# Date 2008-01-16 Time 02:39:16 PST -0800 (1200479956.69 s)
#phil __OFF__

Command line arguments: "../920.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 = 12619
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 920

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.01158
Completeness in resolution range: 0.978276
Completeness with d_max=infinity: 0.975208

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   2.0116

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.01158
Completeness in resolution range: 0.978276
Completeness with d_max=infinity: 0.975208

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1443 -  4.3038 [2102/2126]  1892   210  10.0%
  bin  2:  4.3038 -  3.4291 [2026/2046]  1822   204  10.1%
  bin  3:  3.4291 -  2.9994 [1993/2012]  1795   198   9.9%
  bin  4:  2.9994 -  2.7269 [1962/1992]  1764   198  10.1%
  bin  5:  2.7269 -  2.5325 [1978/1997]  1783   195   9.9%
  bin  6:  2.5325 -  2.3837 [1957/1982]  1758   199  10.2%
  bin  7:  2.3837 -  2.2648 [1941/1969]  1748   193   9.9%
  bin  8:  2.2648 -  2.1665 [1932/1968]  1739   193  10.0%
  bin  9:  2.1665 -  2.0833 [1913/1955]  1722   191  10.0%
  bin 10:  2.0833 -  2.0116 [1785/1977]  1607   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2170
        3.04 -     3.66: 4589
        3.66 -     4.28: 8905
        4.28 -     4.90: 12260
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.955 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.275 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27927 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_920/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4197   ksol= 0.00   Bsol= 0.00   scale= 0.813    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.228172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7999 0.99   1374  152 0.3628 0.3351      6.5337      6.4117|
|  2:  4.7999 -  3.8301 0.99   1303  146 0.3252 0.3387      6.6422      6.7125|
|  3:  3.8301 -  3.3520 0.99   1287  144 0.3775 0.3608      6.5718      6.5603|
|  4:  3.3520 -  3.0482 0.99   1284  142 0.4150 0.3599      6.4652      6.3576|
|  5:  3.0482 -  2.8313 0.99   1267  139 0.4504 0.4344      6.3212      6.3425|
|  6:  2.8313 -  2.6653 0.99   1272  143 0.4621 0.4989      6.2456       6.185|
|  7:  2.6653 -  2.5325 0.99   1269  139 0.4827 0.4712       6.203      6.1796|
|  8:  2.5325 -  2.4227 0.98   1248  141 0.4881 0.4388      6.1658      6.1366|
|  9:  2.4227 -  2.3298 0.98   1253  138 0.4801 0.4820      6.0911      6.1033|
| 10:  2.3298 -  2.2496 1.00   1239  141 0.4961 0.4760       6.103      6.0764|
| 11:  2.2496 -  2.1795 0.97   1254  135 0.4879 0.4586      6.0188      6.0247|
| 12:  2.1795 -  2.1174 0.98   1244  140 0.4967 0.4823      5.9761      5.9996|
| 13:  2.1174 -  2.0618 0.99   1241  136 0.5012 0.4790      5.8856      5.8676|
| 14:  2.0618 -  2.0116 0.86   1095  123 0.5054 0.4548      5.8558      5.7072|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1443 -  4.7999  1374   152  0.75  29.61   0.81     0.77      53536.04|
|  2:  4.7999 -  3.8301  1303   146  0.78  27.89   0.91     0.82      71734.46|
|  3:  3.8301 -  3.3520  1287   144  0.72  34.07   0.86     0.78      75561.86|
|  4:  3.3520 -  3.0482  1284   142  0.65  39.85   0.83     0.70      69105.15|
|  5:  3.0482 -  2.8313  1267   139  0.56  46.90   0.76     0.63      60942.99|
|  6:  2.8313 -  2.6653  1272   143  0.52  50.05   0.75     0.58      56828.09|
|  7:  2.6653 -  2.5325  1269   139  0.49  52.49   0.74     0.55      52869.22|
|  8:  2.5325 -  2.4227  1248   141  0.48  53.60   0.77     0.55      48766.05|
|  9:  2.4227 -  2.3298  1253   138  0.49  52.69   0.74     0.55      43470.90|
| 10:  2.3298 -  2.2496  1239   141  0.50  52.12   0.76     0.56      39407.18|
| 11:  2.2496 -  2.1795  1254   135  0.48  53.73   0.76     0.55      36789.61|
| 12:  2.1795 -  2.1174  1244   140  0.46  55.25   0.77     0.55      35110.45|
| 13:  2.1174 -  2.0618  1241   136  0.47  55.02   0.74     0.53      30098.21|
| 14:  2.0618 -  2.0116  1095   123  0.53  50.28   0.73     0.54      22241.96|
|alpha:            min =        0.53 max =            0.82 mean =         0.62|
|beta:             min =    22241.96 max =        75561.86 mean =     50213.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.44|
|phase err.(test): min =        0.00 max =           89.91 mean =        46.51|
|-----------------------------------------------------------------------------|

============================== 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 = 7.801720              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.534   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.282   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1477 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2579 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3878 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4984 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6527 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7642 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.280 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.618 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4424   r_free= 0.4211   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.233883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4271   r_free= 0.4042   ksol= 0.30   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.64,7.96,9.38,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.223219                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.305061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.031   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633949              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.688   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4271      final r-factor (work) = 0.3137          |
| start r-factor (free) = 0.4042      final r-factor (free) = 0.3368          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.0791 = 7.31 * 0.50 * 6.2420 + 1.00 * 54.2800                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2516 = 7.31 * 0.50 * 6.0589 + 1.00 * 0.1213                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3137      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3368      final r-factor (free) = 0.2872          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8558 = 0.63 * 1.00 * 6.0589 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7411 = 0.63 * 1.00 * 5.8829 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.44   10.44    None  None   None       |
|    all(noH): 2823   0      0.00    73.44   10.44    None  None   None       |
|    Sol.    : 438    0      0.00    73.44   27.37    None  None   None       |
|    Mac.    : 2385   0      0.00    57.56   7.33     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 -   7.344: 1542   |   5:    36.718 -  44.061:   74        |
|      1:     7.344 -  14.687:  677   |   6:    44.061 -  51.405:   44        |
|      2:    14.687 -  22.031:  214   |   7:    51.405 -  58.748:   13        |
|      3:    22.031 -  29.374:  148   |   8:    58.748 -  66.092:    2        |
|      4:    29.374 -  36.718:  108   |   9:    66.092 -  73.435:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2530 r_free = 0.2872             target_work(ml) = 5.815         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2522 r_free = 0.2875             target_work(ml) = 5.814         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2522   r_free= 0.2875   ksol= 0.30   Bsol= 20.00   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.64,7.96,9.38,0.00,0.00,0.00); trace/3= 8.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.813969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2481   r_free= 0.2818   ksol= 0.34   Bsol= 58.19   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.45,4.74,5.97,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.813843                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.254936              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.839   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.346293              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2481      final r-factor (work) = 0.1627          |
