# Date 2008-01-16 Time 02:37:51 PST -0800 (1200479871.63 s)
#phil __OFF__

Command line arguments: "../909.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 = 31416
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 909

-------------------------------------------------------------------------------
  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, 46.93, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.00223
Completeness in resolution range: 0.96956
Completeness with d_max=infinity: 0.966547

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   2.0022

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, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.00223
Completeness in resolution range: 0.96956
Completeness with d_max=infinity: 0.966547

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1443 -  4.2842 [2118/2142]  1905   213  10.1%
  bin  2:  4.2842 -  3.4133 [2037/2057]  1834   203  10.0%
  bin  3:  3.4133 -  2.9856 [2013/2032]  1813   200   9.9%
  bin  4:  2.9856 -  2.7143 [1999/2029]  1799   200  10.0%
  bin  5:  2.7143 -  2.5207 [1988/2007]  1788   200  10.1%
  bin  6:  2.5207 -  2.3727 [1956/1981]  1758   198  10.1%
  bin  7:  2.3727 -  2.2543 [1955/1983]  1762   193   9.9%
  bin  8:  2.2543 -  2.1564 [1966/2002]  1771   195   9.9%
  bin  9:  2.1564 -  2.0736 [1942/1984]  1748   194  10.0%
  bin 10:  2.0736 -  2.0022 [1615/1987]  1452   163  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2176
        3.04 -     3.66: 4598
        3.66 -     4.28: 8938
        4.28 -     4.90: 12277
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.104 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.284 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27992 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_909/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 46.93 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4290   r_free= 0.4141   ksol= 0.00   Bsol= 0.00   scale= 0.818    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.219408                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7783 0.99   1380  153 0.3610 0.3300      6.5334      6.4112|
|  2:  4.7783 -  3.8126 0.99   1325  149 0.3167 0.3276       6.622      6.6783|
|  3:  3.8126 -  3.3365 0.99   1298  142 0.3710 0.3350      6.5466      6.5308|
|  4:  3.3365 -  3.0341 0.99   1288  145 0.4071 0.3562      6.4475      6.3374|
|  5:  3.0341 -  2.8182 0.99   1280  143 0.4439 0.4415       6.304      6.3425|
|  6:  2.8182 -  2.6529 0.99   1296  140 0.4541 0.4920      6.2322      6.1605|
|  7:  2.6529 -  2.5207 0.99   1272  144 0.4866 0.4907      6.2063      6.2193|
|  8:  2.5207 -  2.4114 0.98   1258  137 0.4776 0.4356      6.1434      6.0931|
|  9:  2.4114 -  2.3189 0.98   1261  142 0.4688 0.4951      6.0722      6.1184|
| 10:  2.3189 -  2.2392 1.00   1262  143 0.4923 0.4653      6.0996      6.0503|
| 11:  2.2392 -  2.1694 0.97   1265  137 0.4900 0.4408      6.0124      5.9944|
| 12:  2.1694 -  2.1075 0.98   1237  139 0.4916 0.4700      5.9642      5.9668|
| 13:  2.1075 -  2.0522 0.99   1284  142 0.4979 0.4829      5.8831      5.8349|
| 14:  2.0522 -  2.0022 0.73    924  103 0.4930 0.4520      5.8388      5.7115|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.7783  1380   153  0.76  29.24   0.81     0.78      52718.26|
|  2:  4.7783 -  3.8126  1325   149  0.79  27.01   0.91     0.83      67829.66|
|  3:  3.8126 -  3.3365  1298   142  0.73  33.07   0.87     0.80      71165.73|
|  4:  3.3365 -  3.0341  1288   145  0.66  38.61   0.83     0.72      65257.01|
|  5:  3.0341 -  2.8182  1280   143  0.58  45.90   0.78     0.64      58675.37|
|  6:  2.8182 -  2.6529  1296   140  0.53  49.43   0.76     0.59      55282.80|
|  7:  2.6529 -  2.5207  1272   144  0.49  52.95   0.74     0.55      53087.22|
|  8:  2.5207 -  2.4114  1258   137  0.48  53.82   0.76     0.54      49097.98|
|  9:  2.4114 -  2.3189  1261   142  0.50  52.29   0.74     0.56      43458.95|
| 10:  2.3189 -  2.2392  1262   143  0.51  51.66   0.78     0.57      37811.84|
| 11:  2.2392 -  2.1694  1265   137  0.50  52.32   0.76     0.57      35253.76|
| 12:  2.1694 -  2.1075  1237   139  0.48  53.75   0.77     0.57      33497.55|
| 13:  2.1075 -  2.0522  1284   142  0.48  53.98   0.75     0.56      29098.26|
| 14:  2.0522 -  2.0022   924   103  0.56  47.93   0.73     0.57      20974.36|
|alpha:            min =        0.54 max =            0.83 mean =         0.64|
|beta:             min =    20974.36 max =        71165.73 mean =     48802.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.61|
|phase err.(test): min =        0.00 max =           89.90 mean =        45.68|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.108750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.853   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.609230              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.518   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2580 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3902 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5000 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6511 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7684 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.165 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.621 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4371   r_free= 0.4189   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.225443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4215   r_free= 0.4008   ksol= 0.30   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,7.49,9.43,0.00,0.00,0.00); trace/3= 8.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.214155                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.707204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.493   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.592907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.601   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4215      final r-factor (work) = 0.3087          |
| start r-factor (free) = 0.4008      final r-factor (free) = 0.3265          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.0704 = 6.71 * 0.50 * 6.2336 + 1.00 * 54.1653                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3997 = 6.71 * 0.50 * 6.0484 + 1.00 * 0.1157                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3087      final r-factor (work) = 0.2410          |
| start r-factor (free) = 0.3265      final r-factor (free) = 0.2726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6009 = 0.59 * 1.00 * 6.0484 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4813 = 0.59 * 1.00 * 5.8515 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.06   10.64    None  None   None       |
|    all(noH): 2823   0      0.00    72.06   10.64    None  None   None       |
|    Sol.    : 438    0      0.00    72.06   28.62    None  None   None       |
|    Mac.    : 2385   0      0.00    61.65   7.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.206: 1519   |   5:    36.032 -  43.238:   82        |
|      1:     7.206 -  14.413:  674   |   6:    43.238 -  50.444:   38        |
|      2:    14.413 -  21.619:  217   |   7:    50.444 -  57.651:   26        |
|      3:    21.619 -  28.825:  131   |   8:    57.651 -  64.857:    4        |
|      4:    28.825 -  36.032:  129   |   9:    64.857 -  72.063:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2410 r_free = 0.2726             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2404 r_free = 0.2732             target_work(ml) = 5.773         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2404   r_free= 0.2732   ksol= 0.30   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,7.49,9.43,0.00,0.00,0.00); trace/3= 8.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.773096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2355   r_free= 0.2672   ksol= 0.32   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.57,4.19,6.13,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.771471                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.937131              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.603   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.315758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.958  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2355      final r-factor (work) = 0.1556          |
