# Date 2008-01-16 Time 03:14:52 PST -0800 (1200482092.38 s)
#phil __OFF__

Command line arguments: "../1160.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27292
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1160

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00104
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960669

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2108
                             d_min =   2.0010

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: (71.655, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00104
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960669

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2112 -  4.2821 [2133/2159]  1922   211   9.9%
  bin  2:  4.2821 -  3.4114 [2046/2065]  1840   206  10.1%
  bin  3:  3.4114 -  2.9839 [2029/2048]  1824   205  10.1%
  bin  4:  2.9839 -  2.7127 [2010/2040]  1810   200  10.0%
  bin  5:  2.7127 -  2.5192 [1991/2010]  1797   194   9.7%
  bin  6:  2.5192 -  2.3713 [1981/2006]  1777   204  10.3%
  bin  7:  2.3713 -  2.2529 [1967/1995]  1770   197  10.0%
  bin  8:  2.2529 -  2.1551 [1970/2006]  1774   196   9.9%
  bin  9:  2.1551 -  2.0724 [1971/2013]  1773   198  10.0%
  bin 10:  2.0724 -  2.0010 [1491/1987]  1343   148   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 5
        2.31 -     2.95: 1641
        2.95 -     3.60: 4440
        3.60 -     4.25: 9122
        4.25 -     4.90: 12742
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.657 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.197 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.219 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27945 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_1160/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.16465 86.39 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: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4430   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.243894                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7761 0.99   1386  155 0.3709 0.3478      6.5469      6.4599|
|  2:  4.7761 -  3.8106 0.99   1340  146 0.3418 0.3641      6.6885      6.7128|
|  3:  3.8106 -  3.3347 0.99   1304  144 0.3852 0.3542       6.582      6.5948|
|  4:  3.3347 -  3.0324 0.99   1300  153 0.4205 0.3776       6.473      6.3795|
|  5:  3.0324 -  2.8165 0.99   1297  139 0.4630 0.4714      6.3341       6.377|
|  6:  2.8165 -  2.6514 0.99   1279  142 0.4712 0.4790      6.2441      6.2209|
|  7:  2.6514 -  2.5192 0.99   1287  137 0.4963 0.4832      6.2304      6.2155|
|  8:  2.5192 -  2.4100 0.98   1263  151 0.4961 0.4602      6.1543      6.1407|
|  9:  2.4100 -  2.3176 0.98   1265  142 0.4777 0.5062      6.0989      6.1275|
| 10:  2.3176 -  2.2379 0.99   1276  135 0.4969 0.4649      6.0949      6.0564|
| 11:  2.2379 -  2.1681 0.98   1275  141 0.4976 0.4728      6.0343       6.028|
| 12:  2.1681 -  2.1063 0.97   1237  143 0.5018 0.5229      5.9725      6.0168|
| 13:  2.1063 -  2.0510 1.00   1277  135 0.5187 0.4999      5.8968      5.8478|
| 14:  2.0510 -  2.0010 0.65    844   96 0.5017 0.4372      5.8628      5.6905|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7761  1386   155  0.74  30.96   0.80     0.76      58542.27|
|  2:  4.7761 -  3.8106  1340   146  0.77  29.00   0.90     0.80      77152.83|
|  3:  3.8106 -  3.3347  1304   144  0.69  36.11   0.85     0.77      82512.02|
|  4:  3.3347 -  3.0324  1300   153  0.61  42.72   0.82     0.69      77242.99|
|  5:  3.0324 -  2.8165  1297   139  0.52  50.57   0.75     0.60      68398.17|
|  6:  2.8165 -  2.6514  1279   142  0.48  53.84   0.76     0.55      61965.26|
|  7:  2.6514 -  2.5192  1287   137  0.46  55.01   0.73     0.51      56880.29|
|  8:  2.5192 -  2.4100  1263   151  0.44  57.18   0.73     0.51      52530.75|
|  9:  2.4100 -  2.3176  1265   142  0.46  55.57   0.74     0.51      46827.80|
| 10:  2.3176 -  2.2379  1276   135  0.45  55.78   0.76     0.51      42395.68|
| 11:  2.2379 -  2.1681  1275   141  0.44  56.80   0.76     0.50      38929.43|
| 12:  2.1681 -  2.1063  1237   143  0.44  57.33   0.77     0.51      37130.36|
| 13:  2.1063 -  2.0510  1277   135  0.45  56.02   0.72     0.53      30367.32|
| 14:  2.0510 -  2.0010   844    96  0.57  46.94   0.72     0.61      20594.62|
|alpha:            min =        0.50 max =            0.80 mean =         0.60|
|beta:             min =    20594.62 max =        82512.02 mean =     54742.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.66|
|phase err.(test): min =        0.00 max =           89.92 mean =        48.57|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.541146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.888   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.685933              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1489 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2597 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3861 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4997 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6546 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7587 |
|-----------------------------------------------------------------------------|
|-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 |       54.298 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.617 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    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 = 12.212)------------------------------------------|
|    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: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4499   r_free= 0.4364   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.246743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4181   ksol= 0.30   Bsol= 20.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.51,7.96,7.56,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.238942                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.754666              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.611   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663966              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.684   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4359      final r-factor (work) = 0.3292          |
| start r-factor (free) = 0.4181      final r-factor (free) = 0.3586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.6593 = 8.75 * 0.50 * 6.2506 + 1.00 * 54.2984                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7987 = 8.75 * 0.50 * 6.0927 + 1.00 * 0.1288                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3292      final r-factor (work) = 0.2744          |
| start r-factor (free) = 0.3586      final r-factor (free) = 0.3124          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0601 = 0.66 * 1.00 * 6.0927 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9657 = 0.66 * 1.00 * 5.9557 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.65   10.32    None  None   None       |
|    all(noH): 2823   0      0.00    66.65   10.32    None  None   None       |
|    Sol.    : 438    0      0.00    66.65   26.46    None  None   None       |
|    Mac.    : 2385   0      0.00    59.41   7.36     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 -   6.665: 1458   |   5:    33.326 -  39.991:   70        |
|      1:     6.665 -  13.330:  693   |   6:    39.991 -  46.656:   55        |
|      2:    13.330 -  19.996:  252   |   7:    46.656 -  53.321:   24        |
|      3:    19.996 -  26.661:  146   |   8:    53.321 -  59.987:   10        |
|      4:    26.661 -  33.326:  111   |   9:    59.987 -  66.652:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2744 r_free = 0.3124             target_work(ml) = 5.904         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2737 r_free = 0.3129             target_work(ml) = 5.903         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2737   r_free= 0.3129   ksol= 0.30   Bsol= 20.00   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.51,7.96,7.56,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.902796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2708   r_free= 0.3088   ksol= 0.33   Bsol= 50.05   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.31,4.93,5.18,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.902116                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.483285              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447136              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2708      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.3088      final r-factor (free) = 0.2412          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5015 = 3.48 * 0.50 * 5.9559 + 1.00 * 0.1285                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0895 = 3.48 * 0.50 * 5.7553 + 1.00 * 0.0658                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1938      final r-factor (work) = 0.1792          |
