# Date 2008-01-16 Time 01:45:13 PST -0800 (1200476713.28 s)
#phil __OFF__

Command line arguments: "../548.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 = 17217
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 548

-------------------------------------------------------------------------------
  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: (69.8988, 46.93, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99071
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9907

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: (69.8988, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99071
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2593 [2152/2176]  1933   219  10.2%
  bin  2:  4.2593 -  3.3936 [2059/2078]  1856   203   9.9%
  bin  3:  3.3936 -  2.9684 [2036/2055]  1834   202   9.9%
  bin  4:  2.9684 -  2.6987 [2012/2042]  1807   205  10.2%
  bin  5:  2.6987 -  2.5062 [2011/2030]  1811   200   9.9%
  bin  6:  2.5062 -  2.3590 [2000/2025]  1799   201  10.1%
  bin  7:  2.3590 -  2.2413 [1990/2018]  1795   195   9.8%
  bin  8:  2.2413 -  2.1440 [1975/2011]  1772   203  10.3%
  bin  9:  2.1440 -  2.0617 [1965/2007]  1776   189   9.6%
  bin 10:  2.0617 -  1.9907 [1389/2005]  1247   142  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/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:
        1.60 -     2.26: 12
        2.26 -     2.92: 1469
        2.92 -     3.58: 4413
        3.58 -     4.24: 9119
        4.24 -     4.90: 13075
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.597 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.618 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.770 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.912 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28083 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_548/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/model_refine_001.geo

CPU time processing inputs: 9.03


============================ 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 = 69.89875 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4499   r_free= 0.4356   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.252309                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.3713 0.3374       6.561      6.4564|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.3458 0.3869      6.6784      6.8129|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.4017 0.3705      6.6181      6.5695|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.4403 0.4252      6.4929      6.4284|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.4715 0.4469      6.3339      6.3352|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.4710 0.5539      6.2545      6.2267|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.4854 0.4625      6.2104      6.1448|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.5047 0.4463      6.1759      6.1282|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.4980 0.5142       6.101      6.1439|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.5149 0.4107      6.1165      6.0039|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.5007 0.5204      6.0276      6.0508|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.5099 0.4537      5.9552      5.9895|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.5011 0.4944      5.8834      5.8223|
| 14:  2.0404 -  1.9907 0.58    754   85 0.5135 0.4398      5.9103      5.7133|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.74  30.91   0.81     0.76      59134.50|
|  2:  4.7504 -  3.7905  1340   153  0.75  30.43   0.90     0.81      83221.32|
|  3:  3.7905 -  3.3173  1311   146  0.68  37.03   0.85     0.77      87846.54|
|  4:  3.3173 -  3.0166  1308   139  0.60  43.76   0.81     0.67      79027.32|
|  5:  3.0166 -  2.8019  1306   146  0.50  51.71   0.76     0.57      69403.17|
|  6:  2.8019 -  2.6377  1292   148  0.46  55.20   0.73     0.52      64473.99|
|  7:  2.6377 -  2.5062  1287   144  0.44  56.48   0.75     0.50      58475.02|
|  8:  2.5062 -  2.3976  1282   138  0.47  54.68   0.73     0.54      49832.67|
|  9:  2.3976 -  2.3056  1276   147  0.49  52.66   0.74     0.57      43763.53|
| 10:  2.3056 -  2.2263  1274   139  0.49  52.74   0.75     0.57      39182.10|
| 11:  2.2263 -  2.1569  1268   139  0.46  55.52   0.76     0.55      39255.23|
| 12:  2.1569 -  2.0954  1257   141  0.44  57.04   0.76     0.54      36365.95|
| 13:  2.0954 -  2.0404  1278   141  0.46  55.83   0.73     0.54      30546.51|
| 14:  2.0404 -  1.9907   754    85  0.54  48.92   0.74     0.55      20732.65|
|alpha:            min =        0.50 max =            0.81 mean =         0.61|
|beta:             min =    20732.65 max =        87846.54 mean =     55681.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.56|
|phase err.(test): min =        0.00 max =           89.99 mean =        48.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.287862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.487   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.688904              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.223   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1492 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2587 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3908 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5041 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6534 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7661 |
|-----------------------------------------------------------------------------|
|-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 |       54.059 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.790 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    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 = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4585   r_free= 0.4392   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.257951                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4411   r_free= 0.4252   ksol= 0.33   Bsol= 13.73   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.96,7.63,11.90,0.00,0.00,0.00); trace/3= 8.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.243724                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.386763              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.753   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.699172              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.258   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4411      final r-factor (work) = 0.3416          |
| start r-factor (free) = 0.4252      final r-factor (free) = 0.3595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.3021 = 8.39 * 0.50 * 6.2581 + 1.00 * 54.0594                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7587 = 8.39 * 0.50 * 6.1123 + 1.00 * 0.1275                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3416      final r-factor (work) = 0.2859          |
| start r-factor (free) = 0.3595      final r-factor (free) = 0.3251          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2879 = 0.70 * 1.00 * 6.1123 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1882 = 0.70 * 1.00 * 5.9723 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.28   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    65.28   11.53    None  None   None       |
|    Sol.    : 438    0      0.00    65.28   26.82    None  None   None       |
|    Mac.    : 2385   0      0.00    53.87   8.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.528: 1178   |   5:    32.639 -  39.167:   90        |
|      1:     6.528 -  13.056:  787   |   6:    39.167 -  45.694:   50        |
|      2:    13.056 -  19.583:  343   |   7:    45.694 -  52.222:   31        |
|      3:    19.583 -  26.111:  199   |   8:    52.222 -  58.750:   12        |