| start r-factor (free) = 0.2672      final r-factor (free) = 0.1969          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6476 = 3.94 * 0.50 * 5.8581 + 1.00 * 0.1155                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0701 = 3.94 * 0.50 * 5.5878 + 1.00 * 0.0701                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1556      final r-factor (work) = 0.1416          |
| start r-factor (free) = 0.1969      final r-factor (free) = 0.1842          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7764 = 0.32 * 1.00 * 5.5878 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7025 = 0.32 * 1.00 * 5.3578 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.41   10.92    None  None   None       |
|    all(noH): 2823   0      0.00    71.41   10.92    None  None   None       |
|    Sol.    : 438    0      0.00    71.41   31.50    None  None   None       |
|    Mac.    : 2385   0      0.00    60.40   7.14     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.141: 1594   |   5:    35.706 -  42.847:  123        |
|      1:     7.141 -  14.283:  603   |   6:    42.847 -  49.989:   57        |
|      2:    14.283 -  21.424:  178   |   7:    49.989 -  57.130:   31        |
|      3:    21.424 -  28.565:  115   |   8:    57.130 -  64.271:    9        |
|      4:    28.565 -  35.706:  111   |   9:    64.271 -  71.412:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1416 r_free = 0.1842             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1416 r_free = 0.1842             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1416   r_free= 0.1842   ksol= 0.32   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.57,4.19,6.13,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.326259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1413   r_free= 0.1837   ksol= 0.32   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.47,4.94,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.327641                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.808246              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.852  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.098430              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.336  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1413      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1837      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6047 = 2.81 * 0.50 * 5.3660 + 1.00 * 0.0701                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4564 = 2.81 * 0.50 * 5.2592 + 1.00 * 0.0719                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3058 = 3.10 * 1.00 * 5.2592 + 1.00 * 0.0106                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.0913 = 3.10 * 1.00 * 5.1886 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.69   11.71    None  None   None       |
|    all(noH): 2823   0      0.00    75.69   11.71    None  None   None       |
|    Sol.    : 438    0      0.00    75.66   35.46    None  None   None       |
|    Mac.    : 2385   0      0.00    75.69   7.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.569: 1656   |   5:    37.845 -  45.414:   78        |
|      1:     7.569 -  15.138:  556   |   6:    45.414 -  52.983:   87        |
|      2:    15.138 -  22.707:  163   |   7:    52.983 -  60.551:   51        |
|      3:    22.707 -  30.276:  106   |   8:    60.551 -  68.120:   21        |
|      4:    30.276 -  37.845:   93   |   9:    68.120 -  75.689:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1634             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1634             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1634   ksol= 0.32   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.51,3.47,4.94,0.00,0.00,0.00); trace/3= 3.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1634   ksol= 0.32   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.46,4.83,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.859710              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.406  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.348  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4903 = 2.86 * 0.50 * 5.1882 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4643 = 2.86 * 0.50 * 5.1688 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3867 = 0.27 * 1.00 * 5.1688 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3842 = 0.27 * 1.00 * 5.1705 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.95   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    74.95   11.08    None  None   None       |
|    Sol.    : 438    0      0.66    74.13   32.72    None  None   None       |
|    Mac.    : 2385   0      0.00    74.95   7.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.495: 1685   |   5:    37.473 -  44.967:   77        |
|      1:     7.495 -  14.989:  553   |   6:    44.967 -  52.462:   70        |
|      2:    14.989 -  22.484:  154   |   7:    52.462 -  59.956:   30        |
|      3:    22.484 -  29.978:  113   |   8:    59.956 -  67.451:   16        |
|      4:    29.978 -  37.473:  120   |   9:    67.451 -  74.945:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1136 r_free = 0.1603             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1604             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1604   ksol= 0.32   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.46,4.83,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1598   ksol= 0.32   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.46,4.83,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.810513              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.844  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.318830              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.086   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7544 = 1.81 * 0.50 * 5.1707 + 1.00 * 0.0736                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7406 = 1.81 * 0.50 * 5.1678 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6592 = 0.32 * 1.00 * 5.1678 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6823 = 0.32 * 1.00 * 5.1704 + 1.00 * 0.0338                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.40   11.04    None  None   None       |
|    all(noH): 2823   0      0.00    75.40   11.04    None  None   None       |
|    Sol.    : 438    0      0.64    73.76   32.61    None  None   None       |
|    Mac.    : 2385   0      0.00    75.40   7.08     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.540: 1698   |   5:    37.699 -  45.239:   82        |
|      1:     7.540 -  15.080:  540   |   6:    45.239 -  52.779:   69        |
|      2:    15.080 -  22.620:  156   |   7:    52.779 -  60.319:   27        |
|      3:    22.620 -  30.159:  109   |   8:    60.319 -  67.859:   15        |
|      4:    30.159 -  37.699:  122   |   9:    67.859 -  75.399:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1605             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1606             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1606   ksol= 0.32   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.43,3.46,4.83,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170087                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7783 0.99   1380  153 0.1024 0.1326      5.4027      5.5343|
|  2:  4.7783 -  3.8126 0.99   1325  149 0.0880 0.1149      5.4609      5.6605|
|  3:  3.8126 -  3.3365 0.99   1298  142 0.1070 0.1484      5.4902      5.8409|
|  4:  3.3365 -  3.0341 0.99   1288  145 0.1221 0.1605      5.4686      5.6091|
|  5:  3.0341 -  2.8182 0.99   1280  143 0.1362 0.1750      5.3595       5.592|
|  6:  2.8182 -  2.6529 0.99   1296  140 0.1223 0.2080      5.2399      5.5249|
|  7:  2.6529 -  2.5207 0.99   1272  144 0.1327 0.1597      5.2049      5.3576|