| start r-factor (free) = 0.2412      final r-factor (free) = 0.2267          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6176 = 0.45 * 1.00 * 5.7553 + 1.00 * 0.0442                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7090 = 0.45 * 1.00 * 5.5678 + 1.00 * 0.2194                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.43   11.00    None  None   None       |
|    all(noH): 2823   0      0.00    75.43   11.00    None  None   None       |
|    Sol.    : 438    0      0.00    66.56   30.41    None  None   None       |
|    Mac.    : 2385   0      0.00    75.43   7.43     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 -   7.543: 1585   |   5:    37.713 -  45.255:   87        |
|      1:     7.543 -  15.085:  616   |   6:    45.255 -  52.798:   42        |
|      2:    15.085 -  22.628:  199   |   7:    52.798 -  60.341:   21        |
|      3:    22.628 -  30.170:  127   |   8:    60.341 -  67.883:    5        |
|      4:    30.170 -  37.713:  140   |   9:    67.883 -  75.426:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1792 r_free = 0.2267             target_work(ml) = 5.542         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1790 r_free = 0.2267             target_work(ml) = 5.542         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1790   r_free= 0.2267   ksol= 0.33   Bsol= 50.05   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.31,4.93,5.18,0.00,0.00,0.00); trace/3= 5.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.541701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1780   r_free= 0.2243   ksol= 0.33   Bsol= 50.05   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.09,3.63,4.29,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.541138                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.563982              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.981  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.855318              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.690   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1780      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2243      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2117 = 2.56 * 0.50 * 5.5741 + 1.00 * 0.0658                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0373 = 2.56 * 0.50 * 5.4371 + 1.00 * 0.0669                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1781          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 31.8566 = 5.86 * 1.00 * 5.4371 + 1.00 * 0.0206                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 31.0251 = 5.86 * 1.00 * 5.2957 + 1.00 * 0.0169                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.54   12.40    None  None   None       |
|    all(noH): 2823   0      0.00    91.54   12.40    None  None   None       |
|    Sol.    : 438    0      0.00    91.54   37.67    None  None   None       |
|    Mac.    : 2385   0      0.00    86.05   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 -   9.154: 1795   |   5:    45.770 -  54.924:   80        |
|      1:     9.154 -  18.308:  483   |   6:    54.924 -  64.077:   66        |
|      2:    18.308 -  27.462:  149   |   7:    64.077 -  73.231:   29        |
|      3:    27.462 -  36.616:  113   |   8:    73.231 -  82.385:   11        |
|      4:    36.616 -  45.770:   93   |   9:    82.385 -  91.539:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1297 r_free = 0.1781             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1297 r_free = 0.1781             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1297   r_free= 0.1781   ksol= 0.33   Bsol= 50.05   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.09,3.63,4.29,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.275993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1781   ksol= 0.33   Bsol= 60.70   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.31,4.14,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.276658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.378649              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.884  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1781      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3661 = 2.38 * 0.50 * 5.2964 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3080 = 2.38 * 0.50 * 5.2456 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3963 = 0.26 * 1.00 * 5.2456 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3993 = 0.26 * 1.00 * 5.2214 + 1.00 * 0.0270                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.69   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    88.69   12.01    None  None   None       |
|    Sol.    : 438    0      0.77    88.69   36.17    None  None   None       |
|    Mac.    : 2385   0      0.00    84.77   7.58     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.869: 1805   |   5:    44.345 -  53.214:   78        |
|      1:     8.869 -  17.738:  487   |   6:    53.214 -  62.083:   60        |
|      2:    17.738 -  26.607:  155   |   7:    62.083 -  70.952:   29        |
|      3:    26.607 -  35.476:  103   |   8:    70.952 -  79.821:    9        |
|      4:    35.476 -  44.345:   90   |   9:    79.821 -  88.689:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1670             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1202 r_free = 0.1668             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1668   ksol= 0.33   Bsol= 60.70   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.31,4.14,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206498                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1668   ksol= 0.33   Bsol= 58.34   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.31,4.14,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206460                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.813091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.299  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.756811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.547   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4123 = 2.81 * 0.50 * 5.2207 + 1.00 * 0.0692                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3728 = 2.81 * 0.50 * 5.1877 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9406 = 0.76 * 1.00 * 5.1877 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9250 = 0.76 * 1.00 * 5.1683 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.29   11.95    None  None   None       |
|    all(noH): 2823   0      0.00    90.29   11.95    None  None   None       |
|    Sol.    : 438    0      0.86    90.29   35.77    None  None   None       |
|    Mac.    : 2385   0      0.00    87.56   7.57     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.029: 1810   |   5:    45.144 -  54.172:   91        |
|      1:     9.029 -  18.058:  482   |   6:    54.172 -  63.201:   50        |
|      2:    18.058 -  27.086:  152   |   7:    63.201 -  72.230:   20        |
|      3:    27.086 -  36.115:  115   |   8:    72.230 -  81.259:    9        |
|      4:    36.115 -  45.144:   89   |   9:    81.259 -  90.287:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1628             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1628             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1628   ksol= 0.33   Bsol= 58.34   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.55,3.31,4.14,0.00,0.00,0.00); trace/3= 3.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170387                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7761 0.99   1386  155 0.0991 0.1358      5.3836       5.542|
