# Date 2008-01-16 Time 02:03:16 PST -0800 (1200477796.45 s)
#phil __OFF__

Command line arguments: "../674.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26646
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 674

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.1647, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98115
Completeness in resolution range: 0.963172
Completeness with d_max=infinity: 0.960151

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98115
Completeness in resolution range: 0.963172
Completeness with d_max=infinity: 0.960151

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2389 [2127/2154]  1915   212  10.0%
  bin  2:  4.2389 -  3.3773 [2046/2062]  1840   206  10.1%
  bin  3:  3.3773 -  2.9541 [2033/2052]  1828   205  10.1%
  bin  4:  2.9541 -  2.6857 [2006/2036]  1808   198   9.9%
  bin  5:  2.6857 -  2.4942 [1996/2015]  1800   196   9.8%
  bin  6:  2.4942 -  2.3477 [1963/1999]  1768   195   9.9%
  bin  7:  2.3477 -  2.2305 [1977/2010]  1777   200  10.1%
  bin  8:  2.2305 -  2.1337 [1975/2009]  1774   201  10.2%
  bin  9:  2.1337 -  2.0518 [1958/1986]  1767   191   9.8%
  bin 10:  2.0518 -  1.9812 [1508/2015]  1353   155  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/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: 17
        2.42 -     3.04: 2200
        3.04 -     3.66: 4688
        3.66 -     4.28: 9028
        4.28 -     4.90: 12410
  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 100 " - " O   HOH Z 352 "  2.129 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.194 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 207 " - " O   HOH Z 341 "  2.264 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28338 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_674/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.16465 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4227   r_free= 0.4128   ksol= 0.00   Bsol= 0.00   scale= 0.830    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.212034                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7277 0.99   1380  154 0.3589 0.3403      6.5061      6.4474|
|  2:  4.7277 -  3.7723 0.99   1346  146 0.3180 0.3225      6.6094      6.6354|
|  3:  3.7723 -  3.3013 0.99   1308  150 0.3657 0.3484      6.5434      6.5601|
|  4:  3.3013 -  3.0022 0.99   1295  142 0.3918 0.3725      6.4207      6.3456|
|  5:  3.0022 -  2.7885 0.99   1294  142 0.4340 0.4529      6.2934      6.3278|
|  6:  2.7885 -  2.6250 0.99   1286  144 0.4431 0.5058      6.2122      6.2171|
|  7:  2.6250 -  2.4942 0.99   1282  139 0.4681 0.4147      6.2096      6.1175|
|  8:  2.4942 -  2.3860 0.98   1273  149 0.4704 0.4398      6.1403      6.1016|
|  9:  2.3860 -  2.2945 0.98   1279  138 0.4743 0.4663       6.081      6.0727|
| 10:  2.2945 -  2.2156 0.98   1242  138 0.4780 0.4935      6.0822      6.0845|
| 11:  2.2156 -  2.1465 1.00   1284  143 0.4869 0.4209      6.0148      5.9715|
| 12:  2.1465 -  2.0853 0.97   1244  136 0.4895 0.4815      5.9614      6.0168|
| 13:  2.0853 -  2.0306 0.98   1257  146 0.4960 0.5146      5.8698      5.8506|
| 14:  2.0306 -  1.9812 0.66    860   92 0.5021 0.4701      5.8265       5.733|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7277  1380   154  0.74  30.68   0.82     0.76      56869.94|
|  2:  4.7277 -  3.7723  1346   146  0.78  27.78   0.92     0.83      69893.60|
|  3:  3.7723 -  3.3013  1308   150  0.72  34.02   0.88     0.81      72424.17|
|  4:  3.3013 -  3.0022  1295   142  0.66  38.48   0.85     0.73      64856.79|
|  5:  3.0022 -  2.7885  1294   142  0.57  46.60   0.78     0.64      58843.36|
|  6:  2.7885 -  2.6250  1286   144  0.55  47.99   0.78     0.62      52660.74|
|  7:  2.6250 -  2.4942  1282   139  0.55  48.30   0.76     0.61      47992.41|
|  8:  2.4942 -  2.3860  1273   149  0.54  48.77   0.77     0.62      43142.91|
|  9:  2.3860 -  2.2945  1279   138  0.54  48.90   0.76     0.61      38349.20|
| 10:  2.2945 -  2.2156  1242   138  0.54  49.28   0.78     0.61      35796.28|
| 11:  2.2156 -  2.1465  1284   143  0.51  51.69   0.78     0.59      34140.98|
| 12:  2.1465 -  2.0853  1244   136  0.46  55.24   0.78     0.55      35399.88|
| 13:  2.0853 -  2.0306  1257   146  0.42  58.46   0.76     0.50      31728.77|
| 14:  2.0306 -  1.9812   860    92  0.45  56.25   0.75     0.49      25254.30|
|alpha:            min =        0.49 max =            0.83 mean =         0.65|
|beta:             min =    25254.30 max =        72424.17 mean =     48472.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.96 mean =        45.42|
|phase err.(test): min =        0.00 max =           89.86 mean =        45.47|
|-----------------------------------------------------------------------------|

============================== 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 = 7.251589              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.583796              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.651   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1517 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3925 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5069 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6599 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7722 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.693 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.699 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4316   r_free= 0.4219   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.218989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4141   r_free= 0.4038   ksol= 0.35   Bsol= 20.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.60,8.38,0.00,0.00,0.00); trace/3= 8.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.209534                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.663080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.278   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.591925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.127   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4141      final r-factor (work) = 0.3032          |
| start r-factor (free) = 0.4038      final r-factor (free) = 0.3299          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.4398 = 6.66 * 0.50 * 6.2274 + 1.00 * 53.6931                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2375 = 6.66 * 0.50 * 6.0400 + 1.00 * 0.1148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3032      final r-factor (work) = 0.2370          |
| start r-factor (free) = 0.3299      final r-factor (free) = 0.2715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5900 = 0.59 * 1.00 * 6.0400 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4698 = 0.59 * 1.00 * 5.8437 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    51.26   9.96     None  None   None       |
|    all(noH): 2823   0      0.00    51.26   9.96     None  None   None       |
|    Sol.    : 438    0      0.00    51.26   26.03    None  None   None       |
|    Mac.    : 2385   0      0.00    44.60   7.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.126: 1160   |   5:    25.631 -  30.757:  124        |
|      1:     5.126 -  10.252:  782   |   6:    30.757 -  35.883:   96        |
|      2:    10.252 -  15.378:  306   |   7:    35.883 -  41.009:   79        |
|      3:    15.378 -  20.504:  148   |   8:    41.009 -  46.135:   20        |
|      4:    20.504 -  25.631:  106   |   9:    46.135 -  51.261:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2370 r_free = 0.2715             target_work(ml) = 5.760         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2364 r_free = 0.2715             target_work(ml) = 5.759         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2364   r_free= 0.2715   ksol= 0.35   Bsol= 20.00   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,8.60,8.38,0.00,0.00,0.00); trace/3= 8.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.758753                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2316   r_free= 0.2664   ksol= 0.32   Bsol= 38.91   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,4.81,5.38,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.758172                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.706020              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.405   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.290158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.344  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2316      final r-factor (work) = 0.1602          |
