# Date 2008-01-16 Time 00:52:17 PST -0800 (1200473537.37 s)
#phil __OFF__

Command line arguments: "../199.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6575
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 199

-------------------------------------------------------------------------------
  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: (68.845, 47.3993, 84.6622, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (68.845, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8023 1.96052
Completeness in resolution range: 0.957991
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 =  14.8023
                             d_min =   1.9605

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: (68.845, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8023 1.96052
Completeness in resolution range: 0.957991
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: 14.8027 -  4.1948 [2151/2180]  1935   216  10.0%
  bin  2:  4.1948 -  3.3421 [2053/2076]  1848   205  10.0%
  bin  3:  3.3421 -  2.9233 [2035/2060]  1830   205  10.1%
  bin  4:  2.9233 -  2.6577 [2013/2029]  1812   201  10.0%
  bin  5:  2.6577 -  2.4682 [1997/2035]  1795   202  10.1%
  bin  6:  2.4682 -  2.3233 [1997/2030]  1804   193   9.7%
  bin  7:  2.3233 -  2.2073 [1967/2004]  1770   197  10.0%
  bin  8:  2.2073 -  2.1115 [1993/2035]  1791   202  10.1%
  bin  9:  2.1115 -  2.0304 [1956/1995]  1763   193   9.9%
  bin 10:  2.0304 -  1.9605 [1427/2004]  1282   145  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.32 -     2.04: 21
        2.04 -     2.75: 380
        2.75 -     3.47: 4702
        3.47 -     4.18: 9510
        4.18 -     4.90: 14163
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.322 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.381 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.484 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.539 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.705 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28771 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_199/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/model_refine_001.geo

CPU time processing inputs: 10.16


============================ 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 = 68.845 47.3993 84.6622 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: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4925   r_free= 0.4839   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.289918                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6785 0.99   1391  158 0.4042 0.3971       6.601       6.639|
|  2:  4.6785 -  3.7331 0.99   1343  144 0.4158 0.4043      6.7983      6.8105|
|  3:  3.7331 -  3.2670 0.99   1316  152 0.4481 0.4304      6.6918      6.7488|
|  4:  3.2670 -  2.9709 0.99   1313  136 0.4690 0.4693       6.523      6.5078|
|  5:  2.9709 -  2.7594 0.98   1287  147 0.5197 0.5291      6.3953      6.4027|
|  6:  2.7594 -  2.5977 0.99   1292  142 0.5138 0.5395      6.2848      6.2181|
|  7:  2.5977 -  2.4682 0.99   1278  150 0.5393 0.4777      6.2693      6.1713|
|  8:  2.4682 -  2.3612 0.99   1300  134 0.5321 0.5204      6.1878      6.1675|
|  9:  2.3612 -  2.2706 0.99   1276  148 0.5460 0.5536      6.1257      6.1809|
| 10:  2.2706 -  2.1925 0.98   1264  141 0.5386 0.5329       6.122       6.101|
| 11:  2.1925 -  2.1242 0.98   1254  141 0.5349 0.5723      6.0452      6.0826|
| 12:  2.1242 -  2.0636 1.00   1286  140 0.5442 0.5426      5.9815      6.0019|
| 13:  2.0636 -  2.0094 0.96   1253  132 0.5591 0.5356      5.8925      5.9071|
| 14:  2.0094 -  1.9605 0.61    777   94 0.5471 0.4608      5.9078       5.699|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6785  1391   158  0.66  38.10   0.80     0.68      82996.41|
|  2:  4.6785 -  3.7331  1343   144  0.66  38.48   0.88     0.73     120006.99|
|  3:  3.7331 -  3.2670  1316   152  0.56  46.84   0.85     0.69     127932.67|
|  4:  3.2670 -  2.9709  1313   136  0.48  53.74   0.81     0.59     109823.83|
|  5:  2.9709 -  2.7594  1287   147  0.38  61.06   0.73     0.47      90994.67|
|  6:  2.7594 -  2.5977  1292   142  0.36  62.92   0.73     0.42      74185.78|
|  7:  2.5977 -  2.4682  1278   150  0.36  63.02   0.72     0.41      67067.97|
|  8:  2.4682 -  2.3612  1300   134  0.36  62.68   0.73     0.43      58546.71|
|  9:  2.3612 -  2.2706  1276   148  0.31  66.64   0.72     0.39      57040.91|
| 10:  2.2706 -  2.1925  1264   141  0.27  70.00   0.77     0.32      54226.91|
| 11:  2.1925 -  2.1242  1254   141  0.18  76.58   0.75     0.22      54059.97|
| 12:  2.1242 -  2.0636  1286   140  0.18  76.55   0.74     0.23      50502.40|
| 13:  2.0636 -  2.0094  1253   132  0.25  71.31   0.73     0.32      39390.17|
| 14:  2.0094 -  1.9605   777    94  0.47  54.70   0.73     0.52      24099.03|
|alpha:            min =        0.22 max =            0.73 mean =         0.46|
|beta:             min =    24099.03 max =       127932.67 mean =     74084.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.05|
|phase err.(test): min =        0.00 max =           89.75 mean =        60.29|
|-----------------------------------------------------------------------------|

============================== 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 = 18.177936             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.613   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.376257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.684   (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 |  0.870 -  1.273:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.273 -  1.676:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.676 -  2.079:       69 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.079 -  2.482:      414 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.482 -  2.885:     1186 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.885 -  3.288:     2387 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.288 -  3.691:     3953 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.691 -  4.094:     5317 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.094 -  4.497:     7024 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.497 -  4.900:     8447 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.067 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.870 |       2.737 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    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: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4968   r_free= 0.4921   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.290381                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4837   r_free= 0.4759   ksol= 0.37   Bsol= 11.70   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.53,8.76,8.68,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.285784                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.650505             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.029   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.433183              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.353   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4837      final r-factor (work) = 0.4044          |
| start r-factor (free) = 0.4759      final r-factor (free) = 0.4270          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.2901 = 15.65 * 0.50 * 6.2902 + 1.00 * 53.0674                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.7407 = 15.65 * 0.50 * 6.2068 + 1.00 * 0.1711                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4044      final r-factor (work) = 0.3615          |
| start r-factor (free) = 0.4270      final r-factor (free) = 0.4143          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9098 = 1.43 * 1.00 * 6.2068 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8100 = 1.43 * 1.00 * 6.1335 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.06   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    80.06   13.93    None  None   None       |
|    Sol.    : 438    0      0.00    80.06   26.73    None  None   None       |
|    Mac.    : 2385   0      0.00    69.06   11.58    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 -   8.006: 1134   |   5:    40.032 -  48.038:   74        |
|      1:     8.006 -  16.013:  762   |   6:    48.038 -  56.045:   33        |
|      2:    16.013 -  24.019:  406   |   7:    56.045 -  64.051:   17        |
|      3:    24.019 -  32.026:  243   |   8:    64.051 -  72.057:    9        |