| start r-factor (free) = 0.2818      final r-factor (free) = 0.2023          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6475 = 4.25 * 0.50 * 5.8879 + 1.00 * 0.1213                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0503 = 4.25 * 0.50 * 5.6302 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1477          |
| start r-factor (free) = 0.2023      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9615 = 0.35 * 1.00 * 5.6302 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9575 = 0.35 * 1.00 * 5.3943 + 1.00 * 0.0895                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.48   10.82    None  None   None       |
|    all(noH): 2823   0      0.00    72.48   10.82    None  None   None       |
|    Sol.    : 438    0      0.00    72.48   30.72    None  None   None       |
|    Mac.    : 2385   0      0.00    58.72   7.16     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 -   7.248: 1604   |   5:    36.241 -  43.489:  102        |
|      1:     7.248 -  14.496:  601   |   6:    43.489 -  50.737:   58        |
|      2:    14.496 -  21.744:  182   |   7:    50.737 -  57.985:   20        |
|      3:    21.744 -  28.993:  123   |   8:    57.985 -  65.233:    3        |
|      4:    28.993 -  36.241:  129   |   9:    65.233 -  72.481:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1477 r_free = 0.1896             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1475 r_free = 0.1898             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.1898   ksol= 0.34   Bsol= 58.19   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.45,4.74,5.97,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.361406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1471   r_free= 0.1892   ksol= 0.33   Bsol= 58.19   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.362144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.379281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.853  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.472658              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.968   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1471      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4977 = 2.38 * 0.50 * 5.4012 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3615 = 2.38 * 0.50 * 5.2912 + 1.00 * 0.0668                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0976 = 2.47 * 1.00 * 5.2912 + 1.00 * 0.0141                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8998 = 2.47 * 1.00 * 5.2084 + 1.00 * 0.0212                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.39   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    77.39   11.83    None  None   None       |
|    Sol.    : 438    0      0.00    76.38   35.94    None  None   None       |
|    Mac.    : 2385   0      0.00    77.39   7.40     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 -   7.739: 1671   |   5:    38.695 -  46.434:   68        |
|      1:     7.739 -  15.478:  553   |   6:    46.434 -  54.173:   97        |
|      2:    15.478 -  23.217:  159   |   7:    54.173 -  61.912:   41        |
|      3:    23.217 -  30.956:  103   |   8:    61.912 -  69.651:   29        |
|      4:    30.956 -  38.695:   94   |   9:    69.651 -  77.390:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1646             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1646             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1646   ksol= 0.33   Bsol= 58.19   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201688                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1646   ksol= 0.33   Bsol= 58.19   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201536                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.990334              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.187  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321075              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8537 = 2.99 * 0.50 * 5.2080 + 1.00 * 0.0668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8173 = 2.99 * 0.50 * 5.1763 + 1.00 * 0.0778                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1138          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6804 = 0.32 * 1.00 * 5.1763 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6845 = 0.32 * 1.00 * 5.1688 + 1.00 * 0.0249                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.77   11.44    None  None   None       |
|    all(noH): 2823   0      0.00    76.77   11.44    None  None   None       |
|    Sol.    : 438    0      0.50    74.86   34.19    None  None   None       |
|    Mac.    : 2385   0      0.00    76.77   7.26     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 -   7.677: 1695   |   5:    38.383 -  46.059:   77        |
|      1:     7.677 -  15.353:  542   |   6:    46.059 -  53.736:   85        |
|      2:    15.353 -  23.030:  156   |   7:    53.736 -  61.412:   30        |
|      3:    23.030 -  30.706:  108   |   8:    61.412 -  69.089:   24        |
|      4:    30.706 -  38.383:  100   |   9:    69.089 -  76.766:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1595             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1596             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1596   ksol= 0.33   Bsol= 58.19   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1591   ksol= 0.33   Bsol= 58.19   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.446956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.764  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.565696              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.677   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8179 = 1.45 * 0.50 * 5.1681 + 1.00 * 0.0789                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8028 = 1.45 * 0.50 * 5.1758 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9503 = 0.57 * 1.00 * 5.1758 + 1.00 * 0.0223                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9431 = 0.57 * 1.00 * 5.1794 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.11   11.38    None  None   None       |
|    all(noH): 2823   0      0.00    81.11   11.38    None  None   None       |
|    Sol.    : 438    0      0.54    76.77   33.98    None  None   None       |
|    Mac.    : 2385   0      0.00    81.11   7.23     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.111: 1743   |   5:    40.553 -  48.663:   85        |
|      1:     8.111 -  16.221:  508   |   6:    48.663 -  56.774:   62        |
|      2:    16.221 -  24.332:  157   |   7:    56.774 -  64.885:   25        |
|      3:    24.332 -  32.442:  114   |   8:    64.885 -  72.995:   13        |
|      4:    32.442 -  40.553:  112   |   9:    72.995 -  81.106:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1614             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1615             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1615   ksol= 0.33   Bsol= 58.19   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.39,3.68,4.82,0.00,0.00,0.00); trace/3= 3.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183522                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7999 0.99   1374  152 0.1039 0.1301      5.4113      5.5155|
|  2:  4.7999 -  3.8301 0.99   1303  146 0.0887 0.1122      5.4623      5.6483|
|  3:  3.8301 -  3.3520 0.99   1287  144 0.1075 0.1494      5.5006      5.8422|
|  4:  3.3520 -  3.0482 0.99   1284  142 0.1227 0.1597      5.4729      5.6314|
|  5:  3.0482 -  2.8313 0.99   1267  139 0.1376 0.1723      5.3714      5.5491|
|  6:  2.8313 -  2.6653 0.99   1272  143 0.1263 0.2035      5.2537      5.5501|
|  7:  2.6653 -  2.5325 0.99   1269  139 0.1342 0.1653      5.2169      5.3662|
|  8:  2.5325 -  2.4227 0.98   1248  141 0.1244 0.1786      5.1342      5.4143|
|  9:  2.4227 -  2.3298 0.98   1253  138 0.1223 0.1832      5.0881      5.3041|
| 10:  2.3298 -  2.2496 1.00   1239  141 0.1221 0.1785      5.0364      5.3074|
| 11:  2.2496 -  2.1795 0.97   1254  135 0.1233 0.1725      4.9965      5.2469|
| 12:  2.1795 -  2.1174 0.98   1244  140 0.1206 0.1875      4.9326      5.2911|
| 13:  2.1174 -  2.0618 0.99   1241  136 0.1196 0.1675      4.8479       5.074|