| start r-factor (free) = 0.2664      final r-factor (free) = 0.1971          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0406 = 2.71 * 0.50 * 5.8583 + 1.00 * 0.1143                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6122 = 2.71 * 0.50 * 5.5830 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1602      final r-factor (work) = 0.1457          |
| start r-factor (free) = 0.1971      final r-factor (free) = 0.1839          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6305 = 0.29 * 1.00 * 5.5830 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5705 = 0.29 * 1.00 * 5.3784 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.92   10.79    None  None   None       |
|    all(noH): 2823   0      0.00    56.92   10.79    None  None   None       |
|    Sol.    : 438    0      0.97    54.80   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    56.92   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 -   5.692: 1338   |   5:    28.462 -  34.155:   82        |
|      1:     5.692 -  11.385:  729   |   6:    34.155 -  39.847:  111        |
|      2:    11.385 -  17.077:  227   |   7:    39.847 -  45.539:   92        |
|      3:    17.077 -  22.770:  112   |   8:    45.539 -  51.232:   37        |
|      4:    22.770 -  28.462:   81   |   9:    51.232 -  56.924:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1457 r_free = 0.1839             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1456 r_free = 0.1839             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1456   r_free= 0.1839   ksol= 0.32   Bsol= 38.91   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.75,4.81,5.38,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.345833                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1451   r_free= 0.1833   ksol= 0.32   Bsol= 38.92   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,3.76,4.34,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.345618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.074081              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.537  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.733256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.513  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1451      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1833      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3327 = 3.07 * 0.50 * 5.3833 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1489 = 3.07 * 0.50 * 5.2590 + 1.00 * 0.0656                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8660 = 0.73 * 1.00 * 5.2590 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7994 = 0.73 * 1.00 * 5.1647 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.43   11.40    None  None   None       |
|    all(noH): 2823   0      0.00    73.43   11.40    None  None   None       |
|    Sol.    : 438    0      0.78    70.64   33.84    None  None   None       |
|    Mac.    : 2385   0      0.00    73.43   7.28     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 -   7.343: 1634   |   5:    36.715 -  44.058:  100        |
|      1:     7.343 -  14.686:  580   |   6:    44.058 -  51.401:   80        |
|      2:    14.686 -  22.029:  162   |   7:    51.401 -  58.744:   45        |
|      3:    22.029 -  29.372:  106   |   8:    58.744 -  66.087:   17        |
|      4:    29.372 -  36.715:   92   |   9:    66.087 -  73.430:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1562             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1563             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1563   ksol= 0.32   Bsol= 38.92   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,3.76,4.34,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1563   ksol= 0.32   Bsol= 38.92   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,3.76,4.34,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156857                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.705874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.167612              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.670  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4705 = 1.71 * 0.50 * 5.1645 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4516 = 1.71 * 0.50 * 5.1536 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8761 = 0.17 * 1.00 * 5.1536 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8753 = 0.17 * 1.00 * 5.1594 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.09   11.01    None  None   None       |
|    all(noH): 2823   0      0.00    72.09   11.01    None  None   None       |
|    Sol.    : 438    0      0.86    63.60   31.88    None  None   None       |
|    Mac.    : 2385   0      0.00    72.09   7.17     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 -   7.209: 1641   |   5:    36.047 -  43.256:   94        |
|      1:     7.209 -  14.419:  587   |   6:    43.256 -  50.465:   64        |
|      2:    14.419 -  21.628:  158   |   7:    50.465 -  57.674:   38        |
|      3:    21.628 -  28.837:  105   |   8:    57.674 -  64.884:   11        |
|      4:    28.837 -  36.047:  119   |   9:    64.884 -  72.093:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1146 r_free = 0.1560             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1561             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1561   ksol= 0.32   Bsol= 38.92   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,3.76,4.34,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1562   ksol= 0.32   Bsol= 40.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.52,4.08,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155826                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.629952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.203  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.692707              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.891   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8401 = 2.63 * 0.50 * 5.1592 + 1.00 * 0.0559                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8228 = 2.63 * 0.50 * 5.1354 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5684 = 0.69 * 1.00 * 5.1354 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5810 = 0.69 * 1.00 * 5.1207 + 1.00 * 0.0339                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.04   11.22    None  None   None       |
|    all(noH): 2823   0      0.00    76.04   11.22    None  None   None       |
|    Sol.    : 438    0      0.85    66.61   32.89    None  None   None       |
|    Mac.    : 2385   0      0.00    76.04   7.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.604: 1683   |   5:    38.021 -  45.625:   97        |
|      1:     7.604 -  15.208:  554   |   6:    45.625 -  53.229:   69        |
|      2:    15.208 -  22.812:  148   |   7:    53.229 -  60.833:   27        |
|      3:    22.812 -  30.417:  119   |   8:    60.833 -  68.437:    9        |
|      4:    30.417 -  38.021:  111   |   9:    68.437 -  76.041:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1553             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1552             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1552   ksol= 0.32   Bsol= 40.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,3.52,4.08,0.00,0.00,0.00); trace/3= 3.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7277 0.99   1380  154 0.0986 0.1298      5.3741      5.5181|
|  2:  4.7277 -  3.7723 0.99   1346  146 0.0853 0.1094      5.4279      5.6255|
|  3:  3.7723 -  3.3013 0.99   1308  150 0.1031 0.1498      5.4555      5.8348|
|  4:  3.3013 -  3.0022 0.99   1295  142 0.1165 0.1503      5.4294      5.5811|
|  5:  3.0022 -  2.7885 0.99   1294  142 0.1267 0.1693      5.2999      5.5225|
|  6:  2.7885 -  2.6250 0.99   1286  144 0.1169 0.1787      5.1902      5.4347|
|  7:  2.6250 -  2.4942 0.99   1282  139 0.1213 0.1605      5.1498      5.3608|