|      4:    26.111 -  32.639:  129   |   9:    58.750 -  65.278:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2859 r_free = 0.3251             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2852 r_free = 0.3259             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2852   r_free= 0.3259   ksol= 0.33   Bsol= 13.73   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.96,7.63,11.90,0.00,0.00,0.00); trace/3= 8.83                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.933596                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2806   r_free= 0.3214   ksol= 0.32   Bsol= 42.93   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.89,7.99,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.931793                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.036944              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.207   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.899  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2806      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.3214      final r-factor (free) = 0.2464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1882 = 4.04 * 0.50 * 5.9752 + 1.00 * 0.1275                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7206 = 4.04 * 0.50 * 5.7729 + 1.00 * 0.0681                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2005      final r-factor (work) = 0.1814          |
| start r-factor (free) = 0.2464      final r-factor (free) = 0.2291          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1218 = 0.37 * 1.00 * 5.7729 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0500 = 0.37 * 1.00 * 5.5817 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.76   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    61.76   11.65    None  None   None       |
|    Sol.    : 438    0      0.00    61.76   31.61    None  None   None       |
|    Mac.    : 2385   0      0.00    58.66   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.176: 1262   |   5:    30.881 -  37.058:   98        |
|      1:     6.176 -  12.353:  741   |   6:    37.058 -  43.234:  106        |
|      2:    12.353 -  18.529:  286   |   7:    43.234 -  49.410:   45        |
|      3:    18.529 -  24.705:  123   |   8:    49.410 -  55.587:   30        |
|      4:    24.705 -  30.881:  119   |   9:    55.587 -  61.763:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1814 r_free = 0.2291             target_work(ml) = 5.549         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1813 r_free = 0.2292             target_work(ml) = 5.549         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1813   r_free= 0.2292   ksol= 0.32   Bsol= 42.93   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.89,7.99,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.548911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1797   r_free= 0.2296   ksol= 0.32   Bsol= 53.35   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,3.05,5.36,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.547706                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.270742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.738  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.237068              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.475  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1797      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.2296      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2080 = 3.27 * 0.50 * 5.5889 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9509 = 3.27 * 0.50 * 5.4314 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1369      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7298 = 1.24 * 1.00 * 5.4314 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5437 = 1.24 * 1.00 * 5.2745 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.85   12.46    None  None   None       |
|    all(noH): 2823   0      0.00    78.85   12.46    None  None   None       |
|    Sol.    : 438    0      0.58    78.85   36.80    None  None   None       |
|    Mac.    : 2385   0      0.00    75.62   7.99     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 -   7.885: 1599   |   5:    39.423 -  47.307:   87        |
|      1:     7.885 -  15.769:  602   |   6:    47.307 -  55.192:   75        |
|      2:    15.769 -  23.654:  178   |   7:    55.192 -  63.076:   59        |
|      3:    23.654 -  31.538:   99   |   8:    63.076 -  70.961:   19        |
|      4:    31.538 -  39.423:   98   |   9:    70.961 -  78.845:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1270 r_free = 0.1738             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1268 r_free = 0.1739             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1739   ksol= 0.32   Bsol= 53.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,3.05,5.36,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.253242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1744   ksol= 0.33   Bsol= 59.47   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,2.89,4.72,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.253490                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.279227              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.287  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.487164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.789  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7175 = 3.28 * 0.50 * 5.2748 + 1.00 * 0.0689                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6295 = 3.28 * 0.50 * 5.2174 + 1.00 * 0.0751                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5581 = 0.49 * 1.00 * 5.2174 + 1.00 * 0.0164                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5372 = 0.49 * 1.00 * 5.1818 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.67   12.11    None  None   None       |
|    all(noH): 2823   0      0.00    81.67   12.11    None  None   None       |
|    Sol.    : 438    0      0.84    81.67   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    78.48   7.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.167: 1676   |   5:    40.834 -  49.000:   78        |
|      1:     8.167 -  16.334:  566   |   6:    49.000 -  57.167:   78        |
|      2:    16.334 -  24.500:  161   |   7:    57.167 -  65.334:   33        |
|      3:    24.500 -  32.667:  106   |   8:    65.334 -  73.501:   12        |
|      4:    32.667 -  40.834:  108   |   9:    73.501 -  81.667:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1620             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1619             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1619   ksol= 0.33   Bsol= 59.47   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,2.89,4.72,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173219                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1619   ksol= 0.33   Bsol= 59.47   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,2.96,4.68,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.173230                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.417979              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.330  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7491 = 1.42 * 0.50 * 5.1820 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7334 = 1.42 * 0.50 * 5.1887 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3728 = 0.26 * 1.00 * 5.1887 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3742 = 0.26 * 1.00 * 5.1940 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 1       |    number of function evaluations = 1      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.67   12.11    None  None   None       |
|    all(noH): 2823   0      0.00    81.67   12.11    None  None   None       |
|    Sol.    : 438    0      0.84    81.67   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    78.48   7.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.167: 1676   |   5:    40.834 -  49.000:   78        |
|      1:     8.167 -  16.334:  566   |   6:    49.000 -  57.167:   78        |
|      2:    16.334 -  24.500:  161   |   7:    57.167 -  65.334:   33        |
|      3:    24.500 -  32.667:  106   |   8:    65.334 -  73.501:   12        |
