# Date 2008-01-16 Time 00:27:24 PST -0800 (1200472044.38 s)
#phil __OFF__

Command line arguments: "../22.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25283
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 22

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.2261, 84.2302, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95045
Completeness in resolution range: 0.976715
Completeness with d_max=infinity: 0.973608

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6191
                             d_min =   1.9504

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95045
Completeness in resolution range: 0.976715
Completeness with d_max=infinity: 0.973608

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6195 -  4.1726 [2105/2132]  1895   210  10.0%
  bin  2:  4.1726 -  3.3247 [2025/2041]  1822   203  10.0%
  bin  3:  3.3247 -  2.9082 [1996/2015]  1794   202  10.1%
  bin  4:  2.9082 -  2.6440 [1973/2003]  1781   192   9.7%
  bin  5:  2.6440 -  2.4555 [1964/1983]  1764   200  10.2%
  bin  6:  2.4555 -  2.3113 [1957/1983]  1760   197  10.1%
  bin  7:  2.3113 -  2.1959 [1951/1985]  1763   188   9.6%
  bin  8:  2.1959 -  2.1006 [1937/1967]  1740   197  10.2%
  bin  9:  2.1006 -  2.0200 [1924/1965]  1728   196  10.2%
  bin 10:  2.0200 -  1.9504 [1757/1982]  1583   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.62 -     1.48: 7
        1.48 -     2.33: 73
        2.33 -     3.19: 3192
        3.19 -     4.04: 9759
        4.04 -     4.90: 16335
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.620 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.932 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.309 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.346 3.040 -x+1/2,-y+1,z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.375 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 29361 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_22/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/model_refine_001.geo

CPU time processing inputs: 11.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.22605 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5228   r_free= 0.5135   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.309700                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1373  153 0.4359 0.4403      6.6563       6.692|
|  2:  4.6535 -  3.7135 0.99   1308  146 0.4773 0.4614      6.8753      6.8848|
|  3:  3.7135 -  3.2500 0.99   1294  143 0.5036 0.4810      6.7581      6.8237|
|  4:  3.2500 -  2.9555 0.99   1286  139 0.5124 0.4876       6.587       6.529|
|  5:  2.9555 -  2.7452 0.99   1263  142 0.5548 0.5509      6.4151      6.3893|
|  6:  2.7452 -  2.5843 0.99   1274  144 0.5570 0.5577      6.3189      6.2999|
|  7:  2.5843 -  2.4555 0.99   1258  140 0.5412 0.5186      6.2649       6.186|
|  8:  2.4555 -  2.3490 0.98   1261  141 0.5607 0.5697      6.2137      6.2231|
|  9:  2.3490 -  2.2589 0.98   1251  137 0.5548 0.5570      6.1336      6.1543|
| 10:  2.2589 -  2.1813 0.98   1247  137 0.5716 0.5117      6.1344      6.1301|
| 11:  2.1813 -  2.1133 0.99   1261  144 0.5416 0.5964      6.0577       6.121|
| 12:  2.1133 -  2.0530 0.97   1243  132 0.5421 0.4871      5.9986      6.0254|
| 13:  2.0530 -  1.9991 0.99   1239  138 0.5570 0.5311      5.9105      5.8783|
| 14:  1.9991 -  1.9504 0.85   1072  123 0.5502 0.5193        5.86      5.7704|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6195 -  4.6535  1373   153  0.59  43.84   0.78     0.63     103792.29|
|  2:  4.6535 -  3.7135  1308   146  0.58  45.24   0.84     0.67     156536.04|
|  3:  3.7135 -  3.2500  1294   143  0.46  54.66   0.84     0.61     163456.58|
|  4:  3.2500 -  2.9555  1286   139  0.39  60.56   0.79     0.51     134621.44|
|  5:  2.9555 -  2.7452  1263   142  0.32  66.32   0.71     0.40     100519.25|
|  6:  2.7452 -  2.5843  1274   144  0.29  68.24   0.70     0.35      82851.94|
|  7:  2.5843 -  2.4555  1258   140  0.23  72.93   0.74     0.27      75740.24|
|  8:  2.4555 -  2.3490  1261   141  0.21  74.23   0.73     0.26      69753.53|
|  9:  2.3490 -  2.2589  1251   137  0.19  75.78   0.72     0.24      64648.84|
| 10:  2.2589 -  2.1813  1247   137  0.22  73.61   0.75     0.28      57415.97|
| 11:  2.1813 -  2.1133  1261   144  0.16  78.01   0.78     0.21      55379.12|
| 12:  2.1133 -  2.0530  1243   132  0.16  78.18   0.75     0.21      51082.39|
| 13:  2.0530 -  1.9991  1239   138  0.15  79.15   0.75     0.19      43795.70|
| 14:  1.9991 -  1.9504  1072   123  0.23  72.98   0.74     0.27      32977.85|
|alpha:            min =        0.19 max =            0.67 mean =         0.37|
|beta:             min =    32977.85 max =       163456.58 mean =     86390.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.30|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.07|
|phase err.(test): min =        0.00 max =           90.00 mean =        67.52|
|-----------------------------------------------------------------------------|