|  8:  2.5207 -  2.4114 0.98   1258  137 0.1217 0.1751       5.112      5.3781|
|  9:  2.4114 -  2.3189 0.98   1261  142 0.1209 0.1788      5.0752      5.3077|
| 10:  2.3189 -  2.2392 1.00   1262  143 0.1189 0.1701      5.0008      5.2595|
| 11:  2.2392 -  2.1694 0.97   1265  137 0.1172 0.1767      4.9594      5.2374|
| 12:  2.1694 -  2.1075 0.98   1237  139 0.1157 0.1778      4.8998        5.24|
| 13:  2.1075 -  2.0522 0.99   1284  142 0.1175 0.1782      4.8215       5.086|
| 14:  2.0522 -  2.0022 0.73    924  103 0.1094 0.1782      4.7063      4.9556|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.7783  1380   153  0.94   9.21   0.97     0.95       7261.10|
|  2:  4.7783 -  3.8126  1325   149  0.95   8.09   1.01     0.99       9264.62|
|  3:  3.8126 -  3.3365  1298   142  0.93  11.32   1.01     1.01      10606.47|
|  4:  3.3365 -  3.0341  1288   145  0.92  13.74   1.00     0.98      10572.51|
|  5:  3.0341 -  2.8182  1280   143  0.90  16.08   0.99     0.96       8771.87|
|  6:  2.8182 -  2.6529  1296   140  0.90  16.38   0.98     0.95       7580.89|
|  7:  2.6529 -  2.5207  1272   144  0.90  16.18   0.98     0.96       6565.63|
|  8:  2.5207 -  2.4114  1258   137  0.91  15.61   0.99     0.97       5680.19|
|  9:  2.4114 -  2.3189  1261   142  0.91  15.82   1.00     0.96       5400.11|
| 10:  2.3189 -  2.2392  1262   143  0.90  15.90   1.00     0.96       4618.99|
| 11:  2.2392 -  2.1694  1265   137  0.90  16.55   0.99     0.95       4473.32|
| 12:  2.1694 -  2.1075  1237   139  0.91  15.38   1.01     0.99       4044.37|
| 13:  2.1075 -  2.0522  1284   142  0.90  16.57   0.99     0.97       3540.33|
| 14:  2.0522 -  2.0022   924   103  0.91  14.85   0.98     0.94       2740.80|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2740.80 max =        10606.47 mean =      6614.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.34|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1606   ksol= 0.32   Bsol= 53.84   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.43,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1606   ksol= 0.32   Bsol= 53.84   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.43,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170074                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7783 0.99   1380  153 0.1023 0.1325      5.4024      5.5339|
|  2:  4.7783 -  3.8126 0.99   1325  149 0.0880 0.1149      5.4607      5.6604|
|  3:  3.8126 -  3.3365 0.99   1298  142 0.1070 0.1483      5.4901      5.8407|
|  4:  3.3365 -  3.0341 0.99   1288  145 0.1221 0.1605      5.4686      5.6091|
|  5:  3.0341 -  2.8182 0.99   1280  143 0.1362 0.1750      5.3596      5.5923|
|  6:  2.8182 -  2.6529 0.99   1296  140 0.1223 0.2080        5.24      5.5249|
|  7:  2.6529 -  2.5207 0.99   1272  144 0.1327 0.1596      5.2048      5.3573|
|  8:  2.5207 -  2.4114 0.98   1258  137 0.1217 0.1751      5.1119      5.3782|
|  9:  2.4114 -  2.3189 0.98   1261  142 0.1208 0.1789      5.0752      5.3078|
| 10:  2.3189 -  2.2392 1.00   1262  143 0.1189 0.1701      5.0008      5.2592|
| 11:  2.2392 -  2.1694 0.97   1265  137 0.1172 0.1768      4.9595      5.2375|
| 12:  2.1694 -  2.1075 0.98   1237  139 0.1158 0.1778      4.8999        5.24|
| 13:  2.1075 -  2.0522 0.99   1284  142 0.1175 0.1783      4.8216      5.0862|
| 14:  2.0522 -  2.0022 0.73    924  103 0.1094 0.1782      4.7064      4.9558|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.7783  1380   153  0.94   9.21   0.97     0.95       7255.56|
|  2:  4.7783 -  3.8126  1325   149  0.95   8.08   1.01     0.99       9259.30|
|  3:  3.8126 -  3.3365  1298   142  0.93  11.32   1.01     1.01      10603.18|
|  4:  3.3365 -  3.0341  1288   145  0.92  13.74   1.00     0.98      10572.69|
|  5:  3.0341 -  2.8182  1280   143  0.90  16.08   0.99     0.96       8773.95|
|  6:  2.8182 -  2.6529  1296   140  0.90  16.38   0.98     0.95       7582.11|
|  7:  2.6529 -  2.5207  1272   144  0.90  16.18   0.98     0.95       6565.08|
|  8:  2.5207 -  2.4114  1258   137  0.91  15.61   0.99     0.96       5679.96|
|  9:  2.4114 -  2.3189  1261   142  0.91  15.82   1.00     0.96       5399.00|
| 10:  2.3189 -  2.2392  1262   143  0.90  15.90   1.00     0.96       4619.76|
| 11:  2.2392 -  2.1694  1265   137  0.90  16.55   0.99     0.95       4473.66|
| 12:  2.1694 -  2.1075  1237   139  0.91  15.38   1.00     0.99       4045.00|
| 13:  2.1075 -  2.0522  1284   142  0.90  16.57   0.99     0.97       3541.34|
| 14:  2.0522 -  2.0022   924   103  0.91  14.86   0.97     0.93       2742.51|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2742.51 max =        10603.18 mean =      6613.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.34|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.149)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.84    79.24   14.88    None  None   None       |
|    all(noH): 2823   0      3.84    79.24   14.88    None  None   None       |
|    Sol.    : 438    0      4.48    77.60   36.45    None  None   None       |
|    Mac.    : 2385   0      3.84    79.24   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.839 -  11.379: 1698   |   5:    41.539 -  49.079:   82        |
|      1:    11.379 -  18.919:  540   |   6:    49.079 -  56.618:   69        |
|      2:    18.919 -  26.459:  156   |   7:    56.618 -  64.158:   27        |
|      3:    26.459 -  33.999:  109   |   8:    64.158 -  71.698:   15        |
|      4:    33.999 -  41.539:  122   |   9:    71.698 -  79.238:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.313 - 4.656
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 329
   mapped sites are within: 0.735 - 4.656

peak=   10.833 closest distance to " CG2 VAL A 230 " =    1.473
peak=    7.220 closest distance to " CG2 VAL A 296 " =    1.129
peak=    6.452 closest distance to " NH2 ARG A  56 " =    2.274
peak=    6.143 closest distance to " CG  LEU A   5 " =    1.251
peak=    5.642 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.634 closest distance to " CD2 LEU A   5 " =    1.211
peak=    5.606 closest distance to " CG  LEU A 228 " =    1.183
peak=    5.026 closest distance to " NE2 GLN A  11 " =    1.157
peak=    4.979 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.893 closest distance to " O   HOH Z 232 " =    2.322
peak=    4.742 closest distance to " CG  PRO A 198 " =    1.284
peak=    4.703 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.654 closest distance to " CB  VAL A 230 " =    1.198
peak=    4.651 closest distance to " CB  SER A  63 " =    1.299
peak=    4.637 closest distance to " O   HOH Z 126 " =    1.954
peak=    4.616 closest distance to " O   HOH Z 142 " =    1.705
peak=    4.616 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.595 closest distance to " CZ  PHE A 218 " =    1.095
peak=    4.538 closest distance to " CB  VAL A 296 " =    1.076
peak=    4.498 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.487 closest distance to " O   HOH Z 369 " =    2.057
peak=    4.451 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.395 closest distance to " CB  TRP A 266 " =    0.969
peak=    4.384 closest distance to " ND2 ASN A 187 " =    1.480
peak=    4.379 closest distance to " O   HOH Z 368 " =    2.151
peak=    4.377 closest distance to " CB  ASN A 148 " =    1.330
peak=    4.363 closest distance to " O   HOH Z 265 " =    2.411
peak=    4.335 closest distance to " C   PRO A 198 " =    1.547
peak=    4.314 closest distance to " O   HOH Z 427 " =    3.094
peak=    4.292 closest distance to " O   HOH Z 236 " =    2.025
peak=    4.285 closest distance to " CB  ASP A 124 " =    0.743
peak=    4.266 closest distance to " O   HOH Z  78 " =    1.714
peak=    4.230 closest distance to " CD2 LEU A 228 " =    1.197
peak=    4.217 closest distance to " O   HOH Z 303 " =    2.076
peak=    4.204 closest distance to " O   HOH Z 272 " =    1.896
peak=    4.202 closest distance to " O   HOH Z 261 " =    2.075
peak=    4.197 closest distance to " O   HOH Z  61 " =    1.699
peak=    4.181 closest distance to " O   HOH Z 346 " =    1.622
peak=    4.168 closest distance to " CB  GLU A 152 " =    1.144
peak=    4.138 closest distance to " CB  GLU A 128 " =    1.049
peak=    4.130 closest distance to " O   HOH Z 316 " =    3.153
