# Date 2008-01-16 Time 02:21:58 PST -0800 (1200478918.41 s)
#phil __OFF__

Command line arguments: "../801.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3832
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 801

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.1647, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, 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: (70.6012, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   2.0103

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 2.01025
Completeness in resolution range: 0.972014
Completeness with d_max=infinity: 0.968985

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.3009 [2124/2148]  1909   215  10.1%
  bin  2:  4.3009 -  3.4268 [2031/2051]  1832   199   9.8%
  bin  3:  3.4268 -  2.9975 [2011/2030]  1810   201  10.0%
  bin  4:  2.9975 -  2.7251 [1967/1997]  1766   201  10.2%
  bin  5:  2.7251 -  2.5308 [1991/2010]  1792   199  10.0%
  bin  6:  2.5308 -  2.3822 [1966/1991]  1771   195   9.9%
  bin  7:  2.3822 -  2.2633 [1946/1974]  1751   195  10.0%
  bin  8:  2.2633 -  2.1651 [1960/1996]  1765   195   9.9%
  bin  9:  2.1651 -  2.0819 [1931/1973]  1736   195  10.1%
  bin 10:  2.0819 -  2.0103 [1662/1983]  1498   164   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/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:
        1.73 -     2.37: 10
        2.37 -     3.00: 1893
        3.00 -     3.63: 4502
        3.63 -     4.27: 8963
        4.27 -     4.90: 12481
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.734 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.923 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.923 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.984 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27844 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_801/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.16465 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4565   r_free= 0.4446   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.255674                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.3758 0.3428      6.5692      6.4499|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.3548 0.3923      6.7088      6.8518|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.4127 0.3842      6.6422      6.6039|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.4454 0.3946      6.5052      6.3891|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.4723 0.4628      6.3507      6.3619|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.4767 0.5289      6.2592      6.2047|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.5004 0.4881       6.228      6.1828|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.5092 0.4395      6.1785      6.1264|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.4942 0.5390      6.1022      6.1513|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.5153 0.4541      6.1205      6.0588|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.4973 0.5268      6.0205      6.0799|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.5247 0.4705       5.977       6.008|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.5112 0.5146      5.8971      5.8396|
| 14:  2.0604 -  2.0103 0.77    976  110 0.5186 0.4840      5.8566      5.7493|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7967  1382   152  0.74  30.73   0.80     0.76      57906.02|
|  2:  4.7967 -  3.8276  1312   151  0.75  30.54   0.89     0.80      85030.72|
|  3:  3.8276 -  3.3498  1299   141  0.67  38.04   0.84     0.76      90423.41|
|  4:  3.3498 -  3.0462  1295   141  0.59  44.64   0.80     0.65      81813.10|
|  5:  3.0462 -  2.8294  1267   144  0.50  51.97   0.76     0.56      70044.17|
|  6:  2.8294 -  2.6635  1289   144  0.46  55.18   0.73     0.51      64724.19|
|  7:  2.6635 -  2.5308  1265   142  0.44  56.44   0.73     0.50      58584.68|
|  8:  2.5308 -  2.4211  1271   137  0.45  56.16   0.74     0.51      51603.33|
|  9:  2.4211 -  2.3282  1248   142  0.46  55.23   0.73     0.52      46847.48|
| 10:  2.3282 -  2.2481  1271   139  0.44  56.71   0.74     0.51      43193.84|
| 11:  2.2481 -  2.1781  1252   138  0.43  57.97   0.75     0.49      41079.31|
| 12:  2.1781 -  2.1160  1250   138  0.41  59.32   0.75     0.50      38059.92|
| 13:  2.1160 -  2.0604  1253   140  0.41  59.19   0.73     0.48      32987.90|
| 14:  2.0604 -  2.0103   976   110  0.43  57.86   0.72     0.45      26752.61|
|alpha:            min =        0.45 max =            0.80 mean =         0.58|
|beta:             min =    26752.61 max =        90423.41 mean =     57100.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.97 mean =        50.36|
|phase err.(test): min =        0.00 max =           89.91 mean =        50.62|
|-----------------------------------------------------------------------------|

============================== 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 = 10.385175             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.983   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.092   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1475 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2574 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3847 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5002 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6492 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7603 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.427 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.695 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4626   r_free= 0.4423   ksol= 0.00   Bsol= 0.00   scale= 0.769    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.260349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4473   r_free= 0.4295   ksol= 0.35   Bsol= 50.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.47,7.30,11.26,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.250127                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.405112              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.067   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.811514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.495   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4473      final r-factor (work) = 0.3459          |
| start r-factor (free) = 0.4295      final r-factor (free) = 0.3706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.8655 = 9.41 * 0.50 * 6.2601 + 1.00 * 54.4270                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9179 = 9.41 * 0.50 * 6.1205 + 1.00 * 0.1362                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3459      final r-factor (work) = 0.2935          |
| start r-factor (free) = 0.3706      final r-factor (free) = 0.3347          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9812 = 0.81 * 1.00 * 6.1205 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8752 = 0.81 * 1.00 * 5.9907 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    53.82   11.06    None  None   None       |
|    all(noH): 2823   0      0.00    53.82   11.06    None  None   None       |
|    Sol.    : 438    0      0.00    53.82   25.50    None  None   None       |
|    Mac.    : 2385   0      0.00    50.54   8.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.382:  998   |   5:    26.908 -  32.289:  117        |
|      1:     5.382 -  10.763:  749   |   6:    32.289 -  37.671:   76        |
|      2:    10.763 -  16.145:  417   |   7:    37.671 -  43.053:   50        |
|      3:    16.145 -  21.526:  246   |   8:    43.053 -  48.434:   21        |
|      4:    21.526 -  26.908:  140   |   9:    48.434 -  53.816:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2935 r_free = 0.3347             target_work(ml) = 5.953         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2928 r_free = 0.3356             target_work(ml) = 5.952         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2928   r_free= 0.3356   ksol= 0.35   Bsol= 50.00   scale= 1.070   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.47,7.30,11.26,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.952377                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2906   r_free= 0.3340   ksol= 0.32   Bsol= 48.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,4.51,8.00,0.00,0.00,0.00); trace/3= 5.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.954451                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.624178              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.584   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413163              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.302  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2906      final r-factor (work) = 0.2043          |