============================== 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 = 34.091724             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.999004              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.833   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.577 -  1.009:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.009 -  1.442:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.442 -  1.874:       36 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.874 -  2.306:      228 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.306 -  2.739:      932 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.739 -  3.171:     2201 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.171 -  3.603:     3827 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.603 -  4.035:     5565 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.035 -  4.468:     7485 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.468 -  4.900:     9094 |
|-----------------------------------------------------------------------------|
|-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 |       52.341 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.082    4.900  0.577 |       4.149 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5255   r_free= 0.5161   ksol= 0.00   Bsol= 0.00   scale= 0.751    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.310258                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5149   r_free= 0.5050   ksol= 0.39   Bsol= 0.79   scale= 0.965    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,8.42,8.48,0.00,0.00,0.00); trace/3= 7.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305407                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.179492             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.720   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.249565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.799   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5149      final r-factor (work) = 0.4552          |
| start r-factor (free) = 0.5050      final r-factor (free) = 0.4745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 128.5905 = 24.18 * 0.50 * 6.3069 + 1.00 * 52.3413                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.8396 = 24.18 * 0.50 * 6.2574 + 1.00 * 0.1892                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4552      final r-factor (work) = 0.4171          |
| start r-factor (free) = 0.4745      final r-factor (free) = 0.4698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0908 = 2.25 * 1.00 * 6.2574 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0149 = 2.25 * 1.00 * 6.2192 + 1.00 * 0.0243                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.44   16.06    None  None   None       |
|    all(noH): 2823   0      0.00    81.44   16.06    None  None   None       |
|    Sol.    : 438    0      0.00    81.44   22.46    None  None   None       |
|    Mac.    : 2385   0      0.00    73.96   14.88    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 -   8.144:  905   |   5:    40.719 -  48.863:   78        |
|      1:     8.144 -  16.288:  760   |   6:    48.863 -  57.007:   39        |
|      2:    16.288 -  24.432:  514   |   7:    57.007 -  65.151:   20        |
|      3:    24.432 -  32.576:  339   |   8:    65.151 -  73.295:    6        |
|      4:    32.576 -  40.719:  159   |   9:    73.295 -  81.439:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4171 r_free = 0.4698             target_work(ml) = 6.211         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4168 r_free = 0.4704             target_work(ml) = 6.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4168   r_free= 0.4704   ksol= 0.39   Bsol= 0.79   scale= 1.104    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,8.42,8.48,0.00,0.00,0.00); trace/3= 7.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.210502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4150   r_free= 0.4669   ksol= 0.36   Bsol= 27.99   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,5.02,5.87,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.211659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.572943             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.935230              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.422  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4150      final r-factor (work) = 0.3464          |
| start r-factor (free) = 0.4669      final r-factor (free) = 0.4093          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 67.2345 = 21.57 * 0.50 * 6.2157 + 1.00 * 0.1892                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.4756 = 21.57 * 0.50 * 6.1504 + 1.00 * 0.1344                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3464      final r-factor (work) = 0.3200          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.3895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7780 = 0.94 * 1.00 * 6.1504 + 1.00 * 0.0259                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6854 = 0.94 * 1.00 * 6.0472 + 1.00 * 0.0298                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.43  15.56    None  None   None       |
|    all(noH): 2823   0      0.00    119.43  15.56    None  None   None       |
|    Sol.    : 438    0      0.00    79.53   29.08    None  None   None       |
|    Mac.    : 2385   0      0.00    119.43  13.08    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 -  11.943: 1383   |   5:    59.716 -  71.659:   15        |
|      1:    11.943 -  23.886:  843   |   6:    71.659 -  83.602:    6        |
|      2:    23.886 -  35.830:  372   |   7:    83.602 -  95.546:    0        |
|      3:    35.830 -  47.773:  158   |   8:    95.546 - 107.489:    0        |
|      4:    47.773 -  59.716:   45   |   9:   107.489 - 119.432:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3200 r_free = 0.3895             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3194 r_free = 0.3904             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3194   r_free= 0.3904   ksol= 0.36   Bsol= 27.99   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,5.02,5.87,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.025743                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3162   r_free= 0.3889   ksol= 0.32   Bsol= 33.49   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.46,3.21,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.022702                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.701478              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.376  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.493716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.044   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3162      final r-factor (work) = 0.2483          |
| start r-factor (free) = 0.3889      final r-factor (free) = 0.3099          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4285 = 8.70 * 0.50 * 6.0436 + 1.00 * 0.1344                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9155 = 8.70 * 0.50 * 5.9353 + 1.00 * 0.0924                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2483      final r-factor (work) = 0.2221          |
| start r-factor (free) = 0.3099      final r-factor (free) = 0.2831          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9512 = 0.49 * 1.00 * 5.9353 + 1.00 * 0.0209                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8622 = 0.49 * 1.00 * 5.7738 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.01   15.05    None  None   None       |
|    all(noH): 2823   0      0.00    92.01   15.05    None  None   None       |
|    Sol.    : 438    0      1.84    79.19   36.12    None  None   None       |
|    Mac.    : 2385   0      0.00    92.01   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:     0.000 -   9.201: 1332   |   5:    46.006 -  55.208:   77        |
|      1:     9.201 -  18.403:  767   |   6:    55.208 -  64.409:   42        |
|      2:    18.403 -  27.604:  265   |   7:    64.409 -  73.610:   18        |
|      3:    27.604 -  36.805:  175   |   8:    73.610 -  82.812:    5        |
|      4:    36.805 -  46.006:  140   |   9:    82.812 -  92.013:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2221 r_free = 0.2831             target_work(ml) = 5.733         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2217 r_free = 0.2825             target_work(ml) = 5.732         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2217   r_free= 0.2825   ksol= 0.32   Bsol= 33.49   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.46,3.21,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.731867                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2206   r_free= 0.2816   ksol= 0.32   Bsol= 33.49   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,1.22,1.81,0.00,0.00,0.00); trace/3= 1.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.727233                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.612952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.987  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.152791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.542  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2206      final r-factor (work) = 0.1788          |
| start r-factor (free) = 0.2816      final r-factor (free) = 0.2349          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6377 = 2.61 * 0.50 * 5.7753 + 1.00 * 0.0924                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4343 = 2.61 * 0.50 * 5.6443 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1788      final r-factor (work) = 0.1728          |
| start r-factor (free) = 0.2349      final r-factor (free) = 0.2211          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8740 = 0.15 * 1.00 * 5.6443 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8536 = 0.15 * 1.00 * 5.5339 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.87   14.44    None  None   None       |
