 closest distance to " OG BSER A 164 " =    2.281
peak=    3.387 closest distance to " CA  TYR A 116 " =    1.449
peak=    3.386 closest distance to " CA  THR A 264 " =    0.773
peak=    3.385 closest distance to " O   HOH Z 189 " =    2.606
peak=    3.380 closest distance to " O   HOH Z 209 " =    2.380
peak=    3.379 closest distance to " O   HOH Z 128 " =    1.962
peak=    3.374 closest distance to " O   HOH Z 329 " =    3.814
peak=    3.369 closest distance to " CA  ASN A 215 " =    1.220
peak=    3.364 closest distance to " O   HOH Z 359 " =    1.267
peak=    3.359 closest distance to " CG  MET A 185 " =    1.230
peak=    3.357 closest distance to " O   HOH Z 189 " =    2.935
peak=    3.356 closest distance to " CG  ARG A 159 " =    0.936
peak=    3.355 closest distance to " OG BSER A  99 " =    2.136
peak=    3.348 closest distance to " O   HOH Z 271 " =    1.993
peak=    3.344 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.343 closest distance to " O   HOH Z 109 " =    2.428
peak=    3.336 closest distance to " O   HOH Z 345 " =    3.373
peak=    3.335 closest distance to " O   HOH Z 435 " =    2.172
peak=    3.335 closest distance to " CA  ILE A 234 " =    0.961
peak=    3.334 closest distance to " O   HOH Z  88 " =    2.669
peak=    3.328 closest distance to " CB  SER A  62 " =    1.157
peak=    3.323 closest distance to " N   ALA A 256 " =    1.127
peak=    3.323 closest distance to " O   HOH Z 209 " =    2.328
peak=    3.321 closest distance to " O   MET A 105 " =    1.780
peak=    3.321 closest distance to " O   HOH Z  88 " =    3.398
peak=    3.318 closest distance to " O   HOH Z 303 " =    1.761
peak=    3.317 closest distance to " C   GLU A 277 " =    1.220
peak=    3.308 closest distance to " CB  ARG A 139 " =    1.058
peak=    3.308 closest distance to " CA  LEU A 101 " =    1.613
peak=    3.305 closest distance to " O   HOH Z 340 " =    2.185
peak=    3.304 closest distance to " N   SER A 135 " =    1.335
peak=    3.300 closest distance to " CG1 VAL A 153 " =    0.923
peak=    3.297 closest distance to " CE  MET A  93 " =    1.456
peak=    3.296 closest distance to " CA  ASN A  74 " =    1.272
peak=    3.296 closest distance to " O   HOH Z 409 " =    2.916
peak=    3.295 closest distance to " O   HOH Z   1 " =    1.604
peak=    3.293 closest distance to " CD1 LEU A 228 " =    1.767
peak=    3.293 closest distance to " O   HOH Z 295 " =    1.572
peak=    3.292 closest distance to " CA  ARG A 102 " =    1.104
peak=    3.291 closest distance to " O   HOH Z 276 " =    1.205
peak=    3.289 closest distance to " CD2 LEU A 297 " =    0.911
peak=    3.282 closest distance to " N   GLN A 278 " =    1.077
peak=    3.278 closest distance to " N   ASN A 127 " =    1.386
peak=    3.273 closest distance to " O   HOH Z  64 " =    2.292
peak=    3.273 closest distance to " CB  LEU A 237 " =    0.865
peak=    3.269 closest distance to " O   HOH Z 112 " =    1.674
peak=    3.267 closest distance to " O   HOH Z 184 " =    1.378
peak=    3.267 closest distance to " O   HOH Z  71 " =    1.208
peak=    3.266 closest distance to " O   HOH Z 213 " =    2.487
peak=    3.266 closest distance to " O   HOH Z 181 " =    2.209
peak=    3.265 closest distance to " CB  ASP A 140 " =    0.948
peak=    3.261 closest distance to " O   HOH Z  48 " =    1.415
peak=    3.261 closest distance to " NE2 GLN A  58 " =    3.304
peak=    3.261 closest distance to " O   HOH Z   6 " =    2.105
peak=    3.259 closest distance to " CD2 LEU A 255 " =    1.468
peak=    3.256 closest distance to " O   ALA A 158 " =    1.371
peak=    3.252 closest distance to " OE2 GLU A  53 " =    2.020
peak=    3.247 closest distance to " O   HOH Z 282 " =    2.021
peak=    3.246 closest distance to " N   VAL A 126 " =    1.151
peak=    3.245 closest distance to " CB  ALA A   1 " =    4.449
peak=    3.243 closest distance to " CG1 ILE A 263 " =    1.287
peak=    3.240 closest distance to " CD  LYS A 166 " =    1.383