|  8:  2.4942 -  2.3860 0.98   1273  149 0.1135 0.1784      5.0643      5.3529|
|  9:  2.3860 -  2.2945 0.98   1279  138 0.1144 0.1787      5.0231      5.3257|
| 10:  2.2945 -  2.2156 0.98   1242  138 0.1071 0.1659      4.9516       5.172|
| 11:  2.2156 -  2.1465 1.00   1284  143 0.1086 0.1715      4.9065      5.2758|
| 12:  2.1465 -  2.0853 0.97   1244  136 0.1065 0.1624      4.8569      5.1159|
| 13:  2.0853 -  2.0306 0.98   1257  146 0.1109 0.1739      4.7757      5.0793|
| 14:  2.0306 -  1.9812 0.66    860   92 0.1028 0.1717      4.6562      4.9005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7277  1380   154  0.94   8.92   0.98     0.96       7028.30|
|  2:  4.7277 -  3.7723  1346   146  0.95   7.76   1.02     1.00       8807.67|
|  3:  3.7723 -  3.3013  1308   150  0.94  11.12   1.02     1.02      10120.87|
|  4:  3.3013 -  3.0022  1295   142  0.92  13.13   1.00     0.99       9956.32|
|  5:  3.0022 -  2.7885  1294   142  0.90  15.61   0.99     0.96       7966.09|
|  6:  2.7885 -  2.6250  1286   144  0.90  15.56   0.98     0.95       6830.10|
|  7:  2.6250 -  2.4942  1282   139  0.91  15.34   0.99     0.96       6121.01|
|  8:  2.4942 -  2.3860  1273   149  0.91  15.25   0.99     0.96       5401.72|
|  9:  2.3860 -  2.2945  1279   138  0.91  15.54   1.00     0.97       5011.93|
| 10:  2.2945 -  2.2156  1242   138  0.90  15.39   1.00     0.97       4447.53|
| 11:  2.2156 -  2.1465  1284   143  0.90  16.04   1.00     0.96       4187.63|
| 12:  2.1465 -  2.0853  1244   136  0.92  14.46   1.00     0.98       3794.57|
| 13:  2.0853 -  2.0306  1257   146  0.90  16.03   1.01     1.00       3316.57|
| 14:  2.0306 -  1.9812   860    92  0.91  14.54   0.98     0.95       2524.56|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2524.56 max =        10120.87 mean =      6232.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.83|
|phase err.(test): min =        0.00 max =           88.03 mean =        13.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1553   ksol= 0.32   Bsol= 44.11   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.01,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127295                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1553   ksol= 0.32   Bsol= 44.11   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.01,0.56,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127295                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7277 0.99   1380  154 0.0986 0.1299      5.3746      5.5189|
|  2:  4.7277 -  3.7723 0.99   1346  146 0.0853 0.1094      5.4283      5.6257|
|  3:  3.7723 -  3.3013 0.99   1308  150 0.1031 0.1498      5.4557      5.8353|
|  4:  3.3013 -  3.0022 0.99   1295  142 0.1165 0.1504      5.4293      5.5811|
|  5:  3.0022 -  2.7885 0.99   1294  142 0.1267 0.1692      5.2996       5.522|
|  6:  2.7885 -  2.6250 0.99   1286  144 0.1169 0.1788      5.1901      5.4346|
|  7:  2.6250 -  2.4942 0.99   1282  139 0.1214 0.1607      5.1499      5.3615|
|  8:  2.4942 -  2.3860 0.98   1273  149 0.1135 0.1783      5.0645      5.3527|
|  9:  2.3860 -  2.2945 0.98   1279  138 0.1144 0.1786      5.0231      5.3259|
| 10:  2.2945 -  2.2156 0.98   1242  138 0.1070 0.1660      4.9515      5.1721|
| 11:  2.2156 -  2.1465 1.00   1284  143 0.1085 0.1713      4.9062      5.2752|
| 12:  2.1465 -  2.0853 0.97   1244  136 0.1064 0.1624      4.8565      5.1156|
| 13:  2.0853 -  2.0306 0.98   1257  146 0.1109 0.1736      4.7754      5.0787|
| 14:  2.0306 -  1.9812 0.66    860   92 0.1028 0.1716       4.656      4.9006|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7277  1380   154  0.94   8.92   0.98     0.96       7038.47|
|  2:  4.7277 -  3.7723  1346   146  0.95   7.76   1.02     1.00       8816.75|
|  3:  3.7723 -  3.3013  1308   150  0.94  11.13   1.03     1.02      10128.39|
|  4:  3.3013 -  3.0022  1295   142  0.92  13.13   1.01     0.99       9954.31|
|  5:  3.0022 -  2.7885  1294   142  0.90  15.61   0.99     0.96       7962.96|
|  6:  2.7885 -  2.6250  1286   144  0.90  15.56   0.98     0.95       6826.89|
|  7:  2.6250 -  2.4942  1282   139  0.91  15.34   0.99     0.96       6122.55|
|  8:  2.4942 -  2.3860  1273   149  0.91  15.26   0.99     0.97       5402.74|
|  9:  2.3860 -  2.2945  1279   138  0.91  15.55   1.01     0.98       5014.09|
| 10:  2.2945 -  2.2156  1242   138  0.90  15.38   1.00     0.97       4445.94|
| 11:  2.2156 -  2.1465  1284   143  0.90  16.04   1.00     0.97       4184.84|
| 12:  2.1465 -  2.0853  1244   136  0.92  14.45   1.01     0.99       3791.43|
| 13:  2.0853 -  2.0306  1257   146  0.90  16.02   1.01     1.01       3313.46|
| 14:  2.0306 -  1.9812   860    92  0.91  14.53   0.99     0.95       2522.04|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2522.04 max =        10128.39 mean =      6233.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.83|
|phase err.(test): min =        0.00 max =           88.04 mean =        13.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.861)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.61    79.66   14.83    None  None   None       |
|    all(noH): 2823   0      3.61    79.66   14.83    None  None   None       |
|    Sol.    : 438    0      4.46    70.23   36.50    None  None   None       |
|    Mac.    : 2385   0      3.61    79.66   10.85    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:     3.614 -  11.219: 1683   |   5:    41.635 -  49.239:   97        |
|      1:    11.219 -  18.823:  554   |   6:    49.239 -  56.843:   69        |
|      2:    18.823 -  26.427:  148   |   7:    56.843 -  64.448:   27        |
|      3:    26.427 -  34.031:  119   |   8:    64.448 -  72.052:    9        |
|      4:    34.031 -  41.635:  111   |   9:    72.052 -  79.656:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.333 - 4.665
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 322
   mapped sites are within: 0.705 - 4.665

peak=   10.527 closest distance to " CG2 VAL A 230 " =    1.359
peak=    6.248 closest distance to " CG2 VAL A 296 " =    1.068
peak=    6.229 closest distance to " CG  LEU A   5 " =    1.179
peak=    5.845 closest distance to " CG  LEU A 228 " =    1.151
peak=    5.700 closest distance to " CB  VAL A 296 " =    1.067
peak=    5.513 closest distance to " NH2 ARG A  56 " =    2.213
peak=    5.266 closest distance to " CB  VAL A 230 " =    1.198
peak=    5.229 closest distance to " CB  GLN A 223 " =    1.430
peak=    5.213 closest distance to " CG  PRO A  54 " =    1.201
peak=    5.197 closest distance to " CD2 LEU A   5 " =    1.161
peak=    5.168 closest distance to " NE2 GLN A  11 " =    1.105
peak=    5.126 closest distance to " CB  SER A  63 " =    1.270
peak=    5.029 closest distance to " O   HOH Z 126 " =    1.950
peak=    4.940 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.821 closest distance to " O   HOH Z 272 " =    1.908
peak=    4.778 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.741 closest distance to " CB  ARG A 275 " =    0.911
peak=    4.707 closest distance to " O   HOH Z 142 " =    1.639
peak=    4.574 closest distance to " O   HOH Z 193 " =    1.745
peak=    4.551 closest distance to " CB  PRO A  54 " =    0.882
peak=    4.522 closest distance to " C   PRO A 198 " =    1.479
peak=    4.519 closest distance to " O   HOH Z 209 " =    2.350
peak=    4.481 closest distance to " CB  TYR A 169 " =    0.705
peak=    4.445 closest distance to " CB  GLU A 152 " =    1.175
peak=    4.429 closest distance to " O   HOH Z 298 " =    1.829
peak=    4.387 closest distance to " O   SER A  87 " =    2.207
peak=    4.386 closest distance to " O   HOH Z 236 " =    1.935
peak=    4.378 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.369 closest distance to " O   HOH Z  43 " =    2.071
peak=    4.345 closest distance to " O   HOH Z 316 " =    3.041
peak=    4.328 closest distance to " OD1 ASN A  69 " =    2.614
peak=    4.299 closest distance to " O   HOH Z 303 " =    2.042
peak=    4.295 closest distance to " O   HOH Z 427 " =    2.953
peak=    4.280 closest distance to " O   HOH Z 203 " =    1.692
peak=    4.278 closest distance to " O   HOH Z 369 " =    2.142
peak=    4.254 closest distance to " CB  SER A   3 " =    1.248
peak=    4.216 closest distance to " O   HOH Z 423 " =    1.801