|  2:  4.7761 -  3.8106 0.99   1340  146 0.0872 0.1132      5.4497      5.6454|
|  3:  3.8106 -  3.3347 0.99   1304  144 0.1061 0.1562      5.4845      5.8831|
|  4:  3.3347 -  3.0324 0.99   1300  153 0.1224 0.1554      5.4742      5.5905|
|  5:  3.0324 -  2.8165 0.99   1297  139 0.1374 0.1908      5.3615      5.6189|
|  6:  2.8165 -  2.6514 0.99   1279  142 0.1245 0.1905      5.2444      5.5107|
|  7:  2.6514 -  2.5192 0.99   1287  137 0.1303 0.1661      5.2031      5.3843|
|  8:  2.5192 -  2.4100 0.98   1263  151 0.1206 0.1727       5.094      5.3622|
|  9:  2.4100 -  2.3176 0.98   1265  142 0.1201 0.1873      5.0748      5.3681|
| 10:  2.3176 -  2.2379 0.99   1276  135 0.1160 0.1828      4.9963      5.2464|
| 11:  2.2379 -  2.1681 0.98   1275  141 0.1188 0.1792      4.9815       5.301|
| 12:  2.1681 -  2.1063 0.97   1237  143 0.1122 0.1698      4.9032       5.142|
| 13:  2.1063 -  2.0510 1.00   1277  135 0.1211 0.1850       4.827      5.1424|
| 14:  2.0510 -  2.0010 0.65    844   96 0.1086 0.1713      4.6851      4.9117|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7761  1386   155  0.94   9.02   0.97     0.95       7262.53|
|  2:  4.7761 -  3.8106  1340   146  0.95   8.13   1.00     0.99       9304.62|
|  3:  3.8106 -  3.3347  1304   144  0.93  11.65   1.02     1.01      10775.20|
|  4:  3.3347 -  3.0324  1300   153  0.92  14.06   1.00     0.99      10804.89|
|  5:  3.0324 -  2.8165  1297   139  0.89  16.61   1.00     0.97       8935.29|
|  6:  2.8165 -  2.6514  1279   142  0.90  16.57   0.98     0.96       7774.01|
|  7:  2.6514 -  2.5192  1287   137  0.90  16.06   0.99     0.96       6625.38|
|  8:  2.5192 -  2.4100  1263   151  0.90  15.94   0.98     0.96       5683.22|
|  9:  2.4100 -  2.3176  1265   142  0.90  16.13   1.00     0.97       5462.94|
| 10:  2.3176 -  2.2379  1276   135  0.90  16.13   0.99     0.95       4684.05|
| 11:  2.2379 -  2.1681  1275   141  0.89  17.10   0.99     0.95       4745.32|
| 12:  2.1681 -  2.1063  1237   143  0.91  15.12   1.00     0.99       4185.39|
| 13:  2.1063 -  2.0510  1277   135  0.89  17.23   1.00     0.99       3634.89|
| 14:  2.0510 -  2.0010   844    96  0.91  15.11   0.97     0.94       2635.77|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2635.77 max =        10804.89 mean =      6741.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.56|
|phase err.(test): min =        0.00 max =           89.99 mean =        13.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1628   ksol= 0.32   Bsol= 60.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-0.34,0.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1628   ksol= 0.32   Bsol= 60.49   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-0.34,0.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170398                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7761 0.99   1386  155 0.0990 0.1357      5.3823      5.5409|
|  2:  4.7761 -  3.8106 0.99   1340  146 0.0872 0.1130      5.4489      5.6443|
|  3:  3.8106 -  3.3347 0.99   1304  144 0.1061 0.1561      5.4839      5.8824|
|  4:  3.3347 -  3.0324 0.99   1300  153 0.1224 0.1553      5.4743      5.5904|
|  5:  3.0324 -  2.8165 0.99   1297  139 0.1375 0.1911      5.3622      5.6201|
|  6:  2.8165 -  2.6514 0.99   1279  142 0.1245 0.1903       5.245      5.5103|
|  7:  2.6514 -  2.5192 0.99   1287  137 0.1302 0.1659      5.2029      5.3838|
|  8:  2.5192 -  2.4100 0.98   1263  151 0.1206 0.1727      5.0939      5.3625|
|  9:  2.4100 -  2.3176 0.98   1265  142 0.1201 0.1870      5.0748      5.3676|
| 10:  2.3176 -  2.2379 0.99   1276  135 0.1160 0.1829      4.9967      5.2473|
| 11:  2.2379 -  2.1681 0.98   1275  141 0.1188 0.1795      4.9819      5.3017|
| 12:  2.1681 -  2.1063 0.97   1237  143 0.1123 0.1699       4.904      5.1428|
| 13:  2.1063 -  2.0510 1.00   1277  135 0.1211 0.1854      4.8273      5.1436|
| 14:  2.0510 -  2.0010 0.65    844   96 0.1086 0.1712      4.6852      4.9112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2112 -  4.7761  1386   155  0.94   9.01   0.97     0.95       7249.39|
|  2:  4.7761 -  3.8106  1340   146  0.95   8.12   1.00     0.99       9287.00|
|  3:  3.8106 -  3.3347  1304   144  0.93  11.63   1.02     1.01      10755.66|
|  4:  3.3347 -  3.0324  1300   153  0.92  14.06   1.00     0.98      10809.61|
|  5:  3.0324 -  2.8165  1297   139  0.89  16.62   0.99     0.97       8939.50|
|  6:  2.8165 -  2.6514  1279   142  0.90  16.58   0.98     0.96       7782.27|
|  7:  2.6514 -  2.5192  1287   137  0.90  16.05   0.99     0.96       6623.93|
|  8:  2.5192 -  2.4100  1263   151  0.90  15.95   0.98     0.96       5682.68|
|  9:  2.4100 -  2.3176  1265   142  0.90  16.13   1.00     0.97       5459.63|
| 10:  2.3176 -  2.2379  1276   135  0.90  16.14   0.99     0.95       4689.86|
| 11:  2.2379 -  2.1681  1275   141  0.89  17.11   0.99     0.95       4752.23|
| 12:  2.1681 -  2.1063  1237   143  0.91  15.14   1.00     0.98       4195.92|
| 13:  2.1063 -  2.0510  1277   135  0.89  17.23   1.00     0.98       3638.23|
| 14:  2.0510 -  2.0010   844    96  0.91  15.11   0.97     0.93       2635.72|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2635.72 max =        10809.61 mean =      6740.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.56|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.61    93.90   15.56    None  None   None       |
|    all(noH): 2823   0      3.61    93.90   15.56    None  None   None       |
|    Sol.    : 438    0      4.48    93.90   39.38    None  None   None       |
|    Mac.    : 2385   0      3.61    91.17   11.18    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:     3.613 -  12.642: 1810   |   5:    48.757 -  57.785:   91        |
|      1:    12.642 -  21.671:  482   |   6:    57.785 -  66.814:   50        |
|      2:    21.671 -  30.699:  152   |   7:    66.814 -  75.843:   20        |
|      3:    30.699 -  39.728:  115   |   8:    75.843 -  84.872:    9        |
|      4:    39.728 -  48.757:   89   |   9:    84.872 -  93.900:    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)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.319 - 4.739
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 329
   mapped sites are within: 0.714 - 4.739

peak=   10.539 closest distance to " CG2 VAL A 230 " =    1.435
peak=    7.478 closest distance to " CG2 VAL A 296 " =    1.153
peak=    5.966 closest distance to " CG  LEU A   5 " =    1.178
peak=    5.926 closest distance to " O   HOH Z 111 " =    2.106
peak=    5.730 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.442 closest distance to " CG  LEU A 228 " =    1.145
peak=    5.283 closest distance to " CD2 LEU A   5 " =    1.151
peak=    4.987 closest distance to " CB  SER A  63 " =    1.314
peak=    4.952 closest distance to " CB  GLN A 183 " =    1.258
peak=    4.948 closest distance to " O   HOH Z 232 " =    2.276
peak=    4.745 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.685 closest distance to " O   HOH Z 369 " =    2.118
peak=    4.521 closest distance to " O   HOH Z  54 " =    2.353
peak=    4.487 closest distance to " NE2 GLN A  11 " =    1.116
peak=    4.446 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.395 closest distance to " O   HOH Z 298 " =    1.858
peak=    4.388 closest distance to " O   HOH Z 368 " =    2.273
peak=    4.330 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.325 closest distance to " O   HOH Z 427 " =    3.217
peak=    4.317 closest distance to " CB  TRP A 266 " =    0.971
peak=    4.310 closest distance to " C   PRO A 198 " =    1.567
peak=    4.304 closest distance to " CB  ASP A 140 " =    0.896
peak=    4.275 closest distance to " O   HOH Z 403 " =    1.730
peak=    4.273 closest distance to " O   HOH Z 303 " =    2.097
peak=    4.262 closest distance to " O   HOH Z 236 " =    2.003
peak=    4.211 closest distance to " O   HOH Z 316 " =    3.100
peak=    4.208 closest distance to " CB  ARG A  79 " =    1.485
peak=    4.207 closest distance to " CB  GLU A 152 " =    1.170
peak=    4.198 closest distance to " O   HOH Z 425 " =    1.434
peak=    4.193 closest distance to " CB  GLU A 128 " =    1.128
peak=    4.186 closest distance to " O   HOH Z 247 " =    1.388
peak=    4.185 closest distance to " NH1AARG A 145 " =    1.152