peak=    3.238 closest distance to " OE1 GLN A 240 " =    1.571
peak=    3.236 closest distance to " O   ASN A 209 " =    1.452
peak=    3.236 closest distance to " O   HOH Z 207 " =    2.163
peak=    3.235 closest distance to " NE AARG A 275 " =    1.350
peak=    3.235 closest distance to " CA  LEU A 282 " =    1.102
peak=    3.233 closest distance to " CB  ARG A 190 " =    1.680
peak=    3.233 closest distance to " O   HOH Z 366 " =    2.942
peak=    3.231 closest distance to " O   HOH Z 281 " =    1.706
peak=    3.230 closest distance to " CB  HIS A 108 " =    0.865
peak=    3.229 closest distance to " O   HOH Z  59 " =    2.003
peak=    3.223 closest distance to " N   SER A 271 " =    0.978
peak=    3.221 closest distance to " O   HOH Z 305 " =    3.355
peak=    3.218 closest distance to " O   HOH Z  93 " =    2.549
peak=    3.214 closest distance to " O   ALA A 165 " =    1.342
peak=    3.208 closest distance to " O   HOH Z 302 " =    1.706
peak=    3.205 closest distance to " CA  ALA A 248 " =    1.160
peak=    3.203 closest distance to " CB  LYS A 117 " =    1.184
peak=    3.202 closest distance to " OG BSER A 134 " =    3.163
peak=    3.201 closest distance to " N   TRP A 177 " =    1.639
peak=    3.201 closest distance to " O   HOH Z 130 " =    1.932
peak=    3.201 closest distance to " CZ  PHE A 192 " =    0.997
peak=    3.192 closest distance to " O   HOH Z 373 " =    1.478
peak=    3.192 closest distance to " O   HOH Z  44 " =    1.709
peak=    3.191 closest distance to " O   HOH Z   6 " =    1.457
peak=    3.185 closest distance to " O   HOH Z  44 " =    2.746
peak=    3.183 closest distance to " O   HOH Z 192 " =    2.063
peak=    3.174 closest distance to " OG  SER A  22 " =    2.912
peak=    3.171 closest distance to " O   HOH Z 217 " =    1.653
peak=    3.165 closest distance to " O   HOH Z 110 " =    1.568
peak=    3.162 closest distance to " O   HOH Z  40 " =    2.050
peak=    3.157 closest distance to " O   GLN A  58 " =    1.521
peak=    3.156 closest distance to " CG2 VAL A 197 " =    1.135
peak=    3.155 closest distance to " CB  THR A  31 " =    1.758
peak=    3.152 closest distance to " O   HOH Z 391 " =    3.017
peak=    3.149 closest distance to " O   HOH Z 227 " =    2.131
peak=    3.146 closest distance to " O   HOH Z 325 " =    3.590
peak=    3.146 closest distance to " CB  TYR A  30 " =    1.558
peak=    3.145 closest distance to " CE  LYS A  48 " =    1.063
peak=    3.144 closest distance to " O   HOH Z  64 " =    1.952
peak=    3.140 closest distance to " O   HOH Z 115 " =    1.475
peak=    3.140 closest distance to " CA  VAL A 126 " =    1.283
peak=    3.138 closest distance to " CB  ALA A 104 " =    0.725
peak=    3.137 closest distance to " CG  LYS A  76 " =    1.521
peak=    3.136 closest distance to " O   HOH Z 148 " =    3.450
peak=    3.128 closest distance to " CA  ARG A  36 " =    1.075
peak=    3.127 closest distance to " N   SER A 134 " =    1.399
peak=    3.125 closest distance to " CB  ASN A 110 " =    1.146
peak=    3.124 closest distance to " OD1BASN A 224 " =    2.323
peak=    3.123 closest distance to " O   HOH Z 353 " =    2.652
peak=    3.108 closest distance to " OE2 GLU A   2 " =    1.806
peak=    3.100 closest distance to " CB  TRP A 150 " =    1.362
peak=    3.096 closest distance to " O   HOH Z 323 " =    1.577
peak=    3.095 closest distance to " O   HOH Z 197 " =    3.282
peak=    3.095 closest distance to " CB  GLU A 236 " =    1.254
peak=    3.094 closest distance to " O   HOH Z 116 " =    1.686
peak=    3.094 closest distance to " O   HOH Z 118 " =    1.580
peak=    3.084 closest distance to " CA  ALA A 233 " =    1.106
peak=    3.078 closest distance to " ND1 HIS A  81 " =    1.708
peak=    3.077 closest distance to " O   HOH Z 425 " =    1.900
peak=    3.074 closest distance to " CA  ASP A  50 " =    0.996
peak=    3.068 closest distance to " O   TYR A 116 " =    1.238
peak=    3.062 closest distance to " CG1 ILE A 120 " =    1.385