|      4:    32.667 -  40.834:  108   |   9:    73.501 -  81.667:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1630             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1630             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1630   ksol= 0.33   Bsol= 59.47   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,2.96,4.68,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193711                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.1052 0.1353      5.4459       5.561|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.0890 0.1127      5.4706      5.6623|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.1085 0.1537      5.4971      5.8645|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.1247 0.1650      5.4763      5.6279|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.1382 0.1678      5.3698       5.562|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.1289 0.2116      5.2525      5.5472|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.1363 0.1667      5.2343      5.3688|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.1253 0.1728      5.1387      5.3851|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.1273 0.2022      5.0966      5.3941|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.1214 0.1597      5.0092      5.1681|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.1244 0.1846      4.9976      5.2605|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.1222 0.1827      4.9307      5.3142|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.1187 0.1753       4.831      5.0383|
| 14:  2.0404 -  1.9907 0.58    754   85 0.1058 0.1677      4.6944      4.9371|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.93  10.17   0.97     0.95       8402.30|
|  2:  4.7504 -  3.7905  1340   153  0.95   8.32   1.01     0.99       9582.67|
|  3:  3.7905 -  3.3173  1311   146  0.93  11.33   1.02     1.02      10630.11|
|  4:  3.3173 -  3.0166  1308   139  0.92  13.74   1.01     1.00      10691.33|
|  5:  3.0166 -  2.8019  1306   146  0.90  16.24   1.00     0.97       8824.73|
|  6:  2.8019 -  2.6377  1292   148  0.89  16.83   0.98     0.96       7663.18|
|  7:  2.6377 -  2.5062  1287   144  0.90  16.39   0.99     0.95       6815.22|
|  8:  2.5062 -  2.3976  1282   138  0.90  16.09   0.99     0.96       6032.88|
|  9:  2.3976 -  2.3056  1276   147  0.90  16.64   1.01     0.97       5727.08|
| 10:  2.3056 -  2.2263  1274   139  0.89  16.82   1.00     0.96       4780.34|
| 11:  2.2263 -  2.1569  1268   139  0.89  17.16   1.00     0.96       4852.53|
| 12:  2.1569 -  2.0954  1257   141  0.90  16.50   1.01     1.00       4294.59|
| 13:  2.0954 -  2.0404  1278   141  0.90  16.49   0.99     0.97       3604.27|
| 14:  2.0404 -  1.9907   754    85  0.92  14.42   0.98     0.94       2623.13|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2623.13 max =        10691.33 mean =      6917.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.75|
|phase err.(test): min =        0.00 max =           89.40 mean =        14.31|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1630   ksol= 0.33   Bsol= 59.68   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,-0.41,1.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193660                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1630   ksol= 0.33   Bsol= 59.68   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,-0.41,1.31,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193660                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7504 0.99   1397  153 0.1050 0.1352      5.4437      5.5589|
|  2:  4.7504 -  3.7905 0.99   1340  153 0.0888 0.1125      5.4691      5.6602|
|  3:  3.7905 -  3.3173 0.99   1311  146 0.1084 0.1536      5.4964      5.8645|
|  4:  3.3173 -  3.0166 0.99   1308  139 0.1248 0.1651      5.4768      5.6286|
|  5:  3.0166 -  2.8019 0.99   1306  146 0.1383 0.1680      5.3707       5.563|
|  6:  2.8019 -  2.6377 0.99   1292  148 0.1290 0.2118      5.2533      5.5481|
|  7:  2.6377 -  2.5062 0.99   1287  144 0.1363 0.1668       5.235      5.3696|
|  8:  2.5062 -  2.3976 0.98   1282  138 0.1254 0.1728      5.1391      5.3851|
|  9:  2.3976 -  2.3056 0.98   1276  147 0.1273 0.2022      5.0968      5.3941|
| 10:  2.3056 -  2.2263 0.99   1274  139 0.1214 0.1598      5.0093      5.1684|
| 11:  2.2263 -  2.1569 0.98   1268  139 0.1244 0.1846      4.9977      5.2608|
| 12:  2.1569 -  2.0954 0.97   1257  141 0.1222 0.1827      4.9308      5.3142|
| 13:  2.0954 -  2.0404 1.00   1278  141 0.1187 0.1753      4.8311      5.0383|
| 14:  2.0404 -  1.9907 0.58    754   85 0.1058 0.1677      4.6946      4.9375|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7504  1397   153  0.93  10.14   0.97     0.95       8363.78|
|  2:  4.7504 -  3.7905  1340   153  0.95   8.30   1.01     0.99       9549.15|
|  3:  3.7905 -  3.3173  1311   146  0.93  11.31   1.02     1.02      10609.30|
|  4:  3.3173 -  3.0166  1308   139  0.92  13.75   1.01     1.00      10701.09|
|  5:  3.0166 -  2.8019  1306   146  0.90  16.26   1.00     0.97       8840.67|
|  6:  2.8019 -  2.6377  1292   148  0.89  16.85   0.98     0.96       7676.78|
|  7:  2.6377 -  2.5062  1287   144  0.90  16.40   0.99     0.95       6826.12|
|  8:  2.5062 -  2.3976  1282   138  0.90  16.11   0.99     0.96       6037.67|
|  9:  2.3976 -  2.3056  1276   147  0.90  16.65   1.01     0.97       5730.47|
| 10:  2.3056 -  2.2263  1274   139  0.89  16.82   1.00     0.96       4781.75|
| 11:  2.2263 -  2.1569  1268   139  0.89  17.17   1.00     0.96       4854.58|
| 12:  2.1569 -  2.0954  1257   141  0.90  16.50   1.01     1.00       4295.71|
| 13:  2.0954 -  2.0404  1278   141  0.90  16.49   0.99     0.97       3605.59|
| 14:  2.0404 -  1.9907   754    85  0.92  14.42   0.98     0.94       2624.75|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2624.75 max =        10701.09 mean =      6915.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.75|
|phase err.(test): min =        0.00 max =           89.43 mean =        14.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.020)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.37    85.04   15.48    None  None   None       |
|    all(noH): 2823   0      3.37    85.04   15.48    None  None   None       |
|    Sol.    : 438    0      4.21    85.04   38.97    None  None   None       |
|    Mac.    : 2385   0      3.37    81.85   11.16    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:     3.371 -  11.537: 1676   |   5:    44.204 -  52.371:   78        |
|      1:    11.537 -  19.704:  566   |   6:    52.371 -  60.538:   78        |
|      2:    19.704 -  27.871:  161   |   7:    60.538 -  68.704:   33        |
|      3:    27.871 -  36.038:  106   |   8:    68.704 -  76.871:   12        |
|      4:    36.038 -  44.204:  108   |   9:    76.871 -  85.038:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.226 - 4.457
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 315
   mapped sites are within: 0.709 - 4.457

peak=   10.954 closest distance to " CB  VAL A 230 " =    1.471
peak=    6.044 closest distance to " CG  LEU A   5 " =    1.247
peak=    5.891 closest distance to " CG2 VAL A 296 " =    1.110
peak=    5.661 closest distance to " NH2 ARG A  56 " =    2.162
peak=    5.578 closest distance to " CG  PRO A  54 " =    1.394
peak=    5.481 closest distance to " CD2 LEU A   5 " =    1.233
peak=    5.476 closest distance to " CB  VAL A 296 " =    1.103
peak=    5.378 closest distance to " NE2 GLN A  11 " =    1.134
peak=    5.337 closest distance to " CB  GLN A 223 " =    1.475
peak=    5.282 closest distance to " O   HOH Z 142 " =    1.891
peak=    5.243 closest distance to " CG  LEU A 228 " =    1.192
peak=    5.071 closest distance to " CG  PRO A 198 " =    1.308
peak=    4.993 closest distance to " CB  PRO A  54 " =    1.082
peak=    4.987 closest distance to " CG1 VAL A 296 " =    1.183
peak=    4.801 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.764 closest distance to " CZ  PHE A 218 " =    1.144
peak=    4.549 closest distance to " CB  ASN A 148 " =    1.403
peak=    4.480 closest distance to " O   HOH Z 265 " =    2.099
peak=    4.466 closest distance to " CG  PRO A 243 " =    1.175
peak=    4.452 closest distance to " O   HOH Z 248 " =    1.297
peak=    4.440 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.433 closest distance to " CB  ASN A 142 " =    1.123
peak=    4.430 closest distance to " CB  GLN A 183 " =    1.249
peak=    4.384 closest distance to " ND2 ASN A 187 " =    1.608
peak=    4.384 closest distance to " CB  ARG A 190 " =    1.619
peak=    4.347 closest distance to " O   HOH Z 313 " =    1.953
peak=    4.326 closest distance to " O   SER A  87 " =    2.333
peak=    4.316 closest distance to " O   PRO A 198 " =    1.572