|      4:    32.026 -  40.032:  137   |   9:    72.057 -  80.064:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3615 r_free = 0.4143             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3605 r_free = 0.4144             target_work(ml) = 6.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3605   r_free= 0.4144   ksol= 0.37   Bsol= 11.70   scale= 1.107   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.53,8.76,8.68,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.112551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3585   r_free= 0.4092   ksol= 0.32   Bsol= 20.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.35,5.39,6.00,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.112282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.706105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.270   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.593077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.996  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3585      final r-factor (work) = 0.2760          |
| start r-factor (free) = 0.4092      final r-factor (free) = 0.3294          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7187 = 6.71 * 0.50 * 6.1280 + 1.00 * 0.1711                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2436 = 6.71 * 0.50 * 6.0121 + 1.00 * 0.0848                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2760      final r-factor (work) = 0.2528          |
| start r-factor (free) = 0.3294      final r-factor (free) = 0.3076          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5860 = 0.59 * 1.00 * 6.0121 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4910 = 0.59 * 1.00 * 5.8638 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.92   13.85    None  None   None       |
|    all(noH): 2823   0      0.00    90.92   13.85    None  None   None       |
|    Sol.    : 438    0      2.28    90.92   32.16    None  None   None       |
|    Mac.    : 2385   0      0.00    75.07   10.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.093: 1400   |   5:    45.463 -  54.555:   62        |
|      1:     9.093 -  18.185:  713   |   6:    54.555 -  63.648:   32        |
|      2:    18.185 -  27.278:  295   |   7:    63.648 -  72.740:   13        |
|      3:    27.278 -  36.370:  180   |   8:    72.740 -  81.832:    5        |
|      4:    36.370 -  45.463:  122   |   9:    81.832 -  90.925:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2528 r_free = 0.3076             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2526 r_free = 0.3074             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2526   r_free= 0.3074   ksol= 0.32   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.35,5.39,6.00,0.00,0.00,0.00); trace/3= 5.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.831567                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2494   r_free= 0.3041   ksol= 0.33   Bsol= 34.84   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,3.27,3.55,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.827848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.441923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.815   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.296  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2494      final r-factor (work) = 0.1685          |
| start r-factor (free) = 0.3041      final r-factor (free) = 0.2200          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9827 = 6.44 * 0.50 * 5.8672 + 1.00 * 0.0848                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3850 = 6.44 * 0.50 * 5.6835 + 1.00 * 0.0787                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1685      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2200      final r-factor (free) = 0.1963          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3663 = 0.24 * 1.00 * 5.6835 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3071 = 0.24 * 1.00 * 5.4473 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.65   13.46    None  None   None       |
|    all(noH): 2823   0      0.00    89.65   13.46    None  None   None       |
|    Sol.    : 438    0      3.14    89.65   34.12    None  None   None       |
|    Mac.    : 2385   0      0.00    75.43   9.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.965: 1539   |   5:    44.825 -  53.790:   79        |
|      1:     8.965 -  17.930:  654   |   6:    53.790 -  62.754:   32        |
|      2:    17.930 -  26.895:  214   |   7:    62.754 -  71.719:   13        |
|      3:    26.895 -  35.860:  166   |   8:    71.719 -  80.684:    4        |
|      4:    35.860 -  44.825:  121   |   9:    80.684 -  89.649:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1507 r_free = 0.1963             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1501 r_free = 0.1961             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1501   r_free= 0.1961   ksol= 0.33   Bsol= 34.84   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,3.27,3.55,0.00,0.00,0.00); trace/3= 2.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.378924                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1492   r_free= 0.1939   ksol= 0.33   Bsol= 34.84   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,2.05,2.16,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.376145                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.790087              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.797  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.448674              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.378   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1492      final r-factor (work) = 0.1332          |
| start r-factor (free) = 0.1939      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9622 = 1.79 * 0.50 * 5.4563 + 1.00 * 0.0786                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8255 = 1.79 * 0.50 * 5.3286 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1332      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4011 = 0.45 * 1.00 * 5.3286 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3735 = 0.45 * 1.00 * 5.2624 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.23   13.53    None  None   None       |
|    all(noH): 2823   0      0.00    89.23   13.53    None  None   None       |
|    Sol.    : 438    0      2.70    89.23   35.16    None  None   None       |
|    Mac.    : 2385   0      0.00    76.45   9.55     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 -   8.923: 1522   |   5:    44.614 -  53.537:   93        |
|      1:     8.923 -  17.846:  673   |   6:    53.537 -  62.460:   32        |
|      2:    17.846 -  26.769:  207   |   7:    62.460 -  71.383:   18        |
|      3:    26.769 -  35.691:  150   |   8:    71.383 -  80.306:    3        |
|      4:    35.691 -  44.614:  124   |   9:    80.306 -  89.229:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1734             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1287 r_free = 0.1734             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1734   ksol= 0.33   Bsol= 34.84   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.78,2.05,2.16,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.257265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1734   ksol= 0.32   Bsol= 34.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,1.90,1.98,0.00,0.00,0.00); trace/3= 1.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.256820                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.310320              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.147  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659902              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.749   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1287      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7661 = 3.31 * 0.50 * 5.2623 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7055 = 3.31 * 0.50 * 5.2147 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4532 = 0.66 * 1.00 * 5.2147 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4244 = 0.66 * 1.00 * 5.1732 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.82   13.45    None  None   None       |
|    all(noH): 2823   0      0.00    85.82   13.45    None  None   None       |
|    Sol.    : 438    0      2.07    85.82   36.26    None  None   None       |