| start r-factor (free) = 0.3340      final r-factor (free) = 0.2530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9834 = 4.62 * 0.50 * 5.9890 + 1.00 * 0.1362                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4828 = 4.62 * 0.50 * 5.7985 + 1.00 * 0.0762                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2043      final r-factor (work) = 0.1824          |
| start r-factor (free) = 0.2530      final r-factor (free) = 0.2305          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4257 = 0.41 * 1.00 * 5.7985 + 1.00 * 0.0300                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3760 = 0.41 * 1.00 * 5.5911 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.60   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    65.60   11.50    None  None   None       |
|    Sol.    : 438    0      0.00    60.53   31.88    None  None   None       |
|    Mac.    : 2385   0      0.00    65.60   7.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.560: 1374   |   5:    32.798 -  39.358:  115        |
|      1:     6.560 -  13.119:  715   |   6:    39.358 -  45.917:   87        |
|      2:    13.119 -  19.679:  236   |   7:    45.917 -  52.477:   55        |
|      3:    19.679 -  26.239:  129   |   8:    52.477 -  59.037:   19        |
|      4:    26.239 -  32.798:   90   |   9:    59.037 -  65.596:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1824 r_free = 0.2305             target_work(ml) = 5.554         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1822 r_free = 0.2311             target_work(ml) = 5.555         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1822   r_free= 0.2311   ksol= 0.32   Bsol= 48.80   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,4.51,8.00,0.00,0.00,0.00); trace/3= 5.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.554574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1808   r_free= 0.2308   ksol= 0.33   Bsol= 61.32   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,3.40,5.35,0.00,0.00,0.00); trace/3= 3.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.554730                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.518884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.519723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.447   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1808      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.2308      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9264 = 3.52 * 0.50 * 5.5983 + 1.00 * 0.0765                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6519 = 3.52 * 0.50 * 5.4436 + 1.00 * 0.0742                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2866 = 1.52 * 1.00 * 5.4436 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0342 = 1.52 * 1.00 * 5.2757 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.08   12.39    None  None   None       |
|    all(noH): 2823   0      0.00    81.08   12.39    None  None   None       |
|    Sol.    : 438    0      0.00    81.08   37.22    None  None   None       |
|    Mac.    : 2385   0      0.00    77.61   7.83     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 -   8.108: 1643   |   5:    40.538 -  48.646:   76        |
|      1:     8.108 -  16.215:  581   |   6:    48.646 -  56.753:   86        |
|      2:    16.215 -  24.323:  164   |   7:    56.753 -  64.861:   50        |
|      3:    24.323 -  32.430:  105   |   8:    64.861 -  72.968:   17        |
|      4:    32.430 -  40.538:   94   |   9:    72.968 -  81.076:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1746             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1746             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1746   ksol= 0.33   Bsol= 61.32   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.78,3.40,5.35,0.00,0.00,0.00); trace/3= 3.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.257636                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1745   ksol= 0.33   Bsol= 61.32   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.17,4.80,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.256966                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.679806              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.192106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.249  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5059 = 1.68 * 0.50 * 5.2759 + 1.00 * 0.0747                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4634 = 1.68 * 0.50 * 5.2440 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1239      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0268 = 0.19 * 1.00 * 5.2440 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0339 = 0.19 * 1.00 * 5.2399 + 1.00 * 0.0272                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.82   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    77.82   11.73    None  None   None       |
|    Sol.    : 438    0      0.61    77.82   34.14    None  None   None       |
|    Mac.    : 2385   0      0.00    75.39   7.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.782: 1652   |   5:    38.912 -  46.695:   75        |
|      1:     7.782 -  15.565:  589   |   6:    46.695 -  54.477:   73        |
|      2:    15.565 -  23.347:  159   |   7:    54.477 -  62.259:   38        |
|      3:    23.347 -  31.130:  114   |   8:    62.259 -  70.042:   16        |
|      4:    31.130 -  38.912:  101   |   9:    70.042 -  77.824:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1675             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1674             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1674   ksol= 0.33   Bsol= 61.32   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.17,4.80,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1673   ksol= 0.33   Bsol= 60.03   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,3.04,4.59,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.512167              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.297  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.580   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6382 = 2.51 * 0.50 * 5.2379 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6053 = 2.51 * 0.50 * 5.1980 + 1.00 * 0.0762                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1159          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2696 = 0.43 * 1.00 * 5.1980 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2583 = 0.43 * 1.00 * 5.1761 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.80   11.71    None  None   None       |
|    all(noH): 2823   0      0.00    79.80   11.71    None  None   None       |
|    Sol.    : 438    0      0.86    79.80   34.39    None  None   None       |
|    Mac.    : 2385   0      0.00    76.84   7.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.980: 1678   |   5:    39.900 -  47.881:   86        |
|      1:     7.980 -  15.960:  571   |   6:    47.881 -  55.861:   66        |
|      2:    15.960 -  23.940:  155   |   7:    55.861 -  63.841:   38        |
|      3:    23.940 -  31.920:  105   |   8:    63.841 -  71.821:    6        |