peak=    4.281 closest distance to " O   HOH Z   9 " =    1.450
peak=    4.269 closest distance to " O   HOH Z 369 " =    2.287
peak=    4.238 closest distance to " CB  SER A  63 " =    1.169
peak=    4.230 closest distance to " CB  VAL A 265 " =    1.286
peak=    4.213 closest distance to " CG  PRO A 213 " =    1.256
peak=    4.201 closest distance to " CD2 LEU A 228 " =    1.242
peak=    4.194 closest distance to " O   HOH Z  43 " =    2.045
peak=    4.179 closest distance to " O   HOH Z 427 " =    3.003
peak=    4.175 closest distance to " CZ3 TRP A 266 " =    1.135
peak=    4.153 closest distance to " O   HOH Z  78 " =    1.614
peak=    4.144 closest distance to " O   HOH Z 346 " =    1.577
peak=    4.141 closest distance to " CB  ASP A 124 " =    0.801
peak=    4.139 closest distance to " CA  TYR A  30 " =    1.003
peak=    4.127 closest distance to " O   HOH Z 126 " =    1.527
peak=    4.111 closest distance to " CB  ARG A  79 " =    1.440
peak=    4.089 closest distance to " O   HOH Z 188 " =    2.946
peak=    4.069 closest distance to " O   HOH Z 402 " =    1.454
peak=    4.056 closest distance to " ND2 ASN A 249 " =    0.943
peak=    4.037 closest distance to " O   HOH Z 126 " =    1.970
peak=    4.028 closest distance to " O   HOH Z 251 " =    1.621
peak=    4.020 closest distance to " CG2 VAL A 257 " =    0.949
peak=    4.005 closest distance to " CB  GLU A 277 " =    3.684
peak=    4.002 closest distance to " CB  VAL A 230 " =    1.214
peak=    4.002 closest distance to " CG  MET A 185 " =    1.194
peak=    3.999 closest distance to " O   HOH Z 411 " =    3.915
peak=    3.990 closest distance to " N   ASN A  39 " =    1.198
peak=    3.969 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.960 closest distance to " O   HOH Z 261 " =    2.109
peak=    3.957 closest distance to " O   HOH Z 303 " =    2.083
peak=    3.931 closest distance to " CB  ASN A  39 " =    0.953
peak=    3.929 closest distance to " O   HOH Z  92 " =    2.263
peak=    3.923 closest distance to " O   HOH Z 287 " =    2.141
peak=    3.920 closest distance to " CA  ALA A  51 " =    0.953
peak=    3.918 closest distance to " CA  ARG A  36 " =    1.075
peak=    3.910 closest distance to " O   HOH Z 425 " =    1.424
peak=    3.908 closest distance to " CB  GLU A 152 " =    1.133
peak=    3.905 closest distance to " O   HOH Z  61 " =    1.805
peak=    3.898 closest distance to " CZ  PHE A  38 " =    1.122
peak=    3.893 closest distance to " O   HOH Z 272 " =    1.830
peak=    3.888 closest distance to " O   HOH Z 214 " =    2.335
peak=    3.885 closest distance to " O  BHOH Z 338 " =    2.372
peak=    3.867 closest distance to " O   HOH Z 359 " =    1.578
peak=    3.857 closest distance to " CA  SER A  87 " =    1.024
peak=    3.849 closest distance to " CB  TRP A 266 " =    1.033
peak=    3.841 closest distance to " O   HOH Z 316 " =    3.123
peak=    3.836 closest distance to " CB  GLU A  46 " =    0.963
peak=    3.835 closest distance to " CB  GLU A 128 " =    0.973
peak=    3.831 closest distance to " CG  LEU A 167 " =    1.230
peak=    3.820 closest distance to " CB  VAL A 202 " =    1.582
peak=    3.819 closest distance to " CD  LYS A 166 " =    1.315
peak=    3.818 closest distance to " CB  GLN A  89 " =    1.222
peak=    3.808 closest distance to " CD1 LEU A  96 " =    0.709
peak=    3.805 closest distance to " O   HOH Z 209 " =    2.303
peak=    3.800 closest distance to " CD2 TRP A 179 " =    1.290
peak=    3.767 closest distance to " CD1 ILE A 199 " =    1.011
peak=    3.758 closest distance to " CA  ALA A 295 " =    1.001
peak=    3.758 closest distance to " CE  LYS A  76 " =    0.935
peak=    3.754 closest distance to " OG BSER A 164 " =    2.258
peak=    3.753 closest distance to " O   HOH Z 234 " =    3.707
peak=    3.748 closest distance to " CB  ASN A 110 " =    1.119
peak=    3.745 closest distance to " O   HOH Z 298 " =    1.724
peak=    3.742 closest distance to " O   HOH Z 368 " =    2.210
peak=    3.742 closest distance to " O   HOH Z 423 " =    1.783
peak=    3.733 closest distance to " CA  VAL A  41 " =    0.773
peak=    3.707 closest distance to " O   HOH Z 273 " =    2.898
peak=    3.687 closest distance to " O   HOH Z 353 " =    2.638
peak=    3.686 closest distance to " CB  ARG A  79 " =    0.934
peak=    3.679 closest distance to " CD  ARG A 159 " =    0.735
peak=    3.679 closest distance to " CG1 ILE A  49 " =    1.598
peak=    3.672 closest distance to " O   HOH Z 403 " =    1.545
peak=    3.671 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.668 closest distance to " O   HOH Z 158 " =    3.179
peak=    3.666 closest distance to " NH1AARG A 145 " =    1.237
peak=    3.663 closest distance to " CB  ASN A 173 " =    1.057
peak=    3.662 closest distance to " O   HOH Z  40 " =    1.824
peak=    3.662 closest distance to " CB  THR A  31 " =    1.521
peak=    3.649 closest distance to " CB  SER A 273 " =    0.986
peak=    3.640 closest distance to " O  BHOH Z  74 " =    1.197
peak=    3.638 closest distance to " N   PHE A 130 " =    1.238
peak=    3.634 closest distance to " CB  SER A   3 " =    1.262
peak=    3.632 closest distance to " O   HOH Z 371 " =    2.740
peak=    3.632 closest distance to " CG2AVAL A 121 " =    2.384
peak=    3.630 closest distance to " O   HOH Z 422 " =    2.654
peak=    3.624 closest distance to " O   HOH Z  59 " =    2.144
peak=    3.623 closest distance to " O   HOH Z  80 " =    1.788
peak=    3.618 closest distance to " OD1 ASN A  69 " =    2.532
peak=    3.618 closest distance to " O   HOH Z  68 " =    2.224
peak=    3.615 closest distance to " N   GLY A 133 " =    3.748
peak=    3.609 closest distance to " CG1 VAL A 153 " =    0.974
peak=    3.596 closest distance to " O   HOH Z 290 " =    1.128
peak=    3.596 closest distance to " O   HOH Z  63 " =    1.758
peak=    3.588 closest distance to " O   HOH Z 294 " =    1.580
peak=    3.585 closest distance to " N   SER A 135 " =    1.453
peak=    3.578 closest distance to " O   HOH Z  97 " =    2.354
peak=    3.572 closest distance to " CE1 TYR A 186 " =    1.298
peak=    3.567 closest distance to " CB  ASP A 140 " =    1.166
peak=    3.561 closest distance to " O   HOH Z 180 " =    2.171
peak=    3.555 closest distance to " CA  TYR A  30 " =    1.089
peak=    3.552 closest distance to " CB BVAL A  41 " =    1.203
peak=    3.551 closest distance to " CB  ASN A 187 " =    1.205
peak=    3.550 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.550 closest distance to " O   HOH Z 406 " =    1.560
peak=    3.550 closest distance to " O   HOH Z 365 " =    2.882
peak=    3.545 closest distance to " OG  SER A 276 " =    1.254
peak=    3.544 closest distance to " CB  PRO A  90 " =    1.083
peak=    3.528 closest distance to " O   HOH Z 172 " =    3.533
peak=    3.527 closest distance to " CA  ASN A 217 " =    1.223
peak=    3.527 closest distance to " NZ  LYS A 117 " =    3.136
peak=    3.526 closest distance to " CA  THR A 264 " =    0.824
peak=    3.525 closest distance to " NE2 HIS A 207 " =    1.121
peak=    3.521 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.519 closest distance to " CG  GLN A  58 " =    0.913
peak=    3.517 closest distance to " CA  PHE A 283 " =    1.062
peak=    3.516 closest distance to " CB  ALA A 104 " =    0.740
peak=    3.502 closest distance to " CB  ALA A 248 " =    1.394
peak=    3.490 closest distance to " CA  TYR A 116 " =    1.528
peak=    3.489 closest distance to " O   ASN A  74 " =    1.466
peak=    3.485 closest distance to " O   ASP A 124 " =    1.051
peak=    3.477 closest distance to " CG  ARG A  66 " =    2.754
peak=    3.477 closest distance to " N   ALA A 256 " =    1.012
peak=    3.474 closest distance to " CG  GLU A  37 " =    0.940
peak=    3.474 closest distance to " OE2 GLU A  53 " =    1.877
peak=    3.472 closest distance to " CA  ILE A 234 " =    0.942
peak=    3.469 closest distance to " CA  ASN A 127 " =    1.066
peak=    3.468 closest distance to " CG  MET A 185 " =    0.911
peak=    3.466 closest distance to " CD  LYS A  76 " =    2.064
peak=    3.466 closest distance to " CB  GLN A  88 " =    1.234
peak=    3.461 closest distance to " CB  SER A 212 " =    1.357
peak=    3.461 closest distance to " N   ASP A 162 " =    1.213
peak=    3.461 closest distance to " O   HOH Z 128 " =    2.199
peak=    3.460 closest distance to " CA  LEU A 282 " =    1.144