|    Mac.    : 2385   0      0.00    81.18   9.27     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 -   8.582: 1517   |   5:    42.911 -  51.493:  102        |
|      1:     8.582 -  17.164:  703   |   6:    51.493 -  60.075:   61        |
|      2:    17.164 -  25.747:  177   |   7:    60.075 -  68.657:   23        |
|      3:    25.747 -  34.329:  116   |   8:    68.657 -  77.239:    5        |
|      4:    34.329 -  42.911:  115   |   9:    77.239 -  85.822:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1619             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1619             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1619   ksol= 0.32   Bsol= 34.84   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,1.90,1.98,0.00,0.00,0.00); trace/3= 1.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6785 0.99   1391  158 0.1008 0.1273      5.3988      5.5533|
|  2:  4.6785 -  3.7331 0.99   1343  144 0.0857 0.1127      5.4408        5.66|
|  3:  3.7331 -  3.2670 0.99   1316  152 0.1040 0.1562      5.4735      5.8587|
|  4:  3.2670 -  2.9709 0.99   1313  136 0.1229 0.1569      5.4579      5.6525|
|  5:  2.9709 -  2.7594 0.98   1287  147 0.1316 0.1602      5.3387       5.468|
|  6:  2.7594 -  2.5977 0.99   1292  142 0.1289 0.2100      5.2501      5.5506|
|  7:  2.5977 -  2.4682 0.99   1278  150 0.1176 0.1640      5.1528      5.3817|
|  8:  2.4682 -  2.3612 0.99   1300  134 0.1162 0.1767      5.0899      5.3493|
|  9:  2.3612 -  2.2706 0.99   1276  148 0.1187 0.1828      5.0361      5.3382|
| 10:  2.2706 -  2.1925 0.98   1264  141 0.1161 0.1860        5.01      5.2359|
| 11:  2.1925 -  2.1242 0.98   1254  141 0.1177 0.1840      4.9562      5.2905|
| 12:  2.1242 -  2.0636 1.00   1286  140 0.1130 0.1889      4.8844      5.1929|
| 13:  2.0636 -  2.0094 0.96   1253  132 0.1191 0.1706      4.8103       5.037|
| 14:  2.0094 -  1.9605 0.61    777   94 0.1099 0.1763      4.7184      4.9398|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6785  1391   158  0.94   9.22   0.98     0.97       7546.32|
|  2:  4.6785 -  3.7331  1343   144  0.95   8.32   1.03     1.01       9407.43|
|  3:  3.7331 -  3.2670  1316   152  0.93  11.49   1.04     1.03      10779.85|
|  4:  3.2670 -  2.9709  1313   136  0.92  14.00   1.02     1.01      10520.05|
|  5:  2.9709 -  2.7594  1287   147  0.90  16.31   1.00     0.96       8660.99|
|  6:  2.7594 -  2.5977  1292   142  0.89  17.05   0.98     0.95       7703.82|
|  7:  2.5977 -  2.4682  1278   150  0.90  15.63   0.99     0.95       6205.00|
|  8:  2.4682 -  2.3612  1300   134  0.91  15.66   1.01     0.98       5765.28|
|  9:  2.3612 -  2.2706  1276   148  0.90  16.22   1.01     0.99       5192.38|
| 10:  2.2706 -  2.1925  1264   141  0.90  16.47   1.00     0.97       5022.34|
| 11:  2.1925 -  2.1242  1254   141  0.90  16.43   1.01     0.97       4525.86|
| 12:  2.1242 -  2.0636  1286   140  0.91  15.75   1.01     0.99       4048.15|
| 13:  2.0636 -  2.0094  1253   132  0.89  17.04   1.01     1.01       3522.58|
| 14:  2.0094 -  1.9605   777    94  0.91  15.33   0.99     0.96       2802.73|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2802.73 max =        10779.85 mean =      6698.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.55|
|phase err.(test): min =        0.00 max =           88.78 mean =        14.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1630   ksol= 0.32   Bsol= 37.05   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.35,0.48,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1630   ksol= 0.32   Bsol= 37.05   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.35,0.48,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163193                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6785 0.99   1391  158 0.0986 0.1333      5.4018      5.5845|
|  2:  4.6785 -  3.7331 0.99   1343  144 0.0871 0.1159      5.4621      5.6843|
|  3:  3.7331 -  3.2670 0.99   1316  152 0.1049 0.1557      5.4826      5.8524|
|  4:  3.2670 -  2.9709 0.99   1313  136 0.1233 0.1559      5.4612      5.6475|
|  5:  2.9709 -  2.7594 0.98   1287  147 0.1318 0.1615      5.3395      5.4742|
|  6:  2.7594 -  2.5977 0.99   1292  142 0.1287 0.2101      5.2502      5.5442|
|  7:  2.5977 -  2.4682 0.99   1278  150 0.1170 0.1648      5.1514      5.3857|
|  8:  2.4682 -  2.3612 0.99   1300  134 0.1158 0.1775       5.089      5.3496|
|  9:  2.3612 -  2.2706 0.99   1276  148 0.1185 0.1822       5.034       5.336|
| 10:  2.2706 -  2.1925 0.98   1264  141 0.1155 0.1859      5.0077      5.2334|
| 11:  2.1925 -  2.1242 0.98   1254  141 0.1174 0.1842       4.955      5.2898|
| 12:  2.1242 -  2.0636 1.00   1286  140 0.1126 0.1894      4.8835      5.1962|
| 13:  2.0636 -  2.0094 0.96   1253  132 0.1190 0.1701      4.8093      5.0333|
| 14:  2.0094 -  1.9605 0.61    777   94 0.1101 0.1751      4.7164      4.9373|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6785  1391   158  0.94   9.69   0.98     0.96       8022.33|
|  2:  4.6785 -  3.7331  1343   144  0.95   8.64   1.03     1.01       9894.99|
|  3:  3.7331 -  3.2670  1316   152  0.93  11.70   1.04     1.03      11060.99|
|  4:  3.2670 -  2.9709  1313   136  0.92  13.98   1.02     1.01      10522.71|
|  5:  2.9709 -  2.7594  1287   147  0.90  16.30   1.00     0.97       8645.61|
|  6:  2.7594 -  2.5977  1292   142  0.89  17.11   0.99     0.95       7726.02|
|  7:  2.5977 -  2.4682  1278   150  0.90  15.62   0.99     0.95       6205.57|
|  8:  2.4682 -  2.3612  1300   134  0.91  15.69   1.01     0.98       5777.55|
|  9:  2.3612 -  2.2706  1276   148  0.90  16.23   1.01     0.99       5187.50|
| 10:  2.2706 -  2.1925  1264   141  0.90  16.45   1.01     0.98       5005.33|
| 11:  2.1925 -  2.1242  1254   141  0.90  16.44   1.01     0.97       4521.03|
| 12:  2.1242 -  2.0636  1286   140  0.91  15.74   1.01     0.99       4044.64|
| 13:  2.0636 -  2.0094  1253   132  0.89  17.01   1.01     1.01       3513.30|
| 14:  2.0094 -  1.9605   777    94  0.91  15.25   1.00     0.96       2780.53|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2780.53 max =        11060.99 mean =      6792.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.62|
|phase err.(test): min =        0.00 max =           88.80 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.490)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    87.38   15.01    None  None   None       |
|    all(noH): 2823   0      1.56    87.38   15.01    None  None   None       |
|    Sol.    : 438    0      3.62    87.38   37.82    None  None   None       |
|    Mac.    : 2385   0      1.56    82.74   10.82    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:     1.559 -  10.141: 1517   |   5:    44.469 -  53.052:  102        |
|      1:    10.141 -  18.723:  703   |   6:    53.052 -  61.634:   61        |
|      2:    18.723 -  27.305:  177   |   7:    61.634 -  70.216:   23        |
|      3:    27.305 -  35.887:  116   |   8:    70.216 -  78.798:    5        |
|      4:    35.887 -  44.469:  115   |   9:    78.798 -  87.380:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.605 - 5.941
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 318
   mapped sites are within: 0.765 - 5.941

peak=   10.726 closest distance to " CB  VAL A 230 " =    1.405
peak=    7.466 closest distance to " O   HOH Z 120 " =    1.248
peak=    7.159 closest distance to " CG2 VAL A 296 " =    1.152
peak=    6.146 closest distance to " NH2 ARG A  56 " =    2.212
peak=    5.830 closest distance to " O   HOH Z 278 " =    1.515
peak=    5.780 closest distance to " CB  VAL A 296 " =    1.042
peak=    5.756 closest distance to " CG  LEU A   5 " =    1.215
peak=    5.685 closest distance to " O   HOH Z 124 " =    1.561
peak=    5.538 closest distance to " O   HOH Z 193 " =    1.836
peak=    5.194 closest distance to " O   HOH Z 272 " =    1.890
peak=    5.115 closest distance to " CB  ASN A 187 " =    2.051
peak=    5.012 closest distance to " O   HOH Z 403 " =    1.927
peak=    5.012 closest distance to " O   SER A  87 " =    2.266
peak=    4.979 closest distance to " CD2 LEU A   5 " =    1.169
peak=    4.826 closest distance to " O   HOH Z 406 " =    1.288
peak=    4.815 closest distance to " O   HOH Z  85 " =    1.752
peak=    4.814 closest distance to " O   HOH Z 236 " =    1.522
peak=    4.789 closest distance to " O   HOH Z 402 " =    1.491
peak=    4.773 closest distance to " O   HOH Z 411 " =    3.631
peak=    4.744 closest distance to " CG  LEU A 228 " =    1.163