|      4:    31.920 -  39.900:  113   |   9:    71.821 -  79.801:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1159 r_free = 0.1627             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1627             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1627   ksol= 0.33   Bsol= 60.03   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,3.04,4.59,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176534                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.1039 0.1359      5.4252      5.5561|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.0875 0.1177      5.4662      5.6905|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.1090 0.1482      5.5086      5.8176|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.1230 0.1646      5.4639      5.6252|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.1375 0.1736      5.3643      5.5698|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.1251 0.2128      5.2467      5.5707|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.1352 0.1625      5.2246      5.3665|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.1233 0.1741      5.1318      5.3914|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.1217 0.1915       5.078      5.3456|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.1199 0.1739       5.011      5.2499|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.1179 0.1738      4.9763      5.2163|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.1185 0.1809      4.9055      5.2756|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.1139 0.1803      4.8151      5.0788|
| 14:  2.0604 -  2.0103 0.77    976  110 0.1065 0.1680      4.6808      4.9312|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7967  1382   152  0.94   9.66   0.97     0.94       7958.23|
|  2:  4.7967 -  3.8276  1312   151  0.95   8.37   1.00     0.98       9675.64|
|  3:  3.8276 -  3.3498  1299   141  0.93  11.45   1.01     1.01      10938.77|
|  4:  3.3498 -  3.0462  1295   141  0.92  13.47   0.99     0.97      10289.14|
|  5:  3.0462 -  2.8294  1267   144  0.90  16.01   0.99     0.96       8684.39|
|  6:  2.8294 -  2.6635  1289   144  0.89  16.66   0.97     0.95       7616.60|
|  7:  2.6635 -  2.5308  1265   142  0.90  16.50   0.98     0.94       6829.55|
|  8:  2.5308 -  2.4211  1271   137  0.90  15.87   0.98     0.96       5942.51|
|  9:  2.4211 -  2.3282  1248   142  0.90  16.26   1.00     0.96       5596.73|
| 10:  2.3282 -  2.2481  1271   139  0.89  16.42   0.99     0.94       4718.57|
| 11:  2.2481 -  2.1781  1252   138  0.90  16.63   0.99     0.95       4761.29|
| 12:  2.1781 -  2.1160  1250   138  0.90  16.34   1.00     0.98       4159.30|
| 13:  2.1160 -  2.0604  1253   140  0.90  15.93   0.98     0.96       3476.34|
| 14:  2.0604 -  2.0103   976   110  0.92  14.28   0.96     0.93       2549.04|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2549.04 max =        10938.77 mean =      6762.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.51|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1627   ksol= 0.33   Bsol= 63.54   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.40,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176552                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1627   ksol= 0.33   Bsol= 63.54   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.40,1.15,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176552                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7967 0.99   1382  152 0.1039 0.1359      5.4255      5.5566|
|  2:  4.7967 -  3.8276 0.99   1312  151 0.0875 0.1177      5.4665      5.6906|
|  3:  3.8276 -  3.3498 0.99   1299  141 0.1090 0.1483      5.5087       5.818|
|  4:  3.3498 -  3.0462 0.99   1295  141 0.1231 0.1646       5.464      5.6253|
|  5:  3.0462 -  2.8294 0.99   1267  144 0.1375 0.1735      5.3642      5.5696|
|  6:  2.8294 -  2.6635 0.99   1289  144 0.1251 0.2128      5.2466      5.5707|
|  7:  2.6635 -  2.5308 0.99   1265  142 0.1352 0.1626      5.2247      5.3666|
|  8:  2.5308 -  2.4211 0.98   1271  137 0.1234 0.1740       5.132      5.3915|
|  9:  2.4211 -  2.3282 0.98   1248  142 0.1217 0.1916      5.0779      5.3456|
| 10:  2.3282 -  2.2481 1.00   1271  139 0.1199 0.1739       5.011        5.25|
| 11:  2.2481 -  2.1781 0.97   1252  138 0.1179 0.1737      4.9762       5.216|
| 12:  2.1781 -  2.1160 0.98   1250  138 0.1185 0.1808      4.9054      5.2753|
| 13:  2.1160 -  2.0604 0.99   1253  140 0.1139 0.1803       4.815       5.079|
| 14:  2.0604 -  2.0103 0.77    976  110 0.1065 0.1679      4.6807      4.9307|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7967  1382   152  0.94   9.66   0.97     0.95       7965.15|
|  2:  4.7967 -  3.8276  1312   151  0.95   8.37   1.00     0.99       9681.89|
|  3:  3.8276 -  3.3498  1299   141  0.93  11.45   1.02     1.01      10943.17|
|  4:  3.3498 -  3.0462  1295   141  0.92  13.47   0.99     0.98      10289.27|
|  5:  3.0462 -  2.8294  1267   144  0.90  16.01   0.99     0.96       8683.36|
|  6:  2.8294 -  2.6635  1289   144  0.89  16.66   0.98     0.95       7615.46|
|  7:  2.6635 -  2.5308  1265   142  0.90  16.51   0.98     0.95       6830.79|
|  8:  2.5308 -  2.4211  1271   137  0.90  15.87   0.98     0.96       5943.81|
|  9:  2.4211 -  2.3282  1248   142  0.90  16.26   1.00     0.96       5598.47|
| 10:  2.3282 -  2.2481  1271   139  0.89  16.42   0.99     0.95       4717.14|
| 11:  2.2481 -  2.1781  1252   138  0.90  16.62   0.99     0.95       4759.66|
| 12:  2.1781 -  2.1160  1250   138  0.90  16.33   1.00     0.98       4157.75|
| 13:  2.1160 -  2.0604  1253   140  0.90  15.93   0.99     0.96       3475.00|
| 14:  2.0604 -  2.0103   976   110  0.92  14.27   0.97     0.93       2547.70|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2547.70 max =        10943.17 mean =      6763.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.51|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.230)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.52    83.32   15.22    None  None   None       |
|    all(noH): 2823   0      3.52    83.32   15.22    None  None   None       |
|    Sol.    : 438    0      4.37    83.32   37.91    None  None   None       |
|    Mac.    : 2385   0      3.52    80.36   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.517 -  11.497: 1678   |   5:    43.417 -  51.397:   86        |
|      1:    11.497 -  19.477:  571   |   6:    51.397 -  59.377:   66        |
|      2:    19.477 -  27.457:  155   |   7:    59.377 -  67.357:   38        |
|      3:    27.457 -  35.437:  105   |   8:    67.357 -  75.337:    6        |
|      4:    35.437 -  43.417:  113   |   9:    75.337 -  83.318:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.254 - 4.569
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 317
   mapped sites are within: 0.721 - 4.569

peak=   10.603 closest distance to " CB  VAL A 230 " =    1.490
peak=    6.147 closest distance to " NH2 ARG A  56 " =    2.211
peak=    5.954 closest distance to " CG  LEU A   5 " =    1.235
peak=    5.641 closest distance to " CG  LEU A 228 " =    1.177
peak=    5.560 closest distance to " CB  GLN A 223 " =    1.484
peak=    5.359 closest distance to " CD2 LEU A   5 " =    1.158
peak=    5.037 closest distance to " O   HOH Z 142 " =    1.851
peak=    5.000 closest distance to " CG2 VAL A 296 " =    1.028
peak=    4.949 closest distance to " CB  VAL A 296 " =    1.071
peak=    4.934 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.918 closest distance to " NE2 GLN A  11 " =    1.124
peak=    4.634 closest distance to " O   HOH Z 232 " =    2.321
peak=    4.598 closest distance to " CZ  PHE A 218 " =    1.165
peak=    4.550 closest distance to " CB  SER A  63 " =    1.171
peak=    4.511 closest distance to " O   HOH Z 248 " =    1.493
peak=    4.467 closest distance to " O   HOH Z 265 " =    2.118
peak=    4.456 closest distance to " O   HOH Z 369 " =    2.131
peak=    4.423 closest distance to " O   SER A  87 " =    2.329
peak=    4.348 closest distance to " CB  ARG A 190 " =    1.589
peak=    4.320 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.306 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.265 closest distance to " O   HOH Z 303 " =    2.118
peak=    4.257 closest distance to " CA  ALA A  51 " =    0.993
peak=    4.254 closest distance to " CB  ARG A  79 " =    1.512
peak=    4.249 closest distance to " O   HOH Z 298 " =    1.862
peak=    4.244 closest distance to " ND2 ASN A 187 " =    1.586
peak=    4.226 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.189 closest distance to " O   HOH Z  19 " =    2.244
peak=    4.188 closest distance to " CG  PRO A 198 " =    1.326
peak=    4.171 closest distance to " CB  ASN A 142 " =    1.133