peak=    4.108 closest distance to " CB  ARG A  79 " =    1.439
peak=    4.095 closest distance to " CB  VAL A 265 " =    1.290
peak=    4.095 closest distance to " CA  TYR A  30 " =    0.985
peak=    4.079 closest distance to " O   SER A  87 " =    2.323
peak=    4.018 closest distance to " O   HOH Z 423 " =    1.778
peak=    4.012 closest distance to " O   HOH Z  44 " =    2.268
peak=    3.996 closest distance to " O   HOH Z 234 " =    3.791
peak=    3.982 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.972 closest distance to " OG  SER A  97 " =    3.030
peak=    3.952 closest distance to " CB  ARG A 190 " =    1.562
peak=    3.948 closest distance to " CB  ASN A 142 " =    1.046
peak=    3.945 closest distance to " CB  SER A   3 " =    1.328
peak=    3.944 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.937 closest distance to " O   HOH Z 248 " =    1.685
peak=    3.927 closest distance to " CB  ASP A 140 " =    0.893
peak=    3.921 closest distance to " O   HOH Z 158 " =    3.233
peak=    3.910 closest distance to " O   HOH Z  78 " =    2.223
peak=    3.909 closest distance to " O   HOH Z  43 " =    1.957
peak=    3.908 closest distance to " CB  VAL A 202 " =    1.599
peak=    3.890 closest distance to " OD1 ASN A  69 " =    2.600
peak=    3.885 closest distance to " CA  ALA A  51 " =    0.940
peak=    3.882 closest distance to " O   HOH Z 214 " =    2.076
peak=    3.876 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.874 closest distance to " CA  SER A  87 " =    0.984
peak=    3.852 closest distance to " CA  THR A 264 " =    0.792
peak=    3.851 closest distance to " CB  GLU A  46 " =    0.957
peak=    3.848 closest distance to " CB  PRO A  54 " =    0.846
peak=    3.837 closest distance to " NH1AARG A 145 " =    1.195
peak=    3.835 closest distance to " ND2 ASN A 249 " =    1.884
peak=    3.834 closest distance to " N   ASN A  39 " =    1.172
peak=    3.831 closest distance to " CB  GLU A 277 " =    3.646
peak=    3.816 closest distance to " O   HOH Z 425 " =    1.400
peak=    3.815 closest distance to " O   HOH Z  21 " =    1.742
peak=    3.806 closest distance to " CG  MET A 185 " =    1.180
peak=    3.803 closest distance to " CB  ASN A 187 " =    1.221
peak=    3.798 closest distance to " O   HOH Z 403 " =    1.626
peak=    3.797 closest distance to " CG1 VAL A 296 " =    1.211
peak=    3.795 closest distance to " CD  LYS A 166 " =    1.286
peak=    3.793 closest distance to " O   HOH Z 411 " =    3.819
peak=    3.785 closest distance to " CG2 VAL A 257 " =    0.931
peak=    3.772 closest distance to " CZ  PHE A 192 " =    0.936
peak=    3.755 closest distance to " CG  LEU A 167 " =    1.208
peak=    3.748 closest distance to " N   PHE A 130 " =    1.206
peak=    3.747 closest distance to " CA  ASN A 215 " =    1.124
peak=    3.742 closest distance to " O   HOH Z 126 " =    1.983
peak=    3.731 closest distance to " CD  ARG A 269 " =    1.009
peak=    3.729 closest distance to " CB  ALA A 104 " =    0.765
peak=    3.727 closest distance to " O   HOH Z  68 " =    2.114
peak=    3.724 closest distance to " CB  ALA A 291 " =    1.263
peak=    3.723 closest distance to " CD  ARG A  66 " =    2.484
peak=    3.719 closest distance to " CB  LEU A 228 " =    1.230
peak=    3.711 closest distance to " CG1 VAL A 153 " =    0.960
peak=    3.698 closest distance to " O   HOH Z 126 " =    1.575
peak=    3.693 closest distance to " CB  LEU A 143 " =    1.176
peak=    3.688 closest distance to " CG1 ILE A  49 " =    1.457
peak=    3.687 closest distance to " CB  SER A 212 " =    1.280
peak=    3.673 closest distance to " CA  ARG A 195 " =    1.197
peak=    3.653 closest distance to " O   HOH Z 280 " =    3.025
peak=    3.648 closest distance to " CG1BVAL A  72 " =    1.741
peak=    3.644 closest distance to " CZ  PHE A  38 " =    1.132
peak=    3.637 closest distance to " CB  MET A  40 " =    0.829
peak=    3.637 closest distance to " CB  SER A 216 " =    0.816
peak=    3.637 closest distance to " NE2 HIS A 207 " =    1.255
peak=    3.636 closest distance to " NH2 ARG A 156 " =    1.102
peak=    3.630 closest distance to " O   HOH Z 313 " =    1.762
peak=    3.626 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.621 closest distance to " O   HOH Z 203 " =    1.730
peak=    3.611 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.599 closest distance to " O   HOH Z 171 " =    3.895
peak=    3.595 closest distance to " CA  ARG A  36 " =    1.130
peak=    3.591 closest distance to " O   HOH Z 193 " =    1.929
peak=    3.586 closest distance to " O   TRP A 274 " =    1.856
peak=    3.585 closest distance to " O   HOH Z   9 " =    2.076
peak=    3.580 closest distance to " O   HOH Z 402 " =    1.464
peak=    3.576 closest distance to " O   HOH Z 193 " =    2.064
peak=    3.572 closest distance to " CD BLYS A 290 " =    1.047
peak=    3.566 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.554 closest distance to " CA  LYS A 117 " =    1.216
peak=    3.553 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.549 closest distance to " O  BHOH Z 338 " =    2.411
peak=    3.548 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.542 closest distance to " CA  ALA A  21 " =    1.120
peak=    3.536 closest distance to " O   HOH Z 128 " =    2.170
peak=    3.532 closest distance to " CG2 THR A 221 " =    1.035
peak=    3.531 closest distance to " O   MET A 105 " =    1.761
peak=    3.522 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.515 closest distance to " O   HOH Z 141 " =    1.729
peak=    3.513 closest distance to " O   HOH Z 273 " =    2.801
peak=    3.507 closest distance to " O   ASP A 124 " =    1.132
peak=    3.506 closest distance to " O   HOH Z  92 " =    2.423
peak=    3.495 closest distance to " CB BVAL A  41 " =    1.248
peak=    3.494 closest distance to " CA  ALA A 291 " =    0.922
peak=    3.493 closest distance to " O   HOH Z 353 " =    2.566
peak=    3.484 closest distance to " O   HOH Z 291 " =    1.644
peak=    3.483 closest distance to " O   HOH Z 368 " =    3.553
peak=    3.482 closest distance to " O   HOH Z 285 " =    2.652
peak=    3.480 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.474 closest distance to " CE1 TYR A 186 " =    1.316
peak=    3.473 closest distance to " CA  GLY A 267 " =    0.756
peak=    3.472 closest distance to " O   HOH Z 313 " =    1.734
peak=    3.466 closest distance to " CA  ALA A 295 " =    1.107
peak=    3.463 closest distance to " CG  MET A 185 " =    1.048
peak=    3.458 closest distance to " CG1 ILE A 151 " =    1.106
peak=    3.456 closest distance to " N   SER A 135 " =    1.344
peak=    3.451 closest distance to " O   HOH Z 145 " =    1.911
peak=    3.450 closest distance to " CB  HIS A 108 " =    0.775
peak=    3.449 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.447 closest distance to " O   HOH Z  10 " =    1.768
peak=    3.447 closest distance to " O   HOH Z 422 " =    2.701
peak=    3.443 closest distance to " NE2 GLN A  77 " =    3.412
peak=    3.437 closest distance to " O   HOH Z 371 " =    2.982
peak=    3.437 closest distance to " CB  THR A  31 " =    1.606
peak=    3.436 closest distance to " CA  ASP A 162 " =    0.967
peak=    3.426 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.418 closest distance to " CB  SER A 210 " =    0.802
peak=    3.418 closest distance to " O   HOH Z 166 " =    3.789
peak=    3.413 closest distance to " CA  LEU A 282 " =    1.052
peak=    3.412 closest distance to " O   HOH Z 193 " =    1.717
peak=    3.412 closest distance to " O   HOH Z  48 " =    1.618
peak=    3.410 closest distance to " CB  ALA A  34 " =    1.031
peak=    3.405 closest distance to " O   HOH Z 172 " =    3.515
peak=    3.404 closest distance to " CB  THR A  82 " =    1.406
peak=    3.401 closest distance to " O   HOH Z 197 " =    3.109
peak=    3.400 closest distance to " O   HOH Z  97 " =    2.458
peak=    3.399 closest distance to " OG BSER A 164 " =    2.246
peak=    3.395 closest distance to " CG1 ILE A  33 " =    1.316
peak=    3.395 closest distance to " CB  ALA A 114 " =    1.248
peak=    3.394 closest distance to " CA  MET A 105 " =    0.967
peak=    3.393 closest distance to " O   HOH Z  59 " =    2.102