| 14:  2.0618 -  2.0116 0.86   1095  123 0.1103 0.1907      4.7278      5.0148|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1443 -  4.7999  1374   152  0.94   9.28   0.97     0.94       7317.63|
|  2:  4.7999 -  3.8301  1303   146  0.95   8.03   1.00     0.99       9135.17|
|  3:  3.8301 -  3.3520  1287   144  0.93  11.30   1.02     1.01      10714.22|
|  4:  3.3520 -  3.0482  1284   142  0.92  13.45   1.00     0.98      10427.45|
|  5:  3.0482 -  2.8313  1267   139  0.90  16.18   0.99     0.97       8932.18|
|  6:  2.8313 -  2.6653  1272   143  0.90  16.46   0.99     0.96       7612.63|
|  7:  2.6653 -  2.5325  1269   139  0.90  16.23   0.99     0.96       6682.54|
|  8:  2.5325 -  2.4227  1248   141  0.91  15.65   0.99     0.97       5905.20|
|  9:  2.4227 -  2.3298  1253   138  0.90  16.23   1.00     0.97       5596.30|
| 10:  2.3298 -  2.2496  1239   141  0.90  16.21   1.00     0.95       4889.41|
| 11:  2.2496 -  2.1795  1254   135  0.89  16.90   0.99     0.95       4769.40|
| 12:  2.1795 -  2.1174  1244   140  0.90  16.01   1.01     0.99       4275.69|
| 13:  2.1174 -  2.0618  1241   136  0.90  16.45   0.99     0.97       3698.29|
| 14:  2.0618 -  2.0116  1095   123  0.91  15.52   0.97     0.93       2858.64|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2858.64 max =        10714.22 mean =      6697.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.49|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.01|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1615   ksol= 0.32   Bsol= 59.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.29,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183478                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1615   ksol= 0.32   Bsol= 59.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.29,0.86,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183478                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.7999 0.99   1374  152 0.1038 0.1300      5.4093      5.5136|
|  2:  4.7999 -  3.8301 0.99   1303  146 0.0885 0.1120      5.4608      5.6466|
|  3:  3.8301 -  3.3520 0.99   1287  144 0.1074 0.1494         5.5       5.842|
|  4:  3.3520 -  3.0482 0.99   1284  142 0.1227 0.1598      5.4734      5.6319|
|  5:  3.0482 -  2.8313 0.99   1267  139 0.1376 0.1724      5.3722      5.5498|
|  6:  2.8313 -  2.6653 0.99   1272  143 0.1264 0.2036      5.2544      5.5508|
|  7:  2.6653 -  2.5325 0.99   1269  139 0.1343 0.1654      5.2175      5.3667|
|  8:  2.5325 -  2.4227 0.98   1248  141 0.1244 0.1787      5.1345      5.4146|
|  9:  2.4227 -  2.3298 0.98   1253  138 0.1224 0.1831      5.0883       5.304|
| 10:  2.3298 -  2.2496 1.00   1239  141 0.1221 0.1786      5.0366      5.3078|
| 11:  2.2496 -  2.1795 0.97   1254  135 0.1233 0.1726      4.9966      5.2472|
| 12:  2.1795 -  2.1174 0.98   1244  140 0.1206 0.1875      4.9328      5.2912|
| 13:  2.1174 -  2.0618 0.99   1241  136 0.1196 0.1676       4.848      5.0741|
| 14:  2.0618 -  2.0116 0.86   1095  123 0.1103 0.1908      4.7279       5.015|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1443 -  4.7999  1374   152  0.94   9.26   0.97     0.94       7279.77|
|  2:  4.7999 -  3.8301  1303   146  0.95   8.01   1.00     0.99       9105.38|
|  3:  3.8301 -  3.3520  1287   144  0.93  11.28   1.02     1.01      10699.76|
|  4:  3.3520 -  3.0482  1284   142  0.92  13.46   1.00     0.98      10435.83|
|  5:  3.0482 -  2.8313  1267   139  0.90  16.19   0.99     0.97       8946.17|
|  6:  2.8313 -  2.6653  1272   143  0.90  16.47   0.99     0.96       7624.60|
|  7:  2.6653 -  2.5325  1269   139  0.90  16.24   0.99     0.96       6690.73|
|  8:  2.5325 -  2.4227  1248   141  0.91  15.65   0.99     0.97       5909.33|
|  9:  2.4227 -  2.3298  1253   138  0.90  16.23   1.00     0.97       5598.45|
| 10:  2.3298 -  2.2496  1239   141  0.90  16.21   1.00     0.95       4891.69|
| 11:  2.2496 -  2.1795  1254   135  0.89  16.90   0.99     0.95       4771.56|
| 12:  2.1795 -  2.1174  1244   140  0.90  16.01   1.01     0.99       4277.58|
| 13:  2.1174 -  2.0618  1241   136  0.90  16.45   0.99     0.97       3699.66|
| 14:  2.0618 -  2.0116  1095   123  0.91  15.53   0.97     0.93       2859.74|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2859.74 max =        10699.76 mean =      6695.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.49|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.01|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.209)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.96    85.07   15.34    None  None   None       |
|    all(noH): 2823   0      3.96    85.07   15.34    None  None   None       |
|    Sol.    : 438    0      4.50    80.73   37.94    None  None   None       |
|    Mac.    : 2385   0      3.96    85.07   11.19    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:     3.961 -  12.072: 1743   |   5:    44.514 -  52.624:   85        |
|      1:    12.072 -  20.182:  508   |   6:    52.624 -  60.735:   62        |
|      2:    20.182 -  28.293:  157   |   7:    60.735 -  68.845:   25        |
|      3:    28.293 -  36.403:  114   |   8:    68.845 -  76.956:   13        |
|      4:    36.403 -  44.514:  112   |   9:    76.956 -  85.067:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.285 - 4.774
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 342
   mapped sites are within: 0.701 - 4.774

peak=   10.199 closest distance to " CG2 VAL A 230 " =    1.380
peak=    7.153 closest distance to " CG2 VAL A 296 " =    1.130
peak=    6.156 closest distance to " CG  LEU A   5 " =    1.228
peak=    6.011 closest distance to " NH2 ARG A  56 " =    2.277
peak=    5.894 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.579 closest distance to " CD2 LEU A   5 " =    1.163
peak=    5.535 closest distance to " CG  LEU A 228 " =    1.200
peak=    4.912 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.894 closest distance to " CB  VAL A 230 " =    1.213
peak=    4.863 closest distance to " CG  PRO A 198 " =    1.290
peak=    4.756 closest distance to " CZ  PHE A 218 " =    1.084
peak=    4.723 closest distance to " CB  VAL A 296 " =    1.066
peak=    4.622 closest distance to " O   HOH Z 232 " =    2.333
peak=    4.621 closest distance to " NE2 GLN A  11 " =    1.099
peak=    4.596 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.577 closest distance to " CB  SER A  63 " =    1.289
peak=    4.499 closest distance to " CG  PRO A 243 " =    1.144
peak=    4.470 closest distance to " O   HOH Z 298 " =    1.859
peak=    4.449 closest distance to " O   HOH Z 126 " =    1.939
peak=    4.425 closest distance to " CB  ARG A 275 " =    0.903
peak=    4.398 closest distance to " C   PRO A 198 " =    1.557
peak=    4.382 closest distance to " O   HOH Z 369 " =    2.156
peak=    4.356 closest distance to " CB  GLU A 128 " =    1.058
peak=    4.295 closest distance to " O   HOH Z  78 " =    1.726
peak=    4.273 closest distance to " O   HOH Z 368 " =    2.238
peak=    4.273 closest distance to " O   HOH Z 265 " =    2.341
peak=    4.259 closest distance to " O   HOH Z 142 " =    1.661
peak=    4.236 closest distance to " CB  ARG A 190 " =    1.591
peak=    4.234 closest distance to " CB  ASP A 124 " =    0.790
peak=    4.229 closest distance to " O   HOH Z  43 " =    1.961
peak=    4.226 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.193 closest distance to " CA  TYR A  30 " =    0.979
peak=    4.179 closest distance to " CB  TRP A 266 " =    0.977
peak=    4.164 closest distance to " O   SER A  87 " =    2.298
peak=    4.145 closest distance to " O   HOH Z 427 " =    3.092
peak=    4.144 closest distance to " OG  SER A  97 " =    3.039
peak=    4.131 closest distance to " CD2 LEU A 228 " =    1.405
peak=    4.108 closest distance to " ND2 ASN A 187 " =    1.468
peak=    4.074 closest distance to " CB  ARG A  79 " =    1.433
peak=    4.053 closest distance to " CB  ASP A 140 " =    0.945
peak=    4.047 closest distance to " N   ASN A  39 " =    1.225
peak=    4.032 closest distance to " O   HOH Z 303 " =    2.106
peak=    4.019 closest distance to " O   HOH Z 261 " =    1.945
peak=    4.012 closest distance to " O   HOH Z 236 " =    2.009
peak=    3.977 closest distance to " O   HOH Z 316 " =    3.162
peak=    3.974 closest distance to " OD1 ASN A  69 " =    2.607