|    all(noH): 2823   0      0.00    83.87   14.44    None  None   None       |
|    Sol.    : 438    0      3.31    76.55   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    83.87   10.48    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 -   8.387: 1262   |   5:    41.936 -  50.323:   98        |
|      1:     8.387 -  16.775:  838   |   6:    50.323 -  58.711:   53        |
|      2:    16.775 -  25.162:  265   |   7:    58.711 -  67.098:   21        |
|      3:    25.162 -  33.549:  154   |   8:    67.098 -  75.485:    9        |
|      4:    33.549 -  41.936:  119   |   9:    75.485 -  83.872:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1728 r_free = 0.2211             target_work(ml) = 5.504         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1724 r_free = 0.2203             target_work(ml) = 5.502         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1724   r_free= 0.2203   ksol= 0.32   Bsol= 33.49   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,1.22,1.81,0.00,0.00,0.00); trace/3= 1.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.502327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1723   r_free= 0.2205   ksol= 0.33   Bsol= 33.49   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,0.54,1.26,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.502850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.672126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.756   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1723      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.2205      final r-factor (free) = 0.1893          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6873 = 1.67 * 0.50 * 5.5345 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5950 = 1.67 * 0.50 * 5.4281 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1471      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.1893      final r-factor (free) = 0.1870          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0976 = 0.20 * 1.00 * 5.4281 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0814 = 0.20 * 1.00 * 5.3374 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.69   14.49    None  None   None       |
|    all(noH): 2823   0      0.00    83.69   14.49    None  None   None       |
|    Sol.    : 438    0      3.94    76.65   36.44    None  None   None       |
|    Mac.    : 2385   0      0.00    83.69   10.46    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 -   8.369: 1225   |   5:    41.844 -  50.213:  105        |
|      1:     8.369 -  16.738:  896   |   6:    50.213 -  58.581:   54        |
|      2:    16.738 -  25.106:  242   |   7:    58.581 -  66.950:   20        |
|      3:    25.106 -  33.475:  147   |   8:    66.950 -  75.319:    9        |
|      4:    33.475 -  41.844:  119   |   9:    75.319 -  83.688:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1426 r_free = 0.1870             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1424 r_free = 0.1868             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1424   r_free= 0.1868   ksol= 0.33   Bsol= 33.49   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,0.54,1.26,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.330772                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1373  153 0.1237 0.1536      5.5822      5.7009|
|  2:  4.6535 -  3.7135 0.99   1308  146 0.1131 0.1507      5.6714      5.9396|
|  3:  3.7135 -  3.2500 0.99   1294  143 0.1364 0.1554      5.6992      5.8586|
|  4:  3.2500 -  2.9555 0.99   1286  139 0.1563 0.2069      5.6639      5.8622|
|  5:  2.9555 -  2.7452 0.99   1263  142 0.1635 0.1923      5.5166      5.6146|
|  6:  2.7452 -  2.5843 0.99   1274  144 0.1597 0.2054      5.4074      5.5847|
|  7:  2.5843 -  2.4555 0.99   1258  140 0.1498 0.2032      5.3182      5.5271|
|  8:  2.4555 -  2.3490 0.98   1261  141 0.1539 0.2094      5.2916      5.5283|
|  9:  2.3490 -  2.2589 0.98   1251  137 0.1506 0.2041      5.2179      5.4124|
| 10:  2.2589 -  2.1813 0.98   1247  137 0.1437 0.2179      5.1588       5.382|
| 11:  2.1813 -  2.1133 0.99   1261  144 0.1432 0.1919      5.0891      5.3969|
| 12:  2.1133 -  2.0530 0.97   1243  132 0.1397 0.1826      5.0537      5.2977|
| 13:  2.0530 -  1.9991 0.99   1239  138 0.1381 0.2100      4.9627      5.2389|
| 14:  1.9991 -  1.9504 0.85   1072  123 0.1355 0.2021      4.8623      5.1193|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6195 -  4.6535  1373   153  0.92  12.07   0.99     0.97      10795.15|
|  2:  4.6535 -  3.7135  1308   146  0.94  10.58   1.05     1.03      13179.32|
|  3:  3.7135 -  3.2500  1294   143  0.91  14.61   1.06     1.05      15415.71|
|  4:  3.2500 -  2.9555  1286   139  0.90  16.60   1.02     1.01      14292.86|
|  5:  2.9555 -  2.7452  1263   142  0.88  18.34   1.01     0.97      10995.80|
|  6:  2.7452 -  2.5843  1274   144  0.88  18.82   1.00     0.95       9628.21|
|  7:  2.5843 -  2.4555  1258   140  0.87  19.09   1.01     0.99       8540.46|
|  8:  2.4555 -  2.3490  1261   141  0.88  18.72   1.02     0.99       7909.85|
|  9:  2.3490 -  2.2589  1251   137  0.88  18.63   1.03     1.00       6830.97|
| 10:  2.2589 -  2.1813  1247   137  0.88  18.69   1.03     1.01       6403.25|
| 11:  2.1813 -  2.1133  1261   144  0.88  18.73   1.03     0.98       5565.17|
| 12:  2.1133 -  2.0530  1243   132  0.88  18.50   1.05     1.04       5474.49|
| 13:  2.0530 -  1.9991  1239   138  0.88  18.47   1.04     1.03       4584.21|
| 14:  1.9991 -  1.9504  1072   123  0.88  18.20   1.04     1.00       3689.88|
|alpha:            min =        0.95 max =            1.05 mean =         1.00|
|beta:             min =     3689.88 max =        15415.71 mean =      8919.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.73 mean =        17.08|
|phase err.(test): min =        0.00 max =           87.62 mean =        16.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1860   ksol= 0.33   Bsol= 33.76   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.05,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.329271                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1860   ksol= 0.33   Bsol= 33.76   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.05,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.329271                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1373  153 0.1221 0.1493      5.5698      5.6797|
|  2:  4.6535 -  3.7135 0.99   1308  146 0.1147 0.1523      5.6752      5.9387|
|  3:  3.7135 -  3.2500 0.99   1294  143 0.1362 0.1575      5.7005      5.8658|
|  4:  3.2500 -  2.9555 0.99   1286  139 0.1565 0.2074      5.6639      5.8638|
|  5:  2.9555 -  2.7452 0.99   1263  142 0.1636 0.1909      5.5146      5.6071|
|  6:  2.7452 -  2.5843 0.99   1274  144 0.1596 0.2054      5.4056      5.5838|
|  7:  2.5843 -  2.4555 0.99   1258  140 0.1497 0.2031       5.318      5.5274|
|  8:  2.4555 -  2.3490 0.98   1261  141 0.1540 0.2079      5.2904       5.523|
|  9:  2.3490 -  2.2589 0.98   1251  137 0.1503 0.2051      5.2156      5.4152|
| 10:  2.2589 -  2.1813 0.98   1247  137 0.1434 0.2170      5.1568      5.3799|
| 11:  2.1813 -  2.1133 0.99   1261  144 0.1426 0.1911      5.0875      5.3951|
| 12:  2.1133 -  2.0530 0.97   1243  132 0.1398 0.1826      5.0534      5.2978|
| 13:  2.0530 -  1.9991 0.99   1239  138 0.1378 0.2100      4.9622      5.2365|
| 14:  1.9991 -  1.9504 0.85   1072  123 0.1355 0.2013      4.8612      5.1176|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6195 -  4.6535  1373   153  0.92  11.68   0.99     0.97      10343.63|
|  2:  4.6535 -  3.7135  1308   146  0.94  10.53   1.04     1.02      13019.61|
|  3:  3.7135 -  3.2500  1294   143  0.91  14.66   1.05     1.04      15495.09|
|  4:  3.2500 -  2.9555  1286   139  0.89  16.62   1.02     1.00      14308.21|
|  5:  2.9555 -  2.7452  1263   142  0.88  18.27   1.00     0.96      10917.80|
|  6:  2.7452 -  2.5843  1274   144  0.88  18.73   0.99     0.95       9557.24|
|  7:  2.5843 -  2.4555  1258   140  0.87  19.04   1.00     0.98       8493.53|
|  8:  2.4555 -  2.3490  1261   141  0.88  18.71   1.01     0.98       7883.73|
|  9:  2.3490 -  2.2589  1251   137  0.88  18.58   1.02     0.99       6804.67|
| 10:  2.2589 -  2.1813  1247   137  0.88  18.65   1.02     1.00       6376.74|
| 11:  2.1813 -  2.1133  1261   144  0.88  18.69   1.01     0.97       5551.45|
| 12:  2.1133 -  2.0530  1243   132  0.88  18.47   1.04     1.02       5459.22|
| 13:  2.0530 -  1.9991  1239   138  0.88  18.44   1.02     1.01       4577.53|
| 14:  1.9991 -  1.9504  1072   123  0.88  18.14   1.02     0.98       3671.71|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3671.71 max =        15495.09 mean =      8856.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.01|
|phase err.(test): min =        0.00 max =           89.90 mean =        16.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.089)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    83.96   14.77    None  None   None       |
|    all(noH): 2823   0      0.27    83.96   14.77    None  None   None       |
|    Sol.    : 438    0      4.22    76.92   36.72    None  None   None       |
|    Mac.    : 2385   0      0.27    83.96   10.74    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:     0.274 -   8.643: 1225   |   5:    42.118 -  50.487:  105        |
|      1:     8.643 -  17.012:  896   |   6:    50.487 -  58.855:   54        |
|      2:    17.012 -  25.380:  242   |   7:    58.855 -  67.224:   20        |
|      3:    25.380 -  33.749:  147   |   8:    67.224 -  75.593:    9        |
|      4:    33.749 -  42.118:  119   |   9:    75.593 -  83.962:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.495 - 5.898
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 351
   mapped sites are within: 0.710 - 5.898