peak=    4.161 closest distance to " O   HOH Z 427 " =    3.042
peak=    4.102 closest distance to " O   PRO A 198 " =    1.575
peak=    4.096 closest distance to " O   HOH Z 411 " =    3.793
peak=    4.091 closest distance to " CG1 VAL A 296 " =    1.163
peak=    4.091 closest distance to " O   HOH Z  61 " =    1.722
peak=    4.070 closest distance to " CG  PRO A 213 " =    1.185
peak=    4.069 closest distance to " O   HOH Z 368 " =    2.330
peak=    4.068 closest distance to " O   HOH Z  43 " =    2.107
peak=    4.064 closest distance to " CB  GLU A  46 " =    0.929
peak=    4.063 closest distance to " O   HOH Z 126 " =    1.935
peak=    4.046 closest distance to " CB  VAL A 230 " =    1.185
peak=    4.029 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.029 closest distance to " NH1AARG A 145 " =    1.254
peak=    4.012 closest distance to " CA  TYR A  30 " =    1.010
peak=    4.011 closest distance to " O   HOH Z  78 " =    1.673
peak=    4.011 closest distance to " O   HOH Z 251 " =    1.588
peak=    4.009 closest distance to " O   HOH Z 313 " =    1.858
peak=    4.004 closest distance to " O   HOH Z 214 " =    2.476
peak=    4.002 closest distance to " O   HOH Z 346 " =    1.609
peak=    4.000 closest distance to " CB  GLU A 277 " =    3.713
peak=    3.990 closest distance to " CG  MET A 185 " =    1.203
peak=    3.981 closest distance to " O   HOH Z 425 " =    1.419
peak=    3.974 closest distance to " O   HOH Z 188 " =    2.978
peak=    3.968 closest distance to " CD  LYS A 166 " =    1.292
peak=    3.950 closest distance to " O  BHOH Z 338 " =    2.340
peak=    3.938 closest distance to " CB  TRP A 266 " =    1.011
peak=    3.916 closest distance to " CG1 ILE A  49 " =    1.570
peak=    3.911 closest distance to " O   HOH Z 422 " =    2.665
peak=    3.907 closest distance to " O   HOH Z 353 " =    2.522
peak=    3.905 closest distance to " CB  ASP A 140 " =    1.025
peak=    3.900 closest distance to " O   HOH Z 423 " =    1.748
peak=    3.893 closest distance to " O   HOH Z 272 " =    1.889
peak=    3.892 closest distance to " CB  VAL A 202 " =    1.580
peak=    3.891 closest distance to " CA  ARG A 195 " =    1.239
peak=    3.877 closest distance to " O   HOH Z 234 " =    3.698
peak=    3.875 closest distance to " CB  GLU A 128 " =    0.958
peak=    3.874 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.869 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.859 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.856 closest distance to " O   HOH Z 273 " =    2.894
peak=    3.843 closest distance to " CD  ARG A 159 " =    0.757
peak=    3.838 closest distance to " O   HOH Z 158 " =    3.194
peak=    3.830 closest distance to " O   HOH Z 402 " =    1.457
peak=    3.825 closest distance to " O   HOH Z 236 " =    2.052
peak=    3.813 closest distance to " N   ASN A  39 " =    1.220
peak=    3.811 closest distance to " O   HOH Z 126 " =    1.604
peak=    3.809 closest distance to " CD2 LEU A 228 " =    1.147
peak=    3.788 closest distance to " CZ3 TRP A 266 " =    1.153
peak=    3.783 closest distance to " O   HOH Z 261 " =    1.928
peak=    3.782 closest distance to " CG2 VAL A 257 " =    0.877
peak=    3.778 closest distance to " O   HOH Z   9 " =    1.352
peak=    3.773 closest distance to " O   HOH Z  40 " =    1.777
peak=    3.773 closest distance to " CB  ASN A  39 " =    0.885
peak=    3.770 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.769 closest distance to " O   HOH Z 359 " =    1.566
peak=    3.753 closest distance to " CG1 VAL A 153 " =    0.942
peak=    3.747 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.741 closest distance to " O   HOH Z 285 " =    2.314
peak=    3.730 closest distance to " N   PHE A 130 " =    1.273
peak=    3.724 closest distance to " OG BSER A 164 " =    2.293
peak=    3.720 closest distance to " CB  LEU A  83 " =    0.732
peak=    3.703 closest distance to " CA  VAL A 125 " =    1.233
peak=    3.701 closest distance to " CD  ARG A 269 " =    0.953
peak=    3.677 closest distance to " O   HOH Z  63 " =    1.910
peak=    3.675 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.663 closest distance to " CG  LEU A 167 " =    1.209
peak=    3.659 closest distance to " O   HOH Z 261 " =    1.720
peak=    3.656 closest distance to " OD1 ASN A  69 " =    2.548
peak=    3.651 closest distance to " CB  THR A  31 " =    1.478
peak=    3.647 closest distance to " CB  PRO A  54 " =    0.791
peak=    3.644 closest distance to " O   HOH Z  80 " =    1.781
peak=    3.644 closest distance to " O   HOH Z 406 " =    1.549
peak=    3.639 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.631 closest distance to " O   HOH Z  59 " =    2.300
peak=    3.626 closest distance to " CA  SER A  87 " =    1.016
peak=    3.620 closest distance to " O   HOH Z  44 " =    2.298
peak=    3.611 closest distance to " CA  TYR A 116 " =    1.498
peak=    3.611 closest distance to " ND2 ASN A 249 " =    1.881
peak=    3.605 closest distance to " CA  ALA A 295 " =    1.102
peak=    3.603 closest distance to " O   HOH Z 316 " =    3.149
peak=    3.599 closest distance to " CB  ALA A 104 " =    0.730
peak=    3.582 closest distance to " CB BVAL A  41 " =    1.129
peak=    3.577 closest distance to " O   ASP A 124 " =    1.108
peak=    3.576 closest distance to " CB  ASN A 187 " =    1.196
peak=    3.552 closest distance to " O   HOH Z 371 " =    2.846
peak=    3.551 closest distance to " CB  SER A   3 " =    1.262
peak=    3.544 closest distance to " O   HOH Z  90 " =    2.213
peak=    3.528 closest distance to " CA  ARG A  36 " =    1.073
peak=    3.525 closest distance to " O   HOH Z  21 " =    1.749
peak=    3.515 closest distance to " O   HOH Z 171 " =    3.977
peak=    3.513 closest distance to " CB  LEU A 143 " =    1.220
peak=    3.504 closest distance to " O   HOH Z  97 " =    2.343
peak=    3.504 closest distance to " O   HOH Z 166 " =    3.762
peak=    3.499 closest distance to " O   HOH Z 403 " =    1.606
peak=    3.496 closest distance to " CG  MET A 185 " =    1.018
peak=    3.492 closest distance to " CA  ASP A 162 " =    0.999
peak=    3.485 closest distance to " CG2AVAL A  72 " =    1.770
peak=    3.483 closest distance to " O   HOH Z 250 " =    1.367
peak=    3.482 closest distance to " O   HOH Z 147 " =    1.793
peak=    3.481 closest distance to " O   HOH Z 193 " =    1.998
peak=    3.480 closest distance to " CZ  PHE A  38 " =    1.152
peak=    3.479 closest distance to " N   SER A 135 " =    1.412
peak=    3.477 closest distance to " O   HOH Z 299 " =    4.329
peak=    3.475 closest distance to " CG  PHE A 204 " =    0.926
peak=    3.475 closest distance to " N   ASP A 162 " =    1.235
peak=    3.469 closest distance to " CA  MET A 105 " =    0.950
peak=    3.460 closest distance to " CA  LEU A 282 " =    1.128
peak=    3.456 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.455 closest distance to " CB  ALA A 291 " =    1.299
peak=    3.451 closest distance to " CB  GLN A  89 " =    1.198
peak=    3.450 closest distance to " CB  THR A  82 " =    1.382
peak=    3.450 closest distance to " O   HOH Z 227 " =    1.742
peak=    3.449 closest distance to " O   HOH Z 213 " =    1.859
peak=    3.448 closest distance to " O   HOH Z 193 " =    1.985
peak=    3.445 closest distance to " CG BARG A 102 " =    1.752
peak=    3.444 closest distance to " CB  PRO A  90 " =    1.190
peak=    3.444 closest distance to " CA  THR A 264 " =    0.766
peak=    3.441 closest distance to " CB  GLN A 205 " =    1.094
peak=    3.435 closest distance to " CG BARG A 275 " =    1.349
peak=    3.435 closest distance to " O   GLN A  88 " =    1.687
peak=    3.430 closest distance to " NE2 GLN A  77 " =    3.348
peak=    3.417 closest distance to " CD ALYS A 290 " =    1.060
peak=    3.416 closest distance to " CB  PHE A 204 " =    0.895
peak=    3.416 closest distance to " O   HOH Z 290 " =    1.087
peak=    3.415 closest distance to " CB  SER A 212 " =    1.249
peak=    3.398 closest distance to " CD1 ILE A 199 " =    0.890
peak=    3.398 closest distance to " O   HOH Z 148 " =    3.310
peak=    3.392 closest distance to " O   ASN A 284 " =    1.708
peak=    3.392 closest distance to " NH2AARG A 145 " =    1.305
peak=    3.389 closest distance to " CA  ASP A 191 " =    1.180