peak=    3.051 closest distance to " O   HOH Z 172 " =    3.203
peak=    3.041 closest distance to " CA  ALA A 114 " =    1.782
peak=    3.005 closest distance to " O   HOH Z  43 " =    2.015

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.747 - 5.408
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.747 - 5.408

peak=   -4.562 closest distance to " CG2 VAL A 230 " =    0.847
peak=   -4.450 closest distance to " CD  ARG A  14 " =    3.130
peak=   -4.407 closest distance to " O   HOH Z  52 " =    1.239
peak=   -4.352 closest distance to " CG  ARG A 138 " =    0.929
peak=   -4.296 closest distance to " CD  ARG A 156 " =    1.955
peak=   -4.280 closest distance to " O   HOH Z 377 " =    1.932
peak=   -4.241 closest distance to " OG BSER A 134 " =    1.253
peak=   -4.224 closest distance to " O   HOH Z 231 " =    1.721
peak=   -4.135 closest distance to " O   HOH Z  43 " =    1.794
peak=   -4.123 closest distance to " CD  ARG A 138 " =    1.309
peak=   -4.099 closest distance to " CD1 LEU A 255 " =    2.903
peak=   -4.094 closest distance to " CG2 VAL A 296 " =    1.293
peak=   -4.049 closest distance to " CB  PRO A 243 " =    2.604
peak=   -4.026 closest distance to " O   HOH Z 388 " =    2.209
peak=   -4.001 closest distance to " O   HOH Z 191 " =    5.293
peak=   -3.969 closest distance to " O   HOH Z 266 " =    4.876
peak=   -3.967 closest distance to " OE1 GLU A 277 " =    2.189
peak=   -3.945 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.939 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.896 closest distance to " CD  LYS A 289 " =    2.504
peak=   -3.869 closest distance to " CG1 VAL A 197 " =    2.373
peak=   -3.865 closest distance to " N   ALA A  43 " =    2.461
peak=   -3.845 closest distance to " CA  ASP A  27 " =    2.455
peak=   -3.817 closest distance to " OG ASER A 134 " =    1.201
peak=   -3.808 closest distance to " CA  GLY A 133 " =    1.946
peak=   -3.789 closest distance to " NH1 ARG A  56 " =    2.469
peak=   -3.776 closest distance to " O   HOH Z 298 " =    1.172
peak=   -3.753 closest distance to " O   HOH Z 351 " =    1.548
peak=   -3.750 closest distance to " CD2 LEU A   5 " =    1.035
peak=   -3.749 closest distance to " CE1 PHE A  59 " =    2.029
peak=   -3.748 closest distance to " O   HOH Z  65 " =    1.102
peak=   -3.742 closest distance to " CD1 LEU A 101 " =    2.361
peak=   -3.730 closest distance to " CE2 PHE A 218 " =    2.499
peak=   -3.717 closest distance to " NH2 ARG A  79 " =    1.907
peak=   -3.714 closest distance to " CD2 LEU A 237 " =    2.785
peak=   -3.704 closest distance to " CG  GLN A 223 " =    2.222
peak=   -3.697 closest distance to " CG2 THR A   4 " =    1.959
peak=   -3.693 closest distance to " O   HOH Z 389 " =    1.829
peak=   -3.692 closest distance to " CB  ALA A   7 " =    1.997
peak=   -3.686 closest distance to " N   THR A 157 " =    1.440
peak=   -3.684 closest distance to " OG  SER A  87 " =    1.359
peak=   -3.672 closest distance to " C   ASN A 285 " =    2.278
peak=   -3.662 closest distance to " O   HOH Z 198 " =    2.364
peak=   -3.656 closest distance to " O   HOH Z 290 " =    1.213
peak=   -3.650 closest distance to " O   HOH Z 407 " =    3.190
peak=   -3.606 closest distance to " O   HOH Z 211 " =    1.395
peak=   -3.599 closest distance to " CB  TYR A  15 " =    2.047
peak=   -3.593 closest distance to " O   HOH Z 166 " =    1.414
peak=   -3.586 closest distance to " O   HOH Z 350 " =    1.926
peak=   -3.580 closest distance to " O   GLY A  80 " =    2.363
peak=   -3.567 closest distance to " O   HOH Z  90 " =    2.852
peak=   -3.558 closest distance to " CG  PHE A 283 " =    2.651
peak=   -3.556 closest distance to " O   VAL A  67 " =    2.716
peak=   -3.555 closest distance to " N   GLN A  58 " =    1.838
peak=   -3.547 closest distance to " CD1 LEU A 101 " =    2.562
peak=   -3.545 closest distance to " O   HOH Z 143 " =    1.305
peak=   -3.545 closest distance to " O   SER A 135 " =    1.474