peak=    4.171 closest distance to " O   HOH Z 272 " =    1.914
peak=    4.167 closest distance to " CB  VAL A 296 " =    1.066
peak=    4.167 closest distance to " O   HOH Z  78 " =    1.776
peak=    4.163 closest distance to " OD1 ASN A  69 " =    2.660
peak=    4.133 closest distance to " CZ  PHE A 218 " =    1.059
peak=    4.091 closest distance to " CD1AILE A 234 " =    0.955
peak=    4.090 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.064 closest distance to " CB  ARG A 275 " =    0.888
peak=    4.058 closest distance to " O   HOH Z 158 " =    2.982
peak=    4.051 closest distance to " O   HOH Z 126 " =    1.997
peak=    4.040 closest distance to " CB  GLU A 277 " =    3.692
peak=    4.019 closest distance to " CG  PRO A 243 " =    1.152
peak=    4.019 closest distance to " O   HOH Z  88 " =    3.445
peak=    4.006 closest distance to " O   HOH Z  15 " =    2.106
peak=    3.984 closest distance to " CG2 THR A 221 " =    1.041
peak=    3.979 closest distance to " CD  ARG A 159 " =    0.800
peak=    3.978 closest distance to " O   HOH Z 142 " =    1.568
peak=    3.973 closest distance to " O   HOH Z 112 " =    1.623
peak=    3.973 closest distance to " O   HOH Z 261 " =    1.938
peak=    3.963 closest distance to " ND2 ASN A 249 " =    1.928
peak=    3.958 closest distance to " O   HOH Z 234 " =    3.802
peak=    3.957 closest distance to " CB  SER A 212 " =    1.185
peak=    3.950 closest distance to " CB  LEU A 228 " =    1.206
peak=    3.948 closest distance to " O   HOH Z 411 " =    3.612
peak=    3.945 closest distance to " ND2 ASN A 187 " =    1.483
peak=    3.942 closest distance to " O   MET A 105 " =    1.857
peak=    3.935 closest distance to " CB  LEU A 143 " =    1.208
peak=    3.934 closest distance to " CA  ALA A  51 " =    1.029
peak=    3.919 closest distance to " CD  ARG A  66 " =    2.549
peak=    3.913 closest distance to " CD2 LEU A 228 " =    1.135
peak=    3.908 closest distance to " CB  SER A   3 " =    1.380
peak=    3.904 closest distance to " CA  TYR A  30 " =    0.965
peak=    3.904 closest distance to " O   HOH Z 423 " =    1.700
peak=    3.899 closest distance to " CB  ARG A 190 " =    1.675
peak=    3.884 closest distance to " O   HOH Z 193 " =    2.138
peak=    3.882 closest distance to " O   HOH Z 184 " =    1.454
peak=    3.874 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.848 closest distance to " O   HOH Z  63 " =    1.878
peak=    3.847 closest distance to " O   HOH Z 346 " =    1.539
peak=    3.847 closest distance to " O   SER A  87 " =    2.283
peak=    3.840 closest distance to " O   HOH Z 280 " =    2.921
peak=    3.833 closest distance to " CD1 LEU A   5 " =    1.325
peak=    3.823 closest distance to " O   HOH Z  61 " =    1.669
peak=    3.821 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.818 closest distance to " CB  VAL A 202 " =    1.612
peak=    3.811 closest distance to " CB  SER A 216 " =    0.920
peak=    3.792 closest distance to " NH2 ARG A 156 " =    1.108
peak=    3.789 closest distance to " O   HOH Z 437 " =    1.785
peak=    3.781 closest distance to " O   HOH Z 126 " =    1.597
peak=    3.773 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.768 closest distance to " O   HOH Z  80 " =    1.723
peak=    3.752 closest distance to " CA  ALA A 295 " =    1.111
peak=    3.750 closest distance to " CD ALYS A 290 " =    1.018
peak=    3.748 closest distance to " OG BSER A 164 " =    2.201
peak=    3.746 closest distance to " CZ  PHE A 192 " =    1.016
peak=    3.740 closest distance to " O   HOH Z 163 " =    1.657
peak=    3.736 closest distance to " CD1 LEU A 300 " =    1.169
peak=    3.731 closest distance to " O   ALA A 158 " =    1.395
peak=    3.725 closest distance to " O   HOH Z 290 " =    1.069
peak=    3.722 closest distance to " O   HOH Z 213 " =    1.838
peak=    3.717 closest distance to " CB  PRO A  54 " =    0.768
peak=    3.699 closest distance to " O   HOH Z 295 " =    1.536
peak=    3.698 closest distance to " CB  ASN A 187 " =    1.040
peak=    3.684 closest distance to " O   GLN A 278 " =    1.299
peak=    3.682 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.677 closest distance to " CD  LYS A 166 " =    1.298
peak=    3.675 closest distance to " O   HOH Z  20 " =    1.872
peak=    3.672 closest distance to " CG  MET A 185 " =    1.320
peak=    3.672 closest distance to " OG  SER A  97 " =    3.058
peak=    3.662 closest distance to " CA  MET A  40 " =    1.172
peak=    3.647 closest distance to " CA  THR A 264 " =    0.729
peak=    3.647 closest distance to " CG BARG A 275 " =    1.480
peak=    3.646 closest distance to " CG  GLN A  88 " =    1.046
peak=    3.643 closest distance to " O   HOH Z 203 " =    1.825
peak=    3.642 closest distance to " OD2 ASP A 286 " =    2.895
peak=    3.633 closest distance to " CA  THR A 221 " =    0.908
peak=    3.632 closest distance to " ND1 HIS A  81 " =    1.687
peak=    3.629 closest distance to " CA  ALA A  21 " =    1.229
peak=    3.620 closest distance to " O   HOH Z 197 " =    2.908
peak=    3.618 closest distance to " CA  LYS A 117 " =    1.252
peak=    3.612 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.609 closest distance to " CG1BVAL A  72 " =    1.653
peak=    3.608 closest distance to " CB  ASN A 142 " =    1.010
peak=    3.606 closest distance to " CA  ASN A 215 " =    1.235
peak=    3.604 closest distance to " N   SER A 135 " =    1.421
peak=    3.599 closest distance to " OG  SER A  22 " =    2.920
peak=    3.596 closest distance to " O   HOH Z 102 " =    1.385
peak=    3.596 closest distance to " CD  ARG A 269 " =    0.952
peak=    3.595 closest distance to " CB AVAL A  41 " =    1.234
peak=    3.594 closest distance to " CD  ARG A  66 " =    2.394
peak=    3.588 closest distance to " CG1 VAL A 153 " =    0.975
peak=    3.585 closest distance to " CB  TRP A 179 " =    1.460
peak=    3.584 closest distance to " O   HOH Z 214 " =    2.115
peak=    3.583 closest distance to " CA  ALA A 158 " =    1.168
peak=    3.582 closest distance to " O   HOH Z 133 " =    2.362
peak=    3.569 closest distance to " NZ  LYS A 117 " =    3.164
peak=    3.563 closest distance to " O   HOH Z 133 " =    1.738
peak=    3.561 closest distance to " N   VAL A 126 " =    1.401
peak=    3.552 closest distance to " NH1 ARG A  56 " =    0.993
peak=    3.549 closest distance to " O   ASP A 124 " =    1.154
peak=    3.540 closest distance to " O   TRP A 274 " =    1.872
peak=    3.539 closest distance to " O   HOH Z  97 " =    2.127
peak=    3.539 closest distance to " O   HOH Z 128 " =    2.210
peak=    3.531 closest distance to " O   HOH Z 132 " =    2.656
peak=    3.530 closest distance to " CD2 LEU A 255 " =    1.549
peak=    3.528 closest distance to " O   HOH Z 180 " =    2.086
peak=    3.524 closest distance to " O   HOH Z 313 " =    1.821
peak=    3.524 closest distance to " O   HOH Z  68 " =    2.110
peak=    3.523 closest distance to " CB  ILE A 120 " =    1.379
peak=    3.521 closest distance to " CB  TRP A 150 " =    1.391
peak=    3.518 closest distance to " O   HOH Z  43 " =    1.933
peak=    3.517 closest distance to " O   HOH Z 371 " =    3.217
peak=    3.513 closest distance to " O   HOH Z  19 " =    2.496
peak=    3.510 closest distance to " OE1 GLN A  11 " =    1.887
peak=    3.510 closest distance to " CA  SER A  87 " =    0.949
peak=    3.510 closest distance to " CB  THR A  82 " =    1.365
peak=    3.507 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.505 closest distance to " O   HOH Z 193 " =    1.904
peak=    3.500 closest distance to " CB  ALA A 291 " =    1.415
peak=    3.495 closest distance to " CA  ARG A 195 " =    1.245
peak=    3.489 closest distance to " CB  MET A  40 " =    0.785
peak=    3.487 closest distance to " CB  VAL A 268 " =    0.891
peak=    3.481 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.477 closest distance to " CB  ALA A   1 " =    4.739
peak=    3.473 closest distance to " O   HOH Z 227 " =    1.659
peak=    3.469 closest distance to " CA  LEU A 282 " =    1.057
peak=    3.460 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.460 closest distance to " O   HOH Z 383 " =    2.173
peak=    3.454 closest distance to " O   HOH Z 263 " =    1.600
peak=    3.454 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.451 closest distance to " CG2 THR A 220 " =    0.921