peak=    3.387 closest distance to " CD  ARG A  66 " =    2.629
peak=    3.386 closest distance to " CG2 THR A 221 " =    1.178
peak=    3.380 closest distance to " O   HOH Z 365 " =    2.879
peak=    3.377 closest distance to " CB  MET A  40 " =    0.806
peak=    3.371 closest distance to " CB  ASP A 298 " =    1.189
peak=    3.369 closest distance to " CB  GLN A 103 " =    1.023
peak=    3.367 closest distance to " OE1 GLN A  55 " =    1.512
peak=    3.367 closest distance to " CB  GLN A  88 " =    1.198
peak=    3.363 closest distance to " O   HOH Z 329 " =    4.215
peak=    3.362 closest distance to " O   HOH Z 172 " =    3.830
peak=    3.360 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.359 closest distance to " O   HOH Z 197 " =    2.921
peak=    3.358 closest distance to " OG  SER A 245 " =    1.574
peak=    3.357 closest distance to " O   HOH Z 294 " =    1.580
peak=    3.357 closest distance to " CB  LEU A 228 " =    1.208
peak=    3.355 closest distance to " CA  GLY A 211 " =    1.407
peak=    3.355 closest distance to " O   PHE A 192 " =    1.444
peak=    3.354 closest distance to " CB  ALA A 100 " =    1.244
peak=    3.353 closest distance to " CB  ASN A 110 " =    1.128
peak=    3.353 closest distance to " O   MET A 105 " =    1.826
peak=    3.351 closest distance to " CA  LYS A 117 " =    1.266
peak=    3.350 closest distance to " CD1 LEU A 300 " =    1.167
peak=    3.349 closest distance to " CB  TRP A 150 " =    1.352
peak=    3.348 closest distance to " O   HOH Z   4 " =    1.599
peak=    3.346 closest distance to " O   PHE A  61 " =    1.422
peak=    3.345 closest distance to " O   HOH Z  66 " =    2.183
peak=    3.345 closest distance to " NH2 ARG A 156 " =    1.094
peak=    3.342 closest distance to " CA  ALA A 154 " =    1.017
peak=    3.342 closest distance to " CA  ASN A 217 " =    1.266
peak=    3.341 closest distance to " O   HOH Z 368 " =    3.414
peak=    3.337 closest distance to " NE2 HIS A 207 " =    1.189
peak=    3.329 closest distance to " O   HOH Z 305 " =    3.566
peak=    3.326 closest distance to " CZ  PHE A 192 " =    1.017
peak=    3.324 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.324 closest distance to " O   ALA A 165 " =    1.479
peak=    3.318 closest distance to " O   HOH Z  76 " =    1.217
peak=    3.313 closest distance to " CZ3 TRP A 274 " =    4.569
peak=    3.311 closest distance to " O   HOH Z 187 " =    2.330
peak=    3.308 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.307 closest distance to " CB  VAL A 268 " =    0.816
peak=    3.306 closest distance to " CB  ALA A 242 " =    0.774
peak=    3.301 closest distance to " CB  ARG A 138 " =    0.970
peak=    3.301 closest distance to " O   HOH Z  88 " =    3.049
peak=    3.300 closest distance to " CA  TYR A  30 " =    1.065
peak=    3.299 closest distance to " ND2 ASN A 249 " =    0.853
peak=    3.299 closest distance to " O   HOH Z 130 " =    2.221
peak=    3.298 closest distance to " CE1 TYR A 186 " =    1.240
peak=    3.295 closest distance to " CG  GLU A  37 " =    0.895
peak=    3.295 closest distance to " O   HOH Z 238 " =    3.629
peak=    3.295 closest distance to " CD1 LEU A   5 " =    1.356
peak=    3.291 closest distance to " NZ  LYS A  48 " =    1.246
peak=    3.291 closest distance to " CB  ALA A 248 " =    1.389
peak=    3.290 closest distance to " CB  PRO A 243 " =    1.495
peak=    3.288 closest distance to " CA  ILE A 106 " =    0.748
peak=    3.288 closest distance to " O   HOH Z 154 " =    1.395
peak=    3.287 closest distance to " CZ3 TRP A  85 " =    1.070
peak=    3.287 closest distance to " O   ASN A  74 " =    1.438
peak=    3.287 closest distance to " O   HOH Z 145 " =    2.139
peak=    3.285 closest distance to " CA  ALA A 129 " =    1.422
peak=    3.283 closest distance to " O   ALA A 158 " =    1.383
peak=    3.282 closest distance to " O   HOH Z  97 " =    2.001
peak=    3.282 closest distance to " CB  SER A 273 " =    0.889
peak=    3.278 closest distance to " CG AARG A 275 " =    1.284
peak=    3.277 closest distance to " O   GLU A   2 " =    1.583
peak=    3.276 closest distance to " CA  ALA A  21 " =    1.100
peak=    3.275 closest distance to " O   HOH Z  10 " =    1.750
peak=    3.271 closest distance to " CD1 ILE A  33 " =    1.777
peak=    3.270 closest distance to " CB  HIS A 108 " =    0.782
peak=    3.267 closest distance to " O   HOH Z 258 " =    2.081
peak=    3.266 closest distance to " NH2AARG A 275 " =    3.440
peak=    3.265 closest distance to " CB  SER A  26 " =    1.856
peak=    3.263 closest distance to " CB  ASN A 173 " =    1.055
peak=    3.263 closest distance to " O   HOH Z 128 " =    2.322
peak=    3.263 closest distance to " CG2 ILE A 234 " =    0.902
peak=    3.262 closest distance to " CB  ALA A 227 " =    1.010
peak=    3.261 closest distance to " O   HOH Z  48 " =    1.567
peak=    3.261 closest distance to " O   HOH Z 128 " =    2.229
peak=    3.260 closest distance to " O   PRO A 213 " =    1.489
peak=    3.256 closest distance to " O   HOH Z 417 " =    3.342
peak=    3.251 closest distance to " CA  ASN A 215 " =    1.149
peak=    3.249 closest distance to " O   HOH Z  88 " =    3.385
peak=    3.246 closest distance to " CB  ALA A 114 " =    1.176
peak=    3.245 closest distance to " O   HOH Z 203 " =    1.707
peak=    3.244 closest distance to " O   HOH Z 380 " =    1.856
peak=    3.243 closest distance to " O   HOH Z 141 " =    1.629
peak=    3.236 closest distance to " CB  ALA A 248 " =    1.141
peak=    3.231 closest distance to " O   HOH Z 383 " =    1.905
peak=    3.219 closest distance to " O   LYS A 290 " =    2.412
peak=    3.214 closest distance to " O   HOH Z 350 " =    1.640
peak=    3.212 closest distance to " CE3 TRP A 150 " =    1.043
peak=    3.210 closest distance to " CA  ARG A 159 " =    1.210
peak=    3.207 closest distance to " CA  ASN A 127 " =    1.061
peak=    3.205 closest distance to " O   HOH Z 133 " =    2.631
peak=    3.201 closest distance to " CG2 ILE A  20 " =    1.414
peak=    3.199 closest distance to " CB  PRO A 198 " =    1.105
peak=    3.183 closest distance to " CG  ARG A 138 " =    1.173
peak=    3.182 closest distance to " CD  LYS A 119 " =    2.045
peak=    3.182 closest distance to " OG  SER A  28 " =    1.530
peak=    3.180 closest distance to " ND1 HIS A  81 " =    1.702
peak=    3.180 closest distance to " CG2 ILE A 120 " =    1.152
peak=    3.179 closest distance to " N   ARG A 156 " =    1.391
peak=    3.178 closest distance to " OG  SER A  22 " =    2.798
peak=    3.177 closest distance to " CA  THR A 221 " =    0.905
peak=    3.177 closest distance to " O   HOH Z 390 " =    2.725
peak=    3.175 closest distance to " O   THR A 220 " =    1.254
peak=    3.174 closest distance to " CB  ASN A 215 " =    1.191
peak=    3.169 closest distance to " O   HOH Z 185 " =    1.886
peak=    3.168 closest distance to " CA  ARG A 139 " =    1.089
peak=    3.166 closest distance to " O   ASP A 200 " =    1.601
peak=    3.165 closest distance to " CB  SER A  62 " =    1.128
peak=    3.163 closest distance to " C   ALA A 299 " =    0.874
peak=    3.158 closest distance to " CG2 THR A 220 " =    0.723
peak=    3.158 closest distance to " O   HOH Z 325 " =    2.149
peak=    3.155 closest distance to " CG  GLN A  11 " =    1.791
peak=    3.147 closest distance to " O   TRP A 274 " =    1.833
peak=    3.146 closest distance to " O   ARG A  56 " =    3.027
peak=    3.144 closest distance to " CB  ASN A 285 " =    0.963
peak=    3.141 closest distance to " CB  TYR A 116 " =    0.887
peak=    3.133 closest distance to " O   HOH Z 302 " =    2.027
peak=    3.131 closest distance to " OG1 THR A 264 " =    0.781
peak=    3.131 closest distance to " O   HOH Z  47 " =    1.812
peak=    3.129 closest distance to " CG  GLN A  88 " =    1.070
peak=    3.129 closest distance to " CA  ALA A 233 " =    1.552
peak=    3.129 closest distance to " CB  LEU A 300 " =    0.846
peak=    3.123 closest distance to " CB  ALA A 295 " =    1.386
peak=    3.118 closest distance to " O   TYR A 116 " =    1.306
peak=    3.117 closest distance to " O   HOH Z 171 " =    2.394
peak=    3.114 closest distance to " O   LEU A 228 " =    1.858
peak=    3.113 closest distance to " O   HOH Z 193 " =    1.761