peak=   -3.540 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.538 closest distance to " CE2 TYR A  30 " =    2.670
peak=   -3.527 closest distance to " O   GLY A 211 " =    1.274
peak=   -3.522 closest distance to " O   PRO A 163 " =    1.928
peak=   -3.519 closest distance to " O   HOH Z  47 " =    1.583
peak=   -3.516 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.511 closest distance to " O   HOH Z 359 " =    1.653
peak=   -3.510 closest distance to " O   HOH Z 103 " =    1.748
peak=   -3.510 closest distance to " O   HOH Z 275 " =    1.608
peak=   -3.502 closest distance to " OG  SER A 206 " =    1.696
peak=   -3.501 closest distance to " O   HOH Z 359 " =    3.379
peak=   -3.498 closest distance to " N   SER A 276 " =    1.255
peak=   -3.498 closest distance to " O   HOH Z   9 " =    1.622
peak=   -3.488 closest distance to " CZ  PHE A  59 " =    1.492
peak=   -3.487 closest distance to " CA  GLY A  98 " =    1.940
peak=   -3.487 closest distance to " O   HOH Z 281 " =    3.029
peak=   -3.486 closest distance to " CG  PRO A 163 " =    2.558
peak=   -3.484 closest distance to " CB  ALA A 161 " =    2.608
peak=   -3.481 closest distance to " O   SER A  22 " =    2.402
peak=   -3.478 closest distance to " CE2 TYR A 116 " =    3.050
peak=   -3.470 closest distance to " CA  GLY A  35 " =    1.995
peak=   -3.466 closest distance to " O   HOH Z 348 " =    1.740
peak=   -3.465 closest distance to " CG  TRP A 266 " =    1.604
peak=   -3.462 closest distance to " CB  PRO A 163 " =    2.456
peak=   -3.462 closest distance to " OD2 ASP A  50 " =    1.585
peak=   -3.457 closest distance to " C   ASN A 187 " =    1.731
peak=   -3.455 closest distance to " CG2 VAL A 202 " =    2.658
peak=   -3.452 closest distance to " CG2 THR A 178 " =    2.178
peak=   -3.446 closest distance to " NH2AARG A 275 " =    5.408
peak=   -3.440 closest distance to " CG  GLU A 152 " =    2.239
peak=   -3.436 closest distance to " O   HOH Z 111 " =    4.147
peak=   -3.435 closest distance to " NH2BARG A 275 " =    1.637
peak=   -3.430 closest distance to " N   VAL A  72 " =    1.515
peak=   -3.418 closest distance to " CD1 LEU A 228 " =    2.258
peak=   -3.416 closest distance to " CD2 LEU A 237 " =    2.681
peak=   -3.411 closest distance to " O   HOH Z  71 " =    1.225
peak=   -3.409 closest distance to " O   PRO A 198 " =    1.360
peak=   -3.407 closest distance to " O   HOH Z 185 " =    2.026
peak=   -3.406 closest distance to " O   HOH Z 345 " =    2.074
peak=   -3.399 closest distance to " O   HOH Z 140 " =    1.482
peak=   -3.393 closest distance to " OD1 ASN A 187 " =    1.525
peak=   -3.385 closest distance to " N   ALA A 248 " =    1.599
peak=   -3.377 closest distance to " O   HOH Z  60 " =    2.186
peak=   -3.374 closest distance to " OE1 GLN A  88 " =    1.235
peak=   -3.373 closest distance to " O   HOH Z 148 " =    2.061
peak=   -3.372 closest distance to " CD2 PHE A  61 " =    1.841
peak=   -3.369 closest distance to " OG BSER A 134 " =    1.683
peak=   -3.366 closest distance to " CZ3 TRP A 179 " =    1.222
peak=   -3.363 closest distance to " CA  GLY A 241 " =    2.140
peak=   -3.360 closest distance to " O   HOH Z 435 " =    2.070
peak=   -3.356 closest distance to " O   ALA A 161 " =    1.672
peak=   -3.355 closest distance to " CG2 VAL A 112 " =    2.463
peak=   -3.347 closest distance to " CB  ALA A 244 " =    2.037
peak=   -3.330 closest distance to " SD BMET A  47 " =    2.940
peak=   -3.329 closest distance to " O   ILE A  49 " =    1.791
peak=   -3.329 closest distance to " CE  MET A 105 " =    2.294
peak=   -3.325 closest distance to " CB  ALA A  43 " =    2.473
peak=   -3.324 closest distance to " O   HOH Z  13 " =    1.521
peak=   -3.322 closest distance to " O   PRO A 243 " =    2.502
peak=   -3.317 closest distance to " O   HOH Z 111 " =    0.997
peak=   -3.315 closest distance to " OH  TYR A 214 " =    1.145
peak=   -3.314 closest distance to " O   TYR A  30 " =    2.780
peak=   -3.311 closest distance to " CB  ASN A  39 " =    2.128