peak=    4.716 closest distance to " CD1AILE A 234 " =    0.989
peak=    4.710 closest distance to " O   HOH Z  80 " =    1.744
peak=    4.705 closest distance to " O   HOH Z 279 " =    1.122
peak=    4.693 closest distance to " NE2 GLN A  11 " =    1.015
peak=    4.682 closest distance to " O   HOH Z 209 " =    2.378
peak=    4.619 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.617 closest distance to " CB  ARG A 275 " =    0.964
peak=    4.560 closest distance to " CG  PRO A  54 " =    1.166
peak=    4.544 closest distance to " C   PRO A 198 " =    1.446
peak=    4.538 closest distance to " O   HOH Z  48 " =    1.891
peak=    4.499 closest distance to " O   HOH Z 142 " =    1.616
peak=    4.494 closest distance to " CB  GLN A 223 " =    1.440
peak=    4.451 closest distance to " O   HOH Z 102 " =    1.357
peak=    4.426 closest distance to " O   HOH Z 234 " =    3.647
peak=    4.426 closest distance to " O   HOH Z  47 " =    1.719
peak=    4.425 closest distance to " O   HOH Z 232 " =    2.177
peak=    4.412 closest distance to " CB  SER A  63 " =    1.053
peak=    4.409 closest distance to " CG  PRO A 213 " =    1.154
peak=    4.375 closest distance to " O   HOH Z 414 " =    1.646
peak=    4.366 closest distance to " O   HOH Z 247 " =    1.240
peak=    4.346 closest distance to " O   HOH Z 132 " =    1.134
peak=    4.341 closest distance to " O   HOH Z 155 " =    1.722
peak=    4.339 closest distance to " CB  SER A   3 " =    1.283
peak=    4.329 closest distance to " O   HOH Z 345 " =    2.524
peak=    4.324 closest distance to " CB  VAL A 230 " =    1.164
peak=    4.304 closest distance to " O   HOH Z 368 " =    2.042
peak=    4.298 closest distance to " O   HOH Z 249 " =    1.077
peak=    4.265 closest distance to " O   HOH Z 327 " =    1.835
peak=    4.262 closest distance to " O   HOH Z  54 " =    1.555
peak=    4.256 closest distance to " O   HOH Z 346 " =    1.494
peak=    4.230 closest distance to " CG  ARG A  66 " =    1.119
peak=    4.216 closest distance to " O   HOH Z  97 " =    1.852
peak=    4.199 closest distance to " O   HOH Z 423 " =    1.874
peak=    4.199 closest distance to " CA  ALA A  21 " =    1.199
peak=    4.195 closest distance to " OE1 GLU A   2 " =    2.070
peak=    4.191 closest distance to " CD  ARG A 269 " =    1.044
peak=    4.188 closest distance to " O   HOH Z  59 " =    2.177
peak=    4.180 closest distance to " O   HOH Z 134 " =    1.665
peak=    4.158 closest distance to " O   HOH Z 118 " =    1.613
peak=    4.150 closest distance to " O   HOH Z  68 " =    2.633
peak=    4.149 closest distance to " O   HOH Z 316 " =    2.585
peak=    4.136 closest distance to " CA  TYR A  30 " =    1.011
peak=    4.136 closest distance to " O   HOH Z 154 " =    1.578
peak=    4.131 closest distance to " O   HOH Z 389 " =    1.780
peak=    4.126 closest distance to " O   HOH Z 357 " =    1.929
peak=    4.102 closest distance to " O   HOH Z 394 " =    1.487
peak=    4.098 closest distance to " O   HOH Z 303 " =    2.141
peak=    4.097 closest distance to " O   HOH Z 156 " =    3.219
peak=    4.089 closest distance to " CE  LYS A 119 " =    1.027
peak=    4.079 closest distance to " CG1 ILE A  33 " =    1.258
peak=    4.075 closest distance to " O   HOH Z 120 " =    1.938
peak=    4.065 closest distance to " CB  SER A  26 " =    1.644
peak=    4.057 closest distance to " CD2 LEU A 228 " =    1.239
peak=    4.035 closest distance to " NZ  LYS A 117 " =    3.092
peak=    4.034 closest distance to " O   HOH Z  63 " =    2.194
peak=    4.027 closest distance to " O   HOH Z 128 " =    1.798
peak=    4.016 closest distance to " O   HOH Z  78 " =    1.608
peak=    4.016 closest distance to " CD2 TRP A 179 " =    1.416
peak=    4.011 closest distance to " O   HOH Z  67 " =    1.778
peak=    4.008 closest distance to " O   HOH Z  40 " =    1.630
peak=    4.005 closest distance to " O   HOH Z 366 " =    2.879
peak=    4.000 closest distance to " CG1BVAL A  72 " =    1.608
peak=    3.997 closest distance to " O   HOH Z 345 " =    1.783
peak=    3.976 closest distance to " O   HOH Z 245 " =    1.442
peak=    3.972 closest distance to " O   HOH Z 203 " =    1.639
peak=    3.960 closest distance to " O   HOH Z 248 " =    1.653
peak=    3.946 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.932 closest distance to " CB  TRP A 179 " =    1.160
peak=    3.926 closest distance to " O   HOH Z 427 " =    2.445
peak=    3.909 closest distance to " O   HOH Z 426 " =    1.433
peak=    3.883 closest distance to " CB  GLU A 128 " =    1.130
peak=    3.883 closest distance to " O   HOH Z 214 " =    2.475
peak=    3.877 closest distance to " O   HOH Z 191 " =    1.358
peak=    3.875 closest distance to " CG AARG A 275 " =    1.073
peak=    3.845 closest distance to " O   HOH Z 192 " =    1.727
peak=    3.835 closest distance to " CB  VAL A 265 " =    1.250
peak=    3.832 closest distance to " O   HOH Z  55 " =    2.407
peak=    3.810 closest distance to " CB  VAL A 202 " =    1.592
peak=    3.806 closest distance to " CA  LYS A 117 " =    1.340
peak=    3.796 closest distance to " O   HOH Z 250 " =    1.347
peak=    3.795 closest distance to " O   HOH Z 298 " =    1.900
peak=    3.785 closest distance to " O   HOH Z 408 " =    1.686
peak=    3.782 closest distance to " O   HOH Z  15 " =    2.136
peak=    3.769 closest distance to " O   HOH Z  97 " =    2.421
peak=    3.739 closest distance to " O   HOH Z 227 " =    1.514
peak=    3.738 closest distance to " CG2 THR A 221 " =    1.195
peak=    3.736 closest distance to " CB  GLU A 152 " =    1.047
peak=    3.735 closest distance to " O   HOH Z 273 " =    2.715
peak=    3.730 closest distance to " CB  ALA A   9 " =    1.598
peak=    3.729 closest distance to " NH2BARG A 145 " =    2.396
peak=    3.728 closest distance to " O   HOH Z 284 " =    2.873
peak=    3.727 closest distance to " CB  GLU A 277 " =    3.515
peak=    3.721 closest distance to " O   HOH Z 263 " =    1.568
peak=    3.721 closest distance to " CG  GLN A  77 " =    2.197
peak=    3.713 closest distance to " O   HOH Z 227 " =    1.704
peak=    3.699 closest distance to " CD BLYS A 290 " =    1.121
peak=    3.690 closest distance to " CB AVAL A  41 " =    1.086
peak=    3.689 closest distance to " O   HOH Z 322 " =    2.046
peak=    3.686 closest distance to " O   HOH Z 253 " =    1.875
peak=    3.678 closest distance to " O   HOH Z 420 " =    2.159
peak=    3.672 closest distance to " O   HOH Z   4 " =    1.506
peak=    3.664 closest distance to " O   HOH Z 118 " =    1.543
peak=    3.658 closest distance to " O   HOH Z 197 " =    2.482
peak=    3.658 closest distance to " O   HOH Z 194 " =    2.189
peak=    3.656 closest distance to " CB  ARG A  79 " =    1.577
peak=    3.656 closest distance to " O   HOH Z 137 " =    1.215
peak=    3.655 closest distance to " O   HOH Z 344 " =    1.691
peak=    3.649 closest distance to " OG1 THR A 294 " =    2.317
peak=    3.647 closest distance to " O   HOH Z 326 " =    1.473
peak=    3.643 closest distance to " O   HOH Z 291 " =    1.659
peak=    3.634 closest distance to " CA  ASN A 176 " =    0.987
peak=    3.624 closest distance to " O   HOH Z 417 " =    3.269
peak=    3.623 closest distance to " OG BSER A 210 " =    1.355
peak=    3.621 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.615 closest distance to " O   HOH Z 130 " =    2.740
peak=    3.613 closest distance to " O   HOH Z 189 " =    2.324
peak=    3.610 closest distance to " O   HOH Z 188 " =    0.966
peak=    3.607 closest distance to " O   HOH Z 406 " =    1.385
peak=    3.602 closest distance to " O   HOH Z 283 " =    1.701
peak=    3.601 closest distance to " O   HOH Z 199 " =    1.005
peak=    3.601 closest distance to " O   HOH Z  48 " =    2.370
peak=    3.595 closest distance to " N   ASN A  39 " =    1.240
peak=    3.583 closest distance to " O   HOH Z 255 " =    1.687
peak=    3.581 closest distance to " O   HOH Z 422 " =    2.603
peak=    3.575 closest distance to " O   HOH Z 421 " =    1.681
peak=    3.572 closest distance to " O   HOH Z 193 " =    2.127
peak=    3.571 closest distance to " CG2AVAL A 121 " =    2.160
peak=    3.565 closest distance to " CB  ARG A 139 " =    1.039
peak=    3.564 closest distance to " O   HOH Z 361 " =    3.221
peak=    3.562 closest distance to " CG2 ILE A 120 " =    1.301
peak=    3.549 closest distance to " O   HOH Z 419 " =    1.626
peak=    3.547 closest distance to " CB  THR A  31 " =    1.837
peak=    3.547 closest distance to " O   ASP A 124 " =    1.509