peak=    3.451 closest distance to " CB  ALA A  34 " =    0.736
peak=    3.447 closest distance to " O   HOH Z 134 " =    1.433
peak=    3.441 closest distance to " O   HOH Z 171 " =    3.909
peak=    3.440 closest distance to " CG BARG A 102 " =    1.813
peak=    3.437 closest distance to " O   HOH Z 147 " =    1.692
peak=    3.435 closest distance to " CB  ALA A 161 " =    0.918
peak=    3.433 closest distance to " O   HOH Z  57 " =    1.293
peak=    3.426 closest distance to " O   HOH Z  30 " =    1.145
peak=    3.411 closest distance to " O   HOH Z 368 " =    3.582
peak=    3.409 closest distance to " CE1 TYR A 186 " =    1.268
peak=    3.409 closest distance to " O   HOH Z 126 " =    1.754
peak=    3.408 closest distance to " CD2 TRP A 179 " =    1.328
peak=    3.402 closest distance to " OD1 ASN A 217 " =    1.627
peak=    3.402 closest distance to " CB  ASN A 110 " =    1.321
peak=    3.401 closest distance to " CA  ASP A 191 " =    0.772
peak=    3.400 closest distance to " O   HOH Z 410 " =    1.360
peak=    3.397 closest distance to " CB  GLN A  88 " =    1.274
peak=    3.395 closest distance to " CB  ALA A 248 " =    1.403
peak=    3.394 closest distance to " O   HOH Z 422 " =    2.620
peak=    3.391 closest distance to " N   ASN A 127 " =    1.218
peak=    3.382 closest distance to " O   HOH Z 172 " =    3.856
peak=    3.378 closest distance to " CB  THR A  31 " =    1.777
peak=    3.378 closest distance to " N   ASN A  39 " =    1.302
peak=    3.372 closest distance to " O   HOH Z 271 " =    2.581
peak=    3.371 closest distance to " CB  ALA A 248 " =    1.115
peak=    3.371 closest distance to " O   HOH Z 109 " =    2.601
peak=    3.369 closest distance to " O   HOH Z  21 " =    1.685
peak=    3.365 closest distance to " O   ALA A 291 " =    1.554
peak=    3.361 closest distance to " O   HOH Z 305 " =    3.654
peak=    3.359 closest distance to " CA  ALA A 154 " =    1.031
peak=    3.351 closest distance to " ND1 HIS A  86 " =    1.790
peak=    3.347 closest distance to " O   HOH Z 135 " =    1.982
peak=    3.345 closest distance to " O   HOH Z 313 " =    1.782
peak=    3.345 closest distance to " CG1 ILE A 151 " =    1.144
peak=    3.343 closest distance to " CA  LYS A 290 " =    1.345
peak=    3.342 closest distance to " O   HOH Z 344 " =    3.087
peak=    3.342 closest distance to " CA  LYS A 181 " =    1.090
peak=    3.341 closest distance to " CG  MET A 185 " =    1.062
peak=    3.340 closest distance to " O   HOH Z 116 " =    1.811
peak=    3.339 closest distance to " CB  MET A  47 " =    1.106
peak=    3.338 closest distance to " O   HOH Z  68 " =    1.544
peak=    3.337 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.336 closest distance to " CG1 ILE A  49 " =    1.551
peak=    3.331 closest distance to " O   HOH Z 130 " =    2.227
peak=    3.329 closest distance to " O   HOH Z 285 " =    3.085
peak=    3.329 closest distance to " O   HOH Z 420 " =    2.031
peak=    3.327 closest distance to " O   HOH Z 402 " =    1.485
peak=    3.327 closest distance to " NH1 ARG A  14 " =    0.971
peak=    3.324 closest distance to " CD  GLU A 152 " =    0.880
peak=    3.323 closest distance to " CA  ASP A 140 " =    1.278
peak=    3.321 closest distance to " CG2 ILE A 234 " =    0.927
peak=    3.320 closest distance to " CA  ALA A 291 " =    0.912
peak=    3.318 closest distance to " O   HOH Z 273 " =    2.678
peak=    3.316 closest distance to " O   ALA A 165 " =    1.404
peak=    3.310 closest distance to " CB  THR A 157 " =    1.125
peak=    3.304 closest distance to " O   HOH Z 353 " =    2.783
peak=    3.302 closest distance to " CB  ASP A 140 " =    0.714
peak=    3.297 closest distance to " O   HOH Z  44 " =    2.098
peak=    3.296 closest distance to " CB  ALA A 104 " =    0.812
peak=    3.295 closest distance to " CD1 ILE A 106 " =    0.942
peak=    3.293 closest distance to " CA  ARG A  36 " =    1.181
peak=    3.292 closest distance to " O   HOH Z  10 " =    1.805
peak=    3.291 closest distance to " CG2 VAL A 257 " =    0.872
peak=    3.290 closest distance to " CG  ARG A 138 " =    1.176
peak=    3.289 closest distance to " O   HOH Z 156 " =    2.869
peak=    3.282 closest distance to " O   HOH Z 201 " =    3.102
peak=    3.279 closest distance to " CA  VAL A 112 " =    1.140
peak=    3.277 closest distance to " CB  ALA A 100 " =    1.316
peak=    3.271 closest distance to " O   HOH Z 355 " =    1.772
peak=    3.270 closest distance to " O   HOH Z  97 " =    2.726
peak=    3.266 closest distance to " CB  TYR A 116 " =    0.910
peak=    3.265 closest distance to " O   HOH Z  63 " =    1.194
peak=    3.260 closest distance to " O   ARG A  56 " =    2.812
peak=    3.259 closest distance to " O   HOH Z 298 " =    2.532
peak=    3.259 closest distance to " O   HOH Z 409 " =    3.166
peak=    3.253 closest distance to " O   HOH Z 302 " =    1.876
peak=    3.253 closest distance to " O   HOH Z 185 " =    1.936
peak=    3.252 closest distance to " O   HOH Z 423 " =    2.935
peak=    3.252 closest distance to " CB  MET A 113 " =    1.800
peak=    3.252 closest distance to " OG BSER A 134 " =    2.883
peak=    3.250 closest distance to " N   PHE A 130 " =    1.265
peak=    3.248 closest distance to " O   HOH Z  62 " =    2.355
peak=    3.248 closest distance to " NZ  LYS A  48 " =    1.440
peak=    3.247 closest distance to " O   HOH Z  58 " =    1.421
peak=    3.246 closest distance to " CD1 ILE A  33 " =    1.628
peak=    3.243 closest distance to " CB  SER A  62 " =    1.296
peak=    3.237 closest distance to " CG  GLU A  37 " =    0.828
peak=    3.236 closest distance to " CB  SER A 273 " =    0.870
peak=    3.231 closest distance to " CG AARG A 275 " =    1.197
peak=    3.229 closest distance to " O   HOH Z 271 " =    2.037
peak=    3.228 closest distance to " NE2 HIS A 207 " =    1.398
peak=    3.227 closest distance to " O   HOH Z 248 " =    1.785
peak=    3.226 closest distance to " CB  GLN A  89 " =    1.154
peak=    3.224 closest distance to " O   HOH Z 329 " =    3.859
peak=    3.224 closest distance to " CB  ARG A 139 " =    0.866
peak=    3.220 closest distance to " CD2 LEU A   5 " =    0.747
peak=    3.219 closest distance to " O  BHOH Z 338 " =    2.389
peak=    3.219 closest distance to " CG2 ILE A  20 " =    1.456
peak=    3.211 closest distance to " CE2 TYR A 186 " =    0.914
peak=    3.211 closest distance to " O   HOH Z 155 " =    3.338
peak=    3.210 closest distance to " CG2 ILE A 120 " =    1.228
peak=    3.207 closest distance to " O   HOH Z 175 " =    3.584
peak=    3.207 closest distance to " CG  LEU A  25 " =    1.903
peak=    3.205 closest distance to " CG1 VAL A 296 " =    1.232
peak=    3.205 closest distance to " O   HOH Z 183 " =    1.281
peak=    3.204 closest distance to " CA  MET A 105 " =    1.007
peak=    3.197 closest distance to " CG1 VAL A 174 " =    1.134
peak=    3.195 closest distance to " CA  TYR A 116 " =    1.459
peak=    3.194 closest distance to " O   HOH Z  48 " =    1.772
peak=    3.193 closest distance to " O   HOH Z 327 " =    2.363
peak=    3.192 closest distance to " CD1 LEU A 228 " =    1.814
peak=    3.185 closest distance to " CB  ALA A 242 " =    0.851
peak=    3.183 closest distance to " OH  TYR A 214 " =    1.256
peak=    3.181 closest distance to " O   HOH Z 350 " =    1.633
peak=    3.179 closest distance to " O   HOH Z 245 " =    1.363
peak=    3.178 closest distance to " CZ3 TRP A 274 " =    4.720
peak=    3.178 closest distance to " CA  ILE A 106 " =    0.830
peak=    3.176 closest distance to " CD2 HIS A  81 " =    0.948
peak=    3.175 closest distance to " CA  VAL A  41 " =    0.917
peak=    3.174 closest distance to " O   HOH Z 326 " =    2.238
peak=    3.172 closest distance to " CB  ALA A  43 " =    0.906
peak=    3.171 closest distance to " O   HOH Z 327 " =    1.872
peak=    3.169 closest distance to " O   HOH Z 291 " =    1.599
peak=    3.159 closest distance to " CB  TYR A  30 " =    1.470
peak=    3.159 closest distance to " O   HOH Z 345 " =    3.563
peak=    3.158 closest distance to " CE2 TYR A  30 " =    0.880
peak=    3.157 closest distance to " OG BSER A 212 " =    2.410
peak=    3.156 closest distance to " CA  GLY A 211 " =    1.303
peak=    3.156 closest distance to " O   HOH Z 187 " =    2.292
peak=    3.156 closest distance to " NH2 ARG A  79 " =    1.486
peak=    3.154 closest distance to " O   HOH Z   1 " =    2.148