peak=    3.959 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.954 closest distance to " CB  PRO A  54 " =    0.839
peak=    3.939 closest distance to " O   HOH Z 423 " =    1.759
peak=    3.935 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.930 closest distance to " CG  MET A 185 " =    1.208
peak=    3.930 closest distance to " O   HOH Z 234 " =    3.785
peak=    3.923 closest distance to " CZ  PHE A 192 " =    0.977
peak=    3.919 closest distance to " CB  VAL A 265 " =    1.285
peak=    3.918 closest distance to " CB  ASN A 142 " =    1.063
peak=    3.914 closest distance to " CB  GLU A 277 " =    3.703
peak=    3.910 closest distance to " CD  ARG A 269 " =    0.986
peak=    3.907 closest distance to " NH1AARG A 145 " =    1.241
peak=    3.907 closest distance to " O   HOH Z  78 " =    2.230
peak=    3.903 closest distance to " CG2 VAL A 257 " =    0.924
peak=    3.902 closest distance to " O   HOH Z 346 " =    1.594
peak=    3.888 closest distance to " O   HOH Z  63 " =    1.958
peak=    3.884 closest distance to " O   HOH Z 272 " =    1.893
peak=    3.883 closest distance to " O   HOH Z 411 " =    3.764
peak=    3.878 closest distance to " CD  LYS A 166 " =    1.310
peak=    3.869 closest distance to " O   HOH Z 402 " =    1.498
peak=    3.867 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.859 closest distance to " O   HOH Z  61 " =    1.708
peak=    3.857 closest distance to " ND2 ASN A 249 " =    1.880
peak=    3.855 closest distance to " CB  GLU A 152 " =    1.161
peak=    3.845 closest distance to " O   HOH Z  44 " =    2.204
peak=    3.842 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.840 closest distance to " CD ALYS A 290 " =    1.038
peak=    3.837 closest distance to " CB  ASN A 187 " =    1.262
peak=    3.835 closest distance to " O   HOH Z 158 " =    3.179
peak=    3.834 closest distance to " O   HOH Z 214 " =    2.148
peak=    3.833 closest distance to " CA  THR A 264 " =    0.758
peak=    3.833 closest distance to " CB  LEU A 143 " =    1.202
peak=    3.825 closest distance to " O   HOH Z  19 " =    2.318
peak=    3.814 closest distance to " CD  ARG A 159 " =    0.772
peak=    3.807 closest distance to " CG1 VAL A 153 " =    0.996
peak=    3.802 closest distance to " CA  SER A  87 " =    1.010
peak=    3.793 closest distance to " O   HOH Z 126 " =    1.600
peak=    3.786 closest distance to " O   HOH Z  68 " =    2.144
peak=    3.769 closest distance to " O   MET A 105 " =    1.867
peak=    3.765 closest distance to " O   HOH Z  21 " =    1.772
peak=    3.763 closest distance to " O   HOH Z  80 " =    1.753
peak=    3.761 closest distance to " O   HOH Z 425 " =    1.403
peak=    3.756 closest distance to " CD1 LEU A 300 " =    1.172
peak=    3.737 closest distance to " NH2 ARG A 156 " =    1.116
peak=    3.728 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.728 closest distance to " O   HOH Z   9 " =    2.171
peak=    3.724 closest distance to " O   HOH Z 403 " =    1.644
peak=    3.721 closest distance to " CG1 VAL A 296 " =    1.221
peak=    3.721 closest distance to " CB  ALA A 291 " =    1.281
peak=    3.710 closest distance to " N   PHE A 130 " =    1.226
peak=    3.703 closest distance to " CB  SER A   3 " =    1.295
peak=    3.702 closest distance to " CB  ALA A 104 " =    0.767
peak=    3.695 closest distance to " CB  ALA A   9 " =    1.591
peak=    3.688 closest distance to " O   HOH Z 285 " =    2.669
peak=    3.688 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.687 closest distance to " CB  GLU A  46 " =    0.966
peak=    3.676 closest distance to " O   HOH Z 422 " =    2.691
peak=    3.675 closest distance to " CB BVAL A  41 " =    1.142
peak=    3.674 closest distance to " CA  ASN A 215 " =    1.174
peak=    3.665 closest distance to " O   HOH Z 203 " =    1.809
peak=    3.660 closest distance to " O   HOH Z 353 " =    2.613
peak=    3.658 closest distance to " O   HOH Z 180 " =    2.188
peak=    3.655 closest distance to " O   HOH Z 280 " =    3.001
peak=    3.644 closest distance to " CE  LYS A  76 " =    0.868
peak=    3.641 closest distance to " CG  LEU A 167 " =    1.166
peak=    3.622 closest distance to " CG1 ILE A  49 " =    1.513
peak=    3.620 closest distance to " CD  ARG A  66 " =    2.582
peak=    3.613 closest distance to " CZ  PHE A  38 " =    1.166
peak=    3.609 closest distance to " O   HOH Z  40 " =    1.749
peak=    3.608 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.608 closest distance to " CA  ARG A  36 " =    1.107
peak=    3.602 closest distance to " CE1 TYR A 186 " =    1.309
peak=    3.598 closest distance to " CB  MET A  40 " =    0.785
peak=    3.597 closest distance to " O   HOH Z 155 " =    3.426
peak=    3.596 closest distance to " O   ASP A 124 " =    1.033
peak=    3.594 closest distance to " O   HOH Z 248 " =    1.597
peak=    3.591 closest distance to " CA  ALA A 291 " =    0.874
peak=    3.588 closest distance to " O   TRP A 274 " =    1.806
peak=    3.587 closest distance to " CB  LEU A 228 " =    1.223
peak=    3.579 closest distance to " O   HOH Z 193 " =    2.087
peak=    3.577 closest distance to " CB  ALA A 242 " =    0.801
peak=    3.577 closest distance to " CA  ALA A 295 " =    1.098
peak=    3.563 closest distance to " CB  LEU A  83 " =    0.701
peak=    3.563 closest distance to " NE2 HIS A 207 " =    1.222
peak=    3.555 closest distance to " O   HOH Z  48 " =    1.666
peak=    3.545 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.543 closest distance to " O   HOH Z 273 " =    2.829
peak=    3.541 closest distance to " O   HOH Z 313 " =    1.759
peak=    3.539 closest distance to " CG1BVAL A  72 " =    1.746
peak=    3.539 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.539 closest distance to " CD1 LEU A   5 " =    1.339
peak=    3.534 closest distance to " O   HOH Z 437 " =    1.719
peak=    3.532 closest distance to " O   HOH Z 171 " =    3.844
peak=    3.532 closest distance to " CA  TYR A  30 " =    1.082
peak=    3.530 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.523 closest distance to " CG1 ILE A  33 " =    1.333
peak=    3.509 closest distance to " CB  THR A  31 " =    1.599
peak=    3.499 closest distance to " O   HOH Z 227 " =    1.698
peak=    3.497 closest distance to " N   SER A 135 " =    1.466
peak=    3.496 closest distance to " O   HOH Z 147 " =    1.763
peak=    3.486 closest distance to " O   HOH Z 172 " =    3.673
peak=    3.486 closest distance to " CB  SER A 212 " =    1.277
peak=    3.483 closest distance to " CB  SER A 216 " =    0.838
peak=    3.482 closest distance to " CA  THR A 221 " =    0.899
peak=    3.476 closest distance to " CA  VAL A  41 " =    0.788
peak=    3.474 closest distance to " CB  LYS A 117 " =    1.257
peak=    3.467 closest distance to " CD2 LEU A   5 " =    0.755
peak=    3.463 closest distance to " CB  TRP A 179 " =    1.436
peak=    3.461 closest distance to " CB  SER A 210 " =    0.885
peak=    3.459 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.452 closest distance to " CD  ARG A  66 " =    2.406
peak=    3.450 closest distance to " CA  LEU A 282 " =    1.037
peak=    3.446 closest distance to " O   HOH Z  88 " =    3.173
peak=    3.444 closest distance to " CG1 ILE A 151 " =    1.056
peak=    3.443 closest distance to " O   ALA A 165 " =    1.496
peak=    3.439 closest distance to " CB  THR A  82 " =    1.401
peak=    3.438 closest distance to " O   HOH Z 290 " =    1.087
peak=    3.436 closest distance to " CA  ALA A 154 " =    0.971
peak=    3.436 closest distance to " CB  GLN A  89 " =    1.178
peak=    3.436 closest distance to " CG  MET A 185 " =    1.016
peak=    3.430 closest distance to " OG BSER A 164 " =    2.244
peak=    3.430 closest distance to " CD2 TRP A 179 " =    1.361
peak=    3.428 closest distance to " CG2 THR A 220 " =    0.893
peak=    3.426 closest distance to " O   PRO A 213 " =    1.576
peak=    3.417 closest distance to " O   HOH Z  59 " =    2.255
peak=    3.412 closest distance to " CB  MET A  47 " =    1.036
peak=    3.409 closest distance to " CA  LYS A 181 " =    1.020
peak=    3.408 closest distance to " O   HOH Z 383 " =    2.014
peak=    3.400 closest distance to " O   HOH Z 368 " =    3.559
peak=    3.396 closest distance to " CA  VAL A 125 " =    1.212
peak=    3.393 closest distance to " O   HOH Z 133 " =    2.406