peak=    3.544 closest distance to " CB  PRO A  54 " =    0.859
peak=    3.541 closest distance to " O   HOH Z 374 " =    2.516
peak=    3.538 closest distance to " CA  ALA A  51 " =    1.086
peak=    3.537 closest distance to " O   HOH Z 428 " =    3.796
peak=    3.534 closest distance to " O   HOH Z 214 " =    1.145
peak=    3.531 closest distance to " CB  ASN A 148 " =    1.399
peak=    3.531 closest distance to " O   HOH Z  66 " =    2.262
peak=    3.528 closest distance to " O   HOH Z  50 " =    1.423
peak=    3.513 closest distance to " CB  MET A  47 " =    1.400
peak=    3.513 closest distance to " O   HOH Z  37 " =    1.243
peak=    3.507 closest distance to " OD2 ASP A 298 " =    3.956
peak=    3.504 closest distance to " NZ  LYS A 119 " =    1.561
peak=    3.503 closest distance to " O   HOH Z 334 " =    1.385
peak=    3.492 closest distance to " O   HOH Z 215 " =    1.517
peak=    3.491 closest distance to " O   HOH Z 280 " =    2.533
peak=    3.482 closest distance to " O   HOH Z 299 " =    4.212
peak=    3.480 closest distance to " CD  LYS A 166 " =    1.373
peak=    3.479 closest distance to " O   HOH Z 425 " =    1.398
peak=    3.479 closest distance to " O   HOH Z 197 " =    2.087
peak=    3.476 closest distance to " O   HOH Z 108 " =    2.426
peak=    3.475 closest distance to " O   HOH Z 315 " =    1.872
peak=    3.471 closest distance to " NH2AARG A 145 " =    2.194
peak=    3.470 closest distance to " OD1 ASN A  69 " =    2.552
peak=    3.469 closest distance to " O   HOH Z  40 " =    1.863
peak=    3.466 closest distance to " O   HOH Z 261 " =    1.840
peak=    3.465 closest distance to " O   HOH Z 425 " =    2.180
peak=    3.464 closest distance to " OG BSER A 164 " =    2.279
peak=    3.463 closest distance to " O   HOH Z 303 " =    1.582
peak=    3.462 closest distance to " OD1 ASP A 286 " =    1.728
peak=    3.459 closest distance to " CH2 TRP A 274 " =    2.196
peak=    3.450 closest distance to " OG  SER A  22 " =    2.640
peak=    3.439 closest distance to " O   HOH Z 109 " =    2.259
peak=    3.438 closest distance to " CB  TYR A 169 " =    0.976
peak=    3.438 closest distance to " O   TRP A 274 " =    1.909
peak=    3.435 closest distance to " C   ALA A   1 " =    1.694
peak=    3.429 closest distance to " O   HOH Z 136 " =    1.288
peak=    3.426 closest distance to " O   HOH Z  85 " =    1.671
peak=    3.423 closest distance to " CE AMET A  47 " =    1.578
peak=    3.409 closest distance to " OE1 GLN A  11 " =    1.815
peak=    3.405 closest distance to " O   HOH Z 411 " =    1.766
peak=    3.404 closest distance to " O   HOH Z 261 " =    1.933
peak=    3.400 closest distance to " CD  GLN A  58 " =    5.941
peak=    3.397 closest distance to " O   HOH Z  43 " =    2.126
peak=    3.396 closest distance to " O   GLY A  91 " =    1.479
peak=    3.395 closest distance to " O   HOH Z 380 " =    1.989
peak=    3.392 closest distance to " O   HOH Z 261 " =    2.005
peak=    3.391 closest distance to " O   HOH Z  88 " =    3.404
peak=    3.389 closest distance to " O   HOH Z 344 " =    2.648
peak=    3.386 closest distance to " O   HOH Z 214 " =    1.602
peak=    3.382 closest distance to " O   HOH Z 260 " =    1.405
peak=    3.378 closest distance to " CG  MET A 185 " =    1.216
peak=    3.375 closest distance to " O   HOH Z   9 " =    2.183
peak=    3.374 closest distance to " O   HOH Z  78 " =    1.866
peak=    3.370 closest distance to " O   HOH Z 359 " =    1.404
peak=    3.367 closest distance to " O   HOH Z 404 " =    1.466
peak=    3.366 closest distance to " OD2 ASP A 286 " =    2.629
peak=    3.362 closest distance to " ND2 ASN A 187 " =    1.600
peak=    3.355 closest distance to " CB  TRP A 266 " =    1.193
peak=    3.354 closest distance to " CB  GLN A  88 " =    1.238
peak=    3.352 closest distance to " O   HOH Z 329 " =    3.509
peak=    3.350 closest distance to " CB  SER A 141 " =    1.053
peak=    3.349 closest distance to " CB  ALA A 100 " =    1.163
peak=    3.347 closest distance to " O   HOH Z  44 " =    1.974
peak=    3.346 closest distance to " CB  ALA A 248 " =    1.343
peak=    3.345 closest distance to " O   HOH Z 367 " =    3.517
peak=    3.336 closest distance to " CD  GLN A 194 " =    1.572
peak=    3.335 closest distance to " CD  LYS A  76 " =    1.870
peak=    3.329 closest distance to " O   HOH Z 163 " =    1.302
peak=    3.328 closest distance to " CG  PRO A 198 " =    1.215
peak=    3.324 closest distance to " CD2 TYR A  30 " =    0.870
peak=    3.321 closest distance to " O   HOH Z   1 " =    1.967
peak=    3.320 closest distance to " O   HOH Z 214 " =    2.306
peak=    3.317 closest distance to " CB  ARG A 259 " =    1.894
peak=    3.312 closest distance to " O   HOH Z  43 " =    1.350
peak=    3.309 closest distance to " O   HOH Z 350 " =    1.897
peak=    3.307 closest distance to " O   HOH Z 116 " =    1.602
peak=    3.303 closest distance to " CB  ASN A  39 " =    0.765
peak=    3.302 closest distance to " CB  ASN A 110 " =    1.116
peak=    3.301 closest distance to " CA  VAL A 126 " =    0.904
peak=    3.299 closest distance to " CG  PRO A 243 " =    1.209
peak=    3.298 closest distance to " CG  GLN A  58 " =    2.587
peak=    3.296 closest distance to " CD  ARG A 159 " =    0.779
peak=    3.291 closest distance to " O   HOH Z 353 " =    2.644
peak=    3.289 closest distance to " O   HOH Z 278 " =    1.515
peak=    3.286 closest distance to " NH1AARG A 275 " =    1.048
peak=    3.283 closest distance to " O   HOH Z 427 " =    3.093
peak=    3.282 closest distance to " CE BMET A  47 " =    1.206
peak=    3.282 closest distance to " CB  LEU A   5 " =    1.163
peak=    3.282 closest distance to " O   HOH Z  35 " =    2.348
peak=    3.281 closest distance to " NH2 ARG A 156 " =    1.046
peak=    3.280 closest distance to " O   HOH Z 416 " =    2.699
peak=    3.276 closest distance to " CG  MET A 188 " =    1.308
peak=    3.271 closest distance to " ND1 HIS A  81 " =    1.449
peak=    3.271 closest distance to " O   HOH Z 189 " =    2.720
peak=    3.269 closest distance to " O   HOH Z 276 " =    1.305
peak=    3.267 closest distance to " CZ AARG A 102 " =    1.646
peak=    3.263 closest distance to " CB  ASN A 215 " =    1.046
peak=    3.251 closest distance to " CB  PRO A  90 " =    1.343
peak=    3.243 closest distance to " O   HOH Z 380 " =    2.068
peak=    3.243 closest distance to " CG  ARG A  66 " =    3.252
peak=    3.240 closest distance to " O   HOH Z  38 " =    1.495
peak=    3.236 closest distance to " O   HOH Z 412 " =    3.677
peak=    3.233 closest distance to " CG2 ILE A  20 " =    1.479
peak=    3.230 closest distance to " CB  ALA A  34 " =    0.850
peak=    3.230 closest distance to " CG  MET A  93 " =    1.089
peak=    3.228 closest distance to " CB  ALA A  71 " =    1.300
peak=    3.228 closest distance to " O   HOH Z  59 " =    2.049
peak=    3.228 closest distance to " CG2 THR A 294 " =    1.479
peak=    3.224 closest distance to " C   SER A  32 " =    1.133
peak=    3.221 closest distance to " O   HOH Z 112 " =    1.603
peak=    3.218 closest distance to " O   HOH Z 155 " =    2.611
peak=    3.216 closest distance to " CE BLYS A 290 " =    1.001
peak=    3.214 closest distance to " C   ILE A 106 " =    1.867
peak=    3.211 closest distance to " CA  ASP A 140 " =    1.099
peak=    3.210 closest distance to " O   HOH Z 281 " =    4.297
peak=    3.208 closest distance to " O   HOH Z 266 " =    1.572
peak=    3.206 closest distance to " O   HOH Z 267 " =    1.983
peak=    3.203 closest distance to " CA  ALA A 295 " =    1.035
peak=    3.202 closest distance to " O   HOH Z  10 " =    1.656
peak=    3.201 closest distance to " O   HOH Z  61 " =    1.499
peak=    3.201 closest distance to " O   HOH Z 147 " =    1.760
peak=    3.199 closest distance to " N   ASP A 162 " =    1.350
peak=    3.199 closest distance to " CD2 HIS A  81 " =    1.263
peak=    3.192 closest distance to " O   HOH Z 270 " =    1.787
peak=    3.189 closest distance to " O   HOH Z 148 " =    3.081
peak=    3.185 closest distance to " O   HOH Z  99 " =    1.813
peak=    3.184 closest distance to " O   HOH Z 438 " =    2.813
peak=    3.184 closest distance to " O   HOH Z 409 " =    1.702
peak=    3.180 closest distance to " CG2 ILE A 234 " =    0.997
peak=    3.174 closest distance to " O   THR A  31 " =    1.741
peak=    3.171 closest distance to " O   HOH Z  30 " =    2.329
peak=    3.169 closest distance to " CB  ALA A 295 " =    1.224
peak=    3.169 closest distance to " OG  SER A  62 " =    2.996