peak=    3.148 closest distance to " CB  LEU A 237 " =    0.841
peak=    3.147 closest distance to " O   THR A  31 " =    1.546
peak=    3.136 closest distance to " O   HOH Z 425 " =    1.885
peak=    3.135 closest distance to " O   HOH Z 166 " =    3.446
peak=    3.133 closest distance to " O   HOH Z 435 " =    2.041
peak=    3.129 closest distance to " O   HOH Z 141 " =    1.672
peak=    3.124 closest distance to " NH2BARG A 145 " =    2.114
peak=    3.121 closest distance to " O   HOH Z 426 " =    1.547
peak=    3.111 closest distance to " CA  ARG A 102 " =    1.203
peak=    3.102 closest distance to " ND2 ASN A 110 " =    1.612
peak=    3.100 closest distance to " O   ALA A   1 " =    1.641
peak=    3.099 closest distance to " O   HOH Z 294 " =    1.596
peak=    3.098 closest distance to " O   HOH Z 392 " =    1.873
peak=    3.095 closest distance to " N   ARG A 156 " =    1.364
peak=    3.084 closest distance to " OG  SER A  62 " =    3.044
peak=    3.077 closest distance to " N   TYR A  15 " =    0.792
peak=    3.074 closest distance to " O   HOH Z 391 " =    3.019
peak=    3.073 closest distance to " CB  ALA A 227 " =    0.965
peak=    3.070 closest distance to " CZ3 TRP A  85 " =    1.142
peak=    3.061 closest distance to " CA  VAL A 126 " =    1.005
peak=    3.060 closest distance to " CG  MET A 113 " =    1.828
peak=    3.055 closest distance to " CA  ALA A 299 " =    0.949
peak=    3.047 closest distance to " CB  ARG A 138 " =    1.019
peak=    3.015 closest distance to " O   HOH Z  49 " =    2.877
peak=    3.007 closest distance to " O   HOH Z 213 " =    2.824
peak=    3.003 closest distance to " CB  PRO A  54 " =    1.263

                           ----------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: 0.784 - 5.410
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.784 - 5.410

peak=   -4.989 closest distance to " CG2 VAL A 230 " =    0.868
peak=   -4.279 closest distance to " CD  ARG A 156 " =    2.020
peak=   -4.229 closest distance to " O   HOH Z 266 " =    5.146
peak=   -4.166 closest distance to " OE1 GLN A 223 " =    2.222
peak=   -4.131 closest distance to " O   HOH Z  52 " =    1.637
peak=   -4.123 closest distance to " CG1 VAL A 112 " =    2.622
peak=   -4.059 closest distance to " O   HOH Z 231 " =    1.873
peak=   -3.978 closest distance to " O   ILE A 109 " =    2.657
peak=   -3.947 closest distance to " CD  ARG A  14 " =    3.298
peak=   -3.930 closest distance to " O   SER A 271 " =    2.272
peak=   -3.894 closest distance to " O   HOH Z 196 " =    2.297
peak=   -3.889 closest distance to " CE2 TYR A  30 " =    2.822
peak=   -3.888 closest distance to " OG  SER A  87 " =    1.566
peak=   -3.886 closest distance to " NH2AARG A 275 " =    5.410
peak=   -3.866 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.855 closest distance to " OG  SER A  97 " =    2.201
peak=   -3.854 closest distance to " CG2BVAL A  41 " =    2.565
peak=   -3.853 closest distance to " O   HOH Z 166 " =    2.010
peak=   -3.847 closest distance to " CG  LEU A 101 " =    2.531
peak=   -3.844 closest distance to " CG1 VAL A 296 " =    1.439
peak=   -3.838 closest distance to " CG2 VAL A 296 " =    1.376
peak=   -3.828 closest distance to " O   PRO A 163 " =    2.106
peak=   -3.828 closest distance to " CB  PRO A 243 " =    2.660
peak=   -3.810 closest distance to " O   HOH Z 290 " =    1.316
peak=   -3.798 closest distance to " CG1 VAL A 250 " =    2.707
peak=   -3.789 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.784 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.781 closest distance to " CG  TRP A 266 " =    1.776
peak=   -3.776 closest distance to " N   ALA A  43 " =    2.596
peak=   -3.769 closest distance to " CD1 LEU A 228 " =    2.417
peak=   -3.769 closest distance to " O   HOH Z 377 " =    1.825
peak=   -3.767 closest distance to " CZ3 TRP A 179 " =    1.143
peak=   -3.726 closest distance to " O   HOH Z 389 " =    1.919
peak=   -3.723 closest distance to " CD  GLN A  58 " =    1.052
peak=   -3.712 closest distance to " CG  ASP A 231 " =    0.784
peak=   -3.709 closest distance to " O   HOH Z 350 " =    1.738
peak=   -3.685 closest distance to " O   HOH Z 351 " =    1.467
peak=   -3.682 closest distance to " CA  GLY A 241 " =    2.328
peak=   -3.682 closest distance to " CD2 LEU A 300 " =    2.832
peak=   -3.675 closest distance to " OG ASER A 134 " =    1.314
peak=   -3.674 closest distance to " CG  ARG A 269 " =    2.389
peak=   -3.672 closest distance to " O   HOH Z 394 " =    1.544
peak=   -3.665 closest distance to " CA  GLY A 241 " =    3.055
peak=   -3.660 closest distance to " O   HOH Z  10 " =    1.562
peak=   -3.658 closest distance to " OG BSER A 134 " =    1.263
peak=   -3.635 closest distance to " O   GLY A  80 " =    2.611
peak=   -3.630 closest distance to " O   HOH Z  19 " =    2.362
peak=   -3.628 closest distance to " O   HOH Z  73 " =    2.138
peak=   -3.616 closest distance to " O   HOH Z 184 " =    1.578
peak=   -3.611 closest distance to " OG  SER A  26 " =    1.369
peak=   -3.607 closest distance to " CD2 TYR A 293 " =    2.050
peak=   -3.605 closest distance to " O   HOH Z 426 " =    1.653
peak=   -3.604 closest distance to " ND2 ASN A  60 " =    1.387
peak=   -3.601 closest distance to " O   HOH Z  17 " =    1.490
peak=   -3.596 closest distance to " O   HOH Z 103 " =    1.819
peak=   -3.595 closest distance to " O   HOH Z 241 " =    1.149
peak=   -3.590 closest distance to " CG1 VAL A 197 " =    2.343
peak=   -3.583 closest distance to " OD1 ASN A 148 " =    1.480
peak=   -3.583 closest distance to " N   THR A 157 " =    1.530
peak=   -3.581 closest distance to " CD1 PHE A  59 " =    1.968
peak=   -3.578 closest distance to " CE3 TRP A  70 " =    1.789
peak=   -3.574 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.567 closest distance to " O   HOH Z  11 " =    1.939
peak=   -3.566 closest distance to " NH2 ARG A  66 " =    1.939
peak=   -3.552 closest distance to " N   THR A  18 " =    1.264
peak=   -3.549 closest distance to " CG2 ILE A  49 " =    2.814
peak=   -3.545 closest distance to " O   VAL A 189 " =    2.626
peak=   -3.540 closest distance to " NE2 GLN A  88 " =    2.284
peak=   -3.536 closest distance to " O   HOH Z 128 " =    2.576
peak=   -3.536 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.531 closest distance to " N   ALA A 226 " =    2.156
peak=   -3.530 closest distance to " CB  ALA A  43 " =    2.593
peak=   -3.528 closest distance to " O   HOH Z  38 " =    1.384
peak=   -3.528 closest distance to " O   HOH Z 166 " =    1.550
peak=   -3.524 closest distance to " CD2 LEU A 167 " =    1.745
peak=   -3.523 closest distance to " O   HOH Z  13 " =    1.418
peak=   -3.522 closest distance to " O   HOH Z 435 " =    2.754
peak=   -3.522 closest distance to " O   HOH Z 211 " =    1.501
peak=   -3.521 closest distance to " OXT GLY A 302 " =    3.050
peak=   -3.518 closest distance to " OE1 GLN A  88 " =    0.991
peak=   -3.517 closest distance to " O   HOH Z  44 " =    2.150
peak=   -3.503 closest distance to " CD  GLN A  88 " =    0.876
peak=   -3.502 closest distance to " CA  GLY A 203 " =    2.382
peak=   -3.500 closest distance to " O   HOH Z 353 " =    2.216
peak=   -3.492 closest distance to " CG1 VAL A 112 " =    3.036
peak=   -3.478 closest distance to " O   HOH Z 292 " =    4.669
peak=   -3.474 closest distance to " O   HOH Z  43 " =    1.630
peak=   -3.471 closest distance to " O   HOH Z 275 " =    1.509
peak=   -3.466 closest distance to " CD  LYS A 289 " =    2.516
peak=   -3.465 closest distance to " O   HOH Z 118 " =    3.159
peak=   -3.464 closest distance to " CB  PRO A 163 " =    2.533
peak=   -3.452 closest distance to " O   GLY A 211 " =    1.459
peak=   -3.432 closest distance to " O   HOH Z  60 " =    2.178
peak=   -3.425 closest distance to " O   HOH Z 185 " =    2.399
peak=   -3.421 closest distance to " CG  GLU A 277 " =    1.186
peak=   -3.414 closest distance to " CB  ALA A 291 " =    2.179
peak=   -3.414 closest distance to " C   ASN A 285 " =    2.536
peak=   -3.407 closest distance to " OD2 ASP A  50 " =    2.324
peak=   -3.407 closest distance to " CD1 LEU A 101 " =    2.646
peak=   -3.403 closest distance to " CG2 VAL A 112 " =    2.564
peak=   -3.402 closest distance to " CD1 ILE A 151 " =    2.403
peak=   -3.398 closest distance to " C   ASN A 187 " =    1.717