peak=    3.451 closest distance to " O   HOH Z 171 " =    3.942
peak=    3.450 closest distance to " O   HOH Z 145 " =    2.329
peak=    3.446 closest distance to " NZ  LYS A  48 " =    1.173
peak=    3.445 closest distance to " CB  SER A  26 " =    1.839
peak=    3.442 closest distance to " CA  ALA A 291 " =    0.861
peak=    3.441 closest distance to " O   HOH Z  97 " =    2.109
peak=    3.439 closest distance to " CG2AVAL A  72 " =    1.717
peak=    3.437 closest distance to " CG2 ILE A 120 " =    1.174
peak=    3.437 closest distance to " O   HOH Z 389 " =    1.793
peak=    3.436 closest distance to " CB  PRO A 243 " =    1.363
peak=    3.435 closest distance to " CB  SER A 210 " =    0.809
peak=    3.433 closest distance to " O   HOH Z 258 " =    2.106
peak=    3.430 closest distance to " CB  THR A  52 " =    0.838
peak=    3.424 closest distance to " CG  PHE A 204 " =    0.929
peak=    3.423 closest distance to " CB  LYS A 117 " =    1.204
peak=    3.420 closest distance to " CB  ASN A 215 " =    1.196
peak=    3.412 closest distance to " CD BLYS A 290 " =    1.037
peak=    3.410 closest distance to " O   HOH Z 337 " =    3.510
peak=    3.401 closest distance to " CA  ASN A 215 " =    1.050
peak=    3.398 closest distance to " CA  LYS A 117 " =    1.266
peak=    3.393 closest distance to " CA  VAL A 125 " =    1.239
peak=    3.392 closest distance to " O   GLN A  88 " =    1.632
peak=    3.380 closest distance to " NE2 GLN A  77 " =    3.281
peak=    3.379 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.379 closest distance to " CG  LEU A 281 " =    1.039
peak=    3.378 closest distance to " O   TRP A 274 " =    1.847
peak=    3.375 closest distance to " CB  TRP A 179 " =    1.385
peak=    3.371 closest distance to " CG BARG A 102 " =    1.829
peak=    3.370 closest distance to " O   HOH Z 238 " =    2.311
peak=    3.369 closest distance to " O   HOH Z 368 " =    3.427
peak=    3.361 closest distance to " O   HOH Z   4 " =    1.583
peak=    3.359 closest distance to " CD1 ILE A  33 " =    1.753
peak=    3.358 closest distance to " O   HOH Z   3 " =    1.902
peak=    3.355 closest distance to " O   HOH Z  21 " =    1.792
peak=    3.353 closest distance to " CA  MET A 105 " =    0.980
peak=    3.353 closest distance to " CA  ARG A 139 " =    1.021
peak=    3.348 closest distance to " CB  PHE A 204 " =    0.870
peak=    3.344 closest distance to " ND2BASN A 224 " =    0.758
peak=    3.339 closest distance to " O   HOH Z  10 " =    1.711
peak=    3.335 closest distance to " O   HOH Z 250 " =    1.264
peak=    3.334 closest distance to " CB  ARG A 145 " =    0.925
peak=    3.328 closest distance to " O   HOH Z 187 " =    2.337
peak=    3.327 closest distance to " CG1 ILE A 151 " =    1.086
peak=    3.326 closest distance to " CA  ALA A 154 " =    1.043
peak=    3.325 closest distance to " CG2 ILE A  20 " =    1.517
peak=    3.324 closest distance to " O   PHE A  61 " =    1.378
peak=    3.324 closest distance to " CG AARG A 275 " =    1.286
peak=    3.313 closest distance to " CA  ASP A 191 " =    1.156
peak=    3.310 closest distance to " O   THR A 182 " =    1.370
peak=    3.310 closest distance to " O   HOH Z 250 " =    1.384
peak=    3.302 closest distance to " O   HOH Z 337 " =    1.821
peak=    3.302 closest distance to " O   HOH Z 285 " =    2.341
peak=    3.301 closest distance to " O   HOH Z 193 " =    1.439
peak=    3.301 closest distance to " CA  ASP A 162 " =    0.993
peak=    3.295 closest distance to " O   HOH Z 392 " =    2.929
peak=    3.295 closest distance to " CA  GLY A 211 " =    1.355
peak=    3.285 closest distance to " OE2 GLU A  53 " =    1.331
peak=    3.285 closest distance to " CB  VAL A 268 " =    0.816
peak=    3.283 closest distance to " O   HOH Z 293 " =    1.792
peak=    3.280 closest distance to " CG1 ILE A  20 " =    1.312
peak=    3.274 closest distance to " CB  ALA A 291 " =    1.221
peak=    3.272 closest distance to " O   HOH Z 329 " =    4.179
peak=    3.272 closest distance to " CA  ALA A 233 " =    1.442
peak=    3.271 closest distance to " CE  LYS A  48 " =    1.223
peak=    3.269 closest distance to " NH2AARG A 145 " =    1.156
peak=    3.269 closest distance to " CB  PRO A 198 " =    1.092
peak=    3.267 closest distance to " CA  ALA A 160 " =    0.999
peak=    3.264 closest distance to " CB  MET A  40 " =    0.781
peak=    3.258 closest distance to " CA  ILE A 106 " =    0.734
peak=    3.257 closest distance to " O   HOH Z  30 " =    1.272
peak=    3.256 closest distance to " O   HOH Z 435 " =    2.009
peak=    3.256 closest distance to " O   HOH Z 403 " =    1.574
peak=    3.246 closest distance to " O   HOH Z  88 " =    2.956
peak=    3.244 closest distance to " O   PRO A 213 " =    1.388
peak=    3.243 closest distance to " CD1 LEU A 300 " =    1.108
peak=    3.243 closest distance to " O   HOH Z 344 " =    2.922
peak=    3.239 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.237 closest distance to " O   HOH Z 141 " =    1.680
peak=    3.235 closest distance to " CD  ARG A  66 " =    2.629
peak=    3.233 closest distance to " C   ALA A 299 " =    0.867
peak=    3.230 closest distance to " CB  ALA A 114 " =    1.044
peak=    3.227 closest distance to " O   HOH Z 299 " =    4.167
peak=    3.226 closest distance to " CD1 LEU A  96 " =    1.293
peak=    3.226 closest distance to " NH1 ARG A  14 " =    0.932
peak=    3.225 closest distance to " O   HOH Z 148 " =    3.474
peak=    3.224 closest distance to " OG  SER A  28 " =    1.445
peak=    3.222 closest distance to " O   HOH Z 385 " =    3.974
peak=    3.220 closest distance to " CA  ARG A 102 " =    1.180
peak=    3.219 closest distance to " CE3 TRP A 150 " =    1.098
peak=    3.216 closest distance to " CB  ALA A 227 " =    1.070
peak=    3.215 closest distance to " O   SER A 164 " =    1.326
peak=    3.211 closest distance to " N   GLN A 278 " =    1.418
peak=    3.209 closest distance to " CA  ALA A  21 " =    1.028
peak=    3.201 closest distance to " CB  ARG A 102 " =    0.736
peak=    3.196 closest distance to " CB  GLN A 205 " =    1.117
peak=    3.195 closest distance to " O   HOH Z 361 " =    3.647
peak=    3.194 closest distance to " CG  GLN A  88 " =    1.052
peak=    3.189 closest distance to " CB  ALA A  10 " =    0.896
peak=    3.186 closest distance to " CG2 ILE A 263 " =    1.007
peak=    3.185 closest distance to " O   HOH Z 417 " =    3.280
peak=    3.180 closest distance to " O   MET A 105 " =    1.864
peak=    3.175 closest distance to " CA  LYS A 290 " =    1.154
peak=    3.174 closest distance to " OE1 GLU A  37 " =    1.245
peak=    3.171 closest distance to " O   HOH Z 203 " =    1.705
peak=    3.165 closest distance to " CZ3 TRP A 274 " =    4.457
peak=    3.160 closest distance to " CB  ALA A 242 " =    0.767
peak=    3.159 closest distance to " O   TYR A 116 " =    1.336
peak=    3.157 closest distance to " O   LEU A 228 " =    1.928
peak=    3.157 closest distance to " CA  ALA A 129 " =    1.449
peak=    3.156 closest distance to " O   HOH Z 213 " =    1.896
peak=    3.155 closest distance to " CB  GLN A 278 " =    0.954
peak=    3.154 closest distance to " CD  LYS A 119 " =    1.972
peak=    3.152 closest distance to " CB  SER A 216 " =    0.825
peak=    3.149 closest distance to " CB  ALA A  43 " =    0.844
peak=    3.148 closest distance to " CB  ARG A 139 " =    0.918
peak=    3.141 closest distance to " O   PHE A 192 " =    1.397
peak=    3.136 closest distance to " CB  ARG A 219 " =    0.983
peak=    3.136 closest distance to " O   HOH Z   1 " =    2.137
peak=    3.132 closest distance to " O   HOH Z 345 " =    3.405
peak=    3.129 closest distance to " CB  LEU A 300 " =    0.892
peak=    3.124 closest distance to " O   GLY A  91 " =    1.343
peak=    3.123 closest distance to " CG2 THR A 221 " =    1.069
peak=    3.116 closest distance to " O   HOH Z 421 " =    2.085
peak=    3.115 closest distance to " CG  ARG A 138 " =    1.276
peak=    3.114 closest distance to " O   ILE A  49 " =    1.096
peak=    3.113 closest distance to " O   HOH Z  63 " =    1.831
peak=    3.112 closest distance to " OG  SER A 245 " =    1.587
peak=    3.110 closest distance to " O   HOH Z   9 " =    1.767
peak=    3.109 closest distance to " CD2 LEU A   5 " =    0.773
peak=    3.102 closest distance to " CB  TYR A 172 " =    0.872