peak=    3.392 closest distance to " O   HOH Z 350 " =    1.665
peak=    3.390 closest distance to " CB  TRP A 150 " =    1.428
peak=    3.384 closest distance to " O   HOH Z 365 " =    2.993
peak=    3.384 closest distance to " CA  ALA A 233 " =    1.387
peak=    3.383 closest distance to " CD1 ILE A  33 " =    1.702
peak=    3.382 closest distance to " CG  GLN A  88 " =    1.058
peak=    3.379 closest distance to " CB  ALA A 248 " =    1.337
peak=    3.372 closest distance to " CA  THR A 221 " =    0.914
peak=    3.371 closest distance to " O   HOH Z 290 " =    1.103
peak=    3.371 closest distance to " O   HOH Z 187 " =    2.292
peak=    3.370 closest distance to " O   HOH Z 263 " =    1.671
peak=    3.370 closest distance to " CA  VAL A  41 " =    0.803
peak=    3.369 closest distance to " ND1 HIS A  81 " =    1.706
peak=    3.368 closest distance to " O   HOH Z  40 " =    1.533
peak=    3.363 closest distance to " O   HOH Z  88 " =    3.206
peak=    3.353 closest distance to " CB  LYS A 117 " =    1.237
peak=    3.352 closest distance to " CD1 ILE A 106 " =    0.960
peak=    3.352 closest distance to " O   HOH Z 305 " =    3.582
peak=    3.350 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.350 closest distance to " CB  ASN A 224 " =    0.998
peak=    3.346 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.345 closest distance to " CZ3 TRP A 266 " =    1.071
peak=    3.343 closest distance to " CA  ASN A 127 " =    1.014
peak=    3.342 closest distance to " CB  SER A 273 " =    0.904
peak=    3.339 closest distance to " CZ3 TRP A 274 " =    4.656
peak=    3.334 closest distance to " CA  LYS A 181 " =    1.085
peak=    3.333 closest distance to " CA  VAL A 125 " =    1.117
peak=    3.333 closest distance to " O   HOH Z 245 " =    1.384
peak=    3.332 closest distance to " O   HOH Z 227 " =    1.754
peak=    3.332 closest distance to " O   HOH Z   3 " =    1.827
peak=    3.331 closest distance to " CB  ALA A 248 " =    1.098
peak=    3.330 closest distance to " O   HOH Z 384 " =    3.132
peak=    3.330 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.330 closest distance to " CB  ALA A 242 " =    0.768
peak=    3.326 closest distance to " O   HOH Z 258 " =    2.179
peak=    3.325 closest distance to " O   HOH Z 344 " =    3.004
peak=    3.324 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.322 closest distance to " NZ  LYS A  48 " =    1.329
peak=    3.319 closest distance to " O   HOH Z 171 " =    2.291
peak=    3.305 closest distance to " CD1 LEU A 261 " =    1.245
peak=    3.304 closest distance to " CG2 THR A 220 " =    0.835
peak=    3.302 closest distance to " OH  TYR A 214 " =    1.218
peak=    3.300 closest distance to " CA  ILE A 106 " =    0.735
peak=    3.297 closest distance to " O   TYR A 116 " =    1.336
peak=    3.296 closest distance to " O   HOH Z 294 " =    1.550
peak=    3.293 closest distance to " ND2 ASN A 249 " =    0.876
peak=    3.289 closest distance to " CD1 LEU A   5 " =    1.365
peak=    3.287 closest distance to " O   HOH Z 148 " =    3.342
peak=    3.285 closest distance to " O   HOH Z 260 " =    1.569
peak=    3.285 closest distance to " CE3 TRP A 150 " =    0.994
peak=    3.283 closest distance to " CB  GLN A 103 " =    1.026
peak=    3.282 closest distance to " CA  TYR A 116 " =    1.482
peak=    3.280 closest distance to " CA  ALA A 158 " =    1.207
peak=    3.280 closest distance to " CB  PRO A  90 " =    1.220
peak=    3.276 closest distance to " CG BARG A 275 " =    1.442
peak=    3.275 closest distance to " CA  ILE A 234 " =    0.914
peak=    3.273 closest distance to " O   HOH Z 406 " =    1.568
peak=    3.271 closest distance to " O   HOH Z 421 " =    3.013
peak=    3.266 closest distance to " O   HOH Z 437 " =    1.734
peak=    3.265 closest distance to " NZ  LYS A 117 " =    3.259
peak=    3.264 closest distance to " CA  ASN A 217 " =    1.300
peak=    3.260 closest distance to " CD1 LEU A 228 " =    2.077
peak=    3.257 closest distance to " CB  GLN A  89 " =    1.145
peak=    3.257 closest distance to " O   HOH Z 213 " =    1.808
peak=    3.256 closest distance to " O   HOH Z 435 " =    2.019
peak=    3.251 closest distance to " CB  PRO A 243 " =    1.453
peak=    3.246 closest distance to " O   HOH Z 250 " =    1.323
peak=    3.240 closest distance to " CG BARG A 102 " =    1.824
peak=    3.240 closest distance to " O   HOH Z 302 " =    1.958
peak=    3.238 closest distance to " O   HOH Z 250 " =    1.305
peak=    3.233 closest distance to " OG  SER A  22 " =    2.793
peak=    3.232 closest distance to " CE1 HIS A 108 " =    1.202
peak=    3.229 closest distance to " CB  GLN A 278 " =    0.863
peak=    3.229 closest distance to " N   ARG A 190 " =    1.024
peak=    3.227 closest distance to " C   TYR A 214 " =    1.556
peak=    3.226 closest distance to " O   HOH Z 132 " =    2.792
peak=    3.224 closest distance to " O   ASN A  74 " =    1.566
peak=    3.223 closest distance to " O   HOH Z 329 " =    2.869
peak=    3.221 closest distance to " C   ALA A 299 " =    0.963
peak=    3.221 closest distance to " CB  ALA A 295 " =    1.283
peak=    3.221 closest distance to " O   GLN A 278 " =    1.539
peak=    3.217 closest distance to " OG BSER A 134 " =    2.894
peak=    3.213 closest distance to " N   ARG A 156 " =    1.405
peak=    3.212 closest distance to " O   ALA A 158 " =    1.414
peak=    3.211 closest distance to " O   HOH Z 329 " =    3.982
peak=    3.211 closest distance to " CG  ARG A 269 " =    1.826
peak=    3.207 closest distance to " CZ3 TRP A  85 " =    1.060
peak=    3.204 closest distance to " CB  THR A 157 " =    1.129
peak=    3.202 closest distance to " CB  ALA A 227 " =    1.026
peak=    3.198 closest distance to " O   HOH Z 332 " =    1.509
peak=    3.197 closest distance to " O   HOH Z 261 " =    1.397
peak=    3.196 closest distance to " O   HOH Z 417 " =    2.043
peak=    3.195 closest distance to " CD2 TRP A 179 " =    1.305
peak=    3.195 closest distance to " CB  GLN A 205 " =    0.999
peak=    3.194 closest distance to " CA  LYS A 290 " =    1.209
peak=    3.190 closest distance to " CG  GLN A 278 " =    1.349
peak=    3.189 closest distance to " ND1 HIS A  86 " =    1.628
peak=    3.187 closest distance to " CD1 ILE A 199 " =    0.848
peak=    3.187 closest distance to " OG  SER A  62 " =    2.903
peak=    3.182 closest distance to " N   GLN A 278 " =    1.163
peak=    3.181 closest distance to " O   HOH Z 409 " =    3.127
peak=    3.179 closest distance to " CG2AVAL A 121 " =    2.440
peak=    3.179 closest distance to " CB  PRO A 198 " =    0.989
peak=    3.176 closest distance to " NE  ARG A  79 " =    1.210
peak=    3.176 closest distance to " O   HOH Z 264 " =    1.555
peak=    3.174 closest distance to " N   VAL A 126 " =    1.777
peak=    3.172 closest distance to " CD  ARG A 219 " =    1.114
peak=    3.172 closest distance to " O  BHOH Z  74 " =    1.351
peak=    3.171 closest distance to " O   PHE A  61 " =    1.370
peak=    3.169 closest distance to " O   HOH Z 185 " =    1.893
peak=    3.168 closest distance to " O   HOH Z 247 " =    1.361
peak=    3.164 closest distance to " O   HOH Z 112 " =    1.661
peak=    3.163 closest distance to " CB  TYR A 247 " =    0.979
peak=    3.162 closest distance to " CD2 LEU A 297 " =    0.859
peak=    3.158 closest distance to " O   HOH Z 133 " =    2.361
peak=    3.155 closest distance to " CA  GLY A 211 " =    1.325
peak=    3.152 closest distance to " CB  MET A  47 " =    1.052
peak=    3.151 closest distance to " CB  ASN A 215 " =    1.174
peak=    3.150 closest distance to " O   HOH Z  97 " =    2.033
peak=    3.146 closest distance to " O   HOH Z 337 " =    3.535
peak=    3.145 closest distance to " CD1 ILE A 263 " =    1.204
peak=    3.144 closest distance to " O   HOH Z  80 " =    1.601
peak=    3.140 closest distance to " O   HOH Z  88 " =    2.746
peak=    3.136 closest distance to " O   HOH Z 425 " =    1.998
peak=    3.135 closest distance to " CG2 ILE A  20 " =    1.501
peak=    3.131 closest distance to " O   ALA A 292 " =    1.584
peak=    3.127 closest distance to " CB  ARG A 138 " =    1.000
peak=    3.121 closest distance to " CB  LYS A 193 " =    1.079