peak=    4.209 closest distance to " O   HOH Z 368 " =    2.184
peak=    4.209 closest distance to " CB  ASN A 148 " =    1.353
peak=    4.198 closest distance to " O   HOH Z  78 " =    1.718
peak=    4.196 closest distance to " O   HOH Z 158 " =    3.089
peak=    4.190 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.133 closest distance to " CD2 LEU A 228 " =    1.150
peak=    4.109 closest distance to " O   HOH Z 234 " =    3.591
peak=    4.100 closest distance to " CB  ARG A  79 " =    1.426
peak=    4.053 closest distance to " O   HOH Z 403 " =    1.674
peak=    4.049 closest distance to " O   HOH Z 346 " =    1.576
peak=    4.033 closest distance to " CB  GLU A 128 " =    1.044
peak=    4.024 closest distance to " O   HOH Z 402 " =    1.462
peak=    4.017 closest distance to " O   HOH Z  61 " =    1.646
peak=    4.002 closest distance to " CB  VAL A 265 " =    1.312
peak=    3.998 closest distance to " ND2 ASN A 187 " =    1.461
peak=    3.967 closest distance to " O   HOH Z  63 " =    2.080
peak=    3.962 closest distance to " CB  TRP A 179 " =    1.357
peak=    3.949 closest distance to " O   HOH Z  15 " =    2.093
peak=    3.943 closest distance to " CB  GLU A 277 " =    3.535
peak=    3.943 closest distance to " O   HOH Z 280 " =    2.910
peak=    3.942 closest distance to " O   HOH Z 389 " =    1.908
peak=    3.941 closest distance to " CG1BVAL A  72 " =    1.659
peak=    3.940 closest distance to " O   HOH Z  97 " =    1.980
peak=    3.929 closest distance to " CB  ARG A 139 " =    0.966
peak=    3.926 closest distance to " O   HOH Z  66 " =    2.213
peak=    3.924 closest distance to " CB  ARG A 190 " =    1.656
peak=    3.865 closest distance to " O   HOH Z 371 " =    3.262
peak=    3.860 closest distance to " O   HOH Z  97 " =    2.519
peak=    3.860 closest distance to " O   HOH Z 197 " =    3.004
peak=    3.857 closest distance to " CB  TRP A 266 " =    0.952
peak=    3.854 closest distance to " O   HOH Z  54 " =    1.590
peak=    3.846 closest distance to " O   HOH Z 261 " =    2.154
peak=    3.839 closest distance to " O   HOH Z 248 " =    1.665
peak=    3.823 closest distance to " O   TRP A 274 " =    1.877
peak=    3.820 closest distance to " OD2 ASP A 286 " =    2.790
peak=    3.813 closest distance to " CG  ARG A  66 " =    2.722
peak=    3.810 closest distance to " O   HOH Z  59 " =    2.150
peak=    3.809 closest distance to " O   HOH Z 411 " =    3.777
peak=    3.808 closest distance to " CA  ALA A  21 " =    1.166
peak=    3.804 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.779 closest distance to " NH2 ARG A 156 " =    1.133
peak=    3.777 closest distance to " CG  PRO A 243 " =    1.153
peak=    3.772 closest distance to " O   HOH Z  48 " =    1.469
peak=    3.734 closest distance to " O   HOH Z 214 " =    2.186
peak=    3.729 closest distance to " O   HOH Z 189 " =    2.574
peak=    3.718 closest distance to " O   HOH Z 193 " =    1.988
peak=    3.717 closest distance to " CB  ASN A  39 " =    0.820
peak=    3.713 closest distance to " O   HOH Z 245 " =    1.394
peak=    3.712 closest distance to " O   HOH Z 128 " =    2.083
peak=    3.690 closest distance to " O   HOH Z 263 " =    1.655
peak=    3.685 closest distance to " CG  GLN A  77 " =    2.151
peak=    3.679 closest distance to " O   HOH Z 124 " =    1.335
peak=    3.678 closest distance to " O   HOH Z 344 " =    2.932
peak=    3.666 closest distance to " O   HOH Z 128 " =    2.108
peak=    3.662 closest distance to " O   HOH Z 147 " =    1.710
peak=    3.661 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.657 closest distance to " CG1 ILE A  49 " =    1.424
peak=    3.657 closest distance to " CA  THR A 221 " =    0.938
peak=    3.653 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.650 closest distance to " O   HOH Z  78 " =    2.106
peak=    3.648 closest distance to " O   MET A 105 " =    1.865
peak=    3.644 closest distance to " CG2 ILE A  20 " =    1.424
peak=    3.643 closest distance to " CB  ASP A 140 " =    0.913
peak=    3.643 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.642 closest distance to " OG BSER A 164 " =    2.199
peak=    3.640 closest distance to " O   HOH Z 250 " =    1.332
peak=    3.639 closest distance to " CA  ALA A  51 " =    0.970
peak=    3.630 closest distance to " O   HOH Z 345 " =    3.161
peak=    3.624 closest distance to " O   HOH Z  88 " =    3.039
peak=    3.623 closest distance to " CA  ASN A 215 " =    1.202
peak=    3.623 closest distance to " O   HOH Z 261 " =    2.166
peak=    3.616 closest distance to " CD2 TRP A 179 " =    1.388
peak=    3.609 closest distance to " O   HOH Z 417 " =    3.142
peak=    3.607 closest distance to " OE1 GLU A   2 " =    2.168
peak=    3.603 closest distance to " O   HOH Z 299 " =    4.294
peak=    3.603 closest distance to " CA  VAL A  41 " =    0.815
peak=    3.600 closest distance to " O   HOH Z  80 " =    1.695
peak=    3.594 closest distance to " O   HOH Z 273 " =    2.690
peak=    3.592 closest distance to " O   HOH Z 407 " =    2.498
peak=    3.591 closest distance to " CB  TRP A 150 " =    1.426
peak=    3.588 closest distance to " CZ  PHE A 218 " =    1.097
peak=    3.583 closest distance to " CB  ASN A 142 " =    1.104
peak=    3.581 closest distance to " NH2 ARG A  79 " =    1.319
peak=    3.576 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.554 closest distance to " CB  ALA A 291 " =    1.389
peak=    3.550 closest distance to " CB  ALA A 248 " =    1.362
peak=    3.543 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.541 closest distance to " CB  THR A 157 " =    1.199
peak=    3.540 closest distance to " O   HOH Z  40 " =    1.538
peak=    3.539 closest distance to " CD BLYS A 290 " =    1.083
peak=    3.537 closest distance to " ND2 ASN A 110 " =    1.697
peak=    3.537 closest distance to " CA  THR A 264 " =    0.787
peak=    3.535 closest distance to " CB  ALA A   9 " =    1.572
peak=    3.535 closest distance to " O   HOH Z  48 " =    1.675
peak=    3.531 closest distance to " CB  LEU A 228 " =    1.312
peak=    3.527 closest distance to " O   HOH Z 366 " =    2.976
peak=    3.518 closest distance to " CG  MET A 185 " =    1.155
peak=    3.505 closest distance to " O   HOH Z 426 " =    1.535
peak=    3.504 closest distance to " N   VAL A 126 " =    1.361
peak=    3.502 closest distance to " O   HOH Z 291 " =    1.613
peak=    3.501 closest distance to " N   ASN A  39 " =    1.227
peak=    3.499 closest distance to " CA  ALA A 158 " =    1.227
peak=    3.493 closest distance to " CG2 THR A 221 " =    1.185
peak=    3.484 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.481 closest distance to " CG1 VAL A 296 " =    1.216
peak=    3.476 closest distance to " O   HOH Z 322 " =    2.048
peak=    3.471 closest distance to " CB  ARG A  79 " =    0.879
peak=    3.465 closest distance to " CG  PRO A 198 " =    1.176
peak=    3.457 closest distance to " CA  VAL A 126 " =    0.892
peak=    3.457 closest distance to " O   HOH Z 189 " =    2.713
peak=    3.456 closest distance to " CD1 ILE A 106 " =    1.057
peak=    3.455 closest distance to " CB  SER A 212 " =    1.157
peak=    3.452 closest distance to " CA  ASP A 140 " =    1.181
peak=    3.452 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.452 closest distance to " CD  ARG A 159 " =    0.747
peak=    3.451 closest distance to " O   HOH Z 134 " =    1.380
peak=    3.442 closest distance to " O   HOH Z 286 " =    2.311
peak=    3.438 closest distance to " O   HOH Z 135 " =    1.740
peak=    3.437 closest distance to " CB  LEU A 143 " =    1.135
peak=    3.437 closest distance to " CA  PHE A 283 " =    1.235
peak=    3.435 closest distance to " O   HOH Z 132 " =    2.694
peak=    3.429 closest distance to " CB  THR A  31 " =    1.664
peak=    3.423 closest distance to " CD  LYS A 166 " =    1.320
peak=    3.423 closest distance to " CB  GLN A 278 " =    0.871
peak=    3.420 closest distance to " O   HOH Z 329 " =    3.882
peak=    3.420 closest distance to " CG  GLN A  58 " =    2.779
peak=    3.415 closest distance to " CD  ARG A 269 " =    0.976
peak=    3.412 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.412 closest distance to " CB  SER A  26 " =    1.618
peak=    3.411 closest distance to " O   HOH Z 437 " =    2.029