peak=    3.112 closest distance to " O   HOH Z 234 " =    1.835
peak=    3.102 closest distance to " CB  PRO A  54 " =    1.286
peak=    3.101 closest distance to " CB  SER A 216 " =    0.786
peak=    3.094 closest distance to " O   THR A 182 " =    1.375
peak=    3.091 closest distance to " CD2 LEU A   5 " =    0.736
peak=    3.087 closest distance to " CB  VAL A 257 " =    0.733
peak=    3.084 closest distance to " OH  TYR A 214 " =    1.227
peak=    3.082 closest distance to " CA  VAL A  41 " =    0.811
peak=    3.077 closest distance to " CE1 PHE A 218 " =    1.209
peak=    3.074 closest distance to " CB  ARG A 139 " =    0.923
peak=    3.072 closest distance to " O   HOH Z 409 " =    3.308
peak=    3.067 closest distance to " CB  ALA A  43 " =    0.823
peak=    3.067 closest distance to " CB  ILE A 120 " =    1.341
peak=    3.065 closest distance to " O   HOH Z 116 " =    1.787
peak=    3.062 closest distance to " O   HOH Z 263 " =    1.682
peak=    3.061 closest distance to " O   HOH Z 344 " =    2.961
peak=    3.046 closest distance to " CD  ARG A  79 " =    1.974
peak=    3.045 closest distance to " O   HOH Z 201 " =    2.914
peak=    3.039 closest distance to " O   SER A 164 " =    1.235
peak=    3.037 closest distance to " O   HOH Z 134 " =    2.815
peak=    3.028 closest distance to " O   ASP A 124 " =    1.776
peak=    3.023 closest distance to " CA  ASP A 149 " =    1.124

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.750 - 5.574
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.750 - 5.574

peak=   -5.282 closest distance to " CG2 VAL A 230 " =    0.751
peak=   -4.733 closest distance to " CD  GLN A  58 " =    0.955
peak=   -4.684 closest distance to " CD  ARG A  14 " =    3.390
peak=   -4.545 closest distance to " O   HOH Z 211 " =    1.159
peak=   -4.472 closest distance to " CG1 VAL A 112 " =    2.648
peak=   -4.339 closest distance to " CD  ARG A 156 " =    2.020
peak=   -4.302 closest distance to " CB  PRO A 243 " =    2.688
peak=   -4.189 closest distance to " CB  PHE A 192 " =    2.005
peak=   -4.155 closest distance to " CG1 VAL A 112 " =    2.742
peak=   -4.141 closest distance to " O   HOH Z 411 " =    5.574
peak=   -4.120 closest distance to " CG2BVAL A  41 " =    2.652
peak=   -4.067 closest distance to " O   HOH Z 196 " =    2.272
peak=   -4.046 closest distance to " CA  ASP A 298 " =    1.081
peak=   -4.041 closest distance to " OG  SER A  97 " =    2.367
peak=   -4.031 closest distance to " CG1 VAL A 250 " =    2.811
peak=   -3.990 closest distance to " O   HOH Z  73 " =    2.346
peak=   -3.988 closest distance to " CA  VAL A  67 " =    2.804
peak=   -3.959 closest distance to " O   HOH Z 394 " =    1.568
peak=   -3.938 closest distance to " O   HOH Z 290 " =    1.200
peak=   -3.893 closest distance to " C   HIS A 108 " =    1.180
peak=   -3.881 closest distance to " CD2 TYR A 293 " =    2.021
peak=   -3.871 closest distance to " CG1 VAL A 296 " =    1.228
peak=   -3.866 closest distance to " CZ2 TRP A  92 " =    2.844
peak=   -3.850 closest distance to " CG  ARG A 269 " =    2.349
peak=   -3.847 closest distance to " CG  GLN A 223 " =    2.158
peak=   -3.847 closest distance to " O   HOH Z 351 " =    1.565
peak=   -3.834 closest distance to " OG BSER A 134 " =    1.293
peak=   -3.827 closest distance to " OD1 ASN A 148 " =    1.388
peak=   -3.822 closest distance to " O   HOH Z 231 " =    2.184
peak=   -3.822 closest distance to " O   PRO A 163 " =    2.217
peak=   -3.815 closest distance to " O   HOH Z 216 " =    1.098
peak=   -3.798 closest distance to " O   ILE A 109 " =    2.643
peak=   -3.797 closest distance to " CE2 TYR A  30 " =    2.686
peak=   -3.756 closest distance to " CH2 TRP A 179 " =    1.224
peak=   -3.752 closest distance to " CE3 TRP A 150 " =    2.263
peak=   -3.735 closest distance to " O   HOH Z 133 " =    1.179
peak=   -3.713 closest distance to " O   PRO A 198 " =    1.237
peak=   -3.709 closest distance to " CD2 PHE A  61 " =    2.640
peak=   -3.700 closest distance to " CA  GLY A 241 " =    3.185
peak=   -3.697 closest distance to " CA  GLY A 241 " =    2.391
peak=   -3.695 closest distance to " NH2AARG A 275 " =    5.246
peak=   -3.695 closest distance to " CG  GLU A 277 " =    1.202
peak=   -3.683 closest distance to " O   HOH Z  37 " =    1.862
peak=   -3.682 closest distance to " O   HOH Z 429 " =    2.018
peak=   -3.668 closest distance to " O   HOH Z 166 " =    1.869
peak=   -3.659 closest distance to " N   THR A  52 " =    1.687
peak=   -3.658 closest distance to " CE BMET A  47 " =    1.701
peak=   -3.651 closest distance to " CG  HIS A  86 " =    1.169
peak=   -3.637 closest distance to " O   SER A 271 " =    2.175
peak=   -3.636 closest distance to " NE2 GLN A 194 " =    1.874
peak=   -3.626 closest distance to " O   HOH Z 193 " =    1.450
peak=   -3.622 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.606 closest distance to " O   HOH Z 377 " =    2.075
peak=   -3.603 closest distance to " C   ALA A 158 " =    1.401
peak=   -3.593 closest distance to " O   HOH Z  44 " =    2.357
peak=   -3.580 closest distance to " CB  ALA A 248 " =    2.344
peak=   -3.572 closest distance to " N   ALA A 226 " =    2.082
peak=   -3.571 closest distance to " O   HOH Z 102 " =    1.673
peak=   -3.566 closest distance to " O   HOH Z 185 " =    2.444
peak=   -3.558 closest distance to " CD1 LEU A 101 " =    2.417
peak=   -3.553 closest distance to " CG2BVAL A  41 " =    1.777
peak=   -3.551 closest distance to " CB  ALA A  43 " =    2.548
peak=   -3.547 closest distance to " OXT GLY A 302 " =    3.010
peak=   -3.546 closest distance to " CG2 VAL A 296 " =    1.215
peak=   -3.541 closest distance to " O   HOH Z 357 " =    2.209
peak=   -3.528 closest distance to " O   HOH Z 128 " =    2.606
peak=   -3.522 closest distance to " OE1 GLN A  88 " =    0.942
peak=   -3.514 closest distance to " O   VAL A 189 " =    2.673
peak=   -3.512 closest distance to " O   HOH Z 435 " =    2.789
peak=   -3.505 closest distance to " ND2 ASN A 249 " =    2.486
peak=   -3.486 closest distance to " O   HOH Z  10 " =    1.501
peak=   -3.485 closest distance to " O   HOH Z 359 " =    2.886
peak=   -3.484 closest distance to " OD1 ASN A 249 " =    2.495
peak=   -3.483 closest distance to " C   MET A 188 " =    1.373
peak=   -3.477 closest distance to " O   HOH Z  52 " =    1.639
peak=   -3.477 closest distance to " O   HOH Z 252 " =    3.848
peak=   -3.470 closest distance to " C   LEU A 143 " =    1.010
peak=   -3.469 closest distance to " ND2 ASN A  45 " =    1.534
peak=   -3.467 closest distance to " O   HOH Z  11 " =    1.894
peak=   -3.466 closest distance to " CG1 VAL A 265 " =    2.413
peak=   -3.466 closest distance to " O   HOH Z 136 " =    2.547
peak=   -3.463 closest distance to " O   HOH Z 114 " =    3.033
peak=   -3.455 closest distance to " O   HOH Z 177 " =    1.865
peak=   -3.455 closest distance to " CE3 TRP A  70 " =    1.786
peak=   -3.447 closest distance to " N   ALA A  43 " =    2.632
peak=   -3.440 closest distance to " CD2 LEU A 167 " =    1.864
peak=   -3.438 closest distance to " CB  VAL A 230 " =    1.091
peak=   -3.435 closest distance to " O   HOH Z  38 " =    1.652
peak=   -3.408 closest distance to " CD  PRO A 243 " =    2.053
peak=   -3.406 closest distance to " CA  GLY A 133 " =    2.249
peak=   -3.401 closest distance to " CB  PRO A 163 " =    2.471
peak=   -3.397 closest distance to " CG1 VAL A  67 " =    2.900
peak=   -3.396 closest distance to " NE2 GLN A  88 " =    2.127
peak=   -3.395 closest distance to " O   HOH Z 149 " =    2.145
peak=   -3.394 closest distance to " O   ASP A  27 " =    2.066
peak=   -3.387 closest distance to " CD  PRO A 213 " =    2.114
peak=   -3.377 closest distance to " CD1 PHE A  59 " =    2.084
peak=   -3.376 closest distance to " OD1 ASP A 171 " =    1.683
peak=   -3.371 closest distance to " CD1 LEU A 228 " =    2.302
peak=   -3.362 closest distance to " O   GLY A  17 " =    1.271
peak=   -3.355 closest distance to " CD1 ILE A 199 " =    2.561
peak=   -3.349 closest distance to " O   GLY A  80 " =    2.598
peak=   -3.345 closest distance to " O   GLY A  80 " =    2.539
peak=   -3.331 closest distance to " O   HOH Z 241 " =    1.223
peak=   -3.331 closest distance to " OG  SER A  87 " =    1.533