peak=   -3.310 closest distance to " O   HOH Z  93 " =    2.259
peak=   -3.304 closest distance to " O   VAL A  67 " =    2.576
peak=   -3.304 closest distance to " O   GLY A 203 " =    2.471
peak=   -3.299 closest distance to " O   HOH Z 292 " =    1.600
peak=   -3.297 closest distance to " CB  ALA A 248 " =    1.983
peak=   -3.296 closest distance to " N   VAL A 125 " =    1.091
peak=   -3.288 closest distance to " O   HOH Z 385 " =    2.183
peak=   -3.287 closest distance to " OG  SER A  87 " =    1.565
peak=   -3.285 closest distance to " O   HOH Z 134 " =    2.722
peak=   -3.284 closest distance to " CZ2 TRP A 179 " =    2.354
peak=   -3.276 closest distance to " CG2 ILE A 151 " =    2.549
peak=   -3.273 closest distance to " CB  PHE A 192 " =    1.698
peak=   -3.270 closest distance to " C   LEU A 222 " =    0.761
peak=   -3.270 closest distance to " O   HOH Z 417 " =    2.766
peak=   -3.262 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.259 closest distance to " O   HOH Z  51 " =    1.059
peak=   -3.256 closest distance to " O   TRP A  70 " =    1.480
peak=   -3.255 closest distance to " OG1 THR A 178 " =    1.176
peak=   -3.252 closest distance to " CB  CYS A 254 " =    1.935
peak=   -3.251 closest distance to " CA  ASN A 127 " =    1.223
peak=   -3.251 closest distance to " O   HOH Z 241 " =    1.447
peak=   -3.248 closest distance to " CB  PRO A  90 " =    1.530
peak=   -3.242 closest distance to " O   HOH Z 313 " =    1.608
peak=   -3.237 closest distance to " CB  ALA A 131 " =    1.975
peak=   -3.235 closest distance to " CB  VAL A 230 " =    1.079
peak=   -3.234 closest distance to " CE  LYS A  76 " =    2.785
peak=   -3.229 closest distance to " C   LEU A 143 " =    1.319
peak=   -3.227 closest distance to " O   HOH Z  97 " =    1.680
peak=   -3.220 closest distance to " CG  ASP A 231 " =    0.747
peak=   -3.215 closest distance to " O   HOH Z 427 " =    1.598
peak=   -3.211 closest distance to " O   HOH Z  38 " =    1.898
peak=   -3.211 closest distance to " N   HIS A 115 " =    2.191
peak=   -3.210 closest distance to " O   HOH Z 426 " =    2.282
peak=   -3.210 closest distance to " CG1 VAL A 112 " =    2.557
peak=   -3.209 closest distance to " OE2 GLU A 152 " =    1.010
peak=   -3.204 closest distance to " ND2 ASN A 209 " =    1.948
peak=   -3.203 closest distance to " O   ASN A 301 " =    1.373
peak=   -3.203 closest distance to " O   HOH Z  90 " =    1.867
peak=   -3.202 closest distance to " O   HOH Z 423 " =    2.168
peak=   -3.202 closest distance to " O   HOH Z   1 " =    1.518
peak=   -3.200 closest distance to " O   HOH Z 207 " =    1.913
peak=   -3.198 closest distance to " O   PHE A 218 " =    1.332
peak=   -3.194 closest distance to " N   LYS A 166 " =    1.917
peak=   -3.192 closest distance to " O   GLY A  98 " =    2.019
peak=   -3.192 closest distance to " O   HOH Z 365 " =    1.386
peak=   -3.188 closest distance to " O   HOH Z 222 " =    3.099
peak=   -3.187 closest distance to " ND2 ASN A  39 " =    1.676
peak=   -3.187 closest distance to " OD2 ASP A 191 " =    1.391
peak=   -3.183 closest distance to " CA  SER A 146 " =    2.367
peak=   -3.182 closest distance to " O   HOH Z 102 " =    1.671
peak=   -3.178 closest distance to " O   HOH Z 309 " =    2.298
peak=   -3.176 closest distance to " O   ASP A 270 " =    1.605
peak=   -3.176 closest distance to " C   ARG A 269 " =    1.415
peak=   -3.173 closest distance to " N   GLY A  23 " =    2.185
peak=   -3.172 closest distance to " N   THR A 235 " =    1.229
peak=   -3.160 closest distance to " O   HOH Z 426 " =    1.692
peak=   -3.159 closest distance to " O   HOH Z 166 " =    1.706
peak=   -3.154 closest distance to " O   HOH Z 274 " =    3.006
peak=   -3.152 closest distance to " O   HOH Z 368 " =    1.512
peak=   -3.148 closest distance to " O   HOH Z 414 " =    2.363
peak=   -3.147 closest distance to " O   HOH Z 131 " =    4.047
peak=   -3.142 closest distance to " OE1 GLN A  73 " =    2.397