peak=    9.568 closest distance to " CB  VAL A 230 " =    1.442
peak=    9.395 closest distance to " CB  VAL A 296 " =    1.467
peak=    8.372 closest distance to " O   HOH Z 403 " =    2.410
peak=    7.496 closest distance to " O   HOH Z 138 " =    1.070
peak=    6.919 closest distance to " O   HOH Z  45 " =    1.363
peak=    6.849 closest distance to " O   HOH Z 381 " =    1.515
peak=    6.743 closest distance to " O   HOH Z 199 " =    2.097
peak=    6.516 closest distance to " OD1 ASN A  60 " =    1.051
peak=    6.441 closest distance to " CG  ARG A 138 " =    1.192
peak=    5.878 closest distance to " O   HOH Z 188 " =    1.782
peak=    5.834 closest distance to " O   HOH Z 278 " =    2.471
peak=    5.802 closest distance to " O   HOH Z 130 " =    1.375
peak=    5.742 closest distance to " O   HOH Z 193 " =    1.956
peak=    5.716 closest distance to " CD2 LEU A   5 " =    1.471
peak=    5.681 closest distance to " O   HOH Z 390 " =    1.104
peak=    5.680 closest distance to " O   HOH Z 279 " =    1.337
peak=    5.585 closest distance to " N   PHE A  59 " =    0.727
peak=    5.452 closest distance to " O   HOH Z 138 " =    1.924
peak=    5.393 closest distance to " O   HOH Z 326 " =    1.620
peak=    5.385 closest distance to " O   HOH Z 236 " =    1.841
peak=    5.292 closest distance to " CB  ARG A 275 " =    1.169
peak=    5.213 closest distance to " O   HOH Z 424 " =    1.448
peak=    5.126 closest distance to " O   HOH Z 126 " =    2.097
peak=    4.953 closest distance to " O   HOH Z 124 " =    1.756
peak=    4.932 closest distance to " CG  PRO A 213 " =    1.287
peak=    4.921 closest distance to " O   HOH Z  78 " =    1.611
peak=    4.907 closest distance to " CB  ASN A  60 " =    0.991
peak=    4.808 closest distance to " O   HOH Z 375 " =    1.415
peak=    4.796 closest distance to " O   HOH Z 269 " =    1.689
peak=    4.774 closest distance to " CD1AILE A 234 " =    1.062
peak=    4.770 closest distance to " O   HOH Z  97 " =    1.539
peak=    4.751 closest distance to " O   SER A  62 " =    0.772
peak=    4.742 closest distance to " O   HOH Z  28 " =    2.033
peak=    4.731 closest distance to " NE2 GLN A  55 " =    1.672
peak=    4.707 closest distance to " O   HOH Z  69 " =    2.476
peak=    4.678 closest distance to " O   HOH Z  51 " =    1.923
peak=    4.678 closest distance to " O   HOH Z 214 " =    1.533
peak=    4.643 closest distance to " O   HOH Z 423 " =    1.806
peak=    4.631 closest distance to " O   HOH Z 169 " =    0.929
peak=    4.629 closest distance to " O   HOH Z 385 " =    0.835
peak=    4.501 closest distance to " O   HOH Z 148 " =    2.269
peak=    4.470 closest distance to " O   HOH Z 134 " =    1.720
peak=    4.453 closest distance to " NE2 GLN A  11 " =    1.172
peak=    4.444 closest distance to " O   HOH Z 120 " =    1.064
peak=    4.441 closest distance to " NH2 ARG A  56 " =    2.017
peak=    4.440 closest distance to " O   HOH Z  59 " =    1.760
peak=    4.433 closest distance to " O   PRO A 198 " =    1.360
peak=    4.407 closest distance to " O   HOH Z 414 " =    1.750
peak=    4.402 closest distance to " O   HOH Z 146 " =    1.839
peak=    4.390 closest distance to " O   HOH Z 344 " =    1.556
peak=    4.385 closest distance to " O   HOH Z 291 " =    1.550
peak=    4.374 closest distance to " NH1 ARG A 138 " =    1.073
peak=    4.355 closest distance to " O   HOH Z   9 " =    1.311
peak=    4.353 closest distance to " O   HOH Z 316 " =    2.293
peak=    4.325 closest distance to " NH2BARG A 145 " =    1.689
peak=    4.304 closest distance to " O   HOH Z 263 " =    1.630
peak=    4.304 closest distance to " O   HOH Z 276 " =    1.684
peak=    4.296 closest distance to " N   ASN A  60 " =    0.859
peak=    4.296 closest distance to " O   HOH Z 406 " =    1.493
peak=    4.291 closest distance to " O   HOH Z  58 " =    2.057
peak=    4.272 closest distance to " CA  GLY A 241 " =    3.641
peak=    4.230 closest distance to " O   HOH Z   7 " =    1.578
peak=    4.210 closest distance to " O   HOH Z 222 " =    1.364
peak=    4.208 closest distance to " CD2 LEU A 228 " =    1.244
peak=    4.206 closest distance to " O   HOH Z 205 " =    1.038
peak=    4.200 closest distance to " O   HOH Z 249 " =    1.438
peak=    4.168 closest distance to " CB  VAL A 265 " =    1.277
peak=    4.168 closest distance to " O   HOH Z 410 " =    1.259
peak=    4.166 closest distance to " O   HOH Z 366 " =    1.891
peak=    4.160 closest distance to " O   HOH Z 100 " =    1.410
peak=    4.155 closest distance to " O   HOH Z 132 " =    1.457
peak=    4.153 closest distance to " CG  LEU A   5 " =    1.276
peak=    4.153 closest distance to " O   HOH Z  72 " =    0.991
peak=    4.146 closest distance to " O   HOH Z 112 " =    1.204
peak=    4.119 closest distance to " NH2BARG A 190 " =    1.566
peak=    4.116 closest distance to " O   HOH Z  65 " =    0.973
peak=    4.104 closest distance to " O   HOH Z 357 " =    1.844
peak=    4.057 closest distance to " CA  ILE A 234 " =    0.957
peak=    4.039 closest distance to " O   HOH Z 217 " =    1.980
peak=    4.034 closest distance to " CB  SER A   3 " =    1.099
peak=    4.025 closest distance to " O   HOH Z 117 " =    2.361
peak=    4.021 closest distance to " O   HOH Z 302 " =    1.535
peak=    4.010 closest distance to " O   HOH Z 423 " =    1.945
peak=    4.007 closest distance to " O   HOH Z 202 " =    1.473
peak=    4.003 closest distance to " O   HOH Z 427 " =    2.321
peak=    4.002 closest distance to " CG  PRO A  54 " =    1.340
peak=    4.002 closest distance to " CA  ASN A 284 " =    1.093
peak=    3.995 closest distance to " O   HOH Z 130 " =    2.263
peak=    3.968 closest distance to " O   HOH Z 203 " =    1.590
peak=    3.956 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.953 closest distance to " CB  PRO A 198 " =    1.082
peak=    3.909 closest distance to " CB  GLN A 223 " =    1.576
peak=    3.905 closest distance to " CA  ALA A   1 " =    1.330
peak=    3.905 closest distance to " O   HOH Z 388 " =    1.186
peak=    3.902 closest distance to " O   HOH Z 234 " =    2.067
peak=    3.896 closest distance to " O   HOH Z  88 " =    2.380
peak=    3.895 closest distance to " O   HOH Z 273 " =    1.439
peak=    3.889 closest distance to " O   HOH Z 328 " =    1.253
peak=    3.888 closest distance to " O   HOH Z 185 " =    1.314
peak=    3.886 closest distance to " NH1 ARG A  14 " =    0.874
peak=    3.874 closest distance to " O   HOH Z   8 " =    1.702
peak=    3.866 closest distance to " O   HOH Z 226 " =    0.980
peak=    3.862 closest distance to " CB  TRP A 179 " =    0.930
peak=    3.842 closest distance to " O   HOH Z 238 " =    1.104
peak=    3.832 closest distance to " O   HOH Z 116 " =    1.190
peak=    3.827 closest distance to " NH1AARG A 145 " =    0.729
peak=    3.824 closest distance to " CB  ASN A 148 " =    1.435
peak=    3.821 closest distance to " O   HOH Z 189 " =    2.050
peak=    3.817 closest distance to " CG  PRO A 163 " =    3.492
peak=    3.817 closest distance to " CD  ARG A 269 " =    0.995
peak=    3.799 closest distance to " O   HOH Z  24 " =    1.583
peak=    3.796 closest distance to " CB  MET A  47 " =    1.645
peak=    3.790 closest distance to " O   HOH Z  43 " =    1.471
peak=    3.786 closest distance to " O   HOH Z 223 " =    0.973
peak=    3.786 closest distance to " CA  ARG A 275 " =    1.012