peak=   -3.330 closest distance to " CG  ARG A 269 " =    2.061
peak=   -3.330 closest distance to " ND2 ASN A  45 " =    1.316
peak=   -3.330 closest distance to " CA  GLY A  98 " =    1.977
peak=   -3.327 closest distance to " NE2 GLN A  88 " =    0.983
peak=   -3.324 closest distance to " CD1 ILE A 239 " =    2.124
peak=   -3.323 closest distance to " O   HOH Z 222 " =    1.546
peak=   -3.312 closest distance to " CB  ASP A 171 " =    2.319
peak=   -3.310 closest distance to " O   ALA A 227 " =    1.570
peak=   -3.310 closest distance to " O   HOH Z  60 " =    1.647
peak=   -3.310 closest distance to " CG  TRP A 266 " =    1.771
peak=   -3.309 closest distance to " CG  PHE A 283 " =    2.699
peak=   -3.305 closest distance to " O   HOH Z 251 " =    5.036
peak=   -3.301 closest distance to " O   HOH Z 106 " =    1.830
peak=   -3.300 closest distance to " O   SER A 210 " =    1.907
peak=   -3.300 closest distance to " NE2 GLN A  11 " =    1.777
peak=   -3.299 closest distance to " O   HOH Z 407 " =    3.078
peak=   -3.296 closest distance to " CG  PRO A 163 " =    2.496
peak=   -3.279 closest distance to " C   PHE A  59 " =    1.298
peak=   -3.267 closest distance to " OD2 ASP A  50 " =    2.273
peak=   -3.266 closest distance to " O   HOH Z 145 " =    1.234
peak=   -3.265 closest distance to " O   HOH Z 238 " =    0.975
peak=   -3.257 closest distance to " O   HOH Z 434 " =    1.650
peak=   -3.257 closest distance to " O   HOH Z  44 " =    1.042
peak=   -3.257 closest distance to " ND2 ASN A 187 " =    1.467
peak=   -3.255 closest distance to " C   ASP A 270 " =    1.154
peak=   -3.248 closest distance to " CD2 LEU A 300 " =    2.999
peak=   -3.248 closest distance to " NE2 GLN A 278 " =    1.837
peak=   -3.247 closest distance to " O   SER A 276 " =    1.726
peak=   -3.244 closest distance to " NH2 ARG A  79 " =    1.570
peak=   -3.239 closest distance to " N   ASP A 171 " =    2.311
peak=   -3.234 closest distance to " O   HOH Z 198 " =    2.275
peak=   -3.233 closest distance to " O   HOH Z 285 " =    1.953
peak=   -3.232 closest distance to " O   HOH Z 234 " =    4.309
peak=   -3.229 closest distance to " C   LYS A  76 " =    1.559
peak=   -3.228 closest distance to " CB  ALA A 129 " =    2.508
peak=   -3.228 closest distance to " CB  ASP A 132 " =    2.344
peak=   -3.227 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.225 closest distance to " OH  TYR A 247 " =    1.912
peak=   -3.224 closest distance to " CG1 VAL A 125 " =    1.878
peak=   -3.224 closest distance to " CB  ALA A 291 " =    2.428
peak=   -3.224 closest distance to " N   SER A 276 " =    1.453
peak=   -3.222 closest distance to " CD2 PHE A  61 " =    1.980
peak=   -3.221 closest distance to " O   HOH Z 136 " =    0.801
peak=   -3.218 closest distance to " O   HOH Z 431 " =    1.868
peak=   -3.217 closest distance to " CD2 PHE A 225 " =    1.120
peak=   -3.216 closest distance to " N   SER A   3 " =    2.073
peak=   -3.215 closest distance to " O   GLY A 196 " =    1.237
peak=   -3.211 closest distance to " NE2 GLN A 103 " =    1.850
peak=   -3.210 closest distance to " O   HOH Z   6 " =    1.568
peak=   -3.207 closest distance to " O   HOH Z 396 " =    2.206
peak=   -3.202 closest distance to " O   HOH Z 265 " =    1.832
peak=   -3.198 closest distance to " O   HOH Z 371 " =    2.339
peak=   -3.195 closest distance to " CB  TRP A 177 " =    2.278
peak=   -3.192 closest distance to " CE  MET A 105 " =    2.299
peak=   -3.190 closest distance to " NH2 ARG A  36 " =    2.419
peak=   -3.189 closest distance to " O   HOH Z 191 " =    5.566
peak=   -3.188 closest distance to " O   HOH Z 191 " =    3.369
peak=   -3.187 closest distance to " CD  GLN A 223 " =    1.248
peak=   -3.178 closest distance to " O   HOH Z   9 " =    1.637
peak=   -3.178 closest distance to " CG  MET A 105 " =    0.953
peak=   -3.177 closest distance to " CA  GLY A 203 " =    2.501
peak=   -3.176 closest distance to " O   HOH Z 262 " =    2.868
peak=   -3.173 closest distance to " O   HOH Z 176 " =    0.750
peak=   -3.172 closest distance to " CE  LYS A  76 " =    2.617
peak=   -3.171 closest distance to " OG BSER A 210 " =    1.569
peak=   -3.169 closest distance to " CG1 VAL A 197 " =    2.285
peak=   -3.167 closest distance to " CD1 ILE A  33 " =    2.511
peak=   -3.167 closest distance to " O   HOH Z  47 " =    1.688
peak=   -3.163 closest distance to " CG1 VAL A  67 " =    3.053
peak=   -3.162 closest distance to " CZ  TYR A 169 " =    1.768
peak=   -3.157 closest distance to " O   HOH Z 166 " =    1.735
peak=   -3.155 closest distance to " CD2 LEU A 237 " =    2.912
peak=   -3.154 closest distance to " O   HOH Z 313 " =    1.183
peak=   -3.151 closest distance to " CG2 VAL A 189 " =    1.998
peak=   -3.151 closest distance to " N   ALA A 248 " =    2.439
peak=   -3.146 closest distance to " OD1 ASN A 173 " =    1.365
peak=   -3.140 closest distance to " O   HOH Z 380 " =    1.431
peak=   -3.134 closest distance to " O   HOH Z 123 " =    2.484
peak=   -3.131 closest distance to " N   ALA A 248 " =    1.869
peak=   -3.131 closest distance to " O   MET A  40 " =    2.826
peak=   -3.128 closest distance to " O   HOH Z 326 " =    5.065
peak=   -3.126 closest distance to " N   TRP A 274 " =    1.172
peak=   -3.124 closest distance to " O   GLY A 211 " =    1.376
peak=   -3.121 closest distance to " CA  SER A  62 " =    2.509
peak=   -3.119 closest distance to " O   HOH Z 140 " =    1.575
peak=   -3.119 closest distance to " O   HOH Z  43 " =    1.669
peak=   -3.116 closest distance to " CG  ARG A 259 " =    2.393
peak=   -3.112 closest distance to " CB  TRP A  85 " =    2.649
peak=   -3.110 closest distance to " O   HOH Z 409 " =    4.868
peak=   -3.110 closest distance to " CB  ALA A 291 " =    2.229
peak=   -3.095 closest distance to " CG1BVAL A  72 " =    2.460
peak=   -3.091 closest distance to " O   HOH Z 313 " =    1.575
peak=   -3.078 closest distance to " OG  SER A 206 " =    1.769
peak=   -3.069 closest distance to " OG BSER A 134 " =    1.898
peak=   -3.041 closest distance to " O   PRO A 198 " =    1.354

================= 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    :  0.4565 0.4446   6.255674e+00   6.231570e+00
   1_bss:  0.4473 0.4295   6.250127e+00   6.219315e+00
   1_xyz:  0.3459 0.3706   6.082076e+00   6.117848e+00
   1_adp:  0.2935 0.3347   5.953232e+00   6.047189e+00
   1_occ:  0.2928 0.3356   5.952377e+00   6.048919e+00
   2_bss:  0.2906 0.3340   5.954451e+00   6.049147e+00
   2_xyz:  0.2043 0.2530   5.646187e+00   5.809659e+00
   2_adp:  0.1824 0.2305   5.554392e+00   5.737446e+00
   2_occ:  0.1822 0.2311   5.554574e+00   5.739087e+00
   3_bss:  0.1808 0.2308   5.554730e+00   5.738747e+00
   3_xyz:  0.1380 0.1814   5.310313e+00   5.523902e+00
   3_adp:  0.1283 0.1746   5.257788e+00   5.489645e+00
   3_occ:  0.1282 0.1746   5.257636e+00   5.489677e+00
   4_bss:  0.1283 0.1745   5.256966e+00   5.487593e+00
   4_xyz:  0.1239 0.1701   5.231058e+00   5.461576e+00
   4_adp:  0.1255 0.1675   5.230526e+00   5.445696e+00
   4_occ:  0.1252 0.1674   5.228615e+00   5.443881e+00
   5_bss:  0.1252 0.1673   5.228502e+00   5.443899e+00
   5_xyz:  0.1173 0.1628   5.182860e+00   5.417996e+00
   5_adp:  0.1159 0.1627   5.176767e+00   5.417444e+00
   5_occ:  0.1159 0.1627   5.176534e+00   5.417200e+00
   5_bss:  0.1159 0.1627   5.176552e+00   5.417231e+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:  0.351  50.000   6.471   7.299  11.264   0.000   0.000   0.000
   1_xyz:  0.351  50.000   6.471   7.299  11.264   0.000   0.000   0.000
   1_adp:  0.351  50.000   6.471   7.299  11.264   0.000   0.000   0.000
   1_occ:  0.351  50.000   6.471   7.299  11.264   0.000   0.000   0.000
   2_bss:  0.319  48.804   3.717   4.512   7.997   0.000   0.000   0.000
   2_xyz:  0.319  48.804   3.717   4.512   7.997   0.000   0.000   0.000
   2_adp:  0.319  48.804   3.717   4.512   7.997   0.000   0.000   0.000
   2_occ:  0.319  48.804   3.717   4.512   7.997   0.000   0.000   0.000
   3_bss:  0.331  61.317   2.780   3.396   5.347   0.000   0.000   0.000
   3_xyz:  0.331  61.317   2.780   3.396   5.347   0.000   0.000   0.000
   3_adp:  0.331  61.317   2.780   3.396   5.347   0.000   0.000   0.000
   3_occ:  0.331  61.317   2.780   3.396   5.347   0.000   0.000   0.000