peak=    3.097 closest distance to " CG2BVAL A 121 " =    0.749
peak=    3.096 closest distance to " O   HOH Z 409 " =    3.323
peak=    3.094 closest distance to " O   HOH Z 162 " =    3.459
peak=    3.087 closest distance to " O   ALA A 292 " =    1.705
peak=    3.085 closest distance to " O   HOH Z 263 " =    1.649
peak=    3.083 closest distance to " C   ASN A  39 " =    1.071
peak=    3.078 closest distance to " O   HOH Z 116 " =    1.768
peak=    3.076 closest distance to " CD1 ILE A 263 " =    1.151
peak=    3.071 closest distance to " NH2BARG A 190 " =    1.851
peak=    3.063 closest distance to " CG2 ILE A 234 " =    1.038
peak=    3.056 closest distance to " O   HOH Z  85 " =    1.280
peak=    3.055 closest distance to " O   HOH Z 172 " =    3.934
peak=    3.052 closest distance to " CD1 LEU A 261 " =    1.187
peak=    3.043 closest distance to " OE2 GLU A   2 " =    1.930
peak=    3.037 closest distance to " CA  LEU A  83 " =    1.107
peak=    3.033 closest distance to " CG2 ILE A  20 " =    1.362
peak=    3.027 closest distance to " O   HOH Z 371 " =    3.364
peak=    3.007 closest distance to " O   HOH Z  88 " =    3.046

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.713 - 5.661
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.713 - 5.661

peak=   -5.039 closest distance to " CG2 VAL A 230 " =    0.713
peak=   -4.661 closest distance to " CD  ARG A  14 " =    3.203
peak=   -4.581 closest distance to " CD  GLN A  58 " =    1.034
peak=   -4.472 closest distance to " CB  PRO A 243 " =    2.742
peak=   -4.339 closest distance to " CG1 VAL A 296 " =    1.066
peak=   -4.228 closest distance to " O   VAL A  67 " =    2.582
peak=   -4.221 closest distance to " O   PRO A 198 " =    1.137
peak=   -4.221 closest distance to " CG1 VAL A 112 " =    2.669
peak=   -4.207 closest distance to " CD  ARG A 156 " =    2.050
peak=   -4.144 closest distance to " CB  PHE A 192 " =    1.933
peak=   -4.126 closest distance to " OG BSER A 134 " =    1.309
peak=   -4.098 closest distance to " O   HOH Z 351 " =    1.468
peak=   -4.032 closest distance to " CG1 VAL A 112 " =    2.760
peak=   -4.026 closest distance to " C   HIS A 108 " =    1.133
peak=   -4.015 closest distance to " OE1 GLN A 223 " =    2.194
peak=   -4.002 closest distance to " CD2 TYR A 293 " =    1.977
peak=   -4.001 closest distance to " O   HOH Z 211 " =    1.270
peak=   -3.988 closest distance to " O   HOH Z 166 " =    1.944
peak=   -3.936 closest distance to " O   HOH Z 231 " =    2.114
peak=   -3.929 closest distance to " O   HOH Z 267 " =    5.661
peak=   -3.921 closest distance to " O   HOH Z 196 " =    2.278
peak=   -3.896 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -3.890 closest distance to " CA  VAL A  67 " =    2.960
peak=   -3.888 closest distance to " CZ2 TRP A  92 " =    2.869
peak=   -3.836 closest distance to " O   HOH Z 193 " =    1.229
peak=   -3.831 closest distance to " O   HOH Z 216 " =    1.093
peak=   -3.811 closest distance to " CA  ASP A 298 " =    1.109
peak=   -3.797 closest distance to " O   HOH Z 394 " =    1.536
peak=   -3.791 closest distance to " ND2 ASN A  45 " =    1.162
peak=   -3.778 closest distance to " CG2 VAL A 296 " =    1.076
peak=   -3.767 closest distance to " CB  ALA A 161 " =    2.550
peak=   -3.767 closest distance to " CG1 VAL A 250 " =    2.757
peak=   -3.731 closest distance to " CD1 LEU A 101 " =    2.365
peak=   -3.730 closest distance to " CB  ALA A 248 " =    2.345
peak=   -3.723 closest distance to " CZ3 TRP A 179 " =    1.237
peak=   -3.698 closest distance to " O   SER A 271 " =    2.178
peak=   -3.696 closest distance to " OG  SER A  97 " =    2.375
peak=   -3.672 closest distance to " O   HOH Z  44 " =    2.423
peak=   -3.665 closest distance to " CB  ALA A  43 " =    2.524
peak=   -3.656 closest distance to " CG2 VAL A 202 " =    2.746
peak=   -3.653 closest distance to " O   PRO A 163 " =    2.101
peak=   -3.643 closest distance to " O   HOH Z 103 " =    1.816
peak=   -3.642 closest distance to " O   HOH Z 290 " =    1.190
peak=   -3.639 closest distance to " NE2 GLN A  11 " =    1.800
peak=   -3.620 closest distance to " CB  HIS A  86 " =    1.123
peak=   -3.618 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.617 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.593 closest distance to " O   HOH Z 285 " =    2.019
peak=   -3.588 closest distance to " CD1 LEU A 255 " =    2.879
peak=   -3.579 closest distance to " O   HOH Z 429 " =    2.059
peak=   -3.574 closest distance to " CA  GLY A 241 " =    2.398
peak=   -3.571 closest distance to " CG  ASP A 231 " =    0.834
peak=   -3.566 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.562 closest distance to " CG  GLU A 277 " =    1.302
peak=   -3.556 closest distance to " CE BMET A  47 " =    1.313
peak=   -3.556 closest distance to " O   HOH Z  73 " =    2.259
peak=   -3.524 closest distance to " CG1 VAL A 125 " =    1.935
peak=   -3.517 closest distance to " CA  GLY A 241 " =    3.142
peak=   -3.513 closest distance to " N   THR A  52 " =    1.686
peak=   -3.505 closest distance to " O   HOH Z 102 " =    1.743
peak=   -3.499 closest distance to " O   HOH Z 377 " =    2.108
peak=   -3.493 closest distance to " O   SER A 210 " =    1.969
peak=   -3.491 closest distance to " CA  VAL A 296 " =    0.930
peak=   -3.485 closest distance to " O   HOH Z  11 " =    1.917
peak=   -3.482 closest distance to " O   HOH Z 371 " =    2.300
peak=   -3.480 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.475 closest distance to " CB  VAL A 230 " =    1.143
peak=   -3.470 closest distance to " CE  MET A 105 " =    2.381
peak=   -3.465 closest distance to " OXT GLY A 302 " =    2.930
peak=   -3.460 closest distance to " NE2 GLN A  88 " =    1.054
peak=   -3.459 closest distance to " O   HOH Z 359 " =    2.988
peak=   -3.453 closest distance to " O   ASN A 252 " =    1.350
peak=   -3.450 closest distance to " C   ALA A 158 " =    1.400
peak=   -3.445 closest distance to " NE2 GLN A 194 " =    1.882
peak=   -3.444 closest distance to " CE2 TRP A  70 " =    2.130
peak=   -3.433 closest distance to " NH2AARG A 275 " =    5.144
peak=   -3.428 closest distance to " O   HOH Z 198 " =    2.043
peak=   -3.427 closest distance to " N   ALA A 226 " =    2.035
peak=   -3.417 closest distance to " O   HOH Z 114 " =    3.050
peak=   -3.416 closest distance to " OD1 ASN A 148 " =    1.318
peak=   -3.415 closest distance to " CB  ALA A  10 " =    2.320
peak=   -3.398 closest distance to " O   VAL A 189 " =    2.717
peak=   -3.391 closest distance to " CD  PRO A 243 " =    2.037
peak=   -3.389 closest distance to " CG  LEU A   5 " =    0.889
peak=   -3.383 closest distance to " NH2 ARG A  79 " =    1.491
peak=   -3.382 closest distance to " O   HOH Z   9 " =    1.575
peak=   -3.380 closest distance to " O   HOH Z 232 " =    1.752
peak=   -3.376 closest distance to " CB  TRP A  85 " =    2.593
peak=   -3.376 closest distance to " OG  SER A  63 " =    1.136
peak=   -3.375 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.372 closest distance to " C   MET A 188 " =    1.412
peak=   -3.370 closest distance to " O   HOH Z 421 " =    3.076
peak=   -3.368 closest distance to " N   THR A 157 " =    1.541
peak=   -3.366 closest distance to " O   HOH Z 106 " =    1.843
peak=   -3.364 closest distance to " O   HOH Z 275 " =    1.489
peak=   -3.361 closest distance to " O   HOH Z 133 " =    1.354
peak=   -3.359 closest distance to " N   TRP A 274 " =    1.027
peak=   -3.351 closest distance to " OE1 GLN A  88 " =    1.074
peak=   -3.350 closest distance to " CG  ARG A 269 " =    2.313
peak=   -3.349 closest distance to " O   HOH Z 128 " =    2.358
peak=   -3.347 closest distance to " CG  GLN A 103 " =    2.523
peak=   -3.347 closest distance to " NE2 GLN A 278 " =    1.824
peak=   -3.346 closest distance to " O   ILE A 106 " =    1.955
peak=   -3.345 closest distance to " OH  TYR A 247 " =    2.080
peak=   -3.343 closest distance to " OH  TYR A 172 " =    1.850
peak=   -3.339 closest distance to " N   ALA A 248 " =    1.879
peak=   -3.338 closest distance to " CG1 VAL A 265 " =    2.307
peak=   -3.336 closest distance to " O   HOH Z 174 " =    2.461
peak=   -3.336 closest distance to " ND2 ASN A 249 " =    2.376
peak=   -3.334 closest distance to " ND2 ASN A 187 " =    1.472
peak=   -3.332 closest distance to " O   HOH Z 345 " =    2.094