peak=    3.410 closest distance to " OG  SER A  22 " =    2.770
peak=    3.408 closest distance to " O   HOH Z 175 " =    2.111
peak=    3.403 closest distance to " OG1 THR A 294 " =    2.333
peak=    3.402 closest distance to " NZ  LYS A 117 " =    3.236
peak=    3.400 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.398 closest distance to " CD1 LEU A 300 " =    1.233
peak=    3.396 closest distance to " O   HOH Z  19 " =    2.099
peak=    3.395 closest distance to " O   HOH Z 265 " =    2.404
peak=    3.389 closest distance to " O   HOH Z 420 " =    2.061
peak=    3.388 closest distance to " O   HOH Z  21 " =    1.675
peak=    3.386 closest distance to " O   HOH Z 271 " =    2.485
peak=    3.385 closest distance to " CB BVAL A  41 " =    1.223
peak=    3.383 closest distance to " O   HOH Z 166 " =    3.663
peak=    3.383 closest distance to " O   HOH Z 180 " =    2.121
peak=    3.382 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.379 closest distance to " O   HOH Z 313 " =    1.731
peak=    3.375 closest distance to " CB  GLN A 205 " =    1.216
peak=    3.373 closest distance to " O   ASP A 124 " =    1.213
peak=    3.372 closest distance to " CA  ASP A 162 " =    1.064
peak=    3.369 closest distance to " O   HOH Z  10 " =    1.823
peak=    3.365 closest distance to " O   HOH Z  85 " =    1.338
peak=    3.364 closest distance to " CA  ARG A  36 " =    1.038
peak=    3.363 closest distance to " CD1 ILE A  33 " =    1.600
peak=    3.359 closest distance to " O   ALA A 158 " =    1.379
peak=    3.356 closest distance to " O   HOH Z 337 " =    3.639
peak=    3.356 closest distance to " O   HOH Z 171 " =    2.403
peak=    3.356 closest distance to " O   ALA A 165 " =    1.458
peak=    3.349 closest distance to " NZ  LYS A 166 " =    3.079
peak=    3.349 closest distance to " CG BARG A 102 " =    1.805
peak=    3.346 closest distance to " O   HOH Z 148 " =    3.207
peak=    3.344 closest distance to " O   HOH Z 411 " =    1.774
peak=    3.342 closest distance to " O   HOH Z 133 " =    1.540
peak=    3.331 closest distance to " CG  MET A 185 " =    1.116
peak=    3.331 closest distance to " O   HOH Z 112 " =    1.617
peak=    3.327 closest distance to " N   SER A 135 " =    1.401
peak=    3.321 closest distance to " CA  ALA A 233 " =    1.373
peak=    3.320 closest distance to " CB  GLN A  88 " =    1.216
peak=    3.320 closest distance to " CA  ALA A 291 " =    0.943
peak=    3.319 closest distance to " O   HOH Z 305 " =    3.588
peak=    3.318 closest distance to " O   HOH Z 417 " =    2.172
peak=    3.316 closest distance to " O   HOH Z  40 " =    2.658
peak=    3.307 closest distance to " O   HOH Z 227 " =    1.654
peak=    3.305 closest distance to " O   HOH Z 126 " =    1.731
peak=    3.303 closest distance to " N   ARG A 190 " =    1.063
peak=    3.299 closest distance to " O   HOH Z 261 " =    1.548
peak=    3.297 closest distance to " CB  GLN A  89 " =    1.182
peak=    3.296 closest distance to " CB  ILE A 120 " =    1.396
peak=    3.296 closest distance to " CB  GLU A  46 " =    1.054
peak=    3.291 closest distance to " O   HOH Z 172 " =    3.844
peak=    3.290 closest distance to " O   HOH Z 383 " =    1.999
peak=    3.284 closest distance to " O   HOH Z 258 " =    1.659
peak=    3.284 closest distance to " CG2 ILE A 120 " =    1.241
peak=    3.277 closest distance to " O   HOH Z 423 " =    3.096
peak=    3.275 closest distance to " O   HOH Z  66 " =    2.254
peak=    3.274 closest distance to " O   HOH Z 419 " =    1.625
peak=    3.272 closest distance to " O   HOH Z  48 " =    1.389
peak=    3.271 closest distance to " CD1 LEU A 228 " =    1.853
peak=    3.269 closest distance to " CD  LYS A 119 " =    1.538
peak=    3.266 closest distance to " CG  GLN A  88 " =    1.015
peak=    3.264 closest distance to " CB  ALA A   1 " =    1.196
peak=    3.263 closest distance to " O   HOH Z 193 " =    1.570
peak=    3.259 closest distance to " O   HOH Z 132 " =    3.337
peak=    3.257 closest distance to " CB  ALA A 248 " =    0.996
peak=    3.253 closest distance to " CB  ASN A 110 " =    1.167
peak=    3.253 closest distance to " O   HOH Z  35 " =    2.472
peak=    3.253 closest distance to " CA  TYR A 116 " =    1.394
peak=    3.251 closest distance to " O   GLN A 278 " =    1.273
peak=    3.250 closest distance to " O   HOH Z 359 " =    1.798
peak=    3.249 closest distance to " ND1 HIS A  81 " =    1.681
peak=    3.249 closest distance to " CA  LYS A 290 " =    1.250
peak=    3.248 closest distance to " CA  ASP A 191 " =    0.975
peak=    3.248 closest distance to " CB  ALA A 100 " =    1.189
peak=    3.247 closest distance to " O   HOH Z 227 " =    2.110
peak=    3.239 closest distance to " CB  SER A 273 " =    0.798
peak=    3.237 closest distance to " CD1 LEU A   5 " =    1.376
peak=    3.236 closest distance to " OD1 ASP A 231 " =    1.890
peak=    3.235 closest distance to " O   HOH Z 251 " =    1.628
peak=    3.232 closest distance to " O   HOH Z 425 " =    1.264
peak=    3.231 closest distance to " O   HOH Z   9 " =    2.095
peak=    3.231 closest distance to " N   ASN A 127 " =    1.245
peak=    3.231 closest distance to " CB  SER A 216 " =    0.742
peak=    3.229 closest distance to " O   HOH Z 435 " =    1.937
peak=    3.229 closest distance to " NZ  LYS A  48 " =    1.353
peak=    3.227 closest distance to " CG  LEU A 167 " =    1.178
peak=    3.223 closest distance to " CA  ALA A  84 " =    1.477
peak=    3.223 closest distance to " CZ2 TRP A 179 " =    1.689
peak=    3.218 closest distance to " CB  ILE A  20 " =    1.496
peak=    3.216 closest distance to " O   HOH Z 282 " =    1.941
peak=    3.214 closest distance to " O   HOH Z 406 " =    1.621
peak=    3.214 closest distance to " CB  LEU A 255 " =    0.775
peak=    3.211 closest distance to " O   HOH Z 130 " =    2.348
peak=    3.209 closest distance to " CD2 TYR A  30 " =    0.906
peak=    3.208 closest distance to " O   HOH Z 227 " =    1.529
peak=    3.207 closest distance to " O   HOH Z 286 " =    2.506
peak=    3.203 closest distance to " CB  ALA A 295 " =    1.300
peak=    3.202 closest distance to " O   HOH Z 199 " =    1.554
peak=    3.201 closest distance to " OD1 ASN A 217 " =    1.705
peak=    3.200 closest distance to " CB  MET A  47 " =    1.203
peak=    3.198 closest distance to " CB  ASN A 224 " =    1.053
peak=    3.195 closest distance to " O   HOH Z 357 " =    1.854
peak=    3.191 closest distance to " O   HOH Z  44 " =    1.710
peak=    3.190 closest distance to " CA  LEU A 282 " =    1.072
peak=    3.187 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.176 closest distance to " CZ  PHE A 192 " =    0.999
peak=    3.176 closest distance to " CG2 THR A 294 " =    1.694
peak=    3.175 closest distance to " O   HOH Z 374 " =    2.616
peak=    3.174 closest distance to " NH2BARG A 145 " =    1.951
peak=    3.173 closest distance to " CG2 VAL A 257 " =    0.842
peak=    3.173 closest distance to " N   ASP A 162 " =    1.364
peak=    3.171 closest distance to " CB  LYS A 117 " =    1.137
peak=    3.171 closest distance to " CD  ARG A  79 " =    2.014
peak=    3.166 closest distance to " CG2 VAL A 197 " =    1.044
peak=    3.165 closest distance to " CA  ILE A 106 " =    0.771
peak=    3.163 closest distance to " O   HOH Z 163 " =    1.804
peak=    3.163 closest distance to " O   HOH Z  49 " =    2.493
peak=    3.153 closest distance to " OD1BASN A 224 " =    2.256
peak=    3.151 closest distance to " O   HOH Z 421 " =    1.638
peak=    3.151 closest distance to " CA  ASN A 176 " =    1.094
peak=    3.151 closest distance to " O   HOH Z 427 " =    3.138
peak=    3.148 closest distance to " NZ  LYS A  76 " =    1.439
peak=    3.148 closest distance to " O   HOH Z 133 " =    2.438
peak=    3.146 closest distance to " O   HOH Z 187 " =    2.294
peak=    3.146 closest distance to " O   HOH Z  83 " =    1.591
peak=    3.143 closest distance to " O   HOH Z  71 " =    2.224
peak=    3.140 closest distance to " O   HOH Z 209 " =    2.389
peak=    3.137 closest distance to " O   HOH Z 353 " =    2.718
peak=    3.136 closest distance to " O   HOH Z 313 " =    1.758
peak=    3.132 closest distance to " ND1 HIS A  86 " =    1.683
peak=    3.118 closest distance to " OE2 GLU A  53 " =    2.027