peak=    3.387 closest distance to " CZ3 TRP A 266 " =    1.140
peak=    3.387 closest distance to " O   HOH Z 291 " =    1.634
peak=    3.385 closest distance to " CA  ALA A  21 " =    1.101
peak=    3.384 closest distance to " CA  ASN A 127 " =    1.065
peak=    3.383 closest distance to " O   HOH Z 193 " =    1.713
peak=    3.373 closest distance to " CB  ILE A 120 " =    1.280
peak=    3.369 closest distance to " CA  ALA A 158 " =    1.211
peak=    3.369 closest distance to " O   HOH Z 305 " =    3.701
peak=    3.366 closest distance to " O   HOH Z 247 " =    1.390
peak=    3.364 closest distance to " O   HOH Z 145 " =    2.035
peak=    3.364 closest distance to " O   THR A 220 " =    1.199
peak=    3.358 closest distance to " O   HOH Z  97 " =    2.433
peak=    3.357 closest distance to " ND2 ASN A 249 " =    0.835
peak=    3.355 closest distance to " O  BHOH Z 338 " =    2.462
peak=    3.348 closest distance to " O   HOH Z 365 " =    2.951
peak=    3.348 closest distance to " O   HOH Z 187 " =    2.337
peak=    3.347 closest distance to " O   HOH Z 251 " =    1.509
peak=    3.346 closest distance to " CB  ALA A  34 " =    0.916
peak=    3.345 closest distance to " O   HOH Z 371 " =    3.022
peak=    3.344 closest distance to " O   HOH Z 193 " =    1.904
peak=    3.344 closest distance to " CB  HIS A 108 " =    0.788
peak=    3.342 closest distance to " O   HOH Z 250 " =    1.376
peak=    3.341 closest distance to " O   HOH Z 313 " =    1.716
peak=    3.341 closest distance to " N   VAL A 126 " =    1.467
peak=    3.339 closest distance to " CB  THR A 157 " =    1.135
peak=    3.339 closest distance to " CB  ALA A 248 " =    1.146
peak=    3.324 closest distance to " CG2 ILE A 263 " =    0.882
peak=    3.321 closest distance to " ND1 HIS A  81 " =    1.651
peak=    3.320 closest distance to " CA  MET A 105 " =    0.990
peak=    3.315 closest distance to " O   HOH Z  97 " =    2.106
peak=    3.313 closest distance to " O   HOH Z 102 " =    1.296
peak=    3.311 closest distance to " O   HOH Z 141 " =    1.667
peak=    3.307 closest distance to " O   HOH Z 261 " =    1.555
peak=    3.306 closest distance to " NZ  LYS A  48 " =    1.350
peak=    3.305 closest distance to " CG  PHE A 204 " =    0.920
peak=    3.300 closest distance to " NH1 ARG A  14 " =    0.983
peak=    3.299 closest distance to " CA  TYR A 116 " =    1.511
peak=    3.298 closest distance to " O  BHOH Z  74 " =    1.344
peak=    3.297 closest distance to " CZ3 TRP A 274 " =    4.641
peak=    3.297 closest distance to " O   HOH Z 197 " =    2.945
peak=    3.293 closest distance to " CD1 ILE A  33 " =    1.720
peak=    3.291 closest distance to " O   HOH Z 359 " =    1.389
peak=    3.291 closest distance to " CB  ASN A 110 " =    1.144
peak=    3.287 closest distance to " O   HOH Z 435 " =    2.045
peak=    3.287 closest distance to " O   HOH Z 350 " =    1.631
peak=    3.285 closest distance to " O   HOH Z 325 " =    2.222
peak=    3.284 closest distance to " O   HOH Z 258 " =    2.088
peak=    3.281 closest distance to " O   HOH Z 329 " =    4.007
peak=    3.280 closest distance to " O   HOH Z 406 " =    1.560
peak=    3.275 closest distance to " O   GLN A  88 " =    1.663
peak=    3.275 closest distance to " O   HOH Z 294 " =    1.597
peak=    3.274 closest distance to " CB  PRO A 243 " =    1.456
peak=    3.273 closest distance to " CB  TRP A 150 " =    1.412
peak=    3.271 closest distance to " NZ  LYS A 117 " =    3.279
peak=    3.268 closest distance to " CB  ALA A 137 " =    1.038
peak=    3.268 closest distance to " O   HOH Z  66 " =    2.233
peak=    3.268 closest distance to " O   HOH Z 421 " =    3.082
peak=    3.267 closest distance to " CB  VAL A 268 " =    0.827
peak=    3.267 closest distance to " OG BSER A 134 " =    2.819
peak=    3.262 closest distance to " CG  GLU A  37 " =    0.824
peak=    3.261 closest distance to " O   HOH Z 184 " =    1.510
peak=    3.258 closest distance to " CA  GLY A 211 " =    1.367
peak=    3.258 closest distance to " O   HOH Z 327 " =    2.406
peak=    3.257 closest distance to " CE2 TYR A  30 " =    0.748
peak=    3.256 closest distance to " CB  SER A 273 " =    0.917
peak=    3.248 closest distance to " CA  ASN A 217 " =    1.287
peak=    3.247 closest distance to " CD2 LEU A 297 " =    0.848
peak=    3.245 closest distance to " CB  TYR A 247 " =    0.988
peak=    3.245 closest distance to " CA  ASP A 140 " =    1.292
peak=    3.239 closest distance to " O   ASN A  74 " =    1.541
peak=    3.238 closest distance to " O   HOH Z 403 " =    1.462
peak=    3.238 closest distance to " O   HOH Z 344 " =    3.093
peak=    3.238 closest distance to " CE1 HIS A 108 " =    1.168
peak=    3.236 closest distance to " CA  ILE A 106 " =    0.777
peak=    3.232 closest distance to " OG  SER A  22 " =    2.809
peak=    3.229 closest distance to " O   HOH Z 109 " =    2.696
peak=    3.228 closest distance to " CZ3 TRP A  85 " =    1.041
peak=    3.228 closest distance to " CG  GLN A  88 " =    1.063
peak=    3.227 closest distance to " CB  GLN A 205 " =    1.044
peak=    3.226 closest distance to " CB  GLN A 103 " =    1.030
peak=    3.224 closest distance to " OG1 THR A 294 " =    2.426
peak=    3.222 closest distance to " OG  SER A 276 " =    1.262
peak=    3.221 closest distance to " CB  ALA A 295 " =    1.289
peak=    3.216 closest distance to " CG  ARG A 138 " =    1.150
peak=    3.211 closest distance to " O   HOH Z 245 " =    1.358
peak=    3.210 closest distance to " CD1 ILE A 199 " =    0.825
peak=    3.209 closest distance to " O   HOH Z 238 " =    2.357
peak=    3.208 closest distance to " CB  ALA A 114 " =    1.151
peak=    3.207 closest distance to " CA  ASP A 191 " =    1.088
peak=    3.204 closest distance to " O   HOH Z 234 " =    1.818
peak=    3.204 closest distance to " CG  GLN A 205 " =    0.893
peak=    3.204 closest distance to " O   HOH Z 148 " =    3.328
peak=    3.204 closest distance to " OG1 THR A 294 " =    1.743
peak=    3.201 closest distance to " O   HOH Z 263 " =    1.647
peak=    3.200 closest distance to " CA  ASP A 191 " =    0.748
peak=    3.199 closest distance to " CB  GLN A  88 " =    1.203
peak=    3.193 closest distance to " CD  ARG A 219 " =    1.085
peak=    3.193 closest distance to " CA  ALA A 160 " =    0.925
peak=    3.192 closest distance to " CG  ARG A 159 " =    1.000
peak=    3.191 closest distance to " C   ALA A 299 " =    0.939
peak=    3.190 closest distance to " N   ARG A 156 " =    1.415
peak=    3.189 closest distance to " CA  GLU A 152 " =    0.892
peak=    3.189 closest distance to " CA  ASP A 162 " =    0.977
peak=    3.188 closest distance to " CG2 ILE A 151 " =    0.717
peak=    3.188 closest distance to " O   ALA A 158 " =    1.397
peak=    3.187 closest distance to " O   HOH Z 112 " =    1.644
peak=    3.184 closest distance to " CB  ALA A   1 " =    4.774
peak=    3.181 closest distance to " O   HOH Z 128 " =    1.884
peak=    3.180 closest distance to " CG  MET A 113 " =    1.289
peak=    3.180 closest distance to " CA  GLN A  88 " =    1.389
peak=    3.179 closest distance to " N   GLN A 278 " =    1.085
peak=    3.171 closest distance to " CB  SER A  26 " =    1.825
peak=    3.169 closest distance to " CD1 LEU A 261 " =    1.248
peak=    3.169 closest distance to " CA  LYS A 290 " =    1.142
peak=    3.168 closest distance to " CB  ARG A 145 " =    0.761
peak=    3.164 closest distance to " CB  LYS A 193 " =    1.040
peak=    3.155 closest distance to " CD1 LEU A 281 " =    1.104
peak=    3.152 closest distance to " CA  ALA A 233 " =    1.521
peak=    3.147 closest distance to " O   HOH Z 163 " =    1.574
peak=    3.146 closest distance to " CD1 ILE A 106 " =    0.982
peak=    3.143 closest distance to " O   GLN A 278 " =    1.543
peak=    3.142 closest distance to " CG2 VAL A 296 " =    1.590
peak=    3.141 closest distance to " O   HOH Z 380 " =    1.885
peak=    3.139 closest distance to " CG BARG A 102 " =    1.843
peak=    3.137 closest distance to " O   HOH Z 327 " =    1.899
peak=    3.135 closest distance to " CB  ALA A 227 " =    1.032
peak=    3.135 closest distance to " O   HOH Z 417 " =    2.106
peak=    3.134 closest distance to " O   TYR A 116 " =    1.311
peak=    3.134 closest distance to " N   ASN A 127 " =    1.182
peak=    3.131 closest distance to " O   HOH Z 302 " =    1.966