peak=    3.775 closest distance to " O   HOH Z 325 " =    1.358
peak=    3.766 closest distance to " O   HOH Z 225 " =    1.300
peak=    3.763 closest distance to " O   HOH Z 284 " =    1.715
peak=    3.760 closest distance to " CG  LYS A 166 " =    1.427
peak=    3.751 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.743 closest distance to " O   HOH Z  61 " =    1.426
peak=    3.734 closest distance to " CA  PHE A 283 " =    0.978
peak=    3.733 closest distance to " CG  PRO A 198 " =    1.455
peak=    3.731 closest distance to " CD1 LEU A   5 " =    1.867
peak=    3.730 closest distance to " O   HOH Z 316 " =    1.209
peak=    3.712 closest distance to " OE1 GLN A  58 " =    1.540
peak=    3.712 closest distance to " CA  PHE A  59 " =    0.711
peak=    3.710 closest distance to " O   HOH Z 249 " =    1.765
peak=    3.703 closest distance to " O   HOH Z 427 " =    1.240
peak=    3.688 closest distance to " CB  ARG A 102 " =    0.841
peak=    3.682 closest distance to " O   HOH Z  97 " =    1.959
peak=    3.681 closest distance to " CG  LEU A 281 " =    1.076
peak=    3.675 closest distance to " O   HOH Z 260 " =    1.844
peak=    3.674 closest distance to " CG2 ILE A 234 " =    1.023
peak=    3.670 closest distance to " O   HOH Z  95 " =    1.869
peak=    3.666 closest distance to " OE1 GLU A  44 " =    1.249
peak=    3.662 closest distance to " O   HOH Z 366 " =    2.456
peak=    3.653 closest distance to " O   HOH Z 347 " =    1.086
peak=    3.651 closest distance to " CG2 ILE A  20 " =    1.203
peak=    3.644 closest distance to " O   HOH Z 280 " =    1.593
peak=    3.639 closest distance to " CG  GLN A  11 " =    2.178
peak=    3.637 closest distance to " CA  LEU A 282 " =    1.181
peak=    3.635 closest distance to " O   HOH Z 233 " =    1.463
peak=    3.632 closest distance to " CB  GLN A 278 " =    0.777
peak=    3.630 closest distance to " O   HOH Z 108 " =    1.266
peak=    3.626 closest distance to " OG ASER A 134 " =    1.695
peak=    3.621 closest distance to " CA  VAL A 126 " =    1.277
peak=    3.617 closest distance to " CG  PHE A  59 " =    0.878
peak=    3.614 closest distance to " O   SER A  87 " =    2.373
peak=    3.614 closest distance to " O   HOH Z 371 " =    1.576
peak=    3.613 closest distance to " CB  ASN A 148 " =    2.198
peak=    3.604 closest distance to " O   HOH Z 345 " =    1.591
peak=    3.603 closest distance to " O   HOH Z 365 " =    1.876
peak=    3.602 closest distance to " CD  GLN A  58 " =    5.390
peak=    3.595 closest distance to " NE1 TRP A 274 " =    1.017
peak=    3.582 closest distance to " O   HOH Z 257 " =    1.273
peak=    3.581 closest distance to " O   HOH Z 305 " =    3.196
peak=    3.580 closest distance to " O   HOH Z 153 " =    1.659
peak=    3.576 closest distance to " O   SER A  26 " =    1.943
peak=    3.575 closest distance to " CA  PRO A 163 " =    0.905
peak=    3.572 closest distance to " O   HOH Z  63 " =    1.471
peak=    3.568 closest distance to " O   HOH Z 214 " =    1.944
peak=    3.567 closest distance to " CE AMET A  47 " =    0.960
peak=    3.558 closest distance to " CA  SER A 210 " =    1.502
peak=    3.557 closest distance to " O   HOH Z  53 " =    2.361
peak=    3.555 closest distance to " O   HOH Z 261 " =    1.832
peak=    3.554 closest distance to " CB  VAL A 202 " =    1.690
peak=    3.549 closest distance to " O   HOH Z   1 " =    1.793
peak=    3.546 closest distance to " CD  GLN A 194 " =    1.411
peak=    3.541 closest distance to " OE1 GLN A  77 " =    1.308
peak=    3.530 closest distance to " OD2 ASP A 286 " =    2.299
peak=    3.526 closest distance to " O   HOH Z 176 " =    1.786
peak=    3.525 closest distance to " CE1 PHE A  61 " =    1.207
peak=    3.522 closest distance to " O   HOH Z 425 " =    2.051
peak=    3.521 closest distance to " O   HOH Z  80 " =    2.034
peak=    3.516 closest distance to " CB  ASN A 142 " =    1.146
peak=    3.515 closest distance to " O   HOH Z  11 " =    1.745
peak=    3.513 closest distance to " O   HOH Z 245 " =    1.429
peak=    3.513 closest distance to " O   HOH Z 196 " =    1.619
peak=    3.504 closest distance to " N   PHE A  59 " =    1.280
peak=    3.501 closest distance to " O   HOH Z 269 " =    2.447
peak=    3.498 closest distance to " O   HOH Z 361 " =    1.507
peak=    3.498 closest distance to " O   HOH Z  47 " =    1.757
peak=    3.493 closest distance to " O   GLY A 147 " =    1.261
peak=    3.491 closest distance to " CD1 LEU A  96 " =    0.710
peak=    3.489 closest distance to " O   HOH Z 114 " =    2.241
peak=    3.487 closest distance to " CG  TRP A 179 " =    2.298
peak=    3.486 closest distance to " O   HOH Z 232 " =    2.069
peak=    3.485 closest distance to " O   HOH Z 147 " =    1.688
peak=    3.481 closest distance to " O   HOH Z   6 " =    1.313
peak=    3.477 closest distance to " CG  PRO A 243 " =    1.233
peak=    3.474 closest distance to " CA  GLY A  57 " =    0.924
peak=    3.473 closest distance to " NZ  LYS A 119 " =    2.204
peak=    3.472 closest distance to " O   HOH Z  89 " =    2.118
peak=    3.465 closest distance to " O   HOH Z 392 " =    1.470
peak=    3.465 closest distance to " CG  GLN A  88 " =    1.031
peak=    3.460 closest distance to " CE  MET A  93 " =    1.389
peak=    3.458 closest distance to " CA  GLN A 194 " =    0.922
peak=    3.456 closest distance to " CB  LEU A 255 " =    0.978
peak=    3.451 closest distance to " O   HOH Z 213 " =    1.707
peak=    3.446 closest distance to " O   HOH Z 244 " =    1.610
peak=    3.443 closest distance to " O   HOH Z  44 " =    2.020
peak=    3.438 closest distance to " O   HOH Z 422 " =    2.415
peak=    3.437 closest distance to " O   HOH Z  59 " =    2.121
peak=    3.435 closest distance to " N   ALA A 165 " =    0.900
peak=    3.434 closest distance to " O   HOH Z 156 " =    2.481
peak=    3.434 closest distance to " O   HOH Z 123 " =    1.272
peak=    3.432 closest distance to " O   HOH Z 184 " =    1.569
peak=    3.426 closest distance to " O   HOH Z 289 " =    1.604
peak=    3.424 closest distance to " NE2 GLN A 278 " =    3.630
peak=    3.423 closest distance to " O   HOH Z 364 " =    1.868
peak=    3.423 closest distance to " O   HOH Z 365 " =    5.604
peak=    3.421 closest distance to " O   HOH Z 128 " =    1.902
peak=    3.416 closest distance to " O   HOH Z 389 " =    2.895
peak=    3.416 closest distance to " O   HOH Z 265 " =    1.582
peak=    3.410 closest distance to " O   HOH Z 327 " =    1.648
peak=    3.407 closest distance to " O   HOH Z 234 " =    3.251
peak=    3.400 closest distance to " O   HOH Z 194 " =    2.259
peak=    3.395 closest distance to " O   HOH Z 367 " =    3.947
peak=    3.382 closest distance to " O   HOH Z 369 " =    1.402
peak=    3.380 closest distance to " O   HOH Z 108 " =    1.724
peak=    3.378 closest distance to " CB  ASN A 215 " =    1.088
peak=    3.377 closest distance to " CG  LYS A  76 " =    1.487
peak=    3.372 closest distance to " CA  ARG A  66 " =    0.880
peak=    3.367 closest distance to " NE2 GLN A  73 " =    1.963
peak=    3.359 closest distance to " CA  THR A 264 " =    0.838
peak=    3.355 closest distance to " O   HOH Z 329 " =    2.020
peak=    3.352 closest distance to " N   GLU A   2 " =    1.476
peak=    3.352 closest distance to " NZ  LYS A  48 " =    1.690