peak=    3.117 closest distance to " O   HOH Z 409 " =    3.482
peak=    3.114 closest distance to " CB  ASN A 215 " =    1.189
peak=    3.108 closest distance to " O   THR A  31 " =    1.521
peak=    3.108 closest distance to " O   HOH Z 359 " =    3.771
peak=    3.106 closest distance to " CD2 LEU A 255 " =    1.459
peak=    3.102 closest distance to " O   HOH Z 281 " =    4.665
peak=    3.102 closest distance to " O   HOH Z 128 " =    1.771
peak=    3.100 closest distance to " CA  SER A 146 " =    1.754
peak=    3.100 closest distance to " NE2 HIS A 207 " =    1.681
peak=    3.099 closest distance to " O   HOH Z  85 " =    2.139
peak=    3.099 closest distance to " O   HOH Z 367 " =    3.418
peak=    3.094 closest distance to " O   HOH Z 116 " =    1.756
peak=    3.070 closest distance to " O   HOH Z 201 " =    3.180
peak=    3.066 closest distance to " CG2 VAL A 202 " =    1.180
peak=    3.064 closest distance to " CZ3 TRP A  85 " =    0.936
peak=    3.062 closest distance to " CG  GLN A  89 " =    1.489
peak=    3.060 closest distance to " NH2BARG A 190 " =    2.023
peak=    3.057 closest distance to " C   ALA A 299 " =    0.925
peak=    3.052 closest distance to " O   SER A 164 " =    1.162
peak=    3.044 closest distance to " CA  SER A  87 " =    1.009

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 5.463
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.700 - 5.463

peak=   -5.564 closest distance to " CG2 VAL A 230 " =    0.832
peak=   -4.760 closest distance to " SG  CYS A 254 " =    3.188
peak=   -4.617 closest distance to " O   HOH Z 266 " =    4.762
peak=   -4.615 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.287 closest distance to " CB  ALA A 161 " =    2.570
peak=   -4.161 closest distance to " CG  GLN A 223 " =    2.018
peak=   -4.146 closest distance to " C   HIS A 108 " =    1.198
peak=   -4.145 closest distance to " O   HOH Z 290 " =    1.138
peak=   -4.145 closest distance to " CB  PRO A 243 " =    2.593
peak=   -4.053 closest distance to " O   HOH Z 196 " =    2.136
peak=   -4.006 closest distance to " O   PRO A 163 " =    2.129
peak=   -3.981 closest distance to " CD2 LEU A 300 " =    2.757
peak=   -3.976 closest distance to " CG2BVAL A  41 " =    2.539
peak=   -3.959 closest distance to " OG BSER A 134 " =    1.187
peak=   -3.919 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.915 closest distance to " OXT GLY A 302 " =    2.816
peak=   -3.861 closest distance to " CG2 VAL A 296 " =    1.132
peak=   -3.844 closest distance to " N   GLN A  58 " =    1.578
peak=   -3.824 closest distance to " CG  ASP A 231 " =    0.812
peak=   -3.806 closest distance to " CD  GLN A  58 " =    1.122
peak=   -3.805 closest distance to " O   HOH Z  11 " =    1.884
peak=   -3.794 closest distance to " O   VAL A  67 " =    2.703
peak=   -3.793 closest distance to " O   HOH Z 114 " =    3.134
peak=   -3.786 closest distance to " CZ3 TRP A 179 " =    1.275
peak=   -3.778 closest distance to " NE2 GLN A  88 " =    1.955
peak=   -3.753 closest distance to " OG  SER A  97 " =    2.222
peak=   -3.748 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.742 closest distance to " O   HOH Z 231 " =    2.005
peak=   -3.732 closest distance to " CD  ARG A 139 " =    1.594
peak=   -3.727 closest distance to " NH2AARG A 275 " =    5.113
peak=   -3.718 closest distance to " CB  PRO A 163 " =    2.560
peak=   -3.717 closest distance to " N   ALA A 226 " =    2.029
peak=   -3.714 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.700 closest distance to " O   HOH Z 166 " =    1.957
peak=   -3.676 closest distance to " CG1 VAL A 112 " =    2.741
peak=   -3.662 closest distance to " CB  ALA A 248 " =    2.052
peak=   -3.660 closest distance to " CB  PHE A 192 " =    1.911
peak=   -3.654 closest distance to " CG1 VAL A 250 " =    2.752
peak=   -3.651 closest distance to " CD  LYS A 289 " =    2.533
peak=   -3.650 closest distance to " C   ALA A 158 " =    1.263
peak=   -3.639 closest distance to " O   HOH Z 103 " =    1.772
peak=   -3.629 closest distance to " ND2 ASN A  45 " =    1.334
peak=   -3.626 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.625 closest distance to " OD1 ASN A 187 " =    1.700
peak=   -3.624 closest distance to " CD1 LEU A 101 " =    2.456
peak=   -3.621 closest distance to " CB  ALA A 291 " =    2.288
peak=   -3.616 closest distance to " O   HOH Z 389 " =    1.817
peak=   -3.612 closest distance to " N   THR A 235 " =    1.358
peak=   -3.591 closest distance to " OG ASER A 134 " =    1.187
peak=   -3.584 closest distance to " CD1 PHE A  59 " =    1.945
peak=   -3.576 closest distance to " O   HOH Z 198 " =    2.403
peak=   -3.575 closest distance to " O   HOH Z 394 " =    1.556
peak=   -3.572 closest distance to " ND2 ASN A 187 " =    1.587
peak=   -3.558 closest distance to " CE3 TRP A 150 " =    2.044
peak=   -3.530 closest distance to " OG  SER A  62 " =    1.607
peak=   -3.528 closest distance to " O   HOH Z 211 " =    1.670
peak=   -3.522 closest distance to " O   HOH Z  47 " =    1.614
peak=   -3.518 closest distance to " O   HOH Z  52 " =    1.491
peak=   -3.516 closest distance to " O   HOH Z  17 " =    1.534
peak=   -3.515 closest distance to " CZ  TYR A 169 " =    1.686
peak=   -3.514 closest distance to " CB  PRO A 280 " =    2.146
peak=   -3.514 closest distance to " O   HOH Z  13 " =    1.452
peak=   -3.508 closest distance to " OD2 ASP A  50 " =    2.326
peak=   -3.504 closest distance to " O   HOH Z 407 " =    3.018
peak=   -3.503 closest distance to " O   HOH Z 166 " =    1.427
peak=   -3.501 closest distance to " O   HOH Z 283 " =    2.021
peak=   -3.500 closest distance to " O   HOH Z 165 " =    1.960
peak=   -3.500 closest distance to " O   HOH Z  43 " =    1.743
peak=   -3.499 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.488 closest distance to " OG BSER A 134 " =    1.689
peak=   -3.483 closest distance to " CE  MET A 105 " =    2.094
peak=   -3.482 closest distance to " OD2 ASP A 171 " =    2.284
peak=   -3.480 closest distance to " N   ALA A  43 " =    2.553
peak=   -3.479 closest distance to " O   HOH Z 126 " =    1.929
peak=   -3.478 closest distance to " OG  SER A  26 " =    1.217
peak=   -3.473 closest distance to " O   HOH Z  19 " =    2.185
peak=   -3.467 closest distance to " O   HOH Z 426 " =    1.666
peak=   -3.467 closest distance to " CB  ASN A  69 " =    1.162
peak=   -3.465 closest distance to " O   HOH Z 311 " =    3.694
peak=   -3.460 closest distance to " CG  PHE A 283 " =    2.796
peak=   -3.445 closest distance to " N   THR A 157 " =    1.518
peak=   -3.436 closest distance to " NH2 ARG A  66 " =    1.723
peak=   -3.433 closest distance to " O   HOH Z 353 " =    2.049
peak=   -3.426 closest distance to " CG  TRP A 266 " =    1.880
peak=   -3.425 closest distance to " O   VAL A 189 " =    2.604
peak=   -3.424 closest distance to " O   HOH Z 185 " =    2.347
peak=   -3.412 closest distance to " CB  ASP A 132 " =    2.332
peak=   -3.411 closest distance to " CD1 LEU A 101 " =    2.935
peak=   -3.406 closest distance to " O   HOH Z 102 " =    1.613
peak=   -3.404 closest distance to " C   MET A 188 " =    1.444
peak=   -3.403 closest distance to " NZ  LYS A 119 " =    3.484
peak=   -3.403 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.402 closest distance to " O   HOH Z  63 " =    1.134
peak=   -3.398 closest distance to " O   HOH Z  44 " =    2.155
peak=   -3.386 closest distance to " O   HOH Z 339 " =    1.837
peak=   -3.380 closest distance to " O   HOH Z 435 " =    2.745
peak=   -3.380 closest distance to " CD1 LEU A  25 " =    2.480
peak=   -3.380 closest distance to " CG2 ILE A 263 " =    2.350
peak=   -3.376 closest distance to " CG  GLU A 277 " =    1.128
peak=   -3.374 closest distance to " O   HOH Z  60 " =    2.110
peak=   -3.373 closest distance to " CB  TYR A  15 " =    2.201
peak=   -3.371 closest distance to " O   GLY A 196 " =    1.098
peak=   -3.370 closest distance to " CZ  PHE A  59 " =    1.586
peak=   -3.369 closest distance to " CG  ARG A 269 " =    2.287
peak=   -3.362 closest distance to " O   HOH Z 234 " =    4.063
peak=   -3.362 closest distance to " CD1 LEU A 228 " =    2.189
peak=   -3.361 closest distance to " C   ASP A 231 " =    2.624
peak=   -3.356 closest distance to " O   GLY A  80 " =    2.421