peak=    3.128 closest distance to " N   ALA A 256 " =    1.127
peak=    3.125 closest distance to " CD1 LEU A 228 " =    2.017
peak=    3.115 closest distance to " OH  TYR A 214 " =    1.225
peak=    3.114 closest distance to " CG2 ILE A 120 " =    1.144
peak=    3.109 closest distance to " CB  ARG A 139 " =    0.846
peak=    3.108 closest distance to " CB  ASN A 215 " =    1.194
peak=    3.107 closest distance to " O   PHE A  61 " =    1.342
peak=    3.107 closest distance to " CG2 VAL A 268 " =    0.948
peak=    3.101 closest distance to " O   HOH Z 345 " =    3.416
peak=    3.099 closest distance to " N   ASP A 162 " =    1.256
peak=    3.098 closest distance to " CA  ILE A 234 " =    0.894
peak=    3.093 closest distance to " C   ASN A  39 " =    1.078
peak=    3.091 closest distance to " O   HOH Z 295 " =    1.490
peak=    3.089 closest distance to " CB  TYR A 116 " =    0.830
peak=    3.086 closest distance to " O   HOH Z 201 " =    3.026
peak=    3.082 closest distance to " O   HOH Z 195 " =    4.186
peak=    3.077 closest distance to " O   HOH Z 213 " =    1.791
peak=    3.076 closest distance to " CB  ARG A 138 " =    0.982
peak=    3.075 closest distance to " CB  LEU A 300 " =    0.881
peak=    3.067 closest distance to " O   HOH Z 260 " =    1.565
peak=    3.054 closest distance to " N   GLY A 133 " =    3.754
peak=    3.042 closest distance to " CG  ARG A 269 " =    1.714
peak=    3.033 closest distance to " O   HOH Z 293 " =    1.791
peak=    3.027 closest distance to " O   ALA A 292 " =    1.639
peak=    3.017 closest distance to " CB  ALA A 100 " =    1.226
peak=    3.017 closest distance to " O   GLY A 203 " =    1.488

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.520
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 199
   mapped sites are within: 0.774 - 5.520

peak=   -5.145 closest distance to " CG2 VAL A 230 " =    0.814
peak=   -4.515 closest distance to " CD  ARG A 156 " =    2.058
peak=   -4.477 closest distance to " CD  GLN A  58 " =    1.016
peak=   -4.415 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -4.214 closest distance to " O   HOH Z 266 " =    5.412
peak=   -4.196 closest distance to " SG  CYS A 254 " =    3.400
peak=   -4.181 closest distance to " O   HOH Z 196 " =    2.190
peak=   -4.177 closest distance to " CB  PRO A 243 " =    2.700
peak=   -4.089 closest distance to " CG  GLN A 223 " =    2.126
peak=   -4.089 closest distance to " O   VAL A  67 " =    2.655
peak=   -4.081 closest distance to " CB  ALA A 161 " =    2.570
peak=   -4.011 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.971 closest distance to " O   HOH Z 166 " =    1.953
peak=   -3.959 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.898 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.896 closest distance to " CG2 ILE A  49 " =    2.817
peak=   -3.883 closest distance to " CE2 TYR A  30 " =    2.758
peak=   -3.865 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.862 closest distance to " O   HOH Z  73 " =    2.208
peak=   -3.848 closest distance to " O   HOH Z 290 " =    1.215
peak=   -3.845 closest distance to " O   HOH Z 231 " =    2.138
peak=   -3.838 closest distance to " CG1 VAL A 112 " =    2.879
peak=   -3.816 closest distance to " C   ALA A 158 " =    1.340
peak=   -3.802 closest distance to " O   HOH Z 114 " =    3.067
peak=   -3.801 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.768 closest distance to " CG1 VAL A 250 " =    2.770
peak=   -3.749 closest distance to " OD1 ASN A 148 " =    1.403
peak=   -3.746 closest distance to " CG1 VAL A 296 " =    1.367
peak=   -3.740 closest distance to " CA  GLY A 241 " =    3.134
peak=   -3.737 closest distance to " OG BSER A 134 " =    1.184
peak=   -3.722 closest distance to " CZ3 TRP A 179 " =    1.179
peak=   -3.715 closest distance to " O   HOH Z 211 " =    1.438
peak=   -3.709 closest distance to " O   HOH Z 185 " =    2.357
peak=   -3.704 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.700 closest distance to " N   THR A  18 " =    1.335
peak=   -3.699 closest distance to " O   VAL A  67 " =    2.702
peak=   -3.692 closest distance to " O   HOH Z  11 " =    1.929
peak=   -3.691 closest distance to " CG  HIS A  86 " =    1.103
peak=   -3.690 closest distance to " N   ALA A 226 " =    2.182
peak=   -3.689 closest distance to " CE3 TRP A 150 " =    2.185
peak=   -3.683 closest distance to " NH2AARG A 275 " =    5.289
peak=   -3.681 closest distance to " CB  PHE A 192 " =    1.946
peak=   -3.678 closest distance to " O   HOH Z 394 " =    1.549
peak=   -3.678 closest distance to " CG2 VAL A 296 " =    1.414
peak=   -3.628 closest distance to " ND2 ASN A  45 " =    1.074
peak=   -3.623 closest distance to " NE2 GLN A  88 " =    2.038
peak=   -3.615 closest distance to " O   HOH Z  52 " =    1.625
peak=   -3.613 closest distance to " CD2 TYR A 293 " =    1.989
peak=   -3.605 closest distance to " CG1 VAL A 265 " =    2.435
peak=   -3.601 closest distance to " O   HOH Z  10 " =    1.514
peak=   -3.600 closest distance to " OXT GLY A 302 " =    2.976
peak=   -3.581 closest distance to " O   PRO A 198 " =    1.224
peak=   -3.574 closest distance to " CD1 LEU A 101 " =    2.457
peak=   -3.572 closest distance to " O   PRO A 163 " =    2.198
peak=   -3.558 closest distance to " CG  GLU A 277 " =    1.130
peak=   -3.557 closest distance to " CG  ARG A 269 " =    2.475
peak=   -3.555 closest distance to " CG2 VAL A 296 " =    0.918
peak=   -3.555 closest distance to " O   VAL A 189 " =    2.602
peak=   -3.535 closest distance to " O   HOH Z 435 " =    2.781
peak=   -3.521 closest distance to " CG  TRP A 266 " =    1.849
peak=   -3.518 closest distance to " NH2 ARG A  79 " =    1.571
peak=   -3.518 closest distance to " O   HOH Z  37 " =    1.921
peak=   -3.510 closest distance to " O   HOH Z 426 " =    1.673
peak=   -3.505 closest distance to " C   MET A 188 " =    1.381
peak=   -3.505 closest distance to " CE  MET A 105 " =    2.248
peak=   -3.503 closest distance to " CD2 PHE A  61 " =    2.569
peak=   -3.502 closest distance to " O   HOH Z  19 " =    2.399
peak=   -3.459 closest distance to " N   ALA A  43 " =    2.482
peak=   -3.450 closest distance to " CD2 LEU A 300 " =    2.749
peak=   -3.443 closest distance to " O   HOH Z  44 " =    2.227
peak=   -3.439 closest distance to " CB  ALA A 248 " =    2.155
peak=   -3.436 closest distance to " O   SER A 271 " =    2.236
peak=   -3.436 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -3.432 closest distance to " CB  ALA A  43 " =    2.632
peak=   -3.430 closest distance to " O   HOH Z 222 " =    1.490
peak=   -3.428 closest distance to " O   HOH Z 377 " =    2.035
peak=   -3.426 closest distance to " O   HOH Z 241 " =    1.201
peak=   -3.423 closest distance to " CD1 LEU A 228 " =    2.348
peak=   -3.417 closest distance to " O   GLY A 203 " =    2.332
peak=   -3.417 closest distance to " CB  ALA A 248 " =    2.436
peak=   -3.416 closest distance to " ND2 ASN A  45 " =    1.853
peak=   -3.414 closest distance to " N   THR A 157 " =    1.516
peak=   -3.413 closest distance to " N   THR A  52 " =    1.621
peak=   -3.408 closest distance to " O   HOH Z 113 " =    2.378
peak=   -3.404 closest distance to " O   GLY A  80 " =    2.582
peak=   -3.395 closest distance to " O   HOH Z  38 " =    1.522
peak=   -3.387 closest distance to " NE2 GLN A 194 " =    1.890
peak=   -3.386 closest distance to " O   HOH Z 389 " =    2.012
peak=   -3.385 closest distance to " C   PHE A  59 " =    1.282
peak=   -3.384 closest distance to " C   LEU A 143 " =    1.070
peak=   -3.377 closest distance to " CG1 VAL A 125 " =    1.967
peak=   -3.375 closest distance to " CD2 LEU A 167 " =    1.815
peak=   -3.373 closest distance to " NE2 GLN A 103 " =    1.813
peak=   -3.365 closest distance to " OG  SER A  87 " =    1.524
peak=   -3.360 closest distance to " O   HOH Z 216 " =    1.555
peak=   -3.355 closest distance to " N   MET A 105 " =    2.952
peak=   -3.343 closest distance to " OD2 ASP A  50 " =    2.341
peak=   -3.342 closest distance to " O   HOH Z 350 " =    1.916
peak=   -3.341 closest distance to " O   HOH Z 353 " =    2.112
peak=   -3.333 closest distance to " CE BMET A  47 " =    1.854
peak=   -3.328 closest distance to " O   GLY A 211 " =    1.319
peak=   -3.316 closest distance to " CD1 ILE A 239 " =    2.090