   4_bss:  0.331  61.317   2.700   3.168   4.798   0.000   0.000   0.000
   4_xyz:  0.331  61.317   2.700   3.168   4.798   0.000   0.000   0.000
   4_adp:  0.331  61.317   2.700   3.168   4.798   0.000   0.000   0.000
   4_occ:  0.331  61.317   2.700   3.168   4.798   0.000   0.000   0.000
   5_bss:  0.329  60.026   2.648   3.038   4.592   0.000   0.000   0.000
   5_xyz:  0.329  60.026   2.648   3.038   4.592   0.000   0.000   0.000
   5_adp:  0.329  60.026   2.648   3.038   4.592   0.000   0.000   0.000
   5_occ:  0.329  60.026   2.648   3.038   4.592   0.000   0.000   0.000
   5_bss:  0.329  63.543  -0.749  -0.399   1.148   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.389 0.5168  0.5753    57100.594
   1_bss:  49.063 0.5328  0.7635    54776.213
   1_xyz:  40.607 0.6348  0.8791    37787.876
   1_adp:  35.252 0.6988  0.9643    30480.584
   1_occ:  35.318 0.6981  0.9627    30608.007
   2_bss:  35.248 0.6988  0.8682    30526.760
   2_xyz:  25.063 0.8106  0.9808    16175.717
   2_adp:  22.487 0.8376  0.9989    13648.410
   2_occ:  22.541 0.8370  0.9982    13693.243
   3_bss:  22.489 0.8377  0.9447    13720.619
   3_xyz:  16.943 0.8901  0.9744     8458.662
   3_adp:  16.057 0.8981  0.9718     7865.522
   3_occ:  16.056 0.8981  0.9718     7864.158
   4_bss:  16.028 0.8983  0.9619     7822.164
   4_xyz:  15.377 0.9041  0.9647     7354.857
   4_adp:  15.010 0.9073  0.9651     7170.678
   4_occ:  14.983 0.9076  0.9651     7153.008
   5_bss:  14.981 0.9076  0.9607     7152.575
   5_xyz:  14.484 0.9115  0.9637     6797.729
   5_adp:  14.458 0.9118  0.9603     6767.141
   5_occ:  14.454 0.9118  0.9602     6762.450
   5_bss:  14.454 0.9118  0.9634     6763.443
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4427e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4427e+01
   1_xyz:   1.652  0.013  0.107 18.131  0.006  4.114   1.3616e-01
   1_adp:   1.652  0.013  0.107 18.131  0.006  4.114   1.3616e-01
   1_occ:   1.652  0.013  0.107 18.131  0.006  4.114   1.3616e-01
   2_bss:   1.652  0.013  0.107 18.131  0.006  4.114   1.3616e-01
   2_xyz:   1.110  0.009  0.075 16.525  0.004  4.133   7.6158e-02
   2_adp:   1.110  0.009  0.075 16.525  0.004  4.133   7.6158e-02
   2_occ:   1.110  0.009  0.075 16.525  0.004  4.133   7.6158e-02
   3_bss:   1.110  0.009  0.075 16.525  0.004  4.133   7.6158e-02
   3_xyz:   1.113  0.009  0.085 16.192  0.004  4.135   7.4243e-02
   3_adp:   1.113  0.009  0.085 16.192  0.004  4.135   7.4243e-02
   3_occ:   1.113  0.009  0.085 16.192  0.004  4.135   7.4243e-02
   4_bss:   1.113  0.009  0.085 16.192  0.004  4.135   7.4243e-02
   4_xyz:   0.959  0.007  0.075 15.631  0.003  4.124   5.8965e-02
   4_adp:   0.959  0.007  0.075 15.631  0.003  4.124   5.8965e-02
   4_occ:   0.959  0.007  0.075 15.631  0.003  4.124   5.8965e-02
   5_bss:   0.959  0.007  0.075 15.631  0.003  4.124   5.8965e-02
   5_xyz:   1.116  0.010  0.089 15.701  0.004  4.130   7.6195e-02
   5_adp:   1.116  0.010  0.089 15.701  0.004  4.130   7.6195e-02
   5_occ:   1.116  0.010  0.089 15.701  0.004  4.130   7.6195e-02
   5_bss:   1.116  0.010  0.089 15.701  0.004  4.130   7.6195e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0567e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0567e+00
   1_xyz:  14.650  0.155  0.448 87.379  0.036  2.205   1.0258e-01
   1_adp:  14.650  0.155  0.448 87.379  0.036  2.205   1.0258e-01
   1_occ:  14.650  0.155  0.448 87.379  0.036  2.205   1.0258e-01
   2_bss:  14.650  0.155  0.448 87.379  0.036  2.205   1.0258e-01
   2_xyz:   7.450  0.076  0.263 87.675  0.032  2.337   9.1440e-02
   2_adp:   7.450  0.076  0.263 87.675  0.032  2.337   9.1440e-02
   2_occ:   7.450  0.076  0.263 87.675  0.032  2.337   9.1440e-02
   3_bss:   7.450  0.076  0.263 87.675  0.032  2.337   9.1440e-02
   3_xyz:   7.061  0.050  0.380 85.068  0.040  2.346   5.3656e-02
   3_adp:   7.061  0.050  0.380 85.068  0.040  2.346   5.3656e-02
   3_occ:   7.061  0.050  0.380 85.068  0.040  2.346   5.3656e-02
   4_bss:   7.061  0.050  0.380 85.068  0.040  2.346   5.3656e-02
   4_xyz:   7.155  0.040  0.348 81.659  0.036  2.434   3.2169e-02
   4_adp:   7.155  0.040  0.348 81.659  0.036  2.434   3.2169e-02
   4_occ:   7.155  0.040  0.348 81.659  0.036  2.434   3.2169e-02
   5_bss:   7.155  0.040  0.348 81.659  0.036  2.434   3.2169e-02
   5_xyz:   7.563  0.054  0.499 82.118  0.038  2.334   5.1283e-02
   5_adp:   7.563  0.054  0.499 82.118  0.038  2.334   5.1283e-02
   5_occ:   7.563  0.054  0.499 82.118  0.038  2.334   5.1283e-02
   5_bss:   7.563  0.054  0.499 82.118  0.038  2.334   5.1283e-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:  53.82   0.00  11.06  50.54   0.00   8.41  53.82   0.00  25.50
   1_occ:  53.82   0.00  11.06  50.54   0.00   8.41  53.82   0.00  25.50
   2_bss:  53.82   0.00  11.06  50.54   0.00   8.41  53.82   0.00  25.50
   2_xyz:  53.82   0.00  11.06  50.54   0.00   8.41  53.82   0.00  25.50
   2_adp:  65.60   0.00  11.50  65.60   0.00   7.76  60.53   0.00  31.88
   2_occ:  65.60   0.00  11.50  65.60   0.00   7.76  60.53   0.00  31.88
   3_bss:  65.60   0.00  11.50  65.60   0.00   7.76  60.53   0.00  31.88
   3_xyz:  65.60   0.00  11.50  65.60   0.00   7.76  60.53   0.00  31.88
   3_adp:  81.08   0.00  12.39  77.61   0.00   7.83  81.08   0.00  37.22
   3_occ:  81.08   0.00  12.39  77.61   0.00   7.83  81.08   0.00  37.22
   4_bss:  81.08   0.00  12.39  77.61   0.00   7.83  81.08   0.00  37.22
   4_xyz:  81.08   0.00  12.39  77.61   0.00   7.83  81.08   0.00  37.22
   4_adp:  77.82   0.00  11.73  75.39   0.00   7.61  77.82   0.61  34.14
   4_occ:  77.82   0.00  11.73  75.39   0.00   7.61  77.82   0.61  34.14
   5_bss:  77.82   0.00  11.73  75.39   0.00   7.61  77.82   0.61  34.14
   5_xyz:  77.82   0.00  11.73  75.39   0.00   7.61  77.82   0.61  34.14
   5_adp:  79.80   0.00  11.71  76.84   0.00   7.54  79.80   0.86  34.39
   5_occ:  79.80   0.00  11.71  76.84   0.00   7.54  79.80   0.86  34.39
   5_bss:  83.32   3.52  15.22  80.36   3.52  11.06  83.32   4.37  37.91
------------------------------------------------------------------------
 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:    1.255    0.016    0.412
   1_adp:    1.255    0.016    0.412
   1_occ:    1.255    0.016    0.412
   2_bss:    1.255    0.016    0.412
   2_xyz:    1.741    0.013    0.553
   2_adp:    1.741    0.013    0.553
   2_occ:    1.741    0.013    0.553
   3_bss:    1.741    0.013    0.553
   3_xyz:    1.725    0.029    0.606
   3_adp:    1.725    0.029    0.606
   3_occ:    1.725    0.029    0.606
   4_bss:    1.725    0.029    0.606
   4_xyz:    1.887    0.041    0.621
   4_adp:    1.887    0.041    0.621
   4_occ:    1.887    0.041    0.621
   5_bss:    1.887    0.041    0.621
   5_xyz:    1.848    0.053    0.634
   5_adp:    1.848    0.053    0.634
   5_occ:    1.848    0.053    0.634
   5_bss:    1.848    0.053    0.634
------------------------------------------------------------------------

CPU time actual refinement: 323.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/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_801/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_801/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.00 
  Macro-tasks:
    bulk solvent and scale       = 35.74  
    individual site refinement   = 130.40 
    weights calculation          = 32.63  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.53 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 100.52 
    alpha_beta                      = 8.27   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.55 
    fmodel                         = 6.43   
    r_factors                      = 0.20   
    phase_errors                   = 10.86  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 240.08 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.611 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    646 calls, 100.13 s
gradients_fft:          591 calls,  97.77 s

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

# Date 2008-01-16 Time 02:27:35 PST -0800 (1200479255.14 s)
Start R-work = 0.4565, R-free = 0.4446 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1788 (no bulk solvent and anisotropic scale)

Start R-work = 0.4473, R-free = 0.4295
Final R-work = 0.1159, R-free = 0.1627