peak=    3.160 closest distance to " CG2 ILE A 234 " =    2.002
peak=    3.157 closest distance to " OG ASER A 134 " =    1.755
peak=    3.155 closest distance to " O   HOH Z 250 " =    1.584
peak=    3.149 closest distance to " CA  ARG A  66 " =    0.909
peak=    3.145 closest distance to " CB  GLN A 278 " =    0.852
peak=    3.145 closest distance to " O   HOH Z 144 " =    1.568
peak=    3.142 closest distance to " O   HOH Z 381 " =    1.617
peak=    3.138 closest distance to " CD1 LEU A 228 " =    1.475
peak=    3.135 closest distance to " O   HOH Z 383 " =    1.855
peak=    3.133 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.132 closest distance to " O   HOH Z 217 " =    1.287
peak=    3.129 closest distance to " O   HOH Z 359 " =    1.930
peak=    3.123 closest distance to " CA  ASP A 191 " =    0.930
peak=    3.121 closest distance to " CB  ASN A 148 " =    1.948
peak=    3.110 closest distance to " O   ALA A 158 " =    1.290
peak=    3.110 closest distance to " N   ARG A 156 " =    1.336
peak=    3.109 closest distance to " CB  TYR A 247 " =    0.983
peak=    3.108 closest distance to " N   SER A 135 " =    1.188
peak=    3.108 closest distance to " O   HOH Z   3 " =    1.466
peak=    3.100 closest distance to " O   HOH Z 337 " =    3.638
peak=    3.097 closest distance to " CB  THR A 279 " =    1.553
peak=    3.096 closest distance to " O   HOH Z  59 " =    2.194
peak=    3.096 closest distance to " CA  ASN A 217 " =    1.317
peak=    3.085 closest distance to " O   HOH Z 227 " =    2.165
peak=    3.085 closest distance to " CB  ARG A  79 " =    0.864
peak=    3.081 closest distance to " CA  ALA A 158 " =    1.225
peak=    3.064 closest distance to " CA  ARG A  36 " =    1.002
peak=    3.062 closest distance to " O   HOH Z 115 " =    1.673
peak=    3.053 closest distance to " CA  ARG A 195 " =    1.116
peak=    3.041 closest distance to " O   HOH Z  88 " =    3.086
peak=    3.034 closest distance to " CA  GLY A  80 " =    0.771

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.797
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.780 - 5.797

peak=   -5.104 closest distance to " CG2 VAL A 230 " =    0.780
peak=   -4.736 closest distance to " O   PRO A 163 " =    2.070
peak=   -4.654 closest distance to " CD  ARG A 156 " =    2.114
peak=   -4.484 closest distance to " SG  CYS A 254 " =    3.170
peak=   -4.392 closest distance to " O   HOH Z 266 " =    4.323
peak=   -4.325 closest distance to " OXT GLY A 302 " =    2.870
peak=   -4.298 closest distance to " O   VAL A  67 " =    2.727
peak=   -4.291 closest distance to " CD1 LEU A 101 " =    2.454
peak=   -4.190 closest distance to " O   HOH Z 155 " =    1.649
peak=   -4.152 closest distance to " C   HIS A 108 " =    1.209
peak=   -4.114 closest distance to " N   ALA A 248 " =    1.783
peak=   -4.080 closest distance to " CB  ALA A 161 " =    2.472
peak=   -4.052 closest distance to " O   ASN A  45 " =    1.836
peak=   -4.008 closest distance to " O   HOH Z 250 " =    1.363
peak=   -4.003 closest distance to " O   HOH Z  11 " =    1.853
peak=   -3.997 closest distance to " O   HOH Z 407 " =    2.700
peak=   -3.974 closest distance to " CD1 LEU A 255 " =    2.690
peak=   -3.947 closest distance to " C   GLY A  80 " =    2.374
peak=   -3.933 closest distance to " CD1 PHE A  59 " =    1.930
peak=   -3.929 closest distance to " O   HOH Z  60 " =    2.045
peak=   -3.908 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.891 closest distance to " O   HOH Z  11 " =    1.730
peak=   -3.885 closest distance to " O   HOH Z 290 " =    0.983
peak=   -3.883 closest distance to " N   SER A 276 " =    1.359
peak=   -3.882 closest distance to " O   HOH Z 423 " =    2.264
peak=   -3.861 closest distance to " CB  ALA A 248 " =    1.968
peak=   -3.854 closest distance to " O   HOH Z 166 " =    1.889
peak=   -3.848 closest distance to " O   HOH Z  56 " =    2.306
peak=   -3.845 closest distance to " O   HOH Z 362 " =    5.797
peak=   -3.843 closest distance to " OG BSER A 134 " =    1.281
peak=   -3.827 closest distance to " O   ALA A   8 " =    1.897
peak=   -3.821 closest distance to " O   HOH Z 191 " =    5.032
peak=   -3.815 closest distance to " NH2 ARG A  79 " =    1.889
peak=   -3.812 closest distance to " CD  ARG A 195 " =    5.090
peak=   -3.803 closest distance to " O   SER A 146 " =    0.805
peak=   -3.801 closest distance to " O   HOH Z  92 " =    1.794
peak=   -3.757 closest distance to " C   THR A 279 " =    1.231
peak=   -3.739 closest distance to " O   VAL A  67 " =    2.687
peak=   -3.697 closest distance to " CE  MET A 105 " =    2.136
peak=   -3.688 closest distance to " O   HOH Z 234 " =    4.082
peak=   -3.683 closest distance to " OG ASER A 134 " =    1.192
peak=   -3.682 closest distance to " CD2 LEU A 300 " =    2.762
peak=   -3.680 closest distance to " NE2 GLN A  88 " =    1.194
peak=   -3.670 closest distance to " C   ASN A  69 " =    1.332
peak=   -3.655 closest distance to " O   HOH Z 118 " =    3.113
peak=   -3.640 closest distance to " CE2 TYR A  30 " =    2.774
peak=   -3.623 closest distance to " O   ALA A 160 " =    1.376
peak=   -3.603 closest distance to " OG BSER A 134 " =    1.581
peak=   -3.601 closest distance to " O   ASN A 187 " =    1.434
peak=   -3.593 closest distance to " CG  GLN A  58 " =    1.557
peak=   -3.591 closest distance to " O   HOH Z 431 " =    1.778
peak=   -3.580 closest distance to " O   PRO A 198 " =    1.248
peak=   -3.570 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.564 closest distance to " CB  PRO A 163 " =    2.808
peak=   -3.562 closest distance to " O   ALA A  51 " =    1.368
peak=   -3.561 closest distance to " O   VAL A 197 " =    1.259
peak=   -3.557 closest distance to " O   HOH Z 193 " =    1.711
peak=   -3.553 closest distance to " CD1 LEU A 228 " =    2.103
peak=   -3.549 closest distance to " O   HOH Z  97 " =    1.276
peak=   -3.546 closest distance to " O   LEU A 228 " =    2.340
peak=   -3.540 closest distance to " OD1 ASN A  39 " =    2.108
peak=   -3.539 closest distance to " O   PHE A 218 " =    1.620
peak=   -3.536 closest distance to " N   ALA A 226 " =    1.940
peak=   -3.534 closest distance to " O   MET A  40 " =    2.750
peak=   -3.527 closest distance to " O   HOH Z 231 " =    2.212
peak=   -3.524 closest distance to " N   SER A 206 " =    1.830
peak=   -3.519 closest distance to " O   ALA A 184 " =    1.718
peak=   -3.518 closest distance to " CG  GLU A   2 " =    1.926
peak=   -3.516 closest distance to " O   ALA A 161 " =    1.434
peak=   -3.515 closest distance to " C   ALA A 158 " =    1.110
peak=   -3.513 closest distance to " O   HOH Z 377 " =    1.963
peak=   -3.501 closest distance to " O   HOH Z 265 " =    2.039
peak=   -3.500 closest distance to " OG  SER A  62 " =    1.318
peak=   -3.493 closest distance to " CA  GLY A 133 " =    1.903
peak=   -3.493 closest distance to " O   HOH Z 103 " =    1.796
peak=   -3.491 closest distance to " CD  LYS A 289 " =    2.455
peak=   -3.483 closest distance to " CG  ARG A 219 " =    2.307
peak=   -3.481 closest distance to " CG2 VAL A 189 " =    2.048
peak=   -3.475 closest distance to " CG2 VAL A 296 " =    1.519
peak=   -3.471 closest distance to " O   TRP A  92 " =    1.887
peak=   -3.470 closest distance to " N   HIS A 115 " =    1.999
peak=   -3.466 closest distance to " ND2 ASN A 187 " =    1.466
peak=   -3.466 closest distance to " N   GLN A  58 " =    1.801
peak=   -3.461 closest distance to " O   HOH Z  15 " =    1.528
peak=   -3.460 closest distance to " CB  ALA A 291 " =    2.370
peak=   -3.458 closest distance to " OG  SER A  97 " =    2.193
peak=   -3.456 closest distance to " OD2 ASP A 191 " =    1.487
peak=   -3.453 closest distance to " O   GLY A 196 " =    1.024
peak=   -3.453 closest distance to " O   HOH Z 351 " =    1.480
peak=   -3.453 closest distance to " N   ARG A  66 " =    1.786
peak=   -3.453 closest distance to " ND2 ASN A  45 " =    1.127
peak=   -3.448 closest distance to " O   HOH Z  98 " =    1.714
peak=   -3.448 closest distance to " CZ  TYR A 169 " =    1.852
peak=   -3.446 closest distance to " O   HOH Z  71 " =    1.466
peak=   -3.423 closest distance to " O   HOH Z 137 " =    1.599
peak=   -3.421 closest distance to " O   HOH Z 134 " =    2.658
peak=   -3.416 closest distance to " NH2 ARG A  66 " =    1.506
peak=   -3.416 closest distance to " O   HOH Z 165 " =    1.916
peak=   -3.414 closest distance to " OG1 THR A  82 " =    1.355
peak=   -3.412 closest distance to " CG  LYS A 193 " =    2.103
peak=   -3.402 closest distance to " CB  ASP A 132 " =    2.281