peak=   -3.330 closest distance to " NE  ARG A  66 " =    4.183
peak=   -3.329 closest distance to " O   ALA A 227 " =    1.430
peak=   -3.329 closest distance to " O   GLY A  17 " =    1.239
peak=   -3.329 closest distance to " O   HOH Z 357 " =    2.086
peak=   -3.326 closest distance to " CB  VAL A 296 " =    1.316
peak=   -3.323 closest distance to " O   HOH Z 131 " =    4.099
peak=   -3.322 closest distance to " O   HOH Z 407 " =    3.022
peak=   -3.320 closest distance to " CB  PRO A 163 " =    2.487
peak=   -3.319 closest distance to " O   HOH Z 256 " =    1.439
peak=   -3.316 closest distance to " O   HOH Z  38 " =    1.836
peak=   -3.314 closest distance to " CG  LEU A   5 " =    1.311
peak=   -3.314 closest distance to " OE1 GLU A  44 " =    0.879
peak=   -3.311 closest distance to " CA  GLY A 133 " =    2.324
peak=   -3.305 closest distance to " CD1 ILE A 239 " =    2.318
peak=   -3.305 closest distance to " OG1 THR A  82 " =    1.329
peak=   -3.305 closest distance to " O   HOH Z 165 " =    1.923
peak=   -3.303 closest distance to " CE3 TRP A  70 " =    1.690
peak=   -3.302 closest distance to " O   HOH Z 123 " =    2.474
peak=   -3.296 closest distance to " O   HOH Z 136 " =    2.548
peak=   -3.295 closest distance to " O   MET A  40 " =    2.819
peak=   -3.295 closest distance to " O   HOH Z 191 " =    5.577
peak=   -3.293 closest distance to " O   HOH Z  11 " =    2.206
peak=   -3.292 closest distance to " ND2 ASN A  45 " =    1.766
peak=   -3.289 closest distance to " CD  LYS A 289 " =    2.476
peak=   -3.283 closest distance to " O   HOH Z 295 " =    1.536
peak=   -3.279 closest distance to " NH2 ARG A 159 " =    2.278
peak=   -3.278 closest distance to " NE  ARG A  79 " =    1.060
peak=   -3.272 closest distance to " C   LEU A 143 " =    1.062
peak=   -3.271 closest distance to " O   HOH Z  52 " =    1.637
peak=   -3.268 closest distance to " N   ALA A 248 " =    2.395
peak=   -3.264 closest distance to " O   HOH Z 243 " =    2.012
peak=   -3.258 closest distance to " O   HOH Z 431 " =    1.976
peak=   -3.251 closest distance to " O   HOH Z  13 " =    1.848
peak=   -3.248 closest distance to " O   HOH Z 191 " =    3.339
peak=   -3.247 closest distance to " CE AMET A  47 " =    3.207
peak=   -3.244 closest distance to " CE2 PHE A  61 " =    2.691
peak=   -3.236 closest distance to " CD  PRO A 213 " =    2.033
peak=   -3.234 closest distance to " CD1 ILE A 199 " =    2.486
peak=   -3.226 closest distance to " CA  GLY A 203 " =    2.467
peak=   -3.225 closest distance to " O   HOH Z 252 " =    3.796
peak=   -3.220 closest distance to " CA  GLY A  98 " =    1.950
peak=   -3.219 closest distance to " CG1 VAL A  78 " =    2.739
peak=   -3.216 closest distance to " O   GLY A 196 " =    1.154
peak=   -3.215 closest distance to " O   HOH Z 174 " =    3.976
peak=   -3.213 closest distance to " CZ2 TRP A 274 " =    1.058
peak=   -3.207 closest distance to " N   SER A 276 " =    1.370
peak=   -3.204 closest distance to " O   HOH Z 236 " =    1.514
peak=   -3.201 closest distance to " O   ALA A 180 " =    1.383
peak=   -3.195 closest distance to " CG2 VAL A 189 " =    1.993
peak=   -3.191 closest distance to " CZ2 TRP A 150 " =    1.092
peak=   -3.190 closest distance to " CG  MET A 105 " =    0.938
peak=   -3.181 closest distance to " CD1 LEU A 228 " =    2.264
peak=   -3.176 closest distance to " O   TYR A 247 " =    2.833
peak=   -3.176 closest distance to " CB  ASP A 171 " =    2.315
peak=   -3.175 closest distance to " O   HOH Z  68 " =    1.307
peak=   -3.174 closest distance to " O   HOH Z  10 " =    1.430
peak=   -3.166 closest distance to " CD1 PHE A  59 " =    2.034
peak=   -3.166 closest distance to " N   ASP A 191 " =    1.077
peak=   -3.164 closest distance to " O   HOH Z  60 " =    1.625
peak=   -3.164 closest distance to " CB  ILE A 263 " =    1.262
peak=   -3.162 closest distance to " NE2 GLN A  88 " =    2.049
peak=   -3.161 closest distance to " CA  ASP A  27 " =    2.461
peak=   -3.158 closest distance to " O   HOH Z 346 " =    1.848
peak=   -3.153 closest distance to " CB  GLN A  55 " =    1.304
peak=   -3.152 closest distance to " O   HOH Z 265 " =    1.602
peak=   -3.151 closest distance to " O   HOH Z 149 " =    2.144
peak=   -3.149 closest distance to " O   SER A 276 " =    1.704
peak=   -3.139 closest distance to " OD1 ASN A  39 " =    1.261
peak=   -3.139 closest distance to " CZ  PHE A 155 " =    1.037
peak=   -3.137 closest distance to " O   ALA A  10 " =    1.705
peak=   -3.137 closest distance to " O   HOH Z 390 " =    2.286
peak=   -3.133 closest distance to " CB  SER A 210 " =    0.989
peak=   -3.129 closest distance to " C   LYS A  76 " =    1.432
peak=   -3.123 closest distance to " O   HOH Z 423 " =    2.157
peak=   -3.122 closest distance to " O   SER A 135 " =    1.439
peak=   -3.118 closest distance to " O   ARG A 145 " =    1.654
peak=   -3.116 closest distance to " O   HOH Z 392 " =    1.955
peak=   -3.113 closest distance to " N   HIS A 115 " =    2.219
peak=   -3.112 closest distance to " CD2 PHE A 225 " =    1.076
peak=   -3.104 closest distance to " NH2 ARG A  36 " =    2.478
peak=   -3.104 closest distance to " CZ  TYR A 169 " =    1.751
peak=   -3.103 closest distance to " O   HOH Z 389 " =    1.493
peak=   -3.102 closest distance to " C   ASP A 270 " =    0.992
peak=   -3.098 closest distance to " O   ASP A  27 " =    2.078
peak=   -3.096 closest distance to " O   HOH Z 251 " =    5.036
peak=   -3.094 closest distance to " NE2 GLN A 240 " =    1.675
peak=   -3.091 closest distance to " CE1 TYR A 247 " =    2.619
peak=   -3.089 closest distance to " CA  GLY A 133 " =    1.966
peak=   -3.086 closest distance to " O   GLY A  80 " =    2.536
peak=   -3.079 closest distance to " N   LYS A 289 " =    1.560
peak=   -3.076 closest distance to " O   HOH Z 238 " =    1.033
peak=   -3.070 closest distance to " CD2 HIS A 207 " =    2.251
peak=   -3.060 closest distance to " OD2 ASP A  50 " =    2.220
peak=   -3.057 closest distance to " OG  SER A 206 " =    1.714
peak=   -3.052 closest distance to " O   HOH Z 100 " =    1.088
peak=   -3.052 closest distance to " O   HOH Z 166 " =    1.679
peak=   -3.039 closest distance to " O   HOH Z 110 " =    1.434
peak=   -3.001 closest distance to " O   GLY A  80 " =    2.586

================= 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    :  0.4499 0.4356   6.252309e+00   6.222449e+00
   1_bss:  0.4411 0.4252   6.243724e+00   6.209196e+00
   1_xyz:  0.3416 0.3595   6.072545e+00   6.102849e+00
   1_adp:  0.2859 0.3251   5.934306e+00   6.026899e+00
   1_occ:  0.2852 0.3259   5.933596e+00   6.029381e+00
   2_bss:  0.2806 0.3214   5.931793e+00   6.026148e+00
   2_xyz:  0.2005 0.2464   5.631263e+00   5.792808e+00
   2_adp:  0.1814 0.2291   5.548780e+00   5.726213e+00
   2_occ:  0.1813 0.2292   5.548911e+00   5.727100e+00
   3_bss:  0.1797 0.2296   5.547706e+00   5.726385e+00
   3_xyz:  0.1369 0.1827   5.308658e+00   5.523216e+00
   3_adp:  0.1270 0.1738   5.253749e+00   5.483789e+00
   3_occ:  0.1268 0.1739   5.253242e+00   5.483561e+00
   4_bss:  0.1269 0.1744   5.253490e+00   5.482892e+00
   4_xyz:  0.1158 0.1643   5.185953e+00   5.430664e+00
   4_adp:  0.1145 0.1620   5.173669e+00   5.416373e+00
   4_occ:  0.1145 0.1619   5.173219e+00   5.416030e+00
   5_bss:  0.1144 0.1619   5.173230e+00   5.416150e+00
   5_xyz:  0.1181 0.1630   5.193990e+00   5.425005e+00
   5_adp:  0.1181 0.1630   5.193990e+00   5.425005e+00
   5_occ:  0.1181 0.1630   5.193711e+00   5.424606e+00
   5_bss:  0.1181 0.1630   5.193660e+00   5.424588e+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:  0.335  13.734   6.959   7.628  11.898   0.000   0.000   0.000
   1_xyz:  0.335  13.734   6.959   7.628  11.898   0.000   0.000   0.000
   1_adp:  0.335  13.734   6.959   7.628  11.898   0.000   0.000   0.000
   1_occ:  0.335  13.734   6.959   7.628  11.898   0.000   0.000   0.000
   2_bss:  0.324  42.932   3.451   3.887   7.991   0.000   0.000   0.000
   2_xyz:  0.324  42.932   3.451   3.887   7.991   0.000   0.000   0.000
   2_adp:  0.324  42.932   3.451   3.887   7.991   0.000   0.000   0.000
   2_occ:  0.324  42.932   3.451   3.887   7.991   0.000   0.000   0.000
   3_bss:  0.320  53.346   2.368   3.051   5.363   0.000   0.000   0.000
   3_xyz:  0.320  53.346   2.368   3.051   5.363   0.000   0.000   0.000