peak=   -3.141 closest distance to " C   LYS A  76 " =    1.482
peak=   -3.138 closest distance to " O   GLN A 240 " =    1.947
peak=   -3.129 closest distance to " O   HOH Z 208 " =    2.024
peak=   -3.127 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.125 closest distance to " C   MET A 188 " =    1.633
peak=   -3.125 closest distance to " OD1 ASN A 301 " =    2.011
peak=   -3.118 closest distance to " OD1 ASP A 200 " =    1.449
peak=   -3.115 closest distance to " O   HOH Z 139 " =    3.511
peak=   -3.109 closest distance to " O   MET A  40 " =    2.778
peak=   -3.108 closest distance to " CG1 VAL A 296 " =    1.344
peak=   -3.086 closest distance to " CD1 ILE A 199 " =    2.516
peak=   -3.075 closest distance to " CD  GLN A  88 " =    0.853
peak=   -3.072 closest distance to " CB  ASP A 132 " =    2.319
peak=   -3.068 closest distance to " O   HOH Z 353 " =    1.772
peak=   -3.066 closest distance to " O   VAL A 189 " =    2.585
peak=   -3.059 closest distance to " O   HOH Z 198 " =    1.736
peak=   -3.058 closest distance to " O   HOH Z 377 " =    0.989
peak=   -3.056 closest distance to " O   VAL A 125 " =    2.380
peak=   -3.053 closest distance to " NH2 ARG A  66 " =    4.908
peak=   -3.038 closest distance to " CD2 TYR A 293 " =    1.940
peak=   -3.019 closest distance to " O   HOH Z 417 " =    2.523
peak=   -3.019 closest distance to " O   HOH Z  28 " =    2.263
peak=   -3.010 closest distance to " CD2 LEU A 237 " =    2.219

================= 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    :  0.4705 0.4528   6.270556e+00   6.255599e+00
   1_bss:  0.4607 0.4414   6.264442e+00   6.246169e+00
   1_xyz:  0.3709 0.4004   6.132736e+00   6.169666e+00
   1_adp:  0.3269 0.3769   6.045042e+00   6.135474e+00
   1_occ:  0.3265 0.3772   6.044200e+00   6.135800e+00
   2_bss:  0.3221 0.3705   6.042560e+00   6.131757e+00
   2_xyz:  0.2304 0.2815   5.757632e+00   5.913021e+00
   2_adp:  0.2116 0.2707   5.695849e+00   5.879103e+00
   2_occ:  0.2114 0.2705   5.695185e+00   5.878804e+00
   3_bss:  0.2098 0.2666   5.692402e+00   5.873695e+00
   3_xyz:  0.1605 0.2178   5.465332e+00   5.689693e+00
   3_adp:  0.1381 0.1916   5.328691e+00   5.567603e+00
   3_occ:  0.1380 0.1916   5.328446e+00   5.567262e+00
   4_bss:  0.1380 0.1910   5.326650e+00   5.565229e+00
   4_xyz:  0.1275 0.1767   5.256082e+00   5.497655e+00
   4_adp:  0.1242 0.1729   5.235201e+00   5.474801e+00
   4_occ:  0.1242 0.1728   5.234685e+00   5.473930e+00
   5_bss:  0.1241 0.1728   5.234570e+00   5.473854e+00
   5_xyz:  0.1159 0.1654   5.184636e+00   5.437528e+00
   5_adp:  0.1147 0.1632   5.173960e+00   5.426212e+00
   5_occ:  0.1146 0.1630   5.173545e+00   5.425587e+00
   5_bss:  0.1146 0.1630   5.173583e+00   5.425609e+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:  0.344   0.000   8.056   9.940   8.121   0.000   0.000   0.000
   1_xyz:  0.344   0.000   8.056   9.940   8.121   0.000   0.000   0.000
   1_adp:  0.344   0.000   8.056   9.940   8.121   0.000   0.000   0.000
   1_occ:  0.344   0.000   8.056   9.940   8.121   0.000   0.000   0.000
   2_bss:  0.339  32.081   4.190   5.274   4.727   0.000   0.000   0.000
   2_xyz:  0.339  32.081   4.190   5.274   4.727   0.000   0.000   0.000
   2_adp:  0.339  32.081   4.190   5.274   4.727   0.000   0.000   0.000
   2_occ:  0.339  32.081   4.190   5.274   4.727   0.000   0.000   0.000
   3_bss:  0.326  36.287   2.807   3.003   3.532   0.000   0.000   0.000
   3_xyz:  0.326  36.287   2.807   3.003   3.532   0.000   0.000   0.000
   3_adp:  0.326  36.287   2.807   3.003   3.532   0.000   0.000   0.000
   3_occ:  0.326  36.287   2.807   3.003   3.532   0.000   0.000   0.000
   4_bss:  0.319  42.858   2.259   1.999   2.940   0.000   0.000   0.000
   4_xyz:  0.319  42.858   2.259   1.999   2.940   0.000   0.000   0.000
   4_adp:  0.319  42.858   2.259   1.999   2.940   0.000   0.000   0.000
   4_occ:  0.319  42.858   2.259   1.999   2.940   0.000   0.000   0.000