peak=   -3.400 closest distance to " CE  LYS A 166 " =    2.936
peak=   -3.396 closest distance to " N   THR A 157 " =    1.472
peak=   -3.396 closest distance to " O   HOH Z 126 " =    1.911
peak=   -3.392 closest distance to " O   HOH Z 196 " =    2.130
peak=   -3.390 closest distance to " O   HOH Z 313 " =    1.264
peak=   -3.388 closest distance to " O   HOH Z 422 " =    1.552
peak=   -3.387 closest distance to " CG2 THR A 182 " =    2.201
peak=   -3.384 closest distance to " O   HOH Z 283 " =    1.850
peak=   -3.383 closest distance to " OD2 ASP A  50 " =    1.314
peak=   -3.370 closest distance to " CB  PHE A 208 " =    2.233
peak=   -3.368 closest distance to " OD1 ASP A 200 " =    1.245
peak=   -3.365 closest distance to " OG  SER A   3 " =    1.164
peak=   -3.362 closest distance to " CB  SER A 210 " =    1.370
peak=   -3.358 closest distance to " ND2 ASN A 142 " =    1.923
peak=   -3.354 closest distance to " N   GLN A 122 " =    1.445
peak=   -3.353 closest distance to " ND2 ASN A  39 " =    1.110
peak=   -3.350 closest distance to " N   ALA A 248 " =    2.242
peak=   -3.346 closest distance to " NH2 ARG A  66 " =    4.672
peak=   -3.343 closest distance to " CD  GLN A 103 " =    1.314
peak=   -3.343 closest distance to " CG  ASP A  50 " =    2.335
peak=   -3.342 closest distance to " N   ASP A 270 " =    1.517
peak=   -3.341 closest distance to " O   SER A 273 " =    1.282
peak=   -3.340 closest distance to " CB  ASN A  39 " =    1.952
peak=   -3.337 closest distance to " CD1 TYR A 247 " =    2.385
peak=   -3.335 closest distance to " OG1 THR A 251 " =    2.822
peak=   -3.334 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.328 closest distance to " OG  SER A  63 " =    1.150
peak=   -3.320 closest distance to " OD1 ASN A 301 " =    1.947
peak=   -3.318 closest distance to " NH2 ARG A  66 " =    4.565
peak=   -3.311 closest distance to " O   HOH Z 292 " =    4.399
peak=   -3.308 closest distance to " CB  ALA A 248 " =    2.173
peak=   -3.304 closest distance to " O   HOH Z  43 " =    1.974
peak=   -3.297 closest distance to " O   HOH Z 166 " =    2.003
peak=   -3.291 closest distance to " ND2 ASN A 209 " =    1.585
peak=   -3.284 closest distance to " O   HOH Z 193 " =    1.573
peak=   -3.284 closest distance to " O   HOH Z 427 " =    1.470
peak=   -3.282 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.279 closest distance to " O   HOH Z 174 " =    4.307
peak=   -3.279 closest distance to " CG1 VAL A 197 " =    2.207
peak=   -3.279 closest distance to " O   HOH Z 150 " =    1.545
peak=   -3.275 closest distance to " CE2 TYR A 214 " =    1.409
peak=   -3.270 closest distance to " NE2 GLN A 194 " =    1.756
peak=   -3.269 closest distance to " CZ  TYR A 172 " =    1.741
peak=   -3.267 closest distance to " CE2 TRP A 179 " =    1.349
peak=   -3.265 closest distance to " CE BMET A  47 " =    1.374
peak=   -3.263 closest distance to " O   MET A 188 " =    1.819
peak=   -3.263 closest distance to " O   HOH Z 310 " =    3.500
peak=   -3.259 closest distance to " NE2 GLN A 194 " =    2.338
peak=   -3.259 closest distance to " ND2 ASN A  69 " =    1.646
peak=   -3.249 closest distance to " O   HOH Z 426 " =    1.749
peak=   -3.249 closest distance to " C   GLY A  91 " =    1.311
peak=   -3.235 closest distance to " ND2 ASN A 252 " =    1.764
peak=   -3.235 closest distance to " O   HOH Z 145 " =    1.771
peak=   -3.231 closest distance to " O   HOH Z 251 " =    1.304
peak=   -3.230 closest distance to " NH2AARG A 275 " =    4.740
peak=   -3.230 closest distance to " O   VAL A 174 " =    1.958
peak=   -3.221 closest distance to " O   ALA A 256 " =    1.339
peak=   -3.220 closest distance to " CD2 TRP A 274 " =    1.018
peak=   -3.214 closest distance to " OXT GLY A 302 " =    3.363
peak=   -3.214 closest distance to " NZ  LYS A 119 " =    3.367
peak=   -3.212 closest distance to " CG2 ILE A 263 " =    2.182
peak=   -3.210 closest distance to " CD2 TYR A 293 " =    1.980
peak=   -3.209 closest distance to " CA  GLY A 203 " =    2.097
peak=   -3.205 closest distance to " CD1 PHE A  59 " =    2.170
peak=   -3.205 closest distance to " C   ASN A 285 " =    2.180
peak=   -3.204 closest distance to " CG  GLU A  53 " =    1.465
peak=   -3.203 closest distance to " O   HOH Z  17 " =    1.251
peak=   -3.200 closest distance to " O   ILE A 120 " =    1.251
peak=   -3.196 closest distance to " N   THR A 235 " =    1.351
peak=   -3.196 closest distance to " OXT GLY A 302 " =    0.818
peak=   -3.193 closest distance to " CB  ASP A 162 " =    2.539
peak=   -3.190 closest distance to " O   PRO A 198 " =    1.269
peak=   -3.190 closest distance to " O   HOH Z  44 " =    2.057
peak=   -3.188 closest distance to " CG  ASP A 132 " =    2.262
peak=   -3.177 closest distance to " CG2AVAL A  41 " =    3.006
peak=   -3.175 closest distance to " O   ALA A 100 " =    2.285
peak=   -3.172 closest distance to " O   HOH Z 211 " =    1.480
peak=   -3.170 closest distance to " CE3 TRP A 274 " =    2.306
peak=   -3.167 closest distance to " OD1 ASP A 171 " =    1.621
peak=   -3.160 closest distance to " O   HOH Z   6 " =    1.833
peak=   -3.155 closest distance to " CA  GLY A 133 " =    2.249
peak=   -3.147 closest distance to " O   HOH Z 414 " =    2.616
peak=   -3.142 closest distance to " O   HOH Z 154 " =    1.391
peak=   -3.142 closest distance to " OD2 ASP A 286 " =    2.325
peak=   -3.136 closest distance to " O   HOH Z 174 " =    2.185
peak=   -3.119 closest distance to " CG  ARG A 269 " =    2.150
peak=   -3.103 closest distance to " O   HOH Z  60 " =    1.124
peak=   -3.103 closest distance to " OG  SER A  26 " =    1.313
peak=   -3.101 closest distance to " O   HOH Z 385 " =    3.377
peak=   -3.099 closest distance to " O   HOH Z 310 " =    1.518
peak=   -3.099 closest distance to " O   HOH Z 172 " =    4.948
peak=   -3.086 closest distance to " OD2 ASP A 171 " =    2.367
peak=   -3.084 closest distance to " CE1 HIS A  81 " =    1.280
peak=   -3.080 closest distance to " OD1 ASN A 249 " =    1.579
peak=   -3.078 closest distance to " CB  CYS A 254 " =    2.644
peak=   -3.073 closest distance to " O   HOH Z 113 " =    1.991
peak=   -3.073 closest distance to " O   HOH Z 188 " =    4.711
peak=   -3.071 closest distance to " O   HOH Z 424 " =    2.994
peak=   -3.062 closest distance to " C   MET A 188 " =    1.546
peak=   -3.048 closest distance to " OE1 GLN A 223 " =    2.066
peak=   -3.032 closest distance to " CD1 TYR A 169 " =    1.991
peak=   -3.029 closest distance to " CG  PHE A 283 " =    2.578

================= 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    :  0.4925 0.4839   6.289918e+00   6.281377e+00
   1_bss:  0.4837 0.4759   6.285784e+00   6.273830e+00
   1_xyz:  0.4044 0.4270   6.182509e+00   6.219847e+00
   1_adp:  0.3615 0.4143   6.113796e+00   6.197215e+00
   1_occ:  0.3605 0.4144   6.112551e+00   6.196797e+00
   2_bss:  0.3585 0.4092   6.112282e+00   6.195028e+00
   2_xyz:  0.2760 0.3294   5.902360e+00   6.039341e+00
   2_adp:  0.2528 0.3076   5.832091e+00   5.980845e+00
   2_occ:  0.2526 0.3074   5.831567e+00   5.980638e+00
   3_bss:  0.2494 0.3041   5.827848e+00   5.977184e+00
   3_xyz:  0.1685 0.2200   5.498654e+00   5.712245e+00
   3_adp:  0.1507 0.1963   5.380519e+00   5.591301e+00
   3_occ:  0.1501 0.1961   5.378924e+00   5.590497e+00
   4_bss:  0.1492 0.1939   5.376145e+00   5.584452e+00
   4_xyz:  0.1332 0.1748   5.279668e+00   5.489796e+00
   4_adp:  0.1288 0.1734   5.257946e+00   5.477523e+00
   4_occ:  0.1287 0.1734   5.257265e+00   5.477137e+00
   5_bss:  0.1287 0.1734   5.256820e+00   5.476932e+00
   5_xyz:  0.1163 0.1652   5.185872e+00   5.430197e+00
   5_adp:  0.1131 0.1619   5.161454e+00   5.410133e+00
   5_occ:  0.1130 0.1619   5.161142e+00   5.410039e+00
   5_bss:  0.1130 0.1630   5.163193e+00   5.413307e+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:  0.367  11.702   7.529   8.762   8.676   0.000   0.000   0.000
   1_xyz:  0.367  11.702   7.529   8.762   8.676   0.000   0.000   0.000
   1_adp:  0.367  11.702   7.529   8.762   8.676   0.000   0.000   0.000
   1_occ:  0.367  11.702   7.529   8.762   8.676   0.000   0.000   0.000
   2_bss:  0.324  20.000   4.346   5.386   6.002   0.000   0.000   0.000
   2_xyz:  0.324  20.000   4.346   5.386   6.002   0.000   0.000   0.000
   2_adp:  0.324  20.000   4.346   5.386   6.002   0.000   0.000   0.000
   2_occ:  0.324  20.000   4.346   5.386   6.002   0.000   0.000   0.000
   3_bss:  0.327  34.842   1.982   3.274   3.555   0.000   0.000   0.000