   3_adp:  0.320  53.346   2.368   3.051   5.363   0.000   0.000   0.000
   3_occ:  0.320  53.346   2.368   3.051   5.363   0.000   0.000   0.000
   4_bss:  0.329  59.467   2.301   2.889   4.722   0.000   0.000   0.000
   4_xyz:  0.329  59.467   2.301   2.889   4.722   0.000   0.000   0.000
   4_adp:  0.329  59.467   2.301   2.889   4.722   0.000   0.000   0.000
   4_occ:  0.329  59.467   2.301   2.889   4.722   0.000   0.000   0.000
   5_bss:  0.331  59.467   2.470   2.962   4.679   0.000   0.000   0.000
   5_xyz:  0.331  59.467   2.470   2.962   4.679   0.000   0.000   0.000
   5_adp:  0.331  59.467   2.470   2.962   4.679   0.000   0.000   0.000
   5_occ:  0.331  59.467   2.470   2.962   4.679   0.000   0.000   0.000
   5_bss:  0.326  59.679  -0.900  -0.408   1.309   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.587 0.5398  0.6074    55682.303
   1_bss:  48.198 0.5434  0.7987    53563.337
   1_xyz:  39.213 0.6516  0.9238    35845.521
   1_adp:  33.961 0.7138  1.0103    28700.171
   1_occ:  34.083 0.7124  1.0071    28846.222
   2_bss:  33.745 0.7162  0.8885    28425.821
   2_xyz:  24.483 0.8167  0.9873    15525.119
   2_adp:  22.143 0.8411  1.0062    13386.191
   2_occ:  22.178 0.8408  1.0060    13408.220
   3_bss:  22.074 0.8419  0.9539    13395.386
   3_xyz:  17.104 0.8885  0.9788     8546.347
   3_adp:  16.139 0.8972  0.9755     7888.374
   3_occ:  16.141 0.8972  0.9753     7891.982
   4_bss:  16.119 0.8974  0.9655     7879.165
   4_xyz:  14.953 0.9073  0.9721     7029.322
   4_adp:  14.598 0.9104  0.9701     6830.532
   4_occ:  14.588 0.9105  0.9702     6824.760
   5_bss:  14.589 0.9105  0.9726     6827.866
   5_xyz:  14.709 0.9098  0.9709     6925.051
   5_adp:  14.709 0.9098  0.9709     6925.051
   5_occ:  14.703 0.9099  0.9710     6917.533
   5_bss:  14.704 0.9098  0.9709     6915.168
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4059e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4059e+01
   1_xyz:   1.602  0.012  0.104 17.926  0.006  4.113   1.2749e-01
   1_adp:   1.602  0.012  0.104 17.926  0.006  4.113   1.2749e-01
   1_occ:   1.602  0.012  0.104 17.926  0.006  4.113   1.2749e-01
   2_bss:   1.602  0.012  0.104 17.926  0.006  4.113   1.2749e-01
   2_xyz:   1.060  0.008  0.076 16.112  0.004  4.127   6.8082e-02
   2_adp:   1.060  0.008  0.076 16.112  0.004  4.127   6.8082e-02
   2_occ:   1.060  0.008  0.076 16.112  0.004  4.127   6.8082e-02
   3_bss:   1.060  0.008  0.076 16.112  0.004  4.127   6.8082e-02
   3_xyz:   1.073  0.008  0.082 15.982  0.004  4.132   6.8550e-02
   3_adp:   1.073  0.008  0.082 15.982  0.004  4.132   6.8550e-02
   3_occ:   1.073  0.008  0.082 15.982  0.004  4.132   6.8550e-02
   4_bss:   1.073  0.008  0.082 15.982  0.004  4.132   6.8550e-02
   4_xyz:   1.111  0.010  0.088 15.698  0.004  4.125   7.5077e-02
   4_adp:   1.111  0.010  0.088 15.698  0.004  4.125   7.5077e-02
   4_occ:   1.111  0.010  0.088 15.698  0.004  4.125   7.5077e-02
   5_bss:   1.111  0.010  0.088 15.698  0.004  4.125   7.5077e-02
   5_xyz:   0.928  0.006  0.075 15.302  0.003  4.124   5.4670e-02
   5_adp:   0.928  0.006  0.075 15.302  0.003  4.124   5.4670e-02
   5_occ:   0.928  0.006  0.075 15.302  0.003  4.124   5.4670e-02
   5_bss:   0.928  0.006  0.075 15.302  0.003  4.124   5.4670e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0083e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0083e+00
   1_xyz:  13.166  0.154  0.406 87.927  0.039  2.179   9.6267e-02
   1_adp:  13.166  0.154  0.406 87.927  0.039  2.179   9.6267e-02
   1_occ:  13.166  0.154  0.406 87.927  0.039  2.179   9.6267e-02
   2_bss:  13.166  0.154  0.406 87.927  0.039  2.179   9.6267e-02
   2_xyz:   6.906  0.058  0.282 87.507  0.031  2.335   5.2619e-02
   2_adp:   6.906  0.058  0.282 87.507  0.031  2.335   5.2619e-02
   2_occ:   6.906  0.058  0.282 87.507  0.031  2.335   5.2619e-02
   3_bss:   6.906  0.058  0.282 87.507  0.031  2.335   5.2619e-02
   3_xyz:   8.806  0.052  0.384 84.279  0.038  2.297   4.4562e-02
   3_adp:   8.806  0.052  0.384 84.279  0.038  2.297   4.4562e-02
   3_occ:   8.806  0.052  0.384 84.279  0.038  2.297   4.4562e-02
   4_bss:   8.806  0.052  0.384 84.279  0.038  2.297   4.4562e-02
   4_xyz:   7.115  0.055  0.510 82.470  0.041  2.331   5.6926e-02
   4_adp:   7.115  0.055  0.510 82.470  0.041  2.331   5.6926e-02
   4_occ:   7.115  0.055  0.510 82.470  0.041  2.331   5.6926e-02
   5_bss:   7.115  0.055  0.510 82.470  0.041  2.331   5.6926e-02
   5_xyz:   6.426  0.045  0.337 81.921  0.037  2.384   3.1753e-02
   5_adp:   6.426  0.045  0.337 81.921  0.037  2.384   3.1753e-02
   5_occ:   6.426  0.045  0.337 81.921  0.037  2.384   3.1753e-02
   5_bss:   6.426  0.045  0.337 81.921  0.037  2.384   3.1753e-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:  65.28   0.00  11.53  53.87   0.00   8.72  65.28   0.00  26.82
   1_occ:  65.28   0.00  11.53  53.87   0.00   8.72  65.28   0.00  26.82
   2_bss:  65.28   0.00  11.53  53.87   0.00   8.72  65.28   0.00  26.82
   2_xyz:  65.28   0.00  11.53  53.87   0.00   8.72  65.28   0.00  26.82
   2_adp:  61.76   0.00  11.65  58.66   0.00   7.98  61.76   0.00  31.61
   2_occ:  61.76   0.00  11.65  58.66   0.00   7.98  61.76   0.00  31.61
   3_bss:  61.76   0.00  11.65  58.66   0.00   7.98  61.76   0.00  31.61
   3_xyz:  61.76   0.00  11.65  58.66   0.00   7.98  61.76   0.00  31.61
   3_adp:  78.85   0.00  12.46  75.62   0.00   7.99  78.85   0.58  36.80
   3_occ:  78.85   0.00  12.46  75.62   0.00   7.99  78.85   0.58  36.80
   4_bss:  78.85   0.00  12.46  75.62   0.00   7.99  78.85   0.58  36.80
   4_xyz:  78.85   0.00  12.46  75.62   0.00   7.99  78.85   0.58  36.80
   4_adp:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   4_occ:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   5_bss:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   5_xyz:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   5_adp:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   5_occ:  81.67   0.00  12.11  78.48   0.00   7.79  81.67   0.84  35.60
   5_bss:  85.04   3.37  15.48  81.85   3.37  11.16  85.04   4.21  38.97
------------------------------------------------------------------------
 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:    1.251    0.020    0.408
   1_adp:    1.251    0.020    0.408
   1_occ:    1.251    0.020    0.408
   2_bss:    1.251    0.020    0.408
   2_xyz:    1.744    0.028    0.530
   2_adp:    1.744    0.028    0.530
   2_occ:    1.744    0.028    0.530
   3_bss:    1.744    0.028    0.530
   3_xyz:    1.741    0.058    0.588
   3_adp:    1.741    0.058    0.588
   3_occ:    1.741    0.058    0.588
   4_bss:    1.741    0.058    0.588
   4_xyz:    1.844    0.026    0.608
   4_adp:    1.844    0.026    0.608
   4_occ:    1.844    0.026    0.608
   5_bss:    1.844    0.026    0.608
   5_xyz:    1.861    0.037    0.613
   5_adp:    1.861    0.037    0.613
   5_occ:    1.861    0.037    0.613
   5_bss:    1.861    0.037    0.613
------------------------------------------------------------------------

CPU time actual refinement: 317.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/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_548/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_548/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.17 
  Macro-tasks:
    bulk solvent and scale       = 41.26  
    individual site refinement   = 126.46 
    weights calculation          = 31.39  
    collect and process          = 6.44   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 205.64 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 95.38  
    alpha_beta                      = 7.98   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 106.01 
    fmodel                         = 7.05   
    r_factors                      = 0.21   
    phase_errors                   = 10.95  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 230.66 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.496 micro seconds
Total CPU time: 5.51 minutes
from_scatterers_fft:    643 calls, 95.03 s
gradients_fft:          589 calls, 92.72 s

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

# Date 2008-01-16 Time 01:50:42 PST -0800 (1200477042.56 s)
Start R-work = 0.4499, R-free = 0.4356 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.4411, R-free = 0.4252
Final R-work = 0.1181, R-free = 0.1630