peak=    3.116 closest distance to " OE2 GLU A  53 " =    1.975
peak=    3.114 closest distance to " N   ASN A 127 " =    1.243
peak=    3.114 closest distance to " CB  ARG A 145 " =    0.774
peak=    3.104 closest distance to " CA  ASP A 140 " =    1.313
peak=    3.099 closest distance to " CB  ALA A  43 " =    0.849
peak=    3.099 closest distance to " OE2 GLU A   2 " =    1.838
peak=    3.099 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.094 closest distance to " O   HOH Z 325 " =    2.251
peak=    3.091 closest distance to " CB  ASN A 173 " =    1.047
peak=    3.090 closest distance to " CA  ASP A 191 " =    0.897
peak=    3.088 closest distance to " O   GLN A  88 " =    1.664
peak=    3.084 closest distance to " O   HOH Z 383 " =    2.081
peak=    3.078 closest distance to " O   HOH Z 116 " =    1.833
peak=    3.076 closest distance to " CB  TYR A 116 " =    0.834
peak=    3.074 closest distance to " O   HOH Z 293 " =    1.765
peak=    3.074 closest distance to " CA  GLN A  88 " =    1.415
peak=    3.070 closest distance to " O   SER A 164 " =    1.295
peak=    3.069 closest distance to " CB  ARG A 139 " =    0.904
peak=    3.068 closest distance to " CG  ARG A 159 " =    0.998
peak=    3.063 closest distance to " CG2 ILE A 263 " =    0.933
peak=    3.059 closest distance to " N   ASP A 162 " =    1.261
peak=    3.050 closest distance to " O   HOH Z 152 " =    1.790
peak=    3.031 closest distance to " O   HOH Z 417 " =    2.599
peak=    3.027 closest distance to " O   HOH Z  89 " =    1.757

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 5.527
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 201
   mapped sites are within: 0.738 - 5.527

peak=   -5.504 closest distance to " CG2 VAL A 230 " =    0.738
peak=   -4.549 closest distance to " CG1 VAL A 112 " =    2.616
peak=   -4.400 closest distance to " CD  ARG A  14 " =    3.200
peak=   -4.371 closest distance to " CD  ARG A 156 " =    2.036
peak=   -4.348 closest distance to " CB  PRO A 243 " =    2.673
peak=   -4.296 closest distance to " CD  GLN A  58 " =    0.979
peak=   -4.101 closest distance to " O   VAL A  67 " =    2.645
peak=   -4.088 closest distance to " O   HOH Z 266 " =    5.382
peak=   -4.087 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -4.081 closest distance to " CG  GLN A 223 " =    2.081
peak=   -4.030 closest distance to " O   HOH Z 290 " =    1.200
peak=   -3.980 closest distance to " O   ILE A 109 " =    2.586
peak=   -3.949 closest distance to " C   HIS A 108 " =    1.197
peak=   -3.945 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.867 closest distance to " CG2 VAL A 296 " =    1.327
peak=   -3.862 closest distance to " CB  PHE A 192 " =    2.000
peak=   -3.855 closest distance to " O   HOH Z  73 " =    2.214
peak=   -3.835 closest distance to " OG BSER A 134 " =    1.213
peak=   -3.814 closest distance to " O   HOH Z 196 " =    2.203
peak=   -3.811 closest distance to " CA  GLY A 241 " =    3.145
peak=   -3.806 closest distance to " OG  SER A  97 " =    2.340
peak=   -3.795 closest distance to " OD1 ASN A 148 " =    1.440
peak=   -3.791 closest distance to " O   HOH Z 211 " =    1.472
peak=   -3.785 closest distance to " CG  ASP A 231 " =    0.764
peak=   -3.771 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.764 closest distance to " O   GLY A 203 " =    2.364
peak=   -3.755 closest distance to " CE2 TYR A  30 " =    2.772
peak=   -3.740 closest distance to " CG2 ILE A  49 " =    2.781
peak=   -3.715 closest distance to " CG1 VAL A 296 " =    1.374
peak=   -3.706 closest distance to " O   HOH Z 114 " =    3.062
peak=   -3.703 closest distance to " CE3 TRP A 150 " =    2.071
peak=   -3.701 closest distance to " O   VAL A  67 " =    2.728
peak=   -3.694 closest distance to " O   HOH Z 166 " =    2.032
peak=   -3.691 closest distance to " O   HOH Z  11 " =    1.908
peak=   -3.690 closest distance to " CG1 VAL A 112 " =    2.935
peak=   -3.683 closest distance to " O   HOH Z 435 " =    2.854
peak=   -3.680 closest distance to " O   VAL A 189 " =    2.614
peak=   -3.673 closest distance to " CB  ALA A 248 " =    2.425
peak=   -3.666 closest distance to " NH2AARG A 275 " =    5.332
peak=   -3.662 closest distance to " C   ALA A 158 " =    1.387
peak=   -3.661 closest distance to " CA  GLY A 241 " =    2.380
peak=   -3.654 closest distance to " O   HOH Z 394 " =    1.545
peak=   -3.649 closest distance to " C   MET A 188 " =    1.329
peak=   -3.640 closest distance to " CG  HIS A  86 " =    1.142
peak=   -3.621 closest distance to " O   PRO A 198 " =    1.208
peak=   -3.618 closest distance to " O   HOH Z  52 " =    1.552
peak=   -3.613 closest distance to " CE  MET A 105 " =    2.259
peak=   -3.596 closest distance to " O   HOH Z 231 " =    1.830
peak=   -3.591 closest distance to " N   ALA A  43 " =    2.441
peak=   -3.591 closest distance to " N   ALA A 226 " =    2.232
peak=   -3.583 closest distance to " CG1 VAL A 250 " =    2.805
peak=   -3.575 closest distance to " CB  ALA A 248 " =    2.171
peak=   -3.574 closest distance to " CB  PRO A 163 " =    2.550
peak=   -3.572 closest distance to " CB  ALA A  43 " =    2.560
peak=   -3.569 closest distance to " O   HOH Z  44 " =    2.275
peak=   -3.568 closest distance to " O   HOH Z 426 " =    1.667
peak=   -3.561 closest distance to " OXT GLY A 302 " =    2.952
peak=   -3.555 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.525 closest distance to " CG1 VAL A 265 " =    2.438
peak=   -3.525 closest distance to " N   THR A  18 " =    1.363
peak=   -3.521 closest distance to " CG  TRP A 266 " =    1.853
peak=   -3.520 closest distance to " O   HOH Z 176 " =    0.812
peak=   -3.517 closest distance to " CD2 TYR A 293 " =    2.062
peak=   -3.501 closest distance to " O   HOH Z 407 " =    3.168
peak=   -3.494 closest distance to " ND2 ASN A  45 " =    1.155
peak=   -3.490 closest distance to " CD1 TYR A 247 " =    2.889
peak=   -3.488 closest distance to " CD1 LEU A 228 " =    2.346
peak=   -3.483 closest distance to " CG  LEU A 101 " =    2.470
peak=   -3.481 closest distance to " CE BMET A  47 " =    1.723
peak=   -3.476 closest distance to " O   HOH Z  37 " =    1.911
peak=   -3.465 closest distance to " OG  SER A  87 " =    1.498
peak=   -3.464 closest distance to " O   PRO A 163 " =    2.193
peak=   -3.464 closest distance to " NH2 ARG A  79 " =    1.549
peak=   -3.459 closest distance to " O   HOH Z 389 " =    2.008
peak=   -3.458 closest distance to " CB  ASN A  69 " =    1.266
peak=   -3.448 closest distance to " C   LEU A 222 " =    0.870
peak=   -3.444 closest distance to " O   HOH Z  10 " =    1.502
peak=   -3.443 closest distance to " N   THR A 157 " =    1.477
peak=   -3.441 closest distance to " ND2 ASN A  45 " =    1.427
peak=   -3.440 closest distance to " O   HOH Z 241 " =    1.226
peak=   -3.438 closest distance to " CD2 PHE A  61 " =    2.552
peak=   -3.414 closest distance to " NH2 ARG A 159 " =    2.352
peak=   -3.408 closest distance to " CG  ARG A 269 " =    2.501
peak=   -3.403 closest distance to " O   HOH Z 359 " =    3.178
peak=   -3.401 closest distance to " O   HOH Z  60 " =    2.183
peak=   -3.399 closest distance to " CD2 LEU A 167 " =    1.878
peak=   -3.398 closest distance to " OE1 GLN A  88 " =    0.963
peak=   -3.394 closest distance to " CD2 LEU A 300 " =    2.743
peak=   -3.381 closest distance to " CG1 VAL A 197 " =    2.277
peak=   -3.381 closest distance to " CD  ARG A 139 " =    1.634
peak=   -3.366 closest distance to " O   MET A  40 " =    2.787
peak=   -3.365 closest distance to " N   SER A   3 " =    1.994
peak=   -3.357 closest distance to " NE2 GLN A 194 " =    1.820
peak=   -3.356 closest distance to " O   GLY A 196 " =    1.299
peak=   -3.355 closest distance to " CA  ASP A  27 " =    2.491
peak=   -3.350 closest distance to " CG  GLU A 277 " =    1.224
peak=   -3.348 closest distance to " O   GLY A  80 " =    2.576
peak=   -3.346 closest distance to " O   LEU A 101 " =    2.876
peak=   -3.340 closest distance to " OG BSER A 134 " =    1.869
peak=   -3.336 closest distance to " ND2 ASN A 249 " =    2.409
peak=   -3.335 closest distance to " CB  VAL A 230 " =    1.067
peak=   -3.335 closest distance to " O   HOH Z  38 " =    1.549