   3_xyz:  0.327  34.842   1.982   3.274   3.555   0.000   0.000   0.000
   3_adp:  0.327  34.842   1.982   3.274   3.555   0.000   0.000   0.000
   3_occ:  0.327  34.842   1.982   3.274   3.555   0.000   0.000   0.000
   4_bss:  0.330  34.842   0.784   2.051   2.161   0.000   0.000   0.000
   4_xyz:  0.330  34.842   0.784   2.051   2.161   0.000   0.000   0.000
   4_adp:  0.330  34.842   0.784   2.051   2.161   0.000   0.000   0.000
   4_occ:  0.330  34.842   0.784   2.051   2.161   0.000   0.000   0.000
   5_bss:  0.324  34.842   0.663   1.896   1.984   0.000   0.000   0.000
   5_xyz:  0.324  34.842   0.663   1.896   1.984   0.000   0.000   0.000
   5_adp:  0.324  34.842   0.663   1.896   1.984   0.000   0.000   0.000
   5_occ:  0.324  34.842   0.663   1.896   1.984   0.000   0.000   0.000
   5_bss:  0.320  37.047  -0.825   0.349   0.476   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.069 0.3930  0.4611    74069.135
   1_bss:  59.846 0.3938  0.5852    70940.008
   1_xyz:  51.852 0.4948  0.7257    55141.329
   1_adp:  47.479 0.5506  0.8619    49826.110
   1_occ:  47.430 0.5512  0.8609    49691.576
   2_bss:  47.154 0.5544  0.7779    49121.005
   2_xyz:  35.507 0.6942  0.9567    29613.904
   2_adp:  31.946 0.7355  1.0025    24890.146
   2_occ:  31.925 0.7358  1.0026    24861.467
   3_bss:  31.662 0.7386  0.9253    24506.086
   3_xyz:  21.891 0.8424  1.0105    12602.569
   3_adp:  18.600 0.8751  1.0310     9941.743
   3_occ:  18.564 0.8755  1.0312     9922.128
   4_bss:  18.407 0.8768  0.9840     9721.753
   4_xyz:  16.180 0.8969  0.9928     7859.863
   4_adp:  15.915 0.8994  0.9896     7692.566
   4_occ:  15.899 0.8995  0.9896     7685.223
   5_bss:  15.890 0.8996  0.9841     7676.638
   5_xyz:  14.913 0.9077  0.9863     6993.336
   5_adp:  14.502 0.9110  0.9828     6698.776
   5_occ:  14.497 0.9111  0.9827     6697.548
   5_bss:  14.573 0.9105  0.9839     6791.086
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3067e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3067e+01
   1_xyz:   1.874  0.015  0.117 18.396  0.008  4.106   1.7115e-01
   1_adp:   1.874  0.015  0.117 18.396  0.008  4.106   1.7115e-01
   1_occ:   1.874  0.015  0.117 18.396  0.008  4.106   1.7115e-01
   2_bss:   1.874  0.015  0.117 18.396  0.008  4.106   1.7115e-01
   2_xyz:   1.203  0.009  0.081 16.377  0.005  4.108   8.4787e-02
   2_adp:   1.203  0.009  0.081 16.377  0.005  4.108   8.4787e-02
   2_occ:   1.203  0.009  0.081 16.377  0.005  4.108   8.4787e-02
   3_bss:   1.203  0.009  0.081 16.377  0.005  4.108   8.4787e-02
   3_xyz:   1.187  0.008  0.083 15.765  0.004  4.122   7.8706e-02
   3_adp:   1.187  0.008  0.083 15.765  0.004  4.122   7.8706e-02
   3_occ:   1.187  0.008  0.083 15.765  0.004  4.122   7.8706e-02
   4_bss:   1.187  0.008  0.083 15.765  0.004  4.122   7.8706e-02
   4_xyz:   0.970  0.006  0.071 15.163  0.003  4.112   5.6213e-02
   4_adp:   0.970  0.006  0.071 15.163  0.003  4.112   5.6213e-02
   4_occ:   0.970  0.006  0.071 15.163  0.003  4.112   5.6213e-02
   5_bss:   0.970  0.006  0.071 15.163  0.003  4.112   5.6213e-02
   5_xyz:   1.151  0.008  0.087 15.637  0.004  4.114   7.4283e-02
   5_adp:   1.151  0.008  0.087 15.637  0.004  4.114   7.4283e-02
   5_occ:   1.151  0.008  0.087 15.637  0.004  4.114   7.4283e-02
   5_bss:   1.151  0.008  0.087 15.637  0.004  4.114   7.4283e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.870   6.8726e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.870   6.8726e+00
   1_xyz:  16.920  0.192  0.586 85.995  0.055  2.082   1.1607e-01
   1_adp:  16.920  0.192  0.586 85.995  0.055  2.082   1.1607e-01
   1_occ:  16.920  0.192  0.586 85.995  0.055  2.082   1.1607e-01
   2_bss:  16.920  0.192  0.586 85.995  0.055  2.082   1.1607e-01
   2_xyz:   7.367  0.103  0.415 82.871  0.046  2.243   6.9150e-02
   2_adp:   7.367  0.103  0.415 82.871  0.046  2.243   6.9150e-02
   2_occ:   7.367  0.103  0.415 82.871  0.046  2.243   6.9150e-02
   3_bss:   7.367  0.103  0.415 82.871  0.046  2.243   6.9150e-02
   3_xyz:   8.106  0.055  0.550 80.690  0.028  2.269   7.9711e-02
   3_adp:   8.106  0.055  0.550 80.690  0.028  2.269   7.9711e-02
   3_occ:   8.106  0.055  0.550 80.690  0.028  2.269   7.9711e-02
   4_bss:   8.106  0.055  0.550 80.690  0.028  2.269   7.9711e-02
   4_xyz:   6.213  0.037  0.422 81.006  0.023  2.306   5.4061e-02
   4_adp:   6.213  0.037  0.422 81.006  0.023  2.306   5.4061e-02
   4_occ:   6.213  0.037  0.422 81.006  0.023  2.306   5.4061e-02
   5_bss:   6.213  0.037  0.422 81.006  0.023  2.306   5.4061e-02
   5_xyz:   7.396  0.047  0.638 82.712  0.028  2.266   5.5807e-02
   5_adp:   7.396  0.047  0.638 82.712  0.028  2.266   5.5807e-02
   5_occ:   7.396  0.047  0.638 82.712  0.028  2.266   5.5807e-02
   5_bss:   7.396  0.047  0.638 82.712  0.028  2.266   5.5807e-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:  80.06   0.00  13.93  69.06   0.00  11.58  80.06   0.00  26.73
   1_occ:  80.06   0.00  13.93  69.06   0.00  11.58  80.06   0.00  26.73
   2_bss:  80.06   0.00  13.93  69.06   0.00  11.58  80.06   0.00  26.73
   2_xyz:  80.06   0.00  13.93  69.06   0.00  11.58  80.06   0.00  26.73
   2_adp:  90.92   0.00  13.85  75.07   0.00  10.49  90.92   2.28  32.16
   2_occ:  90.92   0.00  13.85  75.07   0.00  10.49  90.92   2.28  32.16
   3_bss:  90.92   0.00  13.85  75.07   0.00  10.49  90.92   2.28  32.16
   3_xyz:  90.92   0.00  13.85  75.07   0.00  10.49  90.92   2.28  32.16
   3_adp:  89.65   0.00  13.46  75.43   0.00   9.67  89.65   3.14  34.12
   3_occ:  89.65   0.00  13.46  75.43   0.00   9.67  89.65   3.14  34.12
   4_bss:  89.65   0.00  13.46  75.43   0.00   9.67  89.65   3.14  34.12
   4_xyz:  89.65   0.00  13.46  75.43   0.00   9.67  89.65   3.14  34.12
   4_adp:  89.23   0.00  13.53  76.45   0.00   9.55  89.23   2.70  35.16
   4_occ:  89.23   0.00  13.53  76.45   0.00   9.55  89.23   2.70  35.16
   5_bss:  89.23   0.00  13.53  76.45   0.00   9.55  89.23   2.70  35.16
   5_xyz:  89.23   0.00  13.53  76.45   0.00   9.55  89.23   2.70  35.16
   5_adp:  85.82   0.00  13.45  81.18   0.00   9.27  85.82   2.07  36.26
   5_occ:  85.82   0.00  13.45  81.18   0.00   9.27  85.82   2.07  36.26
   5_bss:  87.38   1.56  15.01  82.74   1.56  10.82  87.38   3.62  37.82
------------------------------------------------------------------------
 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:    1.240    0.039    0.430
   1_adp:    1.240    0.039    0.430
   1_occ:    1.240    0.039    0.430
   2_bss:    1.240    0.039    0.430
   2_xyz:    1.732    0.015    0.596
   2_adp:    1.732    0.015    0.596
   2_occ:    1.732    0.015    0.596
   3_bss:    1.732    0.015    0.596
   3_xyz:    1.812    0.056    0.724
   3_adp:    1.812    0.056    0.724
   3_occ:    1.812    0.056    0.724
   4_bss:    1.812    0.056    0.724
   4_xyz:    1.908    0.065    0.746
   4_adp:    1.908    0.065    0.746
   4_occ:    1.908    0.065    0.746
   5_bss:    1.908    0.065    0.746
   5_xyz:    1.813    0.077    0.773
   5_adp:    1.813    0.077    0.773
   5_occ:    1.813    0.077    0.773
   5_bss:    1.813    0.077    0.773
------------------------------------------------------------------------

CPU time actual refinement: 352.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/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_199/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_199/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.89 
  Macro-tasks:
    bulk solvent and scale       = 44.65  
    individual site refinement   = 145.02 
    weights calculation          = 33.12  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 229.55 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 109.13 
    alpha_beta                      = 8.37   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.77 
    fmodel                         = 8.10   
    r_factors                      = 0.26   
    phase_errors                   = 10.35  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 259.86 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.930 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    653 calls, 108.74 s
gradients_fft:          599 calls, 106.22 s

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

# Date 2008-01-16 Time 00:58:22 PST -0800 (1200473902.03 s)
Start R-work = 0.4925, R-free = 0.4839 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1790 (no bulk solvent and anisotropic scale)

Start R-work = 0.4837, R-free = 0.4759
Final R-work = 0.1130, R-free = 0.1630