peak=   -3.395 closest distance to " O   HOH Z 407 " =    3.248
peak=   -3.392 closest distance to " CE3 TRP A 150 " =    2.114
peak=   -3.392 closest distance to " CG  HIS A  86 " =    1.020
peak=   -3.388 closest distance to " OG BSER A 134 " =    1.864
peak=   -3.386 closest distance to " CH2 TRP A 177 " =    2.192
peak=   -3.382 closest distance to " ND2 ASN A  45 " =    1.196
peak=   -3.378 closest distance to " CG2 ILE A 263 " =    2.444
peak=   -3.373 closest distance to " CD  PRO A 213 " =    2.240
peak=   -3.373 closest distance to " O   HOH Z 231 " =    1.337
peak=   -3.364 closest distance to " O   HOH Z 252 " =    4.064
peak=   -3.364 closest distance to " O   GLY A 203 " =    2.313
peak=   -3.358 closest distance to " O   HOH Z 311 " =    3.861
peak=   -3.355 closest distance to " O   HOH Z 377 " =    1.472
peak=   -3.336 closest distance to " O   HOH Z 111 " =    2.228
peak=   -3.323 closest distance to " O   HOH Z 177 " =    1.648
peak=   -3.318 closest distance to " CE BMET A  47 " =    1.913
peak=   -3.317 closest distance to " C   LEU A 143 " =    1.175
peak=   -3.313 closest distance to " N   PHE A  59 " =    2.159
peak=   -3.308 closest distance to " O   HOH Z 308 " =    1.712
peak=   -3.305 closest distance to " CD1 TYR A 247 " =    2.341
peak=   -3.297 closest distance to " CD  ARG A 139 " =    1.631
peak=   -3.297 closest distance to " CA  GLY A 133 " =    2.256
peak=   -3.289 closest distance to " CG  PRO A 163 " =    2.430
peak=   -3.288 closest distance to " NE2 GLN A 103 " =    1.769
peak=   -3.288 closest distance to " CA  ASN A 127 " =    1.051
peak=   -3.287 closest distance to " O   HOH Z 174 " =    2.524
peak=   -3.286 closest distance to " O   HOH Z 113 " =    2.054
peak=   -3.285 closest distance to " O   HOH Z 198 " =    1.525
peak=   -3.284 closest distance to " O   HOH Z 234 " =    4.428
peak=   -3.283 closest distance to " O   HOH Z 295 " =    1.472
peak=   -3.282 closest distance to " CB  ALA A 248 " =    2.051
peak=   -3.269 closest distance to " CD1 ILE A 199 " =    2.642
peak=   -3.266 closest distance to " NE2 GLN A  88 " =    1.080
peak=   -3.263 closest distance to " CD1 LEU A 101 " =    2.959
peak=   -3.260 closest distance to " O   VAL A  67 " =    2.625
peak=   -3.257 closest distance to " CB  ALA A 114 " =    2.491
peak=   -3.256 closest distance to " NH2 ARG A  79 " =    2.058
peak=   -3.254 closest distance to " CD2 PHE A  61 " =    1.953
peak=   -3.244 closest distance to " O   HOH Z 431 " =    1.673
peak=   -3.242 closest distance to " O   HOH Z 368 " =    1.709
peak=   -3.239 closest distance to " O   HOH Z 396 " =    1.849
peak=   -3.237 closest distance to " O   PRO A 198 " =    1.368
peak=   -3.232 closest distance to " NE2 GLN A 194 " =    1.893
peak=   -3.230 closest distance to " O   VAL A 125 " =    2.293
peak=   -3.226 closest distance to " CD  GLN A 223 " =    1.441
peak=   -3.224 closest distance to " OD1 ASN A 187 " =    1.583
peak=   -3.223 closest distance to " CB  ALA A 291 " =    2.262
peak=   -3.221 closest distance to " ND2 ASN A  60 " =    1.859
peak=   -3.221 closest distance to " OG  SER A  62 " =    1.789
peak=   -3.220 closest distance to " O   HOH Z 165 " =    1.907
peak=   -3.217 closest distance to " O   LEU A 167 " =    1.494
peak=   -3.217 closest distance to " CB  TYR A  15 " =    2.224
peak=   -3.216 closest distance to " CB  VAL A 230 " =    1.077
peak=   -3.215 closest distance to " O   HOH Z 388 " =    2.023
peak=   -3.213 closest distance to " O   HOH Z  92 " =    1.717
peak=   -3.203 closest distance to " OG1 THR A 178 " =    1.329
peak=   -3.201 closest distance to " CB  ASP A 132 " =    2.299
peak=   -3.197 closest distance to " O   HOH Z 393 " =    1.491
peak=   -3.196 closest distance to " CA  ALA A 248 " =    2.571
peak=   -3.191 closest distance to " CE1 TYR A 169 " =    2.528
peak=   -3.180 closest distance to " O   GLY A 196 " =    1.188
peak=   -3.176 closest distance to " O   HOH Z 357 " =    2.210
peak=   -3.174 closest distance to " O   HOH Z 222 " =    1.518
peak=   -3.171 closest distance to " N   SER A 212 " =    1.926
peak=   -3.168 closest distance to " CG  GLU A   2 " =    1.863
peak=   -3.165 closest distance to " O   HOH Z 189 " =    2.103
peak=   -3.163 closest distance to " CD1 TRP A 179 " =    1.092
peak=   -3.159 closest distance to " O   HOH Z  60 " =    1.958
peak=   -3.156 closest distance to " N   SER A   3 " =    2.100
peak=   -3.150 closest distance to " CE2 PHE A 218 " =    2.571
peak=   -3.150 closest distance to " O   ASN A 301 " =    1.426
peak=   -3.137 closest distance to " CB  TRP A  85 " =    2.501
peak=   -3.134 closest distance to " N   GLN A  58 " =    1.651
peak=   -3.133 closest distance to " OD1 ASN A 173 " =    1.287
peak=   -3.132 closest distance to " N   ASN A  60 " =    1.253
peak=   -3.132 closest distance to " N   SER A 276 " =    1.395
peak=   -3.130 closest distance to " O   HOH Z 106 " =    1.952
peak=   -3.126 closest distance to " CD1 LEU A 297 " =    2.393
peak=   -3.126 closest distance to " NH1 ARG A 195 " =    2.619
peak=   -3.124 closest distance to " C   MET A 188 " =    1.447
peak=   -3.122 closest distance to " CB  ALA A  10 " =    2.246
peak=   -3.114 closest distance to " O   HOH Z 139 " =    3.012
peak=   -3.113 closest distance to " CD2 LEU A 237 " =    2.848
peak=   -3.109 closest distance to " CE  MET A 105 " =    2.271
peak=   -3.108 closest distance to " CD2 PHE A  61 " =    2.468
peak=   -3.098 closest distance to " OG  SER A 206 " =    1.773
peak=   -3.096 closest distance to " OD1 ASN A 301 " =    1.939
peak=   -3.086 closest distance to " O   HOH Z 128 " =    4.296
peak=   -3.075 closest distance to " O   ASP A 270 " =    1.585
peak=   -3.063 closest distance to " O   HOH Z  40 " =    2.294
peak=   -3.050 closest distance to " CG  ARG A 269 " =    2.072
peak=   -3.046 closest distance to " O   HOH Z  51 " =    1.415
peak=   -3.037 closest distance to " ND2 ASN A 285 " =    2.240
peak=   -3.035 closest distance to " CA  TYR A  68 " =    2.864
peak=   -3.030 closest distance to " N   ALA A 248 " =    1.901
peak=   -3.018 closest distance to " O   HOH Z 120 " =    2.066
peak=   -3.006 closest distance to " CA  SER A  62 " =    2.427

================= 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    :  0.4430 0.4308   6.243894e+00   6.222257e+00
   1_bss:  0.4359 0.4181   6.238942e+00   6.211906e+00
   1_xyz:  0.3292 0.3586   6.048379e+00   6.108606e+00
   1_adp:  0.2744 0.3124   5.903706e+00   6.018080e+00
   1_occ:  0.2737 0.3129   5.902796e+00   6.019473e+00
   2_bss:  0.2708 0.3088   5.902116e+00   6.016121e+00
   2_xyz:  0.1938 0.2412   5.608656e+00   5.778138e+00
   2_adp:  0.1792 0.2267   5.542058e+00   5.726361e+00
   2_occ:  0.1790 0.2267   5.541701e+00   5.726116e+00
   3_bss:  0.1780 0.2243   5.541138e+00   5.724119e+00
   3_xyz:  0.1399 0.1859   5.330053e+00   5.548086e+00
   3_adp:  0.1297 0.1781   5.275944e+00   5.509186e+00
   3_occ:  0.1297 0.1781   5.275993e+00   5.509372e+00
   4_bss:  0.1300 0.1781   5.276658e+00   5.509167e+00
   4_xyz:  0.1208 0.1709   5.219810e+00   5.463972e+00
   4_adp:  0.1204 0.1670   5.206923e+00   5.440280e+00
   4_occ:  0.1202 0.1668   5.206498e+00   5.440196e+00
   5_bss:  0.1202 0.1668   5.206460e+00   5.440158e+00
   5_xyz:  0.1152 0.1624   5.173231e+00   5.416089e+00
   5_adp:  0.1142 0.1628   5.170392e+00   5.418830e+00
   5_occ:  0.1142 0.1628   5.170387e+00   5.418920e+00
   5_bss:  0.1141 0.1628   5.170398e+00   5.418925e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   9.506   7.956   7.556   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.506   7.956   7.556   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.506   7.956   7.556   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.506   7.956   7.556   0.000   0.000   0.000
   2_bss:  0.328  50.051   6.306   4.934   5.177   0.000   0.000   0.000
   2_xyz:  0.328  50.051   6.306   4.934   5.177   0.000   0.000   0.000
   2_adp:  0.328  50.051   6.306   4.934   5.177   0.000   0.000   0.000
   2_occ:  0.328  50.051   6.306   4.934   5.177   0.000   0.000   0.000
   3_bss:  0.328  50.051   4.093   3.630   4.291   0.000   0.000   0.000
   3_xyz:  0.328  50.051   4.093   3.630   4.291   0.000   0.000   0.000
   3_adp:  0.328  50.051   4.093   3.630   4.291   0.000   0.000   0.000