peak=   -3.310 closest distance to " O   ARG A  24 " =    2.139
peak=   -3.309 closest distance to " CA  GLY A 203 " =    2.457
peak=   -3.309 closest distance to " SD BMET A  47 " =    1.065
peak=   -3.308 closest distance to " O   HOH Z 177 " =    1.766
peak=   -3.308 closest distance to " ND2 ASN A 187 " =    1.642
peak=   -3.307 closest distance to " C   LEU A 222 " =    0.885
peak=   -3.306 closest distance to " O   HOH Z 102 " =    1.705
peak=   -3.306 closest distance to " CB  VAL A 230 " =    1.074
peak=   -3.305 closest distance to " NH2 ARG A 159 " =    2.329
peak=   -3.302 closest distance to " O   HOH Z 191 " =    5.520
peak=   -3.300 closest distance to " NH2 ARG A  79 " =    2.116
peak=   -3.300 closest distance to " O   HOH Z 231 " =    1.713
peak=   -3.299 closest distance to " O   HOH Z 128 " =    2.622
peak=   -3.296 closest distance to " O   HOH Z 292 " =    4.696
peak=   -3.294 closest distance to " O   HOH Z 106 " =    1.883
peak=   -3.293 closest distance to " CD1 LEU A   5 " =    2.556
peak=   -3.291 closest distance to " CB  ASN A  39 " =    2.278
peak=   -3.286 closest distance to " O   HOH Z  13 " =    1.459
peak=   -3.285 closest distance to " CA  ALA A 248 " =    2.608
peak=   -3.282 closest distance to " O   VAL A 121 " =    1.298
peak=   -3.282 closest distance to " CA  GLY A 133 " =    2.333
peak=   -3.271 closest distance to " O   HOH Z 407 " =    3.172
peak=   -3.269 closest distance to " CZ  PHE A 192 " =    2.878
peak=   -3.269 closest distance to " CE3 TRP A  70 " =    1.838
peak=   -3.268 closest distance to " O   HOH Z 359 " =    3.111
peak=   -3.267 closest distance to " O   HOH Z 198 " =    2.421
peak=   -3.265 closest distance to " O   HOH Z 176 " =    0.804
peak=   -3.260 closest distance to " O   HOH Z 133 " =    1.370
peak=   -3.257 closest distance to " O   HOH Z 326 " =    5.060
peak=   -3.257 closest distance to " O   HOH Z 275 " =    1.544
peak=   -3.257 closest distance to " O   GLY A 196 " =    1.273
peak=   -3.254 closest distance to " CB  ASN A  69 " =    1.251
peak=   -3.253 closest distance to " O   HOH Z  43 " =    1.769
peak=   -3.251 closest distance to " CZ  TYR A 169 " =    1.694
peak=   -3.248 closest distance to " O   HOH Z  60 " =    2.171
peak=   -3.243 closest distance to " O   ALA A  10 " =    1.699
peak=   -3.241 closest distance to " CG  MET A 105 " =    0.930
peak=   -3.237 closest distance to " ND2 ASN A  60 " =    1.320
peak=   -3.231 closest distance to " C   ASN A 285 " =    2.412
peak=   -3.224 closest distance to " O   HOH Z 313 " =    1.123
peak=   -3.223 closest distance to " OG  SER A  63 " =    1.208
peak=   -3.220 closest distance to " CA  VAL A 296 " =    0.989
peak=   -3.217 closest distance to " CA  ASN A 127 " =    1.117
peak=   -3.212 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.209 closest distance to " O   HOH Z 393 " =    1.441
peak=   -3.209 closest distance to " ND2 ASN A  69 " =    1.861
peak=   -3.207 closest distance to " CB  PRO A 163 " =    2.566
peak=   -3.205 closest distance to " OG  SER A 206 " =    1.741
peak=   -3.203 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.197 closest distance to " O   MET A  40 " =    2.796
peak=   -3.196 closest distance to " NH2 ARG A  66 " =    2.016
peak=   -3.196 closest distance to " CB  GLN A  11 " =    1.697
peak=   -3.194 closest distance to " CD  PRO A 213 " =    2.122
peak=   -3.191 closest distance to " N   SER A 212 " =    1.817
peak=   -3.189 closest distance to " N   SER A   3 " =    2.030
peak=   -3.189 closest distance to " O   HOH Z 123 " =    2.523
peak=   -3.188 closest distance to " O   TYR A 247 " =    2.872
peak=   -3.186 closest distance to " O   HOH Z 243 " =    1.921
peak=   -3.185 closest distance to " CD1 PHE A  59 " =    1.968
peak=   -3.182 closest distance to " O   SER A  95 " =    1.801
peak=   -3.176 closest distance to " CD  ARG A 139 " =    1.672
peak=   -3.168 closest distance to " CG2 THR A 178 " =    2.242
peak=   -3.161 closest distance to " CB  ALA A  10 " =    2.269
peak=   -3.157 closest distance to " NE2 GLN A  88 " =    1.018
peak=   -3.152 closest distance to " N   ALA A 248 " =    1.869
peak=   -3.151 closest distance to " CG2 VAL A 189 " =    2.066
peak=   -3.149 closest distance to " SG  CYS A 254 " =    2.880
peak=   -3.148 closest distance to " O   HOH Z 139 " =    3.076
peak=   -3.145 closest distance to " CH2 TRP A 177 " =    2.181
peak=   -3.145 closest distance to " O   HOH Z 174 " =    2.524
peak=   -3.145 closest distance to " O   HOH Z 298 " =    2.801
peak=   -3.142 closest distance to " OD1 ASN A 187 " =    1.538
peak=   -3.141 closest distance to " O   HOH Z  17 " =    1.478
peak=   -3.139 closest distance to " OD2 ASP A 171 " =    1.840
peak=   -3.136 closest distance to " C   ASN A 187 " =    1.819
peak=   -3.133 closest distance to " CB  TRP A  85 " =    2.542
peak=   -3.127 closest distance to " CG1 VAL A  67 " =    2.900
peak=   -3.125 closest distance to " O   HOH Z 421 " =    3.182
peak=   -3.119 closest distance to " OG BSER A 134 " =    1.922
peak=   -3.117 closest distance to " N   SER A 276 " =    1.361
peak=   -3.116 closest distance to " O   ASP A 270 " =    1.651
peak=   -3.114 closest distance to " O   HOH Z 165 " =    1.856
peak=   -3.114 closest distance to " CD  PRO A 243 " =    2.056
peak=   -3.108 closest distance to " CG2 VAL A 112 " =    2.550
peak=   -3.100 closest distance to " O   HOH Z 252 " =    4.001
peak=   -3.096 closest distance to " N   VAL A 230 " =    1.107
peak=   -3.093 closest distance to " CG1 VAL A 197 " =    2.296
peak=   -3.084 closest distance to " CD1 ILE A 151 " =    2.410
peak=   -3.081 closest distance to " O   ILE A 106 " =    2.038
peak=   -3.072 closest distance to " O   HOH Z 265 " =    1.659
peak=   -3.068 closest distance to " O   HOH Z  90 " =    1.622
peak=   -3.063 closest distance to " CG  PHE A 283 " =    2.739
peak=   -3.054 closest distance to " CB  ASP A 171 " =    2.297
peak=   -3.047 closest distance to " O   HOH Z   6 " =    1.635
peak=   -3.044 closest distance to " CG2 VAL A 296 " =    1.826
peak=   -3.043 closest distance to " C   ASP A 270 " =    1.160
peak=   -3.011 closest distance to " NE2 GLN A 194 " =    1.971

================= 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    :  0.4352 0.4197   6.228172e+00   6.199413e+00
   1_bss:  0.4271 0.4042   6.223219e+00   6.184961e+00
   1_xyz:  0.3137 0.3368   6.003980e+00   6.048588e+00
   1_adp:  0.2530 0.2872   5.815379e+00   5.923720e+00
   1_occ:  0.2522 0.2875   5.813969e+00   5.925246e+00
   2_bss:  0.2481 0.2818   5.813843e+00   5.921553e+00
   2_xyz:  0.1627 0.2023   5.443425e+00   5.620260e+00
   2_adp:  0.1477 0.1896   5.361755e+00   5.556895e+00
   2_occ:  0.1475 0.1898   5.361406e+00   5.557134e+00
   3_bss:  0.1471 0.1892   5.362144e+00   5.556514e+00
   3_xyz:  0.1261 0.1673   5.230989e+00   5.450453e+00
   3_adp:  0.1202 0.1646   5.201959e+00   5.434596e+00
   3_occ:  0.1201 0.1646   5.201688e+00   5.434400e+00
   4_bss:  0.1201 0.1646   5.201536e+00   5.434376e+00
   4_xyz:  0.1133 0.1618   5.165671e+00   5.415603e+00
   4_adp:  0.1138 0.1595   5.161044e+00   5.403702e+00
   4_occ:  0.1135 0.1596   5.160492e+00   5.404096e+00
   5_bss:  0.1138 0.1591   5.159564e+00   5.401157e+00
   5_xyz:  0.1175 0.1609   5.182800e+00   5.413092e+00
   5_adp:  0.1169 0.1614   5.183375e+00   5.417940e+00
   5_occ:  0.1169 0.1615   5.183522e+00   5.418347e+00
   5_bss:  0.1169 0.1615   5.183478e+00   5.418318e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   7.640   7.964   9.384   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.640   7.964   9.384   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.640   7.964   9.384   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.640   7.964   9.384   0.000   0.000   0.000
   2_bss:  0.337  58.189   4.451   4.743   5.966   0.000   0.000   0.000
   2_xyz:  0.337  58.189   4.451   4.743   5.966   0.000   0.000   0.000
   2_adp:  0.337  58.189   4.451   4.743   5.966   0.000   0.000   0.000
   2_occ:  0.337  58.189   4.451   4.743   5.966   0.000   0.000   0.000