peak=   -3.330 closest distance to " OG  SER A 206 " =    1.771
peak=   -3.327 closest distance to " C   ILE A 239 " =    2.093
peak=   -3.322 closest distance to " CD1 LEU A 101 " =    2.424
peak=   -3.321 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.309 closest distance to " CD  PRO A 213 " =    2.121
peak=   -3.309 closest distance to " CB  ALA A 291 " =    2.261
peak=   -3.305 closest distance to " O   HOH Z 134 " =    2.885
peak=   -3.303 closest distance to " CD1 TRP A 274 " =    1.003
peak=   -3.302 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.297 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.297 closest distance to " N   SER A 212 " =    1.833
peak=   -3.297 closest distance to " O   ARG A  24 " =    2.145
peak=   -3.296 closest distance to " CG2 THR A 178 " =    2.228
peak=   -3.295 closest distance to " OH  TYR A 247 " =    2.039
peak=   -3.295 closest distance to " O   HOH Z 140 " =    1.772
peak=   -3.294 closest distance to " OD2 ASP A  50 " =    2.269
peak=   -3.292 closest distance to " CD1 ILE A 239 " =    2.129
peak=   -3.289 closest distance to " NE2 GLN A  88 " =    2.006
peak=   -3.287 closest distance to " O   HOH Z 417 " =    2.979
peak=   -3.275 closest distance to " OD1 ASN A 187 " =    1.630
peak=   -3.274 closest distance to " O   HOH Z 179 " =    2.264
peak=   -3.271 closest distance to " CE  LYS A  76 " =    2.594
peak=   -3.270 closest distance to " CA  GLY A  98 " =    1.952
peak=   -3.264 closest distance to " O   GLY A 211 " =    1.355
peak=   -3.264 closest distance to " CA  ALA A 248 " =    2.559
peak=   -3.263 closest distance to " O   HOH Z  51 " =    1.264
peak=   -3.262 closest distance to " ND2 ASN A  60 " =    1.368
peak=   -3.261 closest distance to " CA  SER A 135 " =    1.332
peak=   -3.261 closest distance to " NE2 GLN A  88 " =    1.011
peak=   -3.260 closest distance to " O   HOH Z 262 " =    2.831
peak=   -3.259 closest distance to " NH2 ARG A  79 " =    2.006
peak=   -3.258 closest distance to " O   HOH Z  43 " =    1.786
peak=   -3.258 closest distance to " N   ALA A 248 " =    1.802
peak=   -3.256 closest distance to " O   HOH Z  13 " =    1.545
peak=   -3.256 closest distance to " O   HOH Z 191 " =    5.527
peak=   -3.256 closest distance to " N   GLN A  58 " =    1.742
peak=   -3.249 closest distance to " N   THR A  52 " =    1.698
peak=   -3.242 closest distance to " C   PHE A  59 " =    1.327
peak=   -3.241 closest distance to " O   HOH Z 390 " =    2.326
peak=   -3.241 closest distance to " O   HOH Z 275 " =    1.532
peak=   -3.240 closest distance to " OG  SER A  63 " =    1.204
peak=   -3.239 closest distance to " C   LEU A 143 " =    1.069
peak=   -3.238 closest distance to " NE2 GLN A 278 " =    1.918
peak=   -3.232 closest distance to " O   HOH Z 231 " =    1.512
peak=   -3.231 closest distance to " CB  VAL A 296 " =    1.193
peak=   -3.231 closest distance to " CG1 VAL A 125 " =    1.968
peak=   -3.231 closest distance to " O   HOH Z 222 " =    1.482
peak=   -3.225 closest distance to " O   VAL A 121 " =    1.455
peak=   -3.224 closest distance to " O   HOH Z 313 " =    1.112
peak=   -3.224 closest distance to " O   HOH Z 298 " =    2.877
peak=   -3.224 closest distance to " N   VAL A 230 " =    1.159
peak=   -3.223 closest distance to " SD BMET A  47 " =    1.064
peak=   -3.222 closest distance to " ND2 ASN A 187 " =    1.505
peak=   -3.218 closest distance to " CB  ALA A 291 " =    2.246
peak=   -3.218 closest distance to " O   HOH Z 353 " =    2.070
peak=   -3.212 closest distance to " O   HOH Z 369 " =    2.285
peak=   -3.210 closest distance to " O   HOH Z 216 " =    1.579
peak=   -3.208 closest distance to " CD1 LEU A   5 " =    2.597
peak=   -3.205 closest distance to " CD  ARG A 195 " =    5.105
peak=   -3.197 closest distance to " O   HOH Z 174 " =    2.548
peak=   -3.192 closest distance to " O   ALA A  34 " =    2.047
peak=   -3.191 closest distance to " O   HOH Z 177 " =    1.763
peak=   -3.190 closest distance to " O   PRO A 198 " =    1.356
peak=   -3.187 closest distance to " CG2 VAL A 202 " =    2.722
peak=   -3.186 closest distance to " CG1 VAL A  67 " =    2.895
peak=   -3.175 closest distance to " O   HOH Z 372 " =    2.388
peak=   -3.173 closest distance to " O   ILE A 106 " =    2.086
peak=   -3.173 closest distance to " O   HOH Z 256 " =    1.340
peak=   -3.159 closest distance to " CB  TRP A  85 " =    2.546
peak=   -3.155 closest distance to " CZ  TYR A 169 " =    1.688
peak=   -3.155 closest distance to " CD  PRO A 243 " =    2.140
peak=   -3.148 closest distance to " CG2 VAL A 189 " =    2.032
peak=   -3.144 closest distance to " CD1 ILE A 151 " =    2.432
peak=   -3.141 closest distance to " O   ARG A 145 " =    1.669
peak=   -3.141 closest distance to " O   HOH Z 210 " =    0.998
peak=   -3.134 closest distance to " O   SER A  22 " =    2.216
peak=   -3.133 closest distance to " NE2 GLN A 103 " =    1.790
peak=   -3.131 closest distance to " CG  PHE A 283 " =    2.731
peak=   -3.129 closest distance to " CB  ASN A 252 " =    1.680
peak=   -3.129 closest distance to " N   MET A 188 " =    1.855
peak=   -3.111 closest distance to " O   HOH Z 166 " =    1.672
peak=   -3.106 closest distance to " O   HOH Z 200 " =    4.368
peak=   -3.099 closest distance to " O   HOH Z 350 " =    1.943
peak=   -3.097 closest distance to " C   ASP A 270 " =    1.332
peak=   -3.096 closest distance to " O   HOH Z  89 " =    3.122
peak=   -3.094 closest distance to " CD1 TYR A 247 " =    2.296
peak=   -3.093 closest distance to " OG1 THR A 246 " =    1.436
peak=   -3.084 closest distance to " O   HOH Z 231 " =    1.644
peak=   -3.080 closest distance to " OD2 ASP A 171 " =    1.845
peak=   -3.080 closest distance to " CD2 TYR A 247 " =    2.346
peak=   -3.061 closest distance to " CB  ASP A 171 " =    2.285
peak=   -3.056 closest distance to " CG2BVAL A  41 " =    1.764
peak=   -3.050 closest distance to " OG  SER A  62 " =    1.749
peak=   -3.049 closest distance to " O   HOH Z 313 " =    1.583
peak=   -3.041 closest distance to " O   LYS A 289 " =    2.987
peak=   -3.010 closest distance to " NH2 ARG A  66 " =    2.173

================= 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    :  0.4290 0.4141   6.219408e+00   6.188625e+00
   1_bss:  0.4215 0.4008   6.214155e+00   6.174808e+00
   1_xyz:  0.3087 0.3265   5.988712e+00   6.031667e+00
   1_adp:  0.2410 0.2726   5.774663e+00   5.890653e+00
   1_occ:  0.2404 0.2732   5.773096e+00   5.892420e+00
   2_bss:  0.2355 0.2672   5.771471e+00   5.887689e+00
   2_xyz:  0.1556 0.1969   5.404988e+00   5.590419e+00
   2_adp:  0.1416 0.1842   5.326676e+00   5.529593e+00
   2_occ:  0.1416 0.1842   5.326259e+00   5.529323e+00
   3_bss:  0.1413 0.1837   5.327641e+00   5.529549e+00
   3_xyz:  0.1215 0.1657   5.207168e+00   5.436468e+00
   3_adp:  0.1167 0.1634   5.183071e+00   5.424532e+00
   3_occ:  0.1166 0.1634   5.182775e+00   5.424419e+00
   4_bss:  0.1166 0.1634   5.182817e+00   5.424475e+00
   4_xyz:  0.1126 0.1621   5.165043e+00   5.418536e+00
   4_adp:  0.1136 0.1603   5.163428e+00   5.407609e+00
   4_occ:  0.1135 0.1604   5.163496e+00   5.408119e+00
   5_bss:  0.1139 0.1598   5.162659e+00   5.404884e+00
   5_xyz:  0.1150 0.1607   5.170769e+00   5.410017e+00
   5_adp:  0.1150 0.1605   5.171153e+00   5.410801e+00
   5_occ:  0.1148 0.1606   5.170087e+00   5.410241e+00
   5_bss:  0.1148 0.1606   5.170074e+00   5.410214e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   7.752   7.493   9.426   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.752   7.493   9.426   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.752   7.493   9.426   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.752   7.493   9.426   0.000   0.000   0.000
   2_bss:  0.323  50.001   4.572   4.190   6.129   0.000   0.000   0.000
   2_xyz:  0.323  50.001   4.572   4.190   6.129   0.000   0.000   0.000
   2_adp:  0.323  50.001   4.572   4.190   6.129   0.000   0.000   0.000
   2_occ:  0.323  50.001   4.572   4.190   6.129   0.000   0.000   0.000
   3_bss:  0.324  50.001   3.511   3.470   4.936   0.000   0.000   0.000
   3_xyz:  0.324  50.001   3.511   3.470   4.936   0.000   0.000   0.000
   3_adp:  0.324  50.001   3.511   3.470   4.936   0.000   0.000   0.000