   3_occ:  0.328  50.051   4.093   3.630   4.291   0.000   0.000   0.000
   4_bss:  0.331  60.695   3.550   3.314   4.136   0.000   0.000   0.000
   4_xyz:  0.331  60.695   3.550   3.314   4.136   0.000   0.000   0.000
   4_adp:  0.331  60.695   3.550   3.314   4.136   0.000   0.000   0.000
   4_occ:  0.331  60.695   3.550   3.314   4.136   0.000   0.000   0.000
   5_bss:  0.327  58.338   3.550   3.314   4.136   0.000   0.000   0.000
   5_xyz:  0.327  58.338   3.550   3.314   4.136   0.000   0.000   0.000
   5_adp:  0.327  58.338   3.550   3.314   4.136   0.000   0.000   0.000
   5_occ:  0.327  58.338   3.550   3.314   4.136   0.000   0.000   0.000
   5_bss:  0.323  60.492  -0.199  -0.343   0.542  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.648 0.5388  0.5999    54746.603
   1_bss:  48.378 0.5404  0.7717    52524.460
   1_xyz:  40.256 0.6382  0.8863    37002.339
   1_adp:  33.392 0.7198  0.9752    27495.254
   1_occ:  33.457 0.7189  0.9737    27566.366
   2_bss:  33.235 0.7214  0.8833    27253.637
   2_xyz:  23.629 0.8257  0.9819    14905.081
   2_adp:  21.864 0.8441  1.0028    13235.073
   2_occ:  21.862 0.8441  1.0025    13234.440
   3_bss:  21.793 0.8447  0.9514    13170.522
   3_xyz:  17.354 0.8865  0.9757     8865.954
   3_adp:  16.486 0.8943  0.9773     8131.518
   3_occ:  16.490 0.8943  0.9771     8132.943
   4_bss:  16.495 0.8943  0.9648     8145.113
   4_xyz:  15.479 0.9031  0.9691     7365.768
   4_adp:  14.902 0.9081  0.9710     7058.510
   4_occ:  14.909 0.9080  0.9707     7056.717
   5_bss:  14.911 0.9080  0.9706     7055.782
   5_xyz:  14.436 0.9118  0.9725     6709.503
   5_adp:  14.494 0.9113  0.9705     6742.455
   5_occ:  14.497 0.9113  0.9704     6742.029
   5_bss:  14.499 0.9113  0.9684     6740.989
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4298e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4298e+01
   1_xyz:   1.597  0.012  0.105 18.024  0.006  4.126   1.2875e-01
   1_adp:   1.597  0.012  0.105 18.024  0.006  4.126   1.2875e-01
   1_occ:   1.597  0.012  0.105 18.024  0.006  4.126   1.2875e-01
   2_bss:   1.597  0.012  0.105 18.024  0.006  4.126   1.2875e-01
   2_xyz:   1.013  0.007  0.072 16.440  0.004  4.129   6.5812e-02
   2_adp:   1.013  0.007  0.072 16.440  0.004  4.129   6.5812e-02
   2_occ:   1.013  0.007  0.072 16.440  0.004  4.129   6.5812e-02
   3_bss:   1.013  0.007  0.072 16.440  0.004  4.129   6.5812e-02
   3_xyz:   1.036  0.007  0.080 16.022  0.004  4.115   6.6931e-02
   3_adp:   1.036  0.007  0.080 16.022  0.004  4.115   6.6931e-02
   3_occ:   1.036  0.007  0.080 16.022  0.004  4.115   6.6931e-02
   4_bss:   1.036  0.007  0.080 16.022  0.004  4.115   6.6931e-02
   4_xyz:   1.057  0.008  0.083 16.028  0.003  4.120   6.9186e-02
   4_adp:   1.057  0.008  0.083 16.028  0.003  4.120   6.9186e-02
   4_occ:   1.057  0.008  0.083 16.028  0.003  4.120   6.9186e-02
   5_bss:   1.057  0.008  0.083 16.028  0.003  4.120   6.9186e-02
   5_xyz:   1.114  0.010  0.088 15.820  0.004  4.124   7.6010e-02
   5_adp:   1.114  0.010  0.088 15.820  0.004  4.124   7.6010e-02
   5_occ:   1.114  0.010  0.088 15.820  0.004  4.124   7.6010e-02
   5_bss:   1.114  0.010  0.088 15.820  0.004  4.124   7.6010e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0407e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0407e+00
   1_xyz:  13.301  0.151  0.428 85.648  0.038  2.243   9.8020e-02
   1_adp:  13.301  0.151  0.428 85.648  0.038  2.243   9.8020e-02
   1_occ:  13.301  0.151  0.428 85.648  0.038  2.243   9.8020e-02
   2_bss:  13.301  0.151  0.428 85.648  0.038  2.243   9.8020e-02
   2_xyz:   6.461  0.067  0.224 87.805  0.038  2.279   4.6888e-02
   2_adp:   6.461  0.067  0.224 87.805  0.038  2.279   4.6888e-02
   2_occ:   6.461  0.067  0.224 87.805  0.038  2.279   4.6888e-02
   3_bss:   6.461  0.067  0.224 87.805  0.038  2.279   4.6888e-02
   3_xyz:   7.897  0.057  0.410 80.807  0.039  2.402   6.9165e-02
   3_adp:   7.897  0.057  0.410 80.807  0.039  2.402   6.9165e-02
   3_occ:   7.897  0.057  0.410 80.807  0.039  2.402   6.9165e-02
   4_bss:   7.897  0.057  0.410 80.807  0.039  2.402   6.9165e-02
   4_xyz:   8.564  0.061  0.475 84.084  0.038  2.346   4.8271e-02
   4_adp:   8.564  0.061  0.475 84.084  0.038  2.346   4.8271e-02
   4_occ:   8.564  0.061  0.475 84.084  0.038  2.346   4.8271e-02
   5_bss:   8.564  0.061  0.475 84.084  0.038  2.346   4.8271e-02
   5_xyz:   8.104  0.047  0.571 83.168  0.041  2.322   5.1357e-02
   5_adp:   8.104  0.047  0.571 83.168  0.041  2.322   5.1357e-02
   5_occ:   8.104  0.047  0.571 83.168  0.041  2.322   5.1357e-02
   5_bss:   8.104  0.047  0.571 83.168  0.041  2.322   5.1357e-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:  66.65   0.00  10.32  59.41   0.00   7.36  66.65   0.00  26.46
   1_occ:  66.65   0.00  10.32  59.41   0.00   7.36  66.65   0.00  26.46
   2_bss:  66.65   0.00  10.32  59.41   0.00   7.36  66.65   0.00  26.46
   2_xyz:  66.65   0.00  10.32  59.41   0.00   7.36  66.65   0.00  26.46
   2_adp:  75.43   0.00  11.00  75.43   0.00   7.43  66.56   0.00  30.41
   2_occ:  75.43   0.00  11.00  75.43   0.00   7.43  66.56   0.00  30.41
   3_bss:  75.43   0.00  11.00  75.43   0.00   7.43  66.56   0.00  30.41
   3_xyz:  75.43   0.00  11.00  75.43   0.00   7.43  66.56   0.00  30.41
   3_adp:  91.54   0.00  12.40  86.05   0.00   7.76  91.54   0.00  37.67
   3_occ:  91.54   0.00  12.40  86.05   0.00   7.76  91.54   0.00  37.67
   4_bss:  91.54   0.00  12.40  86.05   0.00   7.76  91.54   0.00  37.67
   4_xyz:  91.54   0.00  12.40  86.05   0.00   7.76  91.54   0.00  37.67
   4_adp:  88.69   0.00  12.01  84.77   0.00   7.58  88.69   0.77  36.17
   4_occ:  88.69   0.00  12.01  84.77   0.00   7.58  88.69   0.77  36.17
   5_bss:  88.69   0.00  12.01  84.77   0.00   7.58  88.69   0.77  36.17
   5_xyz:  88.69   0.00  12.01  84.77   0.00   7.58  88.69   0.77  36.17
   5_adp:  90.29   0.00  11.95  87.56   0.00   7.57  90.29   0.86  35.77
   5_occ:  90.29   0.00  11.95  87.56   0.00   7.57  90.29   0.86  35.77
   5_bss:  93.90   3.61  15.56  91.17   3.61  11.18  93.90   4.48  39.38
------------------------------------------------------------------------
 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:    1.195    0.028    0.409
   1_adp:    1.195    0.028    0.409
   1_occ:    1.195    0.028    0.409
   2_bss:    1.195    0.028    0.409
   2_xyz:    1.536    0.042    0.519
   2_adp:    1.536    0.042    0.519
   2_occ:    1.536    0.042    0.519
   3_bss:    1.536    0.042    0.519
   3_xyz:    1.520    0.015    0.572
   3_adp:    1.520    0.015    0.572
   3_occ:    1.520    0.015    0.572
   4_bss:    1.520    0.015    0.572
   4_xyz:    1.608    0.043    0.596
   4_adp:    1.608    0.043    0.596
   4_occ:    1.608    0.043    0.596
   5_bss:    1.608    0.043    0.596
   5_xyz:    1.633    0.043    0.606
   5_adp:    1.633    0.043    0.606
   5_occ:    1.633    0.043    0.606
   5_bss:    1.633    0.043    0.606
------------------------------------------------------------------------

CPU time actual refinement: 336.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/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_1160/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1160/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.08 
  Macro-tasks:
    bulk solvent and scale       = 42.81  
    individual site refinement   = 138.44 
    weights calculation          = 32.64  
    collect and process          = 6.79   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 220.84 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 102.06 
    alpha_beta                      = 8.43   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 113.13 
    fmodel                         = 7.41   
    r_factors                      = 0.33   
    phase_errors                   = 10.97  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 245.51 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.703 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    652 calls, 101.66 s
gradients_fft:          597 calls,  99.21 s

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

# Date 2008-01-16 Time 03:20:40 PST -0800 (1200482440.65 s)
Start R-work = 0.4430, R-free = 0.4308 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.4359, R-free = 0.4181
Final R-work = 0.1141, R-free = 0.1628