   3_bss:  0.334  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   3_xyz:  0.334  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   3_adp:  0.334  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   3_occ:  0.334  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   4_bss:  0.326  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   4_xyz:  0.326  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   4_adp:  0.326  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   4_occ:  0.326  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   5_bss:  0.328  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   5_xyz:  0.328  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   5_adp:  0.328  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   5_occ:  0.328  58.189   3.387   3.676   4.820   0.000   0.000   0.000
   5_bss:  0.324  59.494  -0.574  -0.285   0.859   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.445 0.5662  0.6215    50215.181
   1_bss:  45.503 0.5768  0.8136    47828.837
   1_xyz:  36.433 0.6840  0.9333    31070.524
   1_adp:  28.875 0.7709  1.0211    21289.098
   1_occ:  28.915 0.7704  1.0203    21354.347
   2_bss:  28.739 0.7723  0.9097    21161.014
   2_xyz:  19.324 0.8681  0.9906    10347.611
   2_adp:  17.558 0.8850  1.0032     9077.934
   2_occ:  17.569 0.8849  1.0030     9078.222
   3_bss:  17.553 0.8850  0.9635     9067.464
   3_xyz:  15.145 0.9059  0.9725     7198.983
   3_adp:  14.832 0.9086  0.9708     6946.099
   3_occ:  14.827 0.9086  0.9707     6944.341
   4_bss:  14.826 0.9086  0.9706     6944.076
   4_xyz:  14.429 0.9119  0.9729     6710.852
   4_adp:  14.153 0.9142  0.9727     6564.243
   4_occ:  14.164 0.9141  0.9724     6569.301
   5_bss:  14.134 0.9142  0.9718     6497.771
   5_xyz:  14.312 0.9130  0.9701     6629.892
   5_adp:  14.436 0.9120  0.9671     6691.688
   5_occ:  14.445 0.9120  0.9671     6697.405
   5_bss:  14.445 0.9120  0.9670     6695.322
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4280e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4280e+01
   1_xyz:   1.542  0.012  0.103 17.955  0.006  4.128   1.2131e-01
   1_adp:   1.542  0.012  0.103 17.955  0.006  4.128   1.2131e-01
   1_occ:   1.542  0.012  0.103 17.955  0.006  4.128   1.2131e-01
   2_bss:   1.542  0.012  0.103 17.955  0.006  4.128   1.2131e-01
   2_xyz:   1.084  0.009  0.077 16.604  0.004  4.130   7.2198e-02
   2_adp:   1.084  0.009  0.077 16.604  0.004  4.130   7.2198e-02
   2_occ:   1.084  0.009  0.077 16.604  0.004  4.130   7.2198e-02
   3_bss:   1.084  0.009  0.077 16.604  0.004  4.130   7.2198e-02
   3_xyz:   1.037  0.008  0.084 16.046  0.004  4.142   6.6845e-02
   3_adp:   1.037  0.008  0.084 16.046  0.004  4.142   6.6845e-02
   3_occ:   1.037  0.008  0.084 16.046  0.004  4.142   6.6845e-02
   4_bss:   1.037  0.008  0.084 16.046  0.004  4.142   6.6845e-02
   4_xyz:   1.121  0.011  0.092 15.928  0.004  4.148   7.7783e-02
   4_adp:   1.121  0.011  0.092 15.928  0.004  4.148   7.7783e-02
   4_occ:   1.121  0.011  0.092 15.928  0.004  4.148   7.7783e-02
   5_bss:   1.121  0.011  0.092 15.928  0.004  4.148   7.7783e-02
   5_xyz:   0.948  0.007  0.077 15.575  0.003  4.117   5.8170e-02
   5_adp:   0.948  0.007  0.077 15.575  0.003  4.117   5.8170e-02
   5_occ:   0.948  0.007  0.077 15.575  0.003  4.117   5.8170e-02
   5_bss:   0.948  0.007  0.077 15.575  0.003  4.117   5.8170e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0383e+00
   1_xyz:  13.039  0.140  0.410 86.393  0.038  2.304   9.1865e-02
   1_adp:  13.039  0.140  0.410 86.393  0.038  2.304   9.1865e-02
   1_occ:  13.039  0.140  0.410 86.393  0.038  2.304   9.1865e-02
   2_bss:  13.039  0.140  0.410 86.393  0.038  2.304   9.1865e-02
   2_xyz:   8.217  0.081  0.327 86.947  0.038  2.393   5.5356e-02
   2_adp:   8.217  0.081  0.327 86.947  0.038  2.393   5.5356e-02
   2_occ:   8.217  0.081  0.327 86.947  0.038  2.393   5.5356e-02
   3_bss:   8.217  0.081  0.327 86.947  0.038  2.393   5.5356e-02
   3_xyz:   7.028  0.042  0.541 82.958  0.040  2.387   4.1206e-02
   3_adp:   7.028  0.042  0.541 82.958  0.040  2.387   4.1206e-02
   3_occ:   7.028  0.042  0.541 82.958  0.040  2.387   4.1206e-02
   4_bss:   7.028  0.042  0.541 82.958  0.040  2.387   4.1206e-02
   4_xyz:   7.397  0.050  0.637 82.616  0.040  2.312   5.6980e-02
   4_adp:   7.397  0.050  0.637 82.616  0.040  2.312   5.6980e-02
   4_occ:   7.397  0.050  0.637 82.616  0.040  2.312   5.6980e-02
   5_bss:   7.397  0.050  0.637 82.616  0.040  2.312   5.6980e-02
   5_xyz:   7.405  0.045  0.459 82.062  0.037  2.416   3.1841e-02
   5_adp:   7.405  0.045  0.459 82.062  0.037  2.416   3.1841e-02
   5_occ:   7.405  0.045  0.459 82.062  0.037  2.416   3.1841e-02
   5_bss:   7.405  0.045  0.459 82.062  0.037  2.416   3.1841e-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:  73.44   0.00  10.44  57.56   0.00   7.33  73.44   0.00  27.37
   1_occ:  73.44   0.00  10.44  57.56   0.00   7.33  73.44   0.00  27.37
   2_bss:  73.44   0.00  10.44  57.56   0.00   7.33  73.44   0.00  27.37
   2_xyz:  73.44   0.00  10.44  57.56   0.00   7.33  73.44   0.00  27.37
   2_adp:  72.48   0.00  10.82  58.72   0.00   7.16  72.48   0.00  30.72
   2_occ:  72.48   0.00  10.82  58.72   0.00   7.16  72.48   0.00  30.72
   3_bss:  72.48   0.00  10.82  58.72   0.00   7.16  72.48   0.00  30.72
   3_xyz:  72.48   0.00  10.82  58.72   0.00   7.16  72.48   0.00  30.72
   3_adp:  77.39   0.00  11.83  77.39   0.00   7.40  76.38   0.00  35.94
   3_occ:  77.39   0.00  11.83  77.39   0.00   7.40  76.38   0.00  35.94
   4_bss:  77.39   0.00  11.83  77.39   0.00   7.40  76.38   0.00  35.94
   4_xyz:  77.39   0.00  11.83  77.39   0.00   7.40  76.38   0.00  35.94
   4_adp:  76.77   0.00  11.44  76.77   0.00   7.26  74.86   0.50  34.19
   4_occ:  76.77   0.00  11.44  76.77   0.00   7.26  74.86   0.50  34.19
   5_bss:  76.77   0.00  11.44  76.77   0.00   7.26  74.86   0.50  34.19
   5_xyz:  76.77   0.00  11.44  76.77   0.00   7.26  74.86   0.50  34.19
   5_adp:  81.11   0.00  11.38  81.11   0.00   7.23  76.77   0.54  33.98
   5_occ:  81.11   0.00  11.38  81.11   0.00   7.23  76.77   0.54  33.98
   5_bss:  85.07   3.96  15.34  85.07   3.96  11.19  80.73   4.50  37.94
------------------------------------------------------------------------
 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:    1.210    0.017    0.405
   1_adp:    1.210    0.017    0.405
   1_occ:    1.210    0.017    0.405
   2_bss:    1.210    0.017    0.405
   2_xyz:    1.500    0.047    0.509
   2_adp:    1.500    0.047    0.509
   2_occ:    1.500    0.047    0.509
   3_bss:    1.500    0.047    0.509
   3_xyz:    1.487    0.052    0.541
   3_adp:    1.487    0.052    0.541
   3_occ:    1.487    0.052    0.541
   4_bss:    1.487    0.052    0.541
   4_xyz:    1.489    0.054    0.558
   4_adp:    1.489    0.054    0.558
   4_occ:    1.489    0.054    0.558
   5_bss:    1.489    0.054    0.558
   5_xyz:    1.580    0.043    0.563
   5_adp:    1.580    0.043    0.563
   5_occ:    1.580    0.043    0.563
   5_bss:    1.580    0.043    0.563
------------------------------------------------------------------------

CPU time actual refinement: 329.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/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_920/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_920/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.21 
  Macro-tasks:
    bulk solvent and scale       = 43.04  
    individual site refinement   = 131.64 
    weights calculation          = 32.19  
    collect and process          = 6.73   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 213.73 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 99.86  
    alpha_beta                      = 8.51   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 110.60 
    fmodel                         = 7.32   
    r_factors                      = 0.17   
    phase_errors                   = 11.04  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 240.74 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.654 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    643 calls, 99.54 s
gradients_fft:          587 calls, 97.23 s

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

# Date 2008-01-16 Time 02:44:59 PST -0800 (1200480299.77 s)
Start R-work = 0.4352, R-free = 0.4197 (no bulk solvent and anisotropic scale)
Final R-work = 0.1337, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.4271, R-free = 0.4042
Final R-work = 0.1169, R-free = 0.1615