peak=    3.351 closest distance to " O   HOH Z 424 " =    2.065
peak=    3.349 closest distance to " CB  PRO A  90 " =    1.136
peak=    3.338 closest distance to " O   HOH Z 344 " =    2.693
peak=    3.336 closest distance to " O   HOH Z 281 " =    2.020
peak=    3.336 closest distance to " O   HOH Z 358 " =    1.293
peak=    3.335 closest distance to " O   HOH Z 179 " =    1.196
peak=    3.335 closest distance to " O   HOH Z 298 " =    4.389
peak=    3.334 closest distance to " O   HOH Z  28 " =    1.865
peak=    3.334 closest distance to " O   HOH Z 285 " =    1.850
peak=    3.333 closest distance to " CB  VAL A 230 " =    1.094
peak=    3.332 closest distance to " O   HOH Z 356 " =    1.625
peak=    3.330 closest distance to " CB  ASN A  69 " =    1.562
peak=    3.330 closest distance to " O   HOH Z 284 " =    2.399
peak=    3.329 closest distance to " O   HOH Z 194 " =    1.396
peak=    3.327 closest distance to " O   HOH Z 375 " =    2.281
peak=    3.326 closest distance to " O   HOH Z 191 " =    1.721
peak=    3.323 closest distance to " NH1BARG A 145 " =    1.675
peak=    3.323 closest distance to " O   HOH Z  63 " =    1.855
peak=    3.323 closest distance to " CD1 PHE A 130 " =    0.887
peak=    3.322 closest distance to " CG2 THR A 246 " =    1.089
peak=    3.314 closest distance to " O   HOH Z 253 " =    1.649
peak=    3.312 closest distance to " O   HOH Z 143 " =    2.220
peak=    3.301 closest distance to " CB  ARG A  79 " =    1.668
peak=    3.299 closest distance to " O   HOH Z  47 " =    1.788
peak=    3.298 closest distance to " CG2 THR A 279 " =    1.311
peak=    3.293 closest distance to " CG1 VAL A 153 " =    0.925
peak=    3.293 closest distance to " N   GLY A 111 " =    1.217
peak=    3.293 closest distance to " O   SER A 164 " =    1.285
peak=    3.292 closest distance to " CG1BVAL A  72 " =    1.262
peak=    3.286 closest distance to " CB  ALA A 233 " =    1.057
peak=    3.280 closest distance to " O   HOH Z 247 " =    1.325
peak=    3.279 closest distance to " O   HOH Z  13 " =    1.846
peak=    3.274 closest distance to " O   HOH Z 250 " =    1.330
peak=    3.272 closest distance to " O   HOH Z 428 " =    1.454
peak=    3.271 closest distance to " CA  ALA A 299 " =    0.949
peak=    3.267 closest distance to " O   HOH Z 150 " =    2.598
peak=    3.264 closest distance to " O   HOH Z 368 " =    1.902
peak=    3.258 closest distance to " OD1 ASP A 286 " =    1.128
peak=    3.254 closest distance to " O   HOH Z 126 " =    2.247
peak=    3.247 closest distance to " CB  GLN A  88 " =    1.389
peak=    3.247 closest distance to " NH1BARG A 190 " =    1.747
peak=    3.235 closest distance to " O   HOH Z 266 " =    1.405
peak=    3.234 closest distance to " CD BARG A 145 " =    1.184
peak=    3.233 closest distance to " O   HOH Z 143 " =    1.480
peak=    3.230 closest distance to " O   HOH Z 311 " =    1.381
peak=    3.227 closest distance to " O   HOH Z 215 " =    1.583
peak=    3.226 closest distance to " O   HOH Z 258 " =    1.305
peak=    3.225 closest distance to " O   HOH Z 433 " =    2.168
peak=    3.223 closest distance to " O   HOH Z 419 " =    1.765
peak=    3.221 closest distance to " CG1AVAL A 121 " =    1.083
peak=    3.220 closest distance to " CG2 THR A 221 " =    1.227
peak=    3.216 closest distance to " CB  VAL A 268 " =    1.014
peak=    3.213 closest distance to " CB  PRO A  54 " =    1.026
peak=    3.213 closest distance to " CG1BVAL A 121 " =    1.106
peak=    3.212 closest distance to " CA  ARG A 195 " =    1.088
peak=    3.212 closest distance to " CE BMET A  47 " =    1.196
peak=    3.210 closest distance to " O   HOH Z 234 " =    4.165
peak=    3.208 closest distance to " CA  SER A  99 " =    0.834
peak=    3.208 closest distance to " O   ALA A   1 " =    1.366
peak=    3.204 closest distance to " O   LYS A 290 " =    2.458
peak=    3.203 closest distance to " O   HOH Z 353 " =    2.383
peak=    3.203 closest distance to " CZ3 TRP A 179 " =    2.220
peak=    3.200 closest distance to " O   HOH Z  40 " =    2.187
peak=    3.197 closest distance to " O   HOH Z   6 " =    2.271
peak=    3.196 closest distance to " O   HOH Z 426 " =    1.226
peak=    3.191 closest distance to " CG2AVAL A  72 " =    3.081
peak=    3.191 closest distance to " O   HOH Z  73 " =    3.289
peak=    3.188 closest distance to " CB  PHE A 130 " =    0.974
peak=    3.183 closest distance to " O   HOH Z 393 " =    1.556
peak=    3.181 closest distance to " O   HOH Z 232 " =    1.198
peak=    3.180 closest distance to " O   HOH Z 322 " =    1.631
peak=    3.178 closest distance to " CG  ARG A  66 " =    1.209
peak=    3.177 closest distance to " O   HOH Z   9 " =    2.112
peak=    3.171 closest distance to " O   HOH Z  66 " =    1.183
peak=    3.170 closest distance to " O   HOH Z 402 " =    1.483
peak=    3.168 closest distance to " O   HOH Z  77 " =    1.134
peak=    3.167 closest distance to " O   HOH Z 183 " =    1.854
peak=    3.166 closest distance to " CB  ASP A 200 " =    0.923
peak=    3.162 closest distance to " NE AARG A 145 " =    0.955
peak=    3.161 closest distance to " O   HOH Z 209 " =    1.147
peak=    3.160 closest distance to " O   HOH Z  85 " =    1.979
peak=    3.160 closest distance to " O   HOH Z  37 " =    1.113
peak=    3.157 closest distance to " NH1BARG A 190 " =    2.025
peak=    3.154 closest distance to " CA  ALA A 295 " =    1.145
peak=    3.154 closest distance to " CG  LEU A 228 " =    1.225
peak=    3.152 closest distance to " O   HOH Z   4 " =    1.390
peak=    3.140 closest distance to " O   HOH Z 266 " =    1.867
peak=    3.140 closest distance to " CB  ALA A 248 " =    1.335
peak=    3.138 closest distance to " O   HOH Z  54 " =    1.522
peak=    3.137 closest distance to " O   HOH Z 222 " =    2.031
peak=    3.133 closest distance to " O   HOH Z 380 " =    1.611
peak=    3.132 closest distance to " CD1 ILE A  33 " =    1.550
peak=    3.132 closest distance to " CG  ASN A 301 " =    0.775
peak=    3.130 closest distance to " O   LEU A 222 " =    1.855
peak=    3.127 closest distance to " O   HOH Z 143 " =    2.144
peak=    3.126 closest distance to " O   HOH Z 172 " =    3.265
peak=    3.123 closest distance to " CG2 THR A 246 " =    0.934
peak=    3.122 closest distance to " O   HOH Z 112 " =    1.462
peak=    3.121 closest distance to " O   HOH Z 193 " =    1.833
peak=    3.119 closest distance to " O   PHE A  59 " =    2.649
peak=    3.117 closest distance to " CD1 TRP A 179 " =    1.113
peak=    3.110 closest distance to " O   HOH Z 185 " =    1.549
peak=    3.106 closest distance to " CG1BVAL A 121 " =    2.293
peak=    3.103 closest distance to " N   TRP A 177 " =    1.462
peak=    3.101 closest distance to " O   HOH Z  10 " =    1.742
peak=    3.100 closest distance to " CG2 THR A 220 " =    0.912
peak=    3.096 closest distance to " O   HOH Z 366 " =    3.085
peak=    3.096 closest distance to " O   HOH Z 181 " =    1.795
peak=    3.093 closest distance to " CA  ALA A  21 " =    1.086
peak=    3.089 closest distance to " N   THR A  29 " =    1.310
peak=    3.087 closest distance to " NE2 GLN A  58 " =    2.604
peak=    3.086 closest distance to " CG2BVAL A  72 " =    1.462
peak=    3.080 closest distance to " O   HOH Z 409 " =    2.040
peak=    3.078 closest distance to " CA  PHE A 130 " =    1.185
peak=    3.029 closest distance to " O   HOH Z 118 " =    5.898