   5_bss:  0.319  42.858   2.216   1.868   2.933   0.000   0.000   0.000
   5_xyz:  0.319  42.858   2.216   1.868   2.933   0.000   0.000   0.000
   5_adp:  0.319  42.858   2.216   1.868   2.933   0.000   0.000   0.000
   5_occ:  0.319  42.858   2.216   1.868   2.933   0.000   0.000   0.000
   5_bss:  0.320  46.362  -0.116  -0.477   0.593  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.966 0.4715  0.5485    64078.772
   1_bss:  53.789 0.4721  0.7023    61269.465
   1_xyz:  45.635 0.5730  0.8367    46100.227
   1_adp:  41.074 0.6297  0.9589    40647.598
   1_occ:  41.134 0.6290  0.9566    40709.636
   2_bss:  40.659 0.6347  0.8428    40117.883
   2_xyz:  28.915 0.7689  0.9793    20893.623
   2_adp:  27.051 0.7898  1.0111    19154.344
   2_occ:  27.044 0.7898  1.0107    19118.664
   3_bss:  26.795 0.7922  0.9554    18740.906
   3_xyz:  21.025 0.8513  0.9965    11950.572
   3_adp:  18.054 0.8797  1.0051     9331.203
   3_occ:  18.050 0.8798  1.0049     9319.748
   4_bss:  17.989 0.8802  0.9790     9256.733
   4_xyz:  16.328 0.8952  0.9843     7902.829
   4_adp:  15.749 0.9006  0.9807     7556.262
   4_occ:  15.731 0.9008  0.9807     7541.980
   5_bss:  15.728 0.9008  0.9786     7539.985
   5_xyz:  14.966 0.9071  0.9820     6971.967
   5_adp:  14.666 0.9097  0.9781     6811.509
   5_occ:  14.652 0.9098  0.9781     6797.285
   5_bss:  14.653 0.9098  0.9819     6798.829
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3455e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3455e+01
   1_xyz:   1.684  0.013  0.106 18.142  0.006  4.108   1.3961e-01
   1_adp:   1.684  0.013  0.106 18.142  0.006  4.108   1.3961e-01
   1_occ:   1.684  0.013  0.106 18.142  0.006  4.108   1.3961e-01
   2_bss:   1.684  0.013  0.106 18.142  0.006  4.108   1.3961e-01
   2_xyz:   1.102  0.008  0.079 16.103  0.005  4.120   7.7637e-02
   2_adp:   1.102  0.008  0.079 16.103  0.005  4.120   7.7637e-02
   2_occ:   1.102  0.008  0.079 16.103  0.005  4.120   7.7637e-02
   3_bss:   1.102  0.008  0.079 16.103  0.005  4.120   7.7637e-02
   3_xyz:   1.054  0.007  0.079 15.765  0.004  4.109   6.8025e-02
   3_adp:   1.054  0.007  0.079 15.765  0.004  4.109   6.8025e-02
   3_occ:   1.054  0.007  0.079 15.765  0.004  4.109   6.8025e-02
   4_bss:   1.054  0.007  0.079 15.765  0.004  4.109   6.8025e-02
   4_xyz:   0.875  0.005  0.068 15.358  0.003  4.111   5.1048e-02
   4_adp:   0.875  0.005  0.068 15.358  0.003  4.111   5.1048e-02
   4_occ:   0.875  0.005  0.068 15.358  0.003  4.111   5.1048e-02
   5_bss:   0.875  0.005  0.068 15.358  0.003  4.111   5.1048e-02
   5_xyz:   1.005  0.006  0.079 15.615  0.003  4.114   6.0484e-02
   5_adp:   1.005  0.006  0.079 15.615  0.003  4.114   6.0484e-02
   5_occ:   1.005  0.006  0.079 15.615  0.003  4.114   6.0484e-02
   5_bss:   1.005  0.006  0.079 15.615  0.003  4.114   6.0484e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9299e+00
   1_xyz:  13.742  0.167  0.461 88.633  0.036  2.233   1.0158e-01
   1_adp:  13.742  0.167  0.461 88.633  0.036  2.233   1.0158e-01
   1_occ:  13.742  0.167  0.461 88.633  0.036  2.233   1.0158e-01
   2_bss:  13.742  0.167  0.461 88.633  0.036  2.233   1.0158e-01
   2_xyz:   6.876  0.057  0.364 84.776  0.038  2.267   6.4230e-02
   2_adp:   6.876  0.057  0.364 84.776  0.038  2.267   6.4230e-02
   2_occ:   6.876  0.057  0.364 84.776  0.038  2.267   6.4230e-02
   3_bss:   6.876  0.057  0.364 84.776  0.038  2.267   6.4230e-02
   3_xyz:   8.044  0.058  0.426 82.114  0.016  2.204   8.3075e-02
   3_adp:   8.044  0.058  0.426 82.114  0.016  2.204   8.3075e-02
   3_occ:   8.044  0.058  0.426 82.114  0.016  2.204   8.3075e-02
   4_bss:   8.044  0.058  0.426 82.114  0.016  2.204   8.3075e-02
   4_xyz:   7.237  0.044  0.365 83.711  0.030  2.386   3.9736e-02
   4_adp:   7.237  0.044  0.365 83.711  0.030  2.386   3.9736e-02
   4_occ:   7.237  0.044  0.365 83.711  0.030  2.386   3.9736e-02
   5_bss:   7.237  0.044  0.365 83.711  0.030  2.386   3.9736e-02
   5_xyz:   8.408  0.057  0.514 84.571  0.024  2.284   3.4722e-02