peak=   -3.356 closest distance to " O   HOH Z 350 " =    1.831
peak=   -3.355 closest distance to " O   HOH Z 134 " =    2.695
peak=   -3.354 closest distance to " CG  LEU A 228 " =    1.030
peak=   -3.347 closest distance to " CB  ASP A 132 " =    2.263
peak=   -3.347 closest distance to " O   HOH Z 198 " =    1.423
peak=   -3.336 closest distance to " CB  ALA A 291 " =    2.129
peak=   -3.330 closest distance to " N   SER A 276 " =    1.334
peak=   -3.324 closest distance to " OG  SER A  87 " =    1.424
peak=   -3.322 closest distance to " CE2 PHE A 218 " =    2.597
peak=   -3.321 closest distance to " CG1 VAL A 230 " =    1.845
peak=   -3.309 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.306 closest distance to " O   HOH Z 389 " =    4.559
peak=   -3.305 closest distance to " OD1 ASN A 148 " =    1.499
peak=   -3.304 closest distance to " O   HOH Z 292 " =    4.427
peak=   -3.304 closest distance to " CG  GLU A  53 " =    1.536
peak=   -3.302 closest distance to " CA  GLY A 133 " =    2.246
peak=   -3.301 closest distance to " O   HOH Z  38 " =    1.623
peak=   -3.301 closest distance to " O   LEU A 167 " =    1.515
peak=   -3.300 closest distance to " O   VAL A 125 " =    2.333
peak=   -3.299 closest distance to " O   SER A 210 " =    2.014
peak=   -3.298 closest distance to " CG  LYS A 193 " =    2.281
peak=   -3.297 closest distance to " SG ACYS A 201 " =    2.054
peak=   -3.292 closest distance to " CB  ASN A  39 " =    2.181
peak=   -3.291 closest distance to " CD1 ILE A 199 " =    2.461
peak=   -3.290 closest distance to " N   HIS A 115 " =    2.075
peak=   -3.280 closest distance to " CB  ALA A 248 " =    2.359
peak=   -3.278 closest distance to " N   ALA A 248 " =    1.614
peak=   -3.278 closest distance to " CD2 LEU A 167 " =    1.716
peak=   -3.277 closest distance to " O   SER A 271 " =    2.000
peak=   -3.273 closest distance to " N   PHE A  59 " =    2.081
peak=   -3.267 closest distance to " C   GLN A 205 " =    1.932
peak=   -3.266 closest distance to " C   LEU A 143 " =    1.018
peak=   -3.258 closest distance to " O   PHE A 218 " =    1.673
peak=   -3.257 closest distance to " O   HOH Z 193 " =    1.820
peak=   -3.253 closest distance to " O   HOH Z 411 " =    3.739
peak=   -3.253 closest distance to " O   MET A  40 " =    2.645
peak=   -3.251 closest distance to " OG  SER A 206 " =    1.650
peak=   -3.242 closest distance to " O   HOH Z 113 " =    2.366
peak=   -3.236 closest distance to " C   ASN A 285 " =    2.404
peak=   -3.231 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.229 closest distance to " CE BMET A  47 " =    1.908
peak=   -3.223 closest distance to " O   HOH Z 191 " =    5.463
peak=   -3.222 closest distance to " O   HOH Z 222 " =    1.553
peak=   -3.221 closest distance to " O   GLY A  75 " =    1.864
peak=   -3.219 closest distance to " CD2 LEU A 237 " =    2.651
peak=   -3.217 closest distance to " CD  ARG A 195 " =    5.194
peak=   -3.216 closest distance to " OXT GLY A 302 " =    3.405
peak=   -3.214 closest distance to " CD1 TYR A 247 " =    2.359
peak=   -3.214 closest distance to " O   SER A  95 " =    1.631
peak=   -3.214 closest distance to " CA  GLY A 241 " =    3.019
peak=   -3.209 closest distance to " O   PRO A 198 " =    1.323
peak=   -3.201 closest distance to " NE2 GLN A 103 " =    1.721
peak=   -3.201 closest distance to " O   ALA A  51 " =    1.342
peak=   -3.198 closest distance to " O   HOH Z 417 " =    2.750
peak=   -3.197 closest distance to " O   HOH Z 244 " =    2.010
peak=   -3.194 closest distance to " CG1 VAL A 296 " =    1.224
peak=   -3.194 closest distance to " CG2 THR A 221 " =    2.037
peak=   -3.188 closest distance to " O   ALA A 161 " =    1.630
peak=   -3.184 closest distance to " O   HOH Z 359 " =    3.115
peak=   -3.184 closest distance to " OG1 THR A 178 " =    1.299
peak=   -3.178 closest distance to " NH1 ARG A 195 " =    2.569
peak=   -3.178 closest distance to " CG2 ILE A  20 " =    2.795
peak=   -3.178 closest distance to " ND2 ASN A  60 " =    1.450
peak=   -3.177 closest distance to " O   GLY A  80 " =    2.544
peak=   -3.177 closest distance to " O   HOH Z 313 " =    1.833
peak=   -3.174 closest distance to " N   LYS A 289 " =    1.558
peak=   -3.173 closest distance to " N   ASP A 171 " =    2.360
peak=   -3.170 closest distance to " O   LYS A 117 " =    1.656
peak=   -3.161 closest distance to " CD2 TYR A 247 " =    2.304
peak=   -3.159 closest distance to " O   HOH Z 310 " =    1.816
peak=   -3.147 closest distance to " N   GLY A  23 " =    2.214
peak=   -3.144 closest distance to " CD  GLN A 223 " =    0.700
peak=   -3.144 closest distance to " O   HOH Z   6 " =    1.696
peak=   -3.142 closest distance to " O   HOH Z 385 " =    1.937
peak=   -3.125 closest distance to " O   HOH Z 431 " =    1.749
peak=   -3.121 closest distance to " O   HOH Z 295 " =    1.504
peak=   -3.117 closest distance to " O   HOH Z  97 " =    1.447
peak=   -3.117 closest distance to " CG  GLU A   2 " =    1.835
peak=   -3.117 closest distance to " O   SER A  22 " =    2.246
peak=   -3.116 closest distance to " CG  GLU A 152 " =    2.288
peak=   -3.104 closest distance to " CG2 VAL A 189 " =    2.035
peak=   -3.102 closest distance to " O   HOH Z 139 " =    3.071
peak=   -3.090 closest distance to " CB  ASP A 286 " =    2.291
peak=   -3.084 closest distance to " O   HOH Z 128 " =    2.559
peak=   -3.081 closest distance to " CG  GLU A 152 " =    1.374
peak=   -3.079 closest distance to " CG  PRO A 163 " =    2.653
peak=   -3.078 closest distance to " NH2 ARG A  79 " =    1.619
peak=   -3.077 closest distance to " O   HOH Z 175 " =    4.341
peak=   -3.077 closest distance to " N   ALA A 248 " =    2.416
peak=   -3.075 closest distance to " N   ALA A 248 " =    1.889
peak=   -3.073 closest distance to " O   HOH Z 111 " =    2.530
peak=   -3.063 closest distance to " C   LEU A 222 " =    0.852
peak=   -3.049 closest distance to " O   HOH Z 298 " =    2.575
peak=   -3.036 closest distance to " OD1 ASN A 301 " =    2.051
peak=   -3.015 closest distance to " O   HOH Z 241 " =    1.339

================= 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    :  0.4227 0.4128   6.212034e+00   6.192723e+00
   1_bss:  0.4141 0.4038   6.209534e+00   6.177402e+00
   1_xyz:  0.3032 0.3299   5.979262e+00   6.033509e+00
   1_adp:  0.2370 0.2715   5.759992e+00   5.876585e+00
   1_occ:  0.2364 0.2715   5.758753e+00   5.876305e+00
   2_bss:  0.2316 0.2664   5.758172e+00   5.871508e+00
   2_xyz:  0.1602 0.1971   5.427832e+00   5.603906e+00
   2_adp:  0.1457 0.1839   5.346218e+00   5.536867e+00
   2_occ:  0.1456 0.1839   5.345833e+00   5.536914e+00
   3_bss:  0.1451 0.1833   5.345618e+00   5.536171e+00
   3_xyz:  0.1198 0.1591   5.183652e+00   5.406617e+00
   3_adp:  0.1149 0.1562   5.157255e+00   5.391015e+00
   3_occ:  0.1148 0.1563   5.156857e+00   5.390712e+00
   4_bss:  0.1148 0.1563   5.156857e+00   5.390712e+00
   4_xyz:  0.1133 0.1567   5.153271e+00   5.390791e+00
   4_adp:  0.1146 0.1560   5.154488e+00   5.383813e+00
   4_occ:  0.1146 0.1561   5.154499e+00   5.384099e+00
   5_bss:  0.1148 0.1562   5.155826e+00   5.384489e+00
   5_xyz:  0.1099 0.1539   5.126642e+00   5.370728e+00
   5_adp:  0.1088 0.1553   5.128519e+00   5.380799e+00
   5_occ:  0.1085 0.1552   5.127309e+00   5.380131e+00
   5_bss:  0.1085 0.1553   5.127295e+00   5.380145e+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:  0.348  20.001   7.158   8.600   8.377   0.000   0.000   0.000
   1_xyz:  0.348  20.001   7.158   8.600   8.377   0.000   0.000   0.000
   1_adp:  0.348  20.001   7.158   8.600   8.377   0.000   0.000   0.000
   1_occ:  0.348  20.001   7.158   8.600   8.377   0.000   0.000   0.000
   2_bss:  0.324  38.915   3.754   4.806   5.380   0.000   0.000   0.000
   2_xyz:  0.324  38.915   3.754   4.806   5.380   0.000   0.000   0.000
   2_adp:  0.324  38.915   3.754   4.806   5.380   0.000   0.000   0.000
   2_occ:  0.324  38.915   3.754   4.806   5.380   0.000   0.000   0.000
   3_bss:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   3_xyz:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   3_adp:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   3_occ:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   4_bss:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   4_xyz:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   4_adp:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   4_occ:  0.324  38.915   3.022   3.762   4.337   0.000   0.000   0.000