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.288 - 4.884
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 180 from: 199
   mapped sites are within: 0.709 - 4.884

peak=   -4.745 closest distance to " O   HOH Z 419 " =    0.729
peak=   -4.566 closest distance to " N   GLN A  58 " =    1.018
peak=   -4.502 closest distance to " N   PHE A  59 " =    1.191
peak=   -4.365 closest distance to " C   ASN A 285 " =    1.998
peak=   -4.302 closest distance to " O   ALA A 161 " =    1.451
peak=   -4.258 closest distance to " CD  GLU A 277 " =    0.791
peak=   -4.233 closest distance to " CE2 TYR A  30 " =    2.972
peak=   -4.190 closest distance to " O   HOH Z  72 " =    1.078
peak=   -4.182 closest distance to " O   HOH Z  24 " =    1.092
peak=   -4.163 closest distance to " O   HOH Z 290 " =    0.759
peak=   -4.133 closest distance to " NH2 ARG A  79 " =    1.906
peak=   -4.128 closest distance to " CG  ARG A 138 " =    0.880
peak=   -4.121 closest distance to " CA  VAL A  67 " =    2.758
peak=   -4.044 closest distance to " CD  ARG A  14 " =    2.926
peak=   -4.039 closest distance to " N   THR A  52 " =    1.539
peak=   -4.032 closest distance to " O   PRO A 198 " =    0.997
peak=   -3.948 closest distance to " O   HOH Z 377 " =    0.726
peak=   -3.860 closest distance to " O   HOH Z  69 " =    1.785
peak=   -3.840 closest distance to " OG  SER A   3 " =    1.147
peak=   -3.835 closest distance to " O   SER A 135 " =    1.528
peak=   -3.832 closest distance to " O   HOH Z 205 " =    0.875
peak=   -3.826 closest distance to " O   HOH Z  56 " =    1.273
peak=   -3.790 closest distance to " N   HIS A 115 " =    1.959
peak=   -3.789 closest distance to " CD  ARG A 138 " =    1.205
peak=   -3.783 closest distance to " OD2 ASP A  50 " =    1.445
peak=   -3.758 closest distance to " O   HOH Z 385 " =    1.331
peak=   -3.734 closest distance to " CD  GLN A  88 " =    1.064
peak=   -3.709 closest distance to " O   HOH Z  93 " =    1.277
peak=   -3.709 closest distance to " O   HOH Z 235 " =    0.919
peak=   -3.708 closest distance to " O   HOH Z 407 " =    2.526
peak=   -3.707 closest distance to " OG ASER A 134 " =    1.125
peak=   -3.704 closest distance to " O   SER A 245 " =    1.359
peak=   -3.685 closest distance to " C   HIS A 108 " =    1.308
peak=   -3.680 closest distance to " O   HOH Z 423 " =    2.672
peak=   -3.674 closest distance to " O   ALA A  51 " =    1.159
peak=   -3.672 closest distance to " O   HOH Z 164 " =    4.884
peak=   -3.659 closest distance to " N   MET A 188 " =    1.712
peak=   -3.656 closest distance to " OG1 THR A 246 " =    1.216
peak=   -3.649 closest distance to " O   HOH Z 388 " =    1.929
peak=   -3.637 closest distance to " O   HOH Z  88 " =    2.394
peak=   -3.633 closest distance to " O   ARG A  56 " =    0.975
peak=   -3.628 closest distance to " O   HOH Z  60 " =    1.254
peak=   -3.628 closest distance to " O   HOH Z 100 " =    1.404
peak=   -3.624 closest distance to " O   HOH Z 125 " =    3.118
peak=   -3.622 closest distance to " CD  GLU A 152 " =    2.377
peak=   -3.603 closest distance to " O   HOH Z 347 " =    0.909
peak=   -3.576 closest distance to " O   ASN A 215 " =    1.443
peak=   -3.569 closest distance to " CB  ALA A 248 " =    1.821
peak=   -3.567 closest distance to " O   HOH Z 266 " =    4.153
peak=   -3.567 closest distance to " OD2 ASP A 191 " =    1.331
peak=   -3.553 closest distance to " O   HOH Z  63 " =    0.900
peak=   -3.533 closest distance to " N   ASN A  60 " =    1.040
peak=   -3.529 closest distance to " NH1 ARG A 219 " =    2.481
peak=   -3.529 closest distance to " O   HOH Z 137 " =    1.483
peak=   -3.525 closest distance to " CG  ASP A  50 " =    1.792
peak=   -3.523 closest distance to " O   HOH Z   9 " =    1.267
peak=   -3.522 closest distance to " O   MET A 188 " =    1.409
peak=   -3.515 closest distance to " CA  GLN A  58 " =    1.118
peak=   -3.512 closest distance to " OE2 GLU A   2 " =    0.823
peak=   -3.489 closest distance to " CD2 LEU A 237 " =    2.472
peak=   -3.485 closest distance to " CB  ALA A 244 " =    2.016
peak=   -3.469 closest distance to " CG  PRO A 198 " =    1.614
peak=   -3.464 closest distance to " CE2 PHE A 218 " =    2.594
peak=   -3.463 closest distance to " O   GLY A 118 " =    1.301
peak=   -3.462 closest distance to " O   HOH Z 100 " =    0.910
peak=   -3.460 closest distance to " OD1 ASN A  39 " =    1.985
peak=   -3.457 closest distance to " CB  ALA A   1 " =    1.260
peak=   -3.457 closest distance to " CG  PHE A 283 " =    2.384
peak=   -3.452 closest distance to " N   GLN A  58 " =    2.364
peak=   -3.440 closest distance to " CD  ARG A 156 " =    2.052
peak=   -3.438 closest distance to " O   HOH Z  89 " =    1.110
peak=   -3.435 closest distance to " N   ARG A  66 " =    1.563
peak=   -3.435 closest distance to " O   HOH Z 429 " =    1.564
peak=   -3.434 closest distance to " CD1 ILE A 239 " =    2.433
peak=   -3.427 closest distance to " CG BARG A 275 " =    0.799
peak=   -3.427 closest distance to " C   LEU A 143 " =    1.174
peak=   -3.427 closest distance to " O   HOH Z 427 " =    1.657
peak=   -3.426 closest distance to " O   HOH Z 328 " =    0.709
peak=   -3.422 closest distance to " O   PRO A 163 " =    1.737
peak=   -3.416 closest distance to " O   GLN A  58 " =    0.899
peak=   -3.415 closest distance to " O   HOH Z 178 " =    0.812
peak=   -3.408 closest distance to " NE2 GLN A  58 " =    1.859
peak=   -3.405 closest distance to " O   HOH Z 250 " =    1.162
peak=   -3.404 closest distance to " O   HOH Z 256 " =    0.987
peak=   -3.400 closest distance to " O   HOH Z 317 " =    3.007
peak=   -3.395 closest distance to " N   SER A 210 " =    1.161
peak=   -3.393 closest distance to " O   ALA A 100 " =    2.508
peak=   -3.392 closest distance to " O   HOH Z 404 " =    1.502
peak=   -3.386 closest distance to " O   HOH Z 314 " =    1.550
peak=   -3.381 closest distance to " O   HOH Z 211 " =    1.257
peak=   -3.376 closest distance to " O   HOH Z 296 " =    0.954
peak=   -3.376 closest distance to " CG  LEU A 228 " =    0.984
peak=   -3.373 closest distance to " O   SER A  22 " =    2.395
peak=   -3.372 closest distance to " O   HOH Z 117 " =    0.933
peak=   -3.370 closest distance to " CG  PRO A 163 " =    1.359
peak=   -3.368 closest distance to " O   HOH Z 134 " =    1.840
peak=   -3.367 closest distance to " OE1 GLU A 277 " =    2.348
peak=   -3.362 closest distance to " C   GLY A  91 " =    1.388
peak=   -3.359 closest distance to " CA  GLY A  23 " =    1.618
peak=   -3.346 closest distance to " CA  GLY A 133 " =    1.859
peak=   -3.344 closest distance to " O   ALA A 165 " =    1.003
peak=   -3.344 closest distance to " CB  PHE A  59 " =    1.794
peak=   -3.342 closest distance to " C   ALA A 158 " =    1.257
peak=   -3.340 closest distance to " CG  ASN A  60 " =    1.043
peak=   -3.339 closest distance to " OG1 THR A 279 " =    0.971
peak=   -3.331 closest distance to " CB  SER A 273 " =    1.701
peak=   -3.329 closest distance to " O   HOH Z 123 " =    0.884
peak=   -3.329 closest distance to " O   LEU A 101 " =    1.143
peak=   -3.327 closest distance to " NE1 TRP A 274 " =    1.294
peak=   -3.323 closest distance to " OG1 THR A 178 " =    1.047
peak=   -3.322 closest distance to " CA  SER A  63 " =    1.596
peak=   -3.321 closest distance to " CB  ALA A   7 " =    1.961
peak=   -3.320 closest distance to " CB  ALA A 248 " =    1.766
peak=   -3.320 closest distance to " CD  PRO A 198 " =    1.208
peak=   -3.309 closest distance to " O   LYS A 289 " =    1.888
peak=   -3.309 closest distance to " O   HOH Z  54 " =    0.921
peak=   -3.307 closest distance to " O   HOH Z 116 " =    1.077
peak=   -3.301 closest distance to " O   PRO A 163 " =    1.374
peak=   -3.299 closest distance to " O   HOH Z 220 " =    1.115
peak=   -3.297 closest distance to " O   HOH Z 266 " =    4.605
peak=   -3.290 closest distance to " O   HOH Z  37 " =    1.339
peak=   -3.275 closest distance to " OG BSER A 134 " =    1.190
peak=   -3.274 closest distance to " CG  PRO A 163 " =    2.679
peak=   -3.264 closest distance to " O   HOH Z 150 " =    1.033
peak=   -3.257 closest distance to " NH2AARG A 275 " =    4.653
peak=   -3.255 closest distance to " O   HOH Z 431 " =    1.285
peak=   -3.248 closest distance to " O   HOH Z 165 " =    2.125
peak=   -3.244 closest distance to " CG1 VAL A 296 " =    2.070
peak=   -3.242 closest distance to " O   HOH Z 184 " =    0.767
peak=   -3.233 closest distance to " O   HOH Z 153 " =    1.420
peak=   -3.231 closest distance to " C   ILE A 239 " =    2.055
peak=   -3.230 closest distance to " CB  GLU A  44 " =    1.300
peak=   -3.229 closest distance to " O   HOH Z 393 " =    3.216
peak=   -3.229 closest distance to " O   HOH Z 193 " =    1.352
peak=   -3.224 closest distance to " O   HOH Z  60 " =    1.984
peak=   -3.223 closest distance to " CD1 LEU A  25 " =    1.379
peak=   -3.220 closest distance to " O   HOH Z 414 " =    0.917
peak=   -3.218 closest distance to " O   HOH Z 344 " =    2.635
peak=   -3.217 closest distance to " O   HOH Z 248 " =    1.038
peak=   -3.216 closest distance to " OG1 THR A   4 " =    1.900
peak=   -3.209 closest distance to " O   SER A 206 " =    1.272
peak=   -3.200 closest distance to " CG  HIS A 108 " =    0.900
peak=   -3.194 closest distance to " CZ3 TRP A 274 " =    1.047
peak=   -3.192 closest distance to " O   HOH Z 281 " =    4.150
peak=   -3.188 closest distance to " O   HOH Z 372 " =    2.152
peak=   -3.184 closest distance to " OG  SER A 245 " =    1.149
peak=   -3.180 closest distance to " O   HOH Z 385 " =    1.321
peak=   -3.177 closest distance to " CE  MET A  93 " =    1.085
peak=   -3.176 closest distance to " CD1 PHE A  61 " =    2.897
peak=   -3.174 closest distance to " NZ  LYS A 117 " =    4.006
peak=   -3.170 closest distance to " CD  GLN A  11 " =    0.805
peak=   -3.167 closest distance to " O   HOH Z 147 " =    1.175
peak=   -3.165 closest distance to " O   HOH Z 359 " =    1.982
peak=   -3.163 closest distance to " ND2 ASN A  69 " =    1.305
peak=   -3.161 closest distance to " N   ALA A   1 " =    1.659
peak=   -3.158 closest distance to " O   HOH Z 426 " =    2.149
peak=   -3.157 closest distance to " O   HOH Z  65 " =    1.118
peak=   -3.157 closest distance to " CG  GLN A  58 " =    1.049
peak=   -3.143 closest distance to " CD1 LEU A 228 " =    2.020
peak=   -3.143 closest distance to " O   HOH Z 414 " =    2.627
peak=   -3.141 closest distance to " O   HOH Z 131 " =    3.692
peak=   -3.137 closest distance to " O   HOH Z 188 " =    3.851
peak=   -3.134 closest distance to " N   THR A 235 " =    1.542
peak=   -3.132 closest distance to " O   GLU A 152 " =    1.582
peak=   -3.126 closest distance to " CD2 TRP A 150 " =    0.940
peak=   -3.123 closest distance to " O   HOH Z 225 " =    0.754
peak=   -3.120 closest distance to " CG  ARG A 219 " =    1.993
peak=   -3.111 closest distance to " O   HOH Z 314 " =    0.878
peak=   -3.110 closest distance to " OD1 ASN A 284 " =    1.263
peak=   -3.109 closest distance to " CB  ARG A 259 " =    2.370
peak=   -3.107 closest distance to " O   ASP A 200 " =    1.121
peak=   -3.106 closest distance to " O   HOH Z  12 " =    3.109
peak=   -3.106 closest distance to " CE  LYS A  76 " =    2.951
peak=   -3.087 closest distance to " O   HOH Z 283 " =    1.511
peak=   -3.065 closest distance to " O   HOH Z 210 " =    1.868
peak=   -3.064 closest distance to " O   VAL A 125 " =    1.935
peak=   -3.057 closest distance to " O   ASN A 301 " =    1.595
peak=   -3.055 closest distance to " CD1 LEU A 255 " =    2.783
peak=   -3.050 closest distance to " O   ALA A  19 " =    1.158
peak=   -3.039 closest distance to " O   LYS A 289 " =    2.496