   3_occ:  0.324  50.001   3.511   3.470   4.936   0.000   0.000   0.000
   4_bss:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   4_xyz:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   4_adp:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   4_occ:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   5_bss:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   5_xyz:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   5_adp:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   5_occ:  0.324  50.001   3.434   3.461   4.829   0.000   0.000   0.000
   5_bss:  0.324  53.840  -0.495  -0.429   0.924   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.615 0.5763  0.6356    48802.185
   1_bss:  45.212 0.5798  0.8188    46683.973
   1_xyz:  35.141 0.6991  0.9517    29204.328
   1_adp:  27.319 0.7879  1.0366    19406.459
   1_occ:  27.371 0.7872  1.0355    19469.582
   2_bss:  27.119 0.7899  0.9240    19177.530
   2_xyz:  18.453 0.8762  0.9962     9578.298
   2_adp:  16.851 0.8913  1.0048     8487.589
   2_occ:  16.849 0.8913  1.0049     8480.782
   3_bss:  16.870 0.8911  0.9687     8515.156
   3_xyz:  14.911 0.9077  0.9757     6989.805
   3_adp:  14.669 0.9098  0.9741     6813.793
   3_occ:  14.667 0.9098  0.9741     6812.710
   4_bss:  14.668 0.9098  0.9718     6813.489
   4_xyz:  14.485 0.9115  0.9722     6750.152
   4_adp:  14.239 0.9135  0.9716     6630.742
   4_occ:  14.253 0.9134  0.9715     6633.595
   5_bss:  14.222 0.9135  0.9710     6559.873
   5_xyz:  14.284 0.9132  0.9703     6612.976
   5_adp:  14.297 0.9131  0.9676     6620.219
   5_occ:  14.289 0.9131  0.9674     6614.240
   5_bss:  14.289 0.9132  0.9650     6613.571
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4165e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4165e+01
   1_xyz:   1.495  0.011  0.101 17.998  0.006  4.126   1.1565e-01
   1_adp:   1.495  0.011  0.101 17.998  0.006  4.126   1.1565e-01
   1_occ:   1.495  0.011  0.101 17.998  0.006  4.126   1.1565e-01
   2_bss:   1.495  0.011  0.101 17.998  0.006  4.126   1.1565e-01
   2_xyz:   1.066  0.008  0.078 16.588  0.004  4.129   7.0136e-02
   2_adp:   1.066  0.008  0.078 16.588  0.004  4.129   7.0136e-02
   2_occ:   1.066  0.008  0.078 16.588  0.004  4.129   7.0136e-02
   3_bss:   1.066  0.008  0.078 16.588  0.004  4.129   7.0136e-02
   3_xyz:   1.064  0.009  0.087 16.059  0.004  4.142   7.1938e-02
   3_adp:   1.064  0.009  0.087 16.059  0.004  4.142   7.1938e-02
   3_occ:   1.064  0.009  0.087 16.059  0.004  4.142   7.1938e-02
   4_bss:   1.064  0.009  0.087 16.059  0.004  4.142   7.1938e-02
   4_xyz:   1.086  0.010  0.089 15.905  0.004  4.145   7.3567e-02
   4_adp:   1.086  0.010  0.089 15.905  0.004  4.145   7.3567e-02
   4_occ:   1.086  0.010  0.089 15.905  0.004  4.145   7.3567e-02
   5_bss:   1.086  0.010  0.089 15.905  0.004  4.145   7.3567e-02
   5_xyz:   0.987  0.008  0.080 15.609  0.004  4.146   6.2367e-02
   5_adp:   0.987  0.008  0.080 15.609  0.004  4.146   6.2367e-02
   5_occ:   0.987  0.008  0.080 15.609  0.004  4.146   6.2367e-02
   5_bss:   0.987  0.008  0.080 15.609  0.004  4.146   6.2367e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0235e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0235e+00
   1_xyz:  12.327  0.134  0.377 86.537  0.036  2.283   8.6468e-02
   1_adp:  12.327  0.134  0.377 86.537  0.036  2.283   8.6468e-02
   1_occ:  12.327  0.134  0.377 86.537  0.036  2.283   8.6468e-02
   2_bss:  12.327  0.134  0.377 86.537  0.036  2.283   8.6468e-02
   2_xyz:   7.783  0.074  0.349 86.900  0.039  2.356   5.2919e-02
   2_adp:   7.783  0.074  0.349 86.900  0.039  2.356   5.2919e-02
   2_occ:   7.783  0.074  0.349 86.900  0.039  2.356   5.2919e-02
   3_bss:   7.783  0.074  0.349 86.900  0.039  2.356   5.2919e-02
   3_xyz:   7.055  0.044  0.567 82.221  0.040  2.342   7.9549e-02
   3_adp:   7.055  0.044  0.567 82.221  0.040  2.342   7.9549e-02
   3_occ:   7.055  0.044  0.567 82.221  0.040  2.342   7.9549e-02
   4_bss:   7.055  0.044  0.567 82.221  0.040  2.342   7.9549e-02
   4_xyz:   7.463  0.048  0.605 82.588  0.039  2.326   6.1848e-02
   4_adp:   7.463  0.048  0.605 82.588  0.039  2.326   6.1848e-02
   4_occ:   7.463  0.048  0.605 82.588  0.039  2.326   6.1848e-02
   5_bss:   7.463  0.048  0.605 82.588  0.039  2.326   6.1848e-02
   5_xyz:   7.413  0.047  0.499 82.377  0.039  2.357   4.6979e-02
   5_adp:   7.413  0.047  0.499 82.377  0.039  2.357   4.6979e-02
   5_occ:   7.413  0.047  0.499 82.377  0.039  2.357   4.6979e-02
   5_bss:   7.413  0.047  0.499 82.377  0.039  2.357   4.6979e-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:  72.06   0.00  10.64  61.65   0.00   7.34  72.06   0.00  28.62
   1_occ:  72.06   0.00  10.64  61.65   0.00   7.34  72.06   0.00  28.62
   2_bss:  72.06   0.00  10.64  61.65   0.00   7.34  72.06   0.00  28.62
   2_xyz:  72.06   0.00  10.64  61.65   0.00   7.34  72.06   0.00  28.62
   2_adp:  71.41   0.00  10.92  60.40   0.00   7.14  71.41   0.00  31.50
   2_occ:  71.41   0.00  10.92  60.40   0.00   7.14  71.41   0.00  31.50
   3_bss:  71.41   0.00  10.92  60.40   0.00   7.14  71.41   0.00  31.50
   3_xyz:  71.41   0.00  10.92  60.40   0.00   7.14  71.41   0.00  31.50
   3_adp:  75.69   0.00  11.71  75.69   0.00   7.35  75.66   0.00  35.46
   3_occ:  75.69   0.00  11.71  75.69   0.00   7.35  75.66   0.00  35.46
   4_bss:  75.69   0.00  11.71  75.69   0.00   7.35  75.66   0.00  35.46
   4_xyz:  75.69   0.00  11.71  75.69   0.00   7.35  75.66   0.00  35.46
   4_adp:  74.95   0.00  11.08  74.95   0.00   7.11  74.13   0.66  32.72
   4_occ:  74.95   0.00  11.08  74.95   0.00   7.11  74.13   0.66  32.72
   5_bss:  74.95   0.00  11.08  74.95   0.00   7.11  74.13   0.66  32.72
   5_xyz:  74.95   0.00  11.08  74.95   0.00   7.11  74.13   0.66  32.72
   5_adp:  75.40   0.00  11.04  75.40   0.00   7.08  73.76   0.64  32.61
   5_occ:  75.40   0.00  11.04  75.40   0.00   7.08  73.76   0.64  32.61
   5_bss:  79.24   3.84  14.88  79.24   3.84  10.92  77.60   4.48  36.45
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.199    0.017    0.400
   1_adp:    1.199    0.017    0.400
   1_occ:    1.199    0.017    0.400
   2_bss:    1.199    0.017    0.400
   2_xyz:    1.459    0.030    0.494
   2_adp:    1.459    0.030    0.494
   2_occ:    1.459    0.030    0.494
   3_bss:    1.459    0.030    0.494
   3_xyz:    1.456    0.058    0.527
   3_adp:    1.456    0.058    0.527
   3_occ:    1.456    0.058    0.527
   4_bss:    1.456    0.058    0.527
   4_xyz:    1.537    0.056    0.536
   4_adp:    1.537    0.056    0.536
   4_occ:    1.537    0.056    0.536
   5_bss:    1.537    0.056    0.536
   5_xyz:    1.553    0.051    0.545
   5_adp:    1.553    0.051    0.545
   5_occ:    1.553    0.051    0.545
   5_bss:    1.553    0.051    0.545
------------------------------------------------------------------------

CPU time actual refinement: 325.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/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_909/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_909/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.09 
  Macro-tasks:
    bulk solvent and scale       = 39.55  
    individual site refinement   = 135.22 
    weights calculation          = 32.42  
    collect and process          = 6.87   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 214.19 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 97.49  
    alpha_beta                      = 8.30   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 110.21 
    fmodel                         = 7.32   
    r_factors                      = 0.28   
    phase_errors                   = 11.24  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 237.92 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.545 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    654 calls, 97.08 s
gradients_fft:          600 calls, 96.33 s

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

# Date 2008-01-16 Time 02:43:29 PST -0800 (1200480209.66 s)
Start R-work = 0.4290, R-free = 0.4141 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.4215, R-free = 0.4008
Final R-work = 0.1148, R-free = 0.1606