   5_adp:   8.408  0.057  0.514 84.571  0.024  2.284   3.4722e-02
   5_occ:   8.408  0.057  0.514 84.571  0.024  2.284   3.4722e-02
   5_bss:   8.408  0.057  0.514 84.571  0.024  2.284   3.4722e-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:  82.78   0.00  12.36  82.78   0.00   9.96  76.32   0.00  25.43
   1_occ:  82.78   0.00  12.36  82.78   0.00   9.96  76.32   0.00  25.43
   2_bss:  82.78   0.00  12.36  82.78   0.00   9.96  76.32   0.00  25.43
   2_xyz:  82.78   0.00  12.36  82.78   0.00   9.96  76.32   0.00  25.43
   2_adp:  82.95   0.00  12.54  82.95   0.00   9.64  77.30   0.77  28.33
   2_occ:  82.95   0.00  12.54  82.95   0.00   9.64  77.30   0.77  28.33
   3_bss:  82.95   0.00  12.54  82.95   0.00   9.64  77.30   0.77  28.33
   3_xyz:  82.95   0.00  12.54  82.95   0.00   9.64  77.30   0.77  28.33
   3_adp:  94.44   0.00  13.49  94.44   0.00   9.09  86.72   1.39  37.47
   3_occ:  94.44   0.00  13.49  94.44   0.00   9.09  86.72   1.39  37.47
   4_bss:  94.44   0.00  13.49  94.44   0.00   9.09  86.72   1.39  37.47
   4_xyz:  94.44   0.00  13.49  94.44   0.00   9.09  86.72   1.39  37.47
   4_adp: 100.33   0.00  13.37 100.33   0.00   8.87  86.68   1.53  37.91
   4_occ: 100.33   0.00  13.37 100.33   0.00   8.87  86.68   1.53  37.91
   5_bss: 100.33   0.00  13.37 100.33   0.00   8.87  86.68   1.53  37.91
   5_xyz: 100.33   0.00  13.37 100.33   0.00   8.87  86.68   1.53  37.91
   5_adp: 102.77   0.00  13.12 102.77   0.00   8.67  90.00   1.51  37.31
   5_occ: 102.77   0.00  13.12 102.77   0.00   8.67  90.00   1.51  37.31
   5_bss: 105.22   2.45  15.56 105.22   2.45  11.12  92.45   3.96  39.76
------------------------------------------------------------------------
 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:    1.227    0.010    0.413
   1_adp:    1.227    0.010    0.413
   1_occ:    1.227    0.010    0.413
   2_bss:    1.227    0.010    0.413
   2_xyz:    1.409    0.038    0.581
   2_adp:    1.409    0.038    0.581
   2_occ:    1.409    0.038    0.581
   3_bss:    1.409    0.038    0.581
   3_xyz:    1.691    0.046    0.656
   3_adp:    1.691    0.046    0.656
   3_occ:    1.691    0.046    0.656
   4_bss:    1.691    0.046    0.656
   4_xyz:    1.862    0.028    0.676
   4_adp:    1.862    0.028    0.676
   4_occ:    1.862    0.028    0.676
   5_bss:    1.862    0.028    0.676
   5_xyz:    1.926    0.037    0.695
   5_adp:    1.926    0.037    0.695
   5_occ:    1.926    0.037    0.695
   5_bss:    1.926    0.037    0.695
------------------------------------------------------------------------

CPU time actual refinement: 319.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/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_872/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_872/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.82 
  Macro-tasks:
    bulk solvent and scale       = 40.88  
    individual site refinement   = 127.32 
    weights calculation          = 31.05  
    collect and process          = 6.50   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 205.88 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 97.62  
    alpha_beta                      = 8.39   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 107.16 
    fmodel                         = 6.91   
    r_factors                      = 0.29   
    phase_errors                   = 10.81  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 234.31 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.558 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    635 calls, 97.29 s
gradients_fft:          580 calls, 94.20 s

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

# Date 2008-01-16 Time 02:37:44 PST -0800 (1200479864.78 s)
Start R-work = 0.4705, R-free = 0.4528 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1795 (no bulk solvent and anisotropic scale)

Start R-work = 0.4607, R-free = 0.4414
Final R-work = 0.1146, R-free = 0.1630