================= 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    :  0.5228 0.5135   6.309700e+00   6.304764e+00
   1_bss:  0.5149 0.5050   6.305407e+00   6.294617e+00
   1_xyz:  0.4552 0.4745   6.248368e+00   6.270032e+00
   1_adp:  0.4171 0.4698   6.210714e+00   6.264536e+00
   1_occ:  0.4168 0.4704   6.210502e+00   6.264653e+00
   2_bss:  0.4150 0.4669   6.211659e+00   6.263767e+00
   2_xyz:  0.3464 0.4093   6.075109e+00   6.185933e+00
   2_adp:  0.3200 0.3895   6.025914e+00   6.152138e+00
   2_occ:  0.3194 0.3904   6.025743e+00   6.152666e+00
   3_bss:  0.3162 0.3889   6.022702e+00   6.150693e+00
   3_xyz:  0.2483 0.3099   5.822317e+00   5.988449e+00
   3_adp:  0.2221 0.2831   5.732685e+00   5.920449e+00
   3_occ:  0.2217 0.2825   5.731867e+00   5.920130e+00
   4_bss:  0.2206 0.2816   5.727233e+00   5.915767e+00
   4_xyz:  0.1788 0.2349   5.547629e+00   5.753039e+00
   4_adp:  0.1728 0.2211   5.503758e+00   5.696479e+00
   4_occ:  0.1724 0.2203   5.502327e+00   5.694548e+00
   5_bss:  0.1723 0.2205   5.502850e+00   5.694731e+00
   5_xyz:  0.1471 0.1893   5.354346e+00   5.554649e+00
   5_adp:  0.1426 0.1870   5.331914e+00   5.542509e+00
   5_occ:  0.1424 0.1868   5.330772e+00   5.540946e+00
   5_bss:  0.1423 0.1860   5.329271e+00   5.538546e+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:  0.395   0.792   6.841   8.422   8.482   0.000   0.000   0.000
   1_xyz:  0.395   0.792   6.841   8.422   8.482   0.000   0.000   0.000
   1_adp:  0.395   0.792   6.841   8.422   8.482   0.000   0.000   0.000
   1_occ:  0.395   0.792   6.841   8.422   8.482   0.000   0.000   0.000
   2_bss:  0.357  27.989   3.838   5.017   5.867   0.000   0.000   0.000
   2_xyz:  0.357  27.989   3.838   5.017   5.867   0.000   0.000   0.000
   2_adp:  0.357  27.989   3.838   5.017   5.867   0.000   0.000   0.000
   2_occ:  0.357  27.989   3.838   5.017   5.867   0.000   0.000   0.000
   3_bss:  0.318  33.488   1.776   2.460   3.209   0.000   0.000   0.000
   3_xyz:  0.318  33.488   1.776   2.460   3.209   0.000   0.000   0.000
   3_adp:  0.318  33.488   1.776   2.460   3.209   0.000   0.000   0.000
   3_occ:  0.318  33.488   1.776   2.460   3.209   0.000   0.000   0.000
   4_bss:  0.323  33.488   0.382   1.217   1.815   0.000   0.000   0.000
   4_xyz:  0.323  33.488   0.382   1.217   1.815   0.000   0.000   0.000
   4_adp:  0.323  33.488   0.382   1.217   1.815   0.000   0.000   0.000
   4_occ:  0.323  33.488   0.382   1.217   1.815   0.000   0.000   0.000
   5_bss:  0.332  33.488  -0.105   0.541   1.263   0.000   0.000   0.000
   5_xyz:  0.332  33.488  -0.105   0.541   1.263   0.000   0.000   0.000
   5_adp:  0.332  33.488  -0.105   0.541   1.263   0.000   0.000   0.000
   5_occ:  0.332  33.488  -0.105   0.541   1.263   0.000   0.000   0.000
   5_bss:  0.332  33.762  -0.600  -0.051   0.652   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.117 0.3017  0.3669    86378.245
   1_bss:  65.995 0.3149  0.4732    82370.986
   1_xyz:  59.898 0.3938  0.5859    72086.028
   1_adp:  58.308 0.4142  0.6707    70379.407
   1_occ:  58.409 0.4129  0.6679    70529.668
   2_bss:  58.294 0.4141  0.6107    70268.535
   2_xyz:  45.544 0.5754  0.8517    48100.272
   2_adp:  42.296 0.6152  0.9175    42516.319
   2_occ:  42.285 0.6154  0.9169    42550.849
   3_bss:  42.054 0.6180  0.8428    42029.846
   3_xyz:  32.175 0.7335  0.9661    25594.640
   3_adp:  28.458 0.7755  0.9925    21292.158
   3_occ:  28.442 0.7757  0.9926    21268.037
   4_bss:  28.245 0.7776  0.9445    20872.931
   4_xyz:  22.687 0.8359  0.9896    14176.638
   4_adp:  20.764 0.8559  1.0048    12654.513
   4_occ:  20.718 0.8563  1.0048    12581.870
   5_bss:  20.718 0.8563  0.9833    12563.593
   5_xyz:  17.347 0.8874  0.9988     9137.848
   5_adp:  17.047 0.8903  1.0003     8960.216
   5_occ:  17.011 0.8906  1.0005     8918.207
   5_bss:  16.950 0.8911  0.9899     8854.797
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.082   5.2341e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.082   5.2341e+01
   1_xyz:   1.953  0.016  0.119 18.632  0.008  4.100   1.8918e-01
   1_adp:   1.953  0.016  0.119 18.632  0.008  4.100   1.8918e-01
   1_occ:   1.953  0.016  0.119 18.632  0.008  4.100   1.8918e-01
   2_bss:   1.953  0.016  0.119 18.632  0.008  4.100   1.8918e-01
   2_xyz:   1.472  0.012  0.096 17.906  0.007  4.096   1.3443e-01
   2_adp:   1.472  0.012  0.096 17.906  0.007  4.096   1.3443e-01
   2_occ:   1.472  0.012  0.096 17.906  0.007  4.096   1.3443e-01
   3_bss:   1.472  0.012  0.096 17.906  0.007  4.096   1.3443e-01
   3_xyz:   1.246  0.009  0.085 16.908  0.005  4.101   9.2383e-02
   3_adp:   1.246  0.009  0.085 16.908  0.005  4.101   9.2383e-02
   3_occ:   1.246  0.009  0.085 16.908  0.005  4.101   9.2383e-02
   4_bss:   1.246  0.009  0.085 16.908  0.005  4.101   9.2383e-02
   4_xyz:   0.943  0.006  0.063 15.845  0.003  4.110   6.0176e-02
   4_adp:   0.943  0.006  0.063 15.845  0.003  4.110   6.0176e-02
   4_occ:   0.943  0.006  0.063 15.845  0.003  4.110   6.0176e-02
   5_bss:   0.943  0.006  0.063 15.845  0.003  4.110   6.0176e-02
   5_xyz:   0.931  0.005  0.064 15.557  0.003  4.106   5.6732e-02
   5_adp:   0.931  0.005  0.064 15.557  0.003  4.106   5.6732e-02
   5_occ:   0.931  0.005  0.064 15.557  0.003  4.106   5.6732e-02
   5_bss:   0.931  0.005  0.064 15.557  0.003  4.106   5.6732e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.577   6.7673e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.577   6.7673e+00
   1_xyz:  15.808  0.185  0.567 85.802  0.054  1.996   1.1959e-01
   1_adp:  15.808  0.185  0.567 85.802  0.054  1.996   1.1959e-01
   1_occ:  15.808  0.185  0.567 85.802  0.054  1.996   1.1959e-01
   2_bss:  15.808  0.185  0.567 85.802  0.054  1.996   1.1959e-01
   2_xyz:   9.849  0.114  0.333 76.099  0.050  2.087   9.2755e-02
   2_adp:   9.849  0.114  0.333 76.099  0.050  2.087   9.2755e-02
   2_occ:   9.849  0.114  0.333 76.099  0.050  2.087   9.2755e-02
   3_bss:   9.849  0.114  0.333 76.099  0.050  2.087   9.2755e-02
   3_xyz:   7.851  0.063  0.327 83.242  0.031  2.179   7.4250e-02
   3_adp:   7.851  0.063  0.327 83.242  0.031  2.179   7.4250e-02
   3_occ:   7.851  0.063  0.327 83.242  0.031  2.179   7.4250e-02
   4_bss:   7.851  0.063  0.327 83.242  0.031  2.179   7.4250e-02
   4_xyz:   8.117  0.059  0.207 88.798  0.019  2.351   4.9473e-02
   4_adp:   8.117  0.059  0.207 88.798  0.019  2.351   4.9473e-02
   4_occ:   8.117  0.059  0.207 88.798  0.019  2.351   4.9473e-02
   5_bss:   8.117  0.059  0.207 88.798  0.019  2.351   4.9473e-02
   5_xyz:   7.070  0.041  0.230 89.849  0.027  2.374   3.6898e-02
   5_adp:   7.070  0.041  0.230 89.849  0.027  2.374   3.6898e-02
   5_occ:   7.070  0.041  0.230 89.849  0.027  2.374   3.6898e-02
   5_bss:   7.070  0.041  0.230 89.849  0.027  2.374   3.6898e-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:  81.44   0.00  16.06  73.96   0.00  14.88  81.44   0.00  22.46
   1_occ:  81.44   0.00  16.06  73.96   0.00  14.88  81.44   0.00  22.46
   2_bss:  81.44   0.00  16.06  73.96   0.00  14.88  81.44   0.00  22.46
   2_xyz:  81.44   0.00  16.06  73.96   0.00  14.88  81.44   0.00  22.46
   2_adp: 119.43   0.00  15.56 119.43   0.00  13.08  79.53   0.00  29.08
   2_occ: 119.43   0.00  15.56 119.43   0.00  13.08  79.53   0.00  29.08
   3_bss: 119.43   0.00  15.56 119.43   0.00  13.08  79.53   0.00  29.08
   3_xyz: 119.43   0.00  15.56 119.43   0.00  13.08  79.53   0.00  29.08
   3_adp:  92.01   0.00  15.05  92.01   0.00  11.18  79.19   1.84  36.12
   3_occ:  92.01   0.00  15.05  92.01   0.00  11.18  79.19   1.84  36.12
   4_bss:  92.01   0.00  15.05  92.01   0.00  11.18  79.19   1.84  36.12
   4_xyz:  92.01   0.00  15.05  92.01   0.00  11.18  79.19   1.84  36.12
   4_adp:  83.87   0.00  14.44  83.87   0.00  10.48  76.55   3.31  36.00
   4_occ:  83.87   0.00  14.44  83.87   0.00  10.48  76.55   3.31  36.00
   5_bss:  83.87   0.00  14.44  83.87   0.00  10.48  76.55   3.31  36.00
   5_xyz:  83.87   0.00  14.44  83.87   0.00  10.48  76.55   3.31  36.00
   5_adp:  83.69   0.00  14.49  83.69   0.00  10.46  76.65   3.94  36.44
   5_occ:  83.69   0.00  14.49  83.69   0.00  10.46  76.65   3.94  36.44
   5_bss:  83.96   0.27  14.77  83.96   0.27  10.74  76.92   4.22  36.72
------------------------------------------------------------------------
 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:    1.291    0.019    0.438
   1_adp:    1.291    0.019    0.438
   1_occ:    1.291    0.019    0.438
   2_bss:    1.291    0.019    0.438
   2_xyz:    1.766    0.039    0.650
   2_adp:    1.766    0.039    0.650
   2_occ:    1.766    0.039    0.650
   3_bss:    1.766    0.039    0.650
   3_xyz:    1.792    0.043    0.791
   3_adp:    1.792    0.043    0.791
   3_occ:    1.792    0.043    0.791
   4_bss:    1.792    0.043    0.791
   4_xyz:    1.881    0.041    0.856
   4_adp:    1.881    0.041    0.856
   4_occ:    1.881    0.041    0.856
   5_bss:    1.881    0.041    0.856
   5_xyz:    1.933    0.010    0.907
   5_adp:    1.933    0.010    0.907
   5_occ:    1.933    0.010    0.907
   5_bss:    1.933    0.010    0.907
------------------------------------------------------------------------

CPU time actual refinement: 361.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/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_22/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_22/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 360.87 
  Macro-tasks:
    bulk solvent and scale       = 41.37  
    individual site refinement   = 157.76 
    weights calculation          = 33.24  
    collect and process          = 6.48   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 238.99 
  Micro-tasks:
    mask                            = 3.01   
    f_calc                          = 114.01 
    alpha_beta                      = 8.20   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 125.82 
    fmodel                         = 7.43   
    r_factors                      = 0.28   
    phase_errors                   = 9.93   
    foms                           = 0.36   
    TOTAL for micro-tasks          = 270.20 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.081 micro seconds
Total CPU time: 6.27 minutes
from_scatterers_fft:    649 calls, 113.67 s
gradients_fft:          595 calls, 112.43 s

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

# Date 2008-01-16 Time 00:33:42 PST -0800 (1200472422.76 s)
Start R-work = 0.5228, R-free = 0.5135 (no bulk solvent and anisotropic scale)
Final R-work = 0.1587, R-free = 0.2040 (no bulk solvent and anisotropic scale)

Start R-work = 0.5149, R-free = 0.5050
Final R-work = 0.1423, R-free = 0.1860