   5_bss:  0.323  40.500   2.921   3.525   4.085   0.000   0.000   0.000
   5_xyz:  0.323  40.500   2.921   3.525   4.085   0.000   0.000   0.000
   5_adp:  0.323  40.500   2.921   3.525   4.085   0.000   0.000   0.000
   5_occ:  0.323  40.500   2.921   3.525   4.085   0.000   0.000   0.000
   5_bss:  0.323  44.114  -0.544  -0.014   0.558   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.426 0.5789  0.6454    48472.715
   1_bss:  45.209 0.5790  0.8199    45918.304
   1_xyz:  35.063 0.6993  0.9657    29060.826
   1_adp:  26.794 0.7932  1.0558    18632.491
   1_occ:  26.802 0.7931  1.0552    18614.726
   2_bss:  26.606 0.7951  0.9353    18417.755
   2_xyz:  18.829 0.8726  0.9941     9907.960
   2_adp:  17.165 0.8883  1.0060     8626.116
   2_occ:  17.168 0.8883  1.0058     8625.578
   3_bss:  17.152 0.8884  0.9721     8623.816
   3_xyz:  14.414 0.9114  0.9828     6555.996
   3_adp:  14.088 0.9143  0.9840     6381.297
   3_occ:  14.077 0.9144  0.9839     6378.095
   4_bss:  14.077 0.9144  0.9839     6378.095
   4_xyz:  13.954 0.9158  0.9829     6359.892
   4_adp:  13.767 0.9174  0.9839     6285.792
   4_occ:  13.770 0.9173  0.9837     6291.001
   5_bss:  13.796 0.9171  0.9760     6316.266
   5_xyz:  13.567 0.9186  0.9774     6130.895
   5_adp:  13.797 0.9168  0.9741     6238.946
   5_occ:  13.786 0.9169  0.9739     6232.055
   5_bss:  13.785 0.9169  0.9776     6232.952
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3693e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3693e+01
   1_xyz:   1.503  0.011  0.101 17.746  0.006  4.121   1.1483e-01
   1_adp:   1.503  0.011  0.101 17.746  0.006  4.121   1.1483e-01
   1_occ:   1.503  0.011  0.101 17.746  0.006  4.121   1.1483e-01
   2_bss:   1.503  0.011  0.101 17.746  0.006  4.121   1.1483e-01
   2_xyz:   0.952  0.006  0.072 15.911  0.004  4.122   5.8414e-02
   2_adp:   0.952  0.006  0.072 15.911  0.004  4.122   5.8414e-02
   2_occ:   0.952  0.006  0.072 15.911  0.004  4.122   5.8414e-02
   3_bss:   0.952  0.006  0.072 15.911  0.004  4.122   5.8414e-02
   3_xyz:   1.048  0.007  0.085 15.751  0.004  4.128   6.5581e-02
   3_adp:   1.048  0.007  0.085 15.751  0.004  4.128   6.5581e-02
   3_occ:   1.048  0.007  0.085 15.751  0.004  4.128   6.5581e-02
   4_bss:   1.048  0.007  0.085 15.751  0.004  4.128   6.5581e-02
   4_xyz:   0.943  0.006  0.077 15.392  0.003  4.118   5.5891e-02
   4_adp:   0.943  0.006  0.077 15.392  0.003  4.118   5.5891e-02
   4_occ:   0.943  0.006  0.077 15.392  0.003  4.118   5.5891e-02
   5_bss:   0.943  0.006  0.077 15.392  0.003  4.118   5.5891e-02
   5_xyz:   1.086  0.008  0.089 15.611  0.004  4.120   6.9832e-02
   5_adp:   1.086  0.008  0.089 15.611  0.004  4.120   6.9832e-02
   5_occ:   1.086  0.008  0.089 15.611  0.004  4.120   6.9832e-02
   5_bss:   1.086  0.008  0.089 15.611  0.004  4.120   6.9832e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9616e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9616e+00
   1_xyz:  12.770  0.137  0.437 88.069  0.045  2.251   8.6327e-02
   1_adp:  12.770  0.137  0.437 88.069  0.045  2.251   8.6327e-02
   1_occ:  12.770  0.137  0.437 88.069  0.045  2.251   8.6327e-02
   2_bss:  12.770  0.137  0.437 88.069  0.045  2.251   8.6327e-02
   2_xyz:   6.679  0.066  0.320 80.525  0.030  2.369   5.2790e-02
   2_adp:   6.679  0.066  0.320 80.525  0.030  2.369   5.2790e-02
   2_occ:   6.679  0.066  0.320 80.525  0.030  2.369   5.2790e-02
   3_bss:   6.679  0.066  0.320 80.525  0.030  2.369   5.2790e-02
   3_xyz:   6.857  0.049  0.617 83.083  0.039  2.337   4.6061e-02
   3_adp:   6.857  0.049  0.617 83.083  0.039  2.337   4.6061e-02
   3_occ:   6.857  0.049  0.617 83.083  0.039  2.337   4.6061e-02
   4_bss:   6.857  0.049  0.617 83.083  0.039  2.337   4.6061e-02
   4_xyz:   6.602  0.040  0.508 82.342  0.038  2.381   3.3224e-02
   4_adp:   6.602  0.040  0.508 82.342  0.038  2.381   3.3224e-02
   4_occ:   6.602  0.040  0.508 82.342  0.038  2.381   3.3224e-02
   5_bss:   6.602  0.040  0.508 82.342  0.038  2.381   3.3224e-02
   5_xyz:   7.386  0.045  0.679 83.018  0.041  2.249   5.0731e-02
   5_adp:   7.386  0.045  0.679 83.018  0.041  2.249   5.0731e-02
   5_occ:   7.386  0.045  0.679 83.018  0.041  2.249   5.0731e-02
   5_bss:   7.386  0.045  0.679 83.018  0.041  2.249   5.0731e-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:  51.26   0.00   9.96  44.60   0.00   7.01  51.26   0.00  26.03
   1_occ:  51.26   0.00   9.96  44.60   0.00   7.01  51.26   0.00  26.03
   2_bss:  51.26   0.00   9.96  44.60   0.00   7.01  51.26   0.00  26.03
   2_xyz:  51.26   0.00   9.96  44.60   0.00   7.01  51.26   0.00  26.03
   2_adp:  56.92   0.00  10.79  56.92   0.00   7.08  54.80   0.97  30.98
   2_occ:  56.92   0.00  10.79  56.92   0.00   7.08  54.80   0.97  30.98
   3_bss:  56.92   0.00  10.79  56.92   0.00   7.08  54.80   0.97  30.98
   3_xyz:  56.92   0.00  10.79  56.92   0.00   7.08  54.80   0.97  30.98
   3_adp:  73.43   0.00  11.40  73.43   0.00   7.28  70.64   0.78  33.84
   3_occ:  73.43   0.00  11.40  73.43   0.00   7.28  70.64   0.78  33.84
   4_bss:  73.43   0.00  11.40  73.43   0.00   7.28  70.64   0.78  33.84
   4_xyz:  73.43   0.00  11.40  73.43   0.00   7.28  70.64   0.78  33.84
   4_adp:  72.09   0.00  11.01  72.09   0.00   7.17  63.60   0.86  31.88
   4_occ:  72.09   0.00  11.01  72.09   0.00   7.17  63.60   0.86  31.88
   5_bss:  72.09   0.00  11.01  72.09   0.00   7.17  63.60   0.86  31.88
   5_xyz:  72.09   0.00  11.01  72.09   0.00   7.17  63.60   0.86  31.88
   5_adp:  76.04   0.00  11.22  76.04   0.00   7.24  66.61   0.85  32.89
   5_occ:  76.04   0.00  11.22  76.04   0.00   7.24  66.61   0.85  32.89
   5_bss:  79.66   3.61  14.83  79.66   3.61  10.85  70.23   4.46  36.50
------------------------------------------------------------------------
 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:    1.175    0.019    0.402
   1_adp:    1.175    0.019    0.402
   1_occ:    1.175    0.019    0.402
   2_bss:    1.175    0.019    0.402
   2_xyz:    1.467    0.036    0.490
   2_adp:    1.467    0.036    0.490
   2_occ:    1.467    0.036    0.490
   3_bss:    1.467    0.036    0.490
   3_xyz:    1.448    0.028    0.521
   3_adp:    1.448    0.028    0.521
   3_occ:    1.448    0.028    0.521
   4_bss:    1.448    0.028    0.521
   4_xyz:    1.541    0.020    0.533
   4_adp:    1.541    0.020    0.533
   4_occ:    1.541    0.020    0.533
   5_bss:    1.541    0.020    0.533
   5_xyz:    1.471    0.014    0.542
   5_adp:    1.471    0.014    0.542
   5_occ:    1.471    0.014    0.542
   5_bss:    1.471    0.014    0.542
------------------------------------------------------------------------

CPU time actual refinement: 323.27


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/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_674/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_674/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.12 
  Macro-tasks:
    bulk solvent and scale       = 41.23  
    individual site refinement   = 129.77 
    weights calculation          = 32.47  
    collect and process          = 6.58   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.17 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 97.91  
    alpha_beta                      = 8.27   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 108.17 
    fmodel                         = 6.88   
    r_factors                      = 0.23   
    phase_errors                   = 10.95  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 235.68 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.565 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    644 calls, 97.39 s
gradients_fft:          589 calls, 94.90 s

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

# Date 2008-01-16 Time 02:08:52 PST -0800 (1200478132.59 s)
Start R-work = 0.4227, R-free = 0.4128 (no bulk solvent and anisotropic scale)
Final R-work = 0.1261, R-free = 0.1710 (no bulk solvent and anisotropic scale)

Start R-work = 0.4141, R-free = 0.4038
Final R-work = 0.1085, R